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LIAM2 User Guide

1. LIAM2 User Guide Release 0 10 2 is now equivalent to age gt 10 and age lt 20 5 2 Assignments Assignments compute values for existing individuals They have the following general format variable_name expression What this means is compute expression and store the result in the variable named variable_name The variable that is assigned to the endogenous variable will often be one of the variables defined in the fields block of the entity but as we will see later it is not always necessary example age age 1 This process increases the variable age of each individual by one each period 5 3 Functions 5 3 1 Declaration One usually group processes in functions Whenever a function is executed the processes within the function are executed in the order they were declared By using functions one can actually make building blocks or modules in the model Changed in version 0 10 Functions were previously called procedures Each function definition starts at a new line with an extra indentation of four spaces compared to the processes keyword of the current entity Within a function each process should start on a new line with an extra indentation of four spaces compared to the function name and a So the usual setup to declare a function is processes function_name processl process2 example entities person
2. 54 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 100 80 60 40 20 100 80 60 40 20 eduach 55 5 7 Output LIAM2 User Guide Release 0 10 2 5 8 Debugging and the interactive console LIAM2 features an interactive console which allows you to interactively explore the state of the memory either during or after a simulation completed 599 1 You can reach it in two ways You can either pass as the last argument when running the executable in which case the interactive console will launch after the whole simulation is over The alternative is to use breakpoints in your simulation to interrupt the simulation at a specific point see below Type help in the console for the list of available commands In addition to those commands you can type any expression that is allowed in the simulation file and have the result directly Show is implicit for all operations examples gt gt gt avg age Dio TLS ELISS gt gt gt groupby trunc age 20 gender expr count inwork Emuine aciea m E20 gender False True Toral 0 14 18 32 1 SF 496 813 2 318 258 576 3 40 102 142 4 0 0 0 5 0 0 0 total 689 874 1563 5 8 1 breakpoint breakpoint temporarily stops execution of the simulation and launch the interactive console There are two additional commands available in the interactive console when you reach it through a breakpoint
3. duration expr number of consecutive period the expression was True examples duration inwork and earnings gt 2000 duration educationlevel 4 tavg expr average of an expression since the individual was created example tavg income e tsum expr sum of an expression since the individual was created 22 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 5 5 6 random functions LIAM2 includes support for many random number generator functions Like for all other functions in LIAM2 all arguments can be expressions computed at runtime and arguments with default values can be omitted All those functions provide the same interface than and actually internally use the corresponding functions in numpy random examples uniform Pun Eo cm pila O T normal loc 0 0 scale 1 0 standard normal mean 0 stdev 1 normal equivalent normal scale std errsal stdev derived from the errsal variable sanoimme 10 4110 random integer between 0 and 10 excluded beta a b size None The Beta distribution over 0 1 See numpy random beta for details New in version 0 9 binomial n p size None Draw samples from a binomial distribution See numpy random binomial for details New in version 0 9 chisquare df size None Draw samples from a chi square distribution See numpy random chisquare for details New in version 0 9 dirichlet alpha si
4. agegroup if age lt 50 5 gy icicbiaie aie Siy 10 trunc age 10 Note The if function always requires three arguments If you want to leave a variable unchanged if a condition is not met use the variable in the expression_if_false retire people set workstate 9 when aged 65 or more workstate if age gt 65 9 workstate You can nest if functions The example below retires men gender True over 64 and women over 61 workstate if gender if age gt 65 9 workstate if age gt 62 9 workstate could also be written like this workstate if age gt if gender 65 62 9 workstate 5 5 2 mathematical functions e log expr natural logarithm In e exp expr exponential e abs expr absolute value e round expr n returns the rounded value of expr to specified n number of digits after the decimal point If n is not specified 0 is used e trunc expr returns the truncated value by dropping the decimal part of expr as an integer e clip x a b returns a if x lt a x ifa lt x lt b b if x gt b e min x a max x a the minimum or maximum of x and a 20 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 5 5 3 aggregate functions e count condition count individuals It counts the individuals in the current entity If a boolean condition is given it only counts the ones satisfying that condition For e
5. entities person fields RSs int agegroup type int initialdata False processes ageing age age 1 agegroup trunc age 10 simulation processes person ageing we do not specify output so this model is not valid in itself input file input h5 start_period 2015 periods 2 example variantl yml import common yml entities person processes 63 LIAM2 User Guide Release 0 10 2 override the ageing process ageing age age 1 2 agegroup if age lt 50 3 He jcieulore lece 5 5 10 rrine Gace 10y simulation provide the required output section which is missing in common yml OULDUL file variant1 h5 example variant2 yml import common yml entities person fields severe_illness type bool initialdata False processes adding new processes illness severe_illness uniform lt 0 001 death dead logit_regr 0 5 severe_illness align al_p_dead csv show Avg age of death avg age filter dead remove dead simulation since we have new processes we have to override the xentirex process list as LIAM2 would not know where to insert the new processes otherwise processes person ageing illness death COuULpOUL file variant2 h5 Imported models can themselves import other models as for example in variant3 yml example variant3 yml
6. step to execute only the next process and resume to resume normal execution general format breakpoint period the period argument is optional and if given will make the breakpoint interrupt the simulation only for that period example marriage in_couple MARRIED or COHAB breakpoint 2002 5 8 2 assertions Assertions can be used to check that your model really produce the results it should produce The behavior when an assertion fails is determined by the assertions simulation option e assertTrue expr evaluates the expression and check its result is True e assertFalse expr evaluates the expression and check its result is False e assertEqual expr1 expr2 evaluates both expressions and check their results are equal e assertNanEqual exprl expr2 evaluates both expressions and check their results are equal even in the presence of nans because normally nan nan 56 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 e assertEquiv expr1 expr2 evaluates both expressions and check their results are equal tolerating a differ ence in shape though they must be compatible e assertIsClose expr1 expr2 evaluates both expressions and check their results are almost equal 5 8 Debugging and the interactive console 57 LIAM2 User Guide Release 0 10 2 58 Chapter 5 Processes CHAPTER SIX LINKS Individuals can be linked with each other or wi
7. fields Sages emits processes ageing age age 1 agegroup trunc age 10 10 display show agegroup agegroup In this example there are two functions one with two processes and one with only one process If the ageing function is executed then both processes will be executed in turn age then agegroup Note Function names have to be unique for each entity 16 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 Within a function it is possible for several assignment processes to modify the same variable Like all processes within the function they will be executed in turn Splitting an expression into smaller bits overwriting the same variable over and over can make some long expressions much more readable example processes ageing age age 1 agegroup trunc age 10 agegroup agegroup 10 New in version 0 10 Since version 0 10 functions can optionally also take arguments and return a value So the general setup to declare a function is processes function_name argumentl argument2 processl process2 return value example plusika D bow Wercleliliovs gi anda return a b Note There are currently two ways to define a function without arguments with or without the parentheses after the function name The version without parentheses is going to be deprecated at some point in the futur
8. matplotlib Even though we have tried to stay as close as possible to their API their implementation in LIAM2 has a few differences in particular we added a few arguments which are available in most functions e fname name of the file to save the chart to The file format is automatically deduced from the file extension You can optionally use the entity and period key words to customize the name You can save the same chart to several formats at once by using amp in the extension For example plot expr fname plot03 png amp pdf will write the chart to both plot03 png and plot03 pdf If the fname argument is not used a window will open to view and interact with the figure using a navigation toolbar See matplotlib navigation toolbar documentation for more details Note Keyboard shortcuts mentioned on that page currently do not work e suffix a more concise alternative to set the name of the file the chart will be saved to When it is used the files are named using the following pattern entity _ period _ suffix png For example bar expr suffix income 99 66 would create person_2002_income png person_2003_income png etc colors a list of the colors to be used for the chart See matplotlib colors documentation for the different ways you can specify colors For example logue Saqere Colors Vie Ye Wo will make a bar chart with red green an
9. 23 if 20 importing data 65 importing models 61 interactive console 55 known issues 75 lag 22 laplace 23 leave 27 lifecycle functions 33 link methods 21 link avg 21 link count 21 link max 21 link min 21 link sum 21 links 57 log 20 logit 26 logit_regr 31 logit_score 26 lognormal 23 logseries 23 macros 8 many2one 59 matching 32 matching functions 32 mathematical functions 20 max 20 21 median 21 min 20 21 multinomial 24 multivariate_normal 24 negative_binomial 24 new 34 noncentral_chisquare 24 101 LIAM2 User Guide Release 0 10 2 noncentral_f 24 normal 22 24 notepad 2 one2many 60 pareto 24 percentile 21 pie 51 pie charts 51 plot 45 poisson 24 power 24 processes 13 python 79 qshow 37 randint 22 24 random 22 rank_matching 33 rayleigh 24 remove 35 round 20 scatter 52 scatter plots 52 show 36 stackplot 50 standard_cauchy 24 standard_exponential 24 standard_gamma 24 standard_normal 24 standard_t 25 std 21 sum 21 take 27 tavg 22 temporal functions 22 triangular 25 trunc 20 tsum 22 uniform 22 25 value_for_period 22 vonmises 25 wald 25 weibull 25 while 35 yaml 79 zipf 25 102 Index
10. For example the mother_age process uses the mother link to assign the age of the mother to the mother_age field If an individual s link does not point to anything eg a person has no known mother trying to use the link would yield the missing value eg for orphans mother age is 1 and parents_income is nan 59 LIAM2 User Guide Release 0 10 2 As another example the process below sets a variable to_separate to True if the variable separate is True for either the individual or his her partner LO_LSe parave Separate Or parinmer separate Note that it is perfectly valid to chain links as for example in grand_parents_income mother mother income mother father income father mother income father father income Another option to get values in the linked individual is to use the form link_name get expr this syntax is a bit more verbose in the simple case but is much more powerful as it allows to evaluate almost any expression on the linked individual For example if you want to get the average age of both parents of the mother of each individual you can do it so mother get mother age father age 2 6 2 one2many A one2many link links an individual of the entity to at least one other individual in the same eg a person to his her children or another entity a household to its members entities household Enkski persons type one2
11. integer when summing integer or boolean expressions and a float for float expressions implemented using the value of a periodic global at a specific period That period can be either a constant eg MINR 2005 or an expression eg MINR period 10 or MINR year_of_birth 20 added trunc function which takes a float expression and returns an int dropping everything after the decimal point Miscellaneous improvements made integer division int int return floats eg 1 2 0 5 instead of 0 processes which do not return any value csv and show do not need to be named anymore when they are inside of a procedure the array used to run the first period is constructed by merging the individuals present in all previous periods print timing for sub processes in procedures This is quite verbose but makes debugging performance problems regressions easier made error messages more understandable in some cases manually flush the console output every time we write to it not only within the interactive console as some environments namely when using the notepad bundle do not flush the buffer themselves disable compression of the output simulation file as it hurts performance quite a bit the simulation time can be increased by more than 60 Previously it was using the same compression settings as the input file allowed align to work on a constant eg 10 4 Change log 97 LIAM2 User
12. or keeping a job inwork work score men work_score if ISMALE and ACTIVEAGE and ISINWORK logit_score 0 196599 age 0 0086552 age 2 0 000988 age x x3 Ome O27 Iowa ESMARRIEED Sr 5 54 612 work_score work_score if ISMALE and ACTIVEAGE and ISUNEMPLOYED or ISOTHERINACTIVE logit_score 0 9780908 age 0 0261765 age 2 0 000199 age x x3 IZ 39108 work_score women work_score if ISFEMALE and ACTIVEAGE and ISINWORK logit_score 0 2740483 age 0 0109883 age 2 0 0001159 age x3 0 0906834 ISMARRIED 3 648706 work_score 5 5 Built in Functions 29 LIAM2 User Guide Release 0 10 2 work_score if ISFEMALE and ACTIVEAGE and ISUNEMPLOYED or ISOTHERINACTIVE logit_score 0 8217638 age 0 0219761 age 2 0 000166 x 4 Oss S0S7 5 ss LSMARREED OMA 310 43 work_score work if ACTIVEAGE if ISMALE align work_score al_p_inwork_m csv leave ISSTUDENT or ISRETIRED align work_score al_p_inwork_f csv leave ISSTUDENT or ISRETIRED False The first sub process illustrates a soft leave by setting the score variable work_score to 1 This makes sure that the a priori selection probability is very low but not zero as in t
13. 5 5 5 temporal functions e lag expr num_periods missing value value at previous period expr any expression num_periods optional argument specifying the number of periods to go back to This can be either a constant or a scalar expression Defaults to 1 missing the value to return for individuals which were not present in the past period By default it returns the missing value corresponding to the type of the expression 1 for an integer expression nan for a float or False for a boolean example lag age lag age missing 0 the age each person had last year 1 if newborn avg lag age the age each person had last year 0 if newborn average age that the current population had last year average age of the population of last year the age each person had two years ago 1 for newborns lag avg age lag age 2 I i i iS lag lag age this is equivalent but slightly less efficient value_for_period expr period missing value value at a specific period expr any expression period the period used to evaluate the expression This can be either a constant or a scalar expression missing the value to return for individuals which were not present in the period By default it returns the missing value corresponding to the type of the expression 1 for an integer expression nan for a float or False for a boolean example value_for_period inwork and not male 2002
14. Guide Release 0 10 2 align 0 0 fname al_p_dead_m csv made the tavg function work with boolean and float expressions in addition to integer expressions allowed links to be used in expression given in the new function to initialise the fields of the new individ uals using __parent__ in the new function is no longer necessary made the init section optional it was never intended to be mandatory added progress bar for copying table optimised some parts for speed making the whole simulation roughly as fast as 0 1 even though more work is done Fixes e fixed tavg function the result was wrong because the number of values used in the division was one less than it should it yielded random values when some individuals were present in a past period but not in the current period fixed duration function it crashed when a past period contained no individuals it yielded random values when some individuals were present in a past period but not in the current period fixed many2one links returning seemingly random values instead of missing when they were pointing to an individual which was not present anymore usually because the individual was dead fixed min max functions fields which are not given an explicit value in new are initialised to missing instead of 0 the result of the new function which returns the id of
15. alone for debugging or in combination with autodiff in a later run This option can take either a filename or a boolean in which case autodump h5 is used as the filename Defaults to False 3 6 13 autodiff If this option is used at the end of each function all non scalar variables changed during the function including temporaries will be compared with the values stored previously by autodump in another run of the model or a variant of it This can be used to precisely compare two versions variants of a model and see exactly where they start to differ This option can take either a filename or a boolean in which case autodump h5 is used as the filename Defaults to False 3 6 simulation 11 LIAM2 User Guide Release 0 10 2 12 Chapier 3 Model Definition CHAPTER FOUR RUNNING A MODEL SIMULATION e If you are using the bundled editor simply open the simulation file and press F6 e If you are using the command line use BUNDLEPATH liam2 main run lt path_to_simulation_file gt 13 LIAM2 User Guide Release 0 10 2 14 Chapter 4 Running a model simulation CHAPTER FIVE PROCESSES The processes define how individuals of each entity evolve over time LIAM2 supports several kinds of processes assignments which change the value of a variable predictor using an expression actions which don t but have other effects and control flow operators which specify which
16. e OHS See 6 w BAS me OUDE een e EE a ee R a E 5 8 Debugging and the interactive console o oo e Links 6l MANVZONE sze i i aeea ee i e a ae Heed de eae ee es BWR Sie ee ww a 62 ONEZMANyY e a 3 b 4a es eh eee Se ha be eee be nee eee ea Be es Importing other models Importing data 8 1 data niles 4 2 4 0 245 62648 46 bb bate dae eee bak be ee ee od 2 description Mle cu Je Qk ek e ee GO A A a we SE he Bo ew ee A 3 impor ne thedata ps v6 aranesa 6 RA ok eS OE EA SE Oe Re ee Ow E A Indices and tables 10 Appendix 10 1 KNOWN ISSUES e o os a dees Ee els es ek BO OR he a A re wl See BOM ws Be el lk E 10 2 Code architecture x onsa Re ae He lee ae Gt BCR a etek He AL GO he RA eh O R jm 63 67 67 67 71 73 10 3 Technical choices 10 4 Changelog 10 5 Credits Index CHAPTER ONE INTRODUCTION 1 1 About LIAM2 LIAM2 is a tool to develop different kinds of microsimulation models The goal of the project is to let modellers concentrate on what is strictly specific to their model without having to worry about the technical details This is achieved by providing a generic microsimulation toolbox which is not tied to a particular model By making it available for free our hope is to greatly reduce the development costs in terms of both time and money of microsimulation models The toolbox is made as generic as possible so that it can be used to develop almost any microsimulati
17. for the patch Fixes e fixed a performance regression in 0 8 when using very large negative numbers as indices for a global eg MINR bad_index where bad_indix contains several 2147483648 values Closes issue 121 e fixed the debug interactive console to not produce a useless warning if a global temporary was run before entering the console regression in 0 8 Closes issue 120 e added missing documentation for assertFalse and assertNanEqual 84 Chapter 10 Appendix LIAM2 User Guide Release 0 10 2 10 4 9 Version 0 8 Released on 2014 02 05 New features added a few functions to create charts courtesy of matplotlib bar plot pie stackplot boxplot and scatter As with all other functions in liam2 they are available both during a simulation and in the interactive console The charts can either be visualized directly or saved to a file See the charts section for details added a view command line option to LIAM2 to open ViTables an hdf5 viewer as well as a correspond ing menu entry and keyboard shortcut F9 in Notepad It is meant to be used when editing a model file and it will open both the input dataset and the result file if any document boolean aggregate functions all and any which were added in 0 7 but were not yet docu mented added assertFalse assert function Miscellaneous improvements improved the first few demonstration models quite a bit A recommended read for all users add
18. in version 0 9 randint low high None size None Return random integers between low inclusive and high exclusive See numpy random randint for details rayleigh scale 1 0 size None Draw samples from a Rayleigh distribution See numpy random rayleigh for details New in version 0 9 standard_cauchy size None Standard Cauchy distribution with mode 0 See numpy random standard_cauchy for details New in version 0 9 standard_exponential size None Draw samples from the standard exponential distribution See numpy random standard_exponential for details New in version 0 9 standard_gamma shape size None Draw samples from a Standard Gamma distribution See numpy random standard_gamma for details New in version 0 9 24 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 standard_normal size None Returns samples from a Standard Normal distribution mean 0 stdev 1 See numpy random standard_normal for details New in version 0 9 standard_t df size None Standard Student s t distribution with df degrees of freedom See numpy random standard_t for details New in version 0 9 triangular left mode right size None Draw samples from the triangular distribution See numpy random triangular for details New in version 0 9 uniform low 0 0 high 1 0 size None Draw random samples between low inclusive and high exclusive from a uniform distribution See numpy random uniform for details
19. individuals are taken The methodology used for now by LIAM2 is called alignment by sorting that is for each category the N individuals with the highest scores are selected The score computation is not done internally by the align function but is rather computed by an expression given by the modeller One will usually use logit_score to compute it but it can be computed in any other way a modeller choose Note It is usually a good idea to include a random component like in logit_score in the score expression because otherwise the individuals with the smaller scores will never be selected To know more about the alignment process reading Evaluating Alignment Methods in Dynamic Microsimulation Models by Li and O Donoghue is advised An alignment expression takes the following general form align score proportions filter conditions take conditions leave conditions expressions expressions possible_values pvalues 7 iieelicl_inersiok WV iinabacouenl H rora emoes For example it could look like unemp align unemp_score al_p_unemployed_m csv filter not ISINWORK and age gt 15 and age lt 65 take ISUNEMPLOYED leave ISSTUDENT or ISRETIRED Now let us examine each argument in turn 5 5 Built in Functions 27 LIAM2 User Guide Release 0 10 2 e score it must be an expression or a simple
20. numbers 10 Chapter 3 Model Definition LIAM2 User Guide Release 0 10 2 3 6 8 skip shows If set to True makes all show functions do nothing This can speed up simulations which include many shows usually for debugging Defaults to False 3 6 9 assertions This option can take any of the following values raise interrupt the simulation if an assertion fails this is the default warn display a warning message skip do not run the assertions at all 3 6 10 default_entity If set to the name of an entity the interactive console will start in that entity 3 6 11 logging level Sets logging level If set it should be one of the three following values by increasing level of verbosity periods show only periods functions show periods and functions this is the default Changed in version 0 10 Renamed from procedures to functions procedures Deprecated since version 0 10 Please use functions instead processes show periods functions and individual processes timings If set to False hide all timings from the simulation log so that two simulation log files are more easily comparable for example with diff tools like WinMerge Defaults to True 3 6 12 autodump If this option is used at the end of each function all non scalar variables changed during the function including temporaries will be dumped in an hdf5 file named autodump h5 by default This option can be used
21. option to make all show functions do nothing allowed expressions in addition to variable names in alignment files added keyword arguments to dump missing to convert nans into the given value header to determine whether column names should be in the dump or not improved import functionality compression is now configurable any csv file can be transposed not just globals globals fields can be selected renamed and inverted like in normal entities added explore command to the main executable to launch the interactive console on a completed simula tion without re simulating it Miscellaneous improvements expressions do not need to be quoted anymore reverted init to old semantic it happens in start_period 1 so that lag variable_set_in_init works even for the first period purge all local variables after each process to lower memory usage allowed the result of new to not be stored in a variable allowed using temporary variables in matching function using a string for matching expressions is deprecated added a tolerance of le 6 to the sum of choice s probabilities to be equal 1 0 added explicit message about alignment over and underflows nicer display for small lt 5ms and large gt 1 hour timings improved error message on missing parenthesis around operands of boolean operators improved error message on duplicate fields improved error message when
22. option is to pass an expression returning a two dimensional array plot 2d_expr in which case there will be one line for each possible value of the first dimension and the second dimension will be plotted along the x axis For example plot groupby gender age 5 7 Output 47 LIAM2 User Guide Release 0 10 2 100 O 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 age and using a few of the many possible options to customize the appearance plot groupby gender agegroup grid False linestyle dashed marker o linewidth 5 48 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 800 700 600 500 400 300 200 0 5 10 15 20 25 30 35 40 45 50 60 70 80 90 agegroup And the fourth and last option is to alternate expressions returning one dimensional arrays with styles strings plot ld_exprl style_strl ld_expr2 style_str2 which allows each line array to be plotted with a different style See plot documentation for a description of possible styles strings Note Styles including a color as explained in the matplotlib documentation eg bo are not supported by our implementation Colors should rather be set using the colors argument as explained above and shown in the example below Example plot groupby agegroup expr count not gender o groupby agegroup expr count gender s
23. or round x uniform draws a random number u from an uniform distribution and adds one individual if u lt fractional_need uniform is the default behavior x round simply rounds needs to the nearest integer In other words one individual is added for a category if the fractional need for that category is gt 0 5 x cutoff tries to match the total need as closely as possible at the expense of a slight loss of precision for individual categories by searching for the cutoff point that yields count frac_need gt cutoff sum frac_need changed the order of align arguments proportions is now the second argument instead of filter which means you can omit the fname or proportions keywords and write something like align score my_csv_file csv made align and by extension logit_regr always return False for individuals outside the filter instead of trying to modify the target variable only where the filter is True That feature seemed like a good idea on paper but had a very confusing side effect the result was different when it was stored in an existing variable than in a new temporary variable it is no longer possible to use expressions in alignment files If you need to align on an expression instead of a simple variable you should specify the expression in the alignment function eg align 0 0 fname al_p_dead csv xpressions
24. possible_values False True False True e frac_need control how fractional needs are handled This argument can take any of three values uni form default cutoff or round uniform draws a random number u from an uniform distribution and adds one individual if u lt fractional_need uniform is the default behavior round simply rounds needs to the nearest integer In other words one individual is added for a category if the fractional need for that category is gt 0 5 cutoff tries to match the total need as closely as possible at the expense of a slight loss of precision for individual categories by searching for the cutoff point that yields count frac_need gt cutoff sum frac_need In practice alignment data is often separate for men and women In that case one will usually use the following form variable if condition if gender align score_expr filename_m csv align score_expr filename_f csv False Since LIAM2 supports alignment with any number of dimensions one could also merge both data files in a single file with one more dimension and use a single align expression variable if condition align score_expr filename_m_and_f csv False or even variable align score_expr filename_m_and_f csv filter condition The example below describes the process of getting
25. the default or processes which corresponds to the behavior in earlier versions Miscellaneous improvements decreased memory usage for models with many periods It used to keep the index of individuals of past periods forever in memory which had approximately the same effect than adding one column for each period Since it is only useful when going back in time more than one period it now flushes it to disk for periods lt period 1 This change has two consequences it will decrease memory use for models with many periods but will slow down models going back in time more than one period This closes issue 130 the top times at the end of the simulation now also include the of total after each period a very rough estimate of the remaining time for the simulation is displayed closes issue 127 in combination with the logging level option updated all dependencies provided in the bundle improved the release script Fixes e Using links or other non simple variables in the score expression of the matching function was a lot slower and memory hungry than necessary because some system temporary variables kept accumulating It is still a lot slower than it should though see issue 128 10 4 8 Version 0 8 1 Released on 2014 03 19 New features e added the gumbel function to draw random numbers from the Gumbel distribution also known as the Smallest Extreme Value SEV distribution Thanks to Gijs Dekkers
26. to merge several files use this format files lt path gt lt to gt lt filel gt lt ext gt any option renamings specified here will override the corresponding options defined at the level of the entity transposed newnames True Fals lt fieldX_oldname gt lt fieldX_newname gt lt fieldY_oldname gt lt fieldY_newname gt 68 Chapier 8 Importing data LIAM2 User Guide Release 0 10 2 if you don t have any specific option for a file use lt path gt lt to gt lt file2 gt lt ext gt OR if all the files use the global options the options defined at the level of the entity files lt path gt lt to gt lt filel gt lt ext gt lt path gt lt to gt lt file2 gt lt ext gt if you want to fill missing values for some fields this only works when files is used interpolate lt fieldX_name gt previous_value if you want to invert the value of some boolean fields True gt False and False gt True add them to the invert list below invert list of boolean fields to invert lt entity2_name gt Most elements of this description file are optional The only required elements are output and entities If an element is not specified it uses the following default value e if path is omitted it defaults to a file named after the entity in the same directory than the descriptio
27. variable returning a numerical value It will be used to rank individuals One will usually use logit_score to compute the score but it can be computed in any other way a modeller choose Note that the score is not modified in any way within the align function so if one wants a random factor it should be added manually or through the use of a function like logit_score which includes one proportions the target proportions for each category This argument can take many forms The most common one will probably be a string holding the name of a file containing the alignment data like in the example above but it can be any of the following asingle scalar for aligning with a constant proportion alist of scalars for aligning with constant proportions per category an expression returning a single scalar an expression returning an n dimensional array expressions and possible values will be retrieved from that array so you can simply use align score_expr array_expr alist of expressions returning scalars expr1 expr2 a string treated as a filename That file should be in the array format described in the Importing data section In that case the proportions expressions column names and possible values are read from that file The fname argument which used to be the way to define this is still supported for backward compatibility There is no technical restriction on names for
28. vectors and scalars and it might be confusing do users realize they are assigning a value for each individual even if that is only one of two values In an expression like the following age_sum if gender sum age sum age 75 LIAM2 User Guide Release 0 10 2 do users realize they are assigning a different value for both branches When I see an expression like this I think it returns the same value whether the condition is True or not let s simplify it by removing the condition age_sum sum age which will not have the same result Another smaller point is that implementing this contextual filter feature means one cannot escape the filter of an if function so for example difficult_match if to_marry and not gender abs age avg age filter to_marry and gender nan would not work and would need to be rewritten as avg_age_men avg age filter to_marry and gender difficult_match if to_marry and not gender abs age avg_age_men nan I would greatly appreciate more input on the subject so please make your voice heard if you have an opinion about this on the dev mailing list 10 1 2 31 different variables per expression Within a single expression one may only use 31 different variables There is a simple workaround though split your expression in several pieces each one using less than 31 variables Examp
29. 4 2eo01 58 95 ee VG Oe Al eee a of Al OS coral 50 15 429 85 100 00 example groupby workstate gender xpr avg age gives the average age by workstate and gender workstate gender False True total aL Ail S29 40 53 40 88 2 40 28 44 51 41 88 3 hs 32 Te TO 8 02 4 72 48 T2627 V2 5 38 5 42 35 46 56 43 48 Boran 42 67 42 38 42 53 40 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 As of version 0 6 groupby can also be used in larger expressions This can be used for example to compute alignment targets on the fly see note below about expr count condition vs filter condition men_by_age groupby age expr count gender men_prop_by_age men_by_age groupby age aligned align proportions men_prop_by_age Note that there is a subtle difference between using filter condition and expr count condition The former will not take the filtered individuals into account at all while the later will take them into account but not count them This can make a difference on the output if there are some empty categories and this can be important when using the result of a groupby inside a larger expression as above because it can only work with arrays of the same size Compare groupby civilstate filter age gt 80 Civilstate 3 4 toral Sda a150 l 5 yyy with groupby civils
30. EAA TORN 38 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 You can also output several rows with a single command by enclosing values between brackets csv rowlvaluel rowlvalueN rowNvaluel rowNvalueN fname several_rows csv example esv this is a header with several lines fname person_age_aggregates csv Will produce a file with a layout like this this is a header with several lines 5 7 4 dump dump produces a table with the expressions given as argument evaluated over many possibly all individuals of the dataset general format Gump fesspisl es 1e2 7 eee ty filter filterexpression missing value header True If no expression is given all fields of the current entity will be dumped including temporary variables available at that point otherwise each expression will be evaluated on the objects which satisfy the filter and produce a table The filter argument allows to evaluate the expressions only on the individuals which satisfy the filter Defaults to None evaluate on all individuals The missing argument can be used to transform nan values to another value Defaults to None no transforma tion The header argument determine whether column names should be in the dump or not Defaults to True example show dump age partner age gender fil
31. The context is passed around to the evaluation functions methods A context must present a simple dictionary interface key value There are a few keys with special meanings period should be the period currently being evaluated __len__ if present should be an int representing the number of rows in the context __entity___ current entity __globals__ if present should be a dictionary of global tables periodic The kind of context which is most used is the EntityContext which provides a context interface to an Entity 10 2 2 Other files Main code config py Stores some global configuration variables console py Handles the interactive console cpartition pyx Cython source to speed up our partitioning function group_indices_nd which is used in groupby and alignment cpartition c generated from cpartition pyx using Cython cpartition pyd cpartition c compiled cutils pyx Cython source to speed up some commonly used utility functions cutils c generated from cutils pyx using Cython cutils pyd cutils c compiled data py handles loading indexing checking merging copying or modifying adding or removing fields tables or subsets of them It tries to provide a uniform interface from different data sources but it is a work in progress exprtools py parsing code for expressions importer py code to import csv files in our own hdf5 subformat by reading an import file in yaml khash h Generic hash table from Klib
32. a Logarithmic Series distribution See numpy random logseries for details New in version 0 9 multinomial n pvals size None Draw samples from a multinomial distribution See numpy random multinomial for details New in version 0 9 multivariate_normal mean cov size None Draw random samples from a multivariate normal distribution See numpy random multivariate_normal for details New in version 0 9 negative_binomial n p size None Draw samples from a negative_binomial distribution See numpy random negative_binomial for details New in version 0 9 noncentral_chisquare df nonc size None Draw samples from a noncentral chi square distribution See numpy random noncentral_chisquare for details New in version 0 9 noncentral_f dfnum dfden nonc size None Draw samples from the noncentral F distribution See numpy random noncentral_f for details New in version 0 9 normal loc 0 0 scale 1 0 size None Draw random samples from a normal Gaussian distribution See numpy random normal for details pareto a size None Draw samples from a Pareto II or Lomax distribution with specified shape See numpy random pareto for details New in version 0 9 poisson lam 1 0 size None Draw samples from a Poisson distribution See numpy random poisson for details New in version 0 9 power a size None Draws samples in 0 1 from a power distribution with positive exponent a 1 See numpy random power for details New
33. a variable which is not computed yet is used 10 4 Change log 95 LIAM2 User Guide Release 0 10 2 e added more information to the console log number of individuals at the start and end of each period more stats at the end of the simulation e excluded unused components in the executable to make it smaller Fixes fixed logit_regr align float fixed grpavg bool filter cond fixed groupby a b c expr grpsum d percent True fixed having several grpavg with a filter argument in the same expression fixed calling the main executable without argument simply display usage fixed dump with some kind of aggregate values in combination with a filter fixed void data source 10 4 18 Version 0 3 Released on 2011 06 29 New features e added ability to import csv files directly with the main executable Miscellaneous improvements e made periodic globals optional e improved a few sections of the documentation Fixes e fixed non assignment actions in interactive console csv remove e fixed error_var argument to cont_regr clip_regr and log_regr 10 4 19 Version 0 2 1 Released on 2011 06 20 Miscellaneous improvements e simplified and cleaned up the demonstration models e improved the error message when a link points to an unknown entity e the evaluator creates fewer internal temporary variables in some cases 96 Chapter 10 Appendix LIAM2 User Guide Releas
34. ad from person csv only the fields listed above The data will be converted if necessary to the type declared In this case person csv should contain at least the following columns not necessarily in this order period id age male workstate civilstate partner_id If the fields of an entity are scattered in several files you can use the files key to list them as in this fourth example output example4 h5 entities person fields Geis int gender bool workstate int CILL STAC aine renamings applying to all files of this entity newnames time period files param p_age csv additional renamings for this file only newnames value age param p_workstate csv newnames value workstate person csv should have at least 4 columns period id age and gender param person csv newnames we override the global renaming period period interpolate workstate previous_value 70 Chapier 8 Importing data LIAM2 User Guide Release 0 10 2 civilstate previous_value But this can become tedious if you have a lot of files to import and they all have the same column names If the name of the field can be extracted from the name of the file you can automate the process like this example 5 output example5 h5 entities person fields ages mat Wes OOS newnames time period valuates to th basename e
35. ade the operator precedence for and or and not more sensible which means that for example age gt 10 and age lt 20 is now equivalent to age gt 10 and age lt 20 instead of raising an error e many2one links are now 30 faster for large datasets e during import when a column is entirely empty and its type is not specified manually assume a float column instead of failing to import e allow id and period columns to be defined explicitly even though they are still implicit by default e allow period in any dimension in alignment files not only in the last one e disabled all warnings for x 0 and 0 0 This is not an ideal situation but it is still an improvement because they appeared in LIAM2 code and not in user code and as such confused users more than anything e the num_periods argument of lag lag age num_periods can now be a scalar expression it must have the same value for all individuals e changed output format of groupby to match input format for alignments e added Warning in grpgini when all values for the filter are zeros e when an unrecoverable error happens save the technical error log to the output directory for run and explore commands instead of the directory from where liam2 was run and display on the console where the file has been saved e better error message when an input file has inconsistent row lengths e better error mess
36. age when using a one2many function in a groupby expression Miscellaneous improvements for developers e added a code architecture section to the documentation e python tracebacks can be re activated by setting the DEBUG environment variable to True e added a script to automate much of the release process 90 Chapter 10 Appendix LIAM2 User Guide Release 0 10 2 added source files for creating liam2 bundle ie add our custom version of notepad to the source distribu tion updated INSTALL file and include sections on how to build the documentation and the C extensions added many tests fixed a few existing ones and generally greatly improved our test suite Fixes fixed transposed option on import The number of lines to copy was computed on the untransposed data which meant too few data points were copied if the number columns was greater than the number of lines and it crashed if it was smaller fixed all aggregate functions except grpcount and grpsum with a filter argument equal to a simple variable eg filter gender in the presence of missing nan values in the expression being aggregated the filter variable was modified fixed duration on a simple variable eg duration work the variable was modified by the function fixed a nasty bug which made that each variable that needed to be read on disk lag of more than one period duration value_for_period was read 2 or 3 times inst
37. alse 0 51 0 49 The first sub process to_give_birth is a logit regression over women not gender between 15 and 50 which returns a boolean value whether that person should give birth or not The logit itself does not have a deterministic part 0 0 which means that all women that meet the above condition are equally likely to give birth they are selected randomly This process is also aligned on the data in al_p_birth csv In the above case a new person is created for each time a woman is selected to give birth Secondly a number of links are established the value for the mother_id field of the child is set to the id number of his her mother the child s father is set to the partner of the mother the child receives the household number of his her mother Finally some variables of the child are set to specific initial values the most important of these is its gender which is the result of a simple choice process new can create individuals of different entities the below function get_a_life makes sure that all those who are single when they are 24 year old leave their parents household for their own household The region of this new household is created randomly through a choice process example 2 get_a_life household_id if ISSINGLE and age 24 new household 34 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 region_id choice 0 1 2 3 h
38. ame income period csv would create income2002 csv and income2003 csv e mode allows appending mode a to a csv file instead of overwriting it mode w by default This allows you for example to store the value of some expression for all periods in the same file instead of one file per period by default example csv period avg income fname avg_income csv mode a Note Unless you erase overwrite the file one way or another between two runs of a simulation you will append the data of the current simulation to that of the previous one One way to do overwrite the file automatically at the start of a simulation is to have a function in the init section without mode a If you want that file to start empty you can do so this way csv fname avg_income csv If you want some headers in your file you could write them at that point csv period average income fname avg_income csv When you use the csv function in combination with at least one table expressions see dump and groupby functions below the results are appended below each other csv table_exprl and here goes another table table_expr2 fname tables csv Will produce a file with a layout like this table 1 value at row 1 col 1 EOL 2 EN COMEN ROWEN ECON col 2 Greet COMEN and here goes another table table 2 value at row 1 col 1 ay col N Powe Nae CONN
39. and efficient I O and for high volume and complex data HDF5 is portable and is extensible allowing applications to evolve in their use of HDF5 The HDF5 Technology suite includes tools and applications for managing manipulating viewing and analyzing data in the HDF5 format HDF is open source and the software is distributed at no cost Potential users can evaluate HDF without any financial investment Projects that adopt HDF are assured that the technology they rely on to manage their data is not dependent upon a proprietary format and binary only software that a company may dramatically increase the price of or decide to stop supporting altogether This allows us to handle important data sets 10 3 3 YAML The definition of the data and the model is done in the YAML language http www yaml org YAML YAML Ain t Markup Language What It Is YAML is a human friendly data serialization standard for all programming languages 10 4 Change log 10 4 1 Version 0 10 2 Released on 2015 06 24 Fixes e fixed the fields command in the interactive console closes issue 176 e if there is only one entity defined start the interactive console in that entity even if default_entity is not set closes issue 175 10 3 Technical choices 79 LIAM2 User Guide Release 0 10 2 10 4 2 Version 0 10 1 Released on 2015 06 22 New features e allowed to override all simulation options except init and processes using th
40. asily achieved by setting a very high score for individuals to be taken first leave an expression specifying individuals which should never be selected regardless of their score This argument should be used with care as those individuals will never be selected even if that cause the target number of individuals for some categories to not be reached A softer alternative can be easily achieved by setting a very low score for individuals to be taken last Note Note that even if the score for an individual is 1 or any other negative number it can still be selected by the alignment expression This happens when there are not enough candidates selected by the filter to meet the alignment needs 28 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 e expressions specify the expressions used to partition the individuals into the different alignment categories If proportions is a file name the column names declared in the file are used by default but they can be overridden using this argument For example align 0 0 al_p_dead csv expressions gender age 1 e possible_values specify the different values for each of the expressions in the expressions argument that should be evaluated The combination of the different lists of possible values will form all the alignment categories For example align 0 0 QeoCoomclLomMs O i O 2 Oss Os4 xpressions gender age lt 50
41. bal lt num_migrants total_population MIG_PERCENT MIG is a 3d array age gender period but we want only the 2d array for this period currently we need to manually compute the index 0 based for the current period in the array We know the first period in our array is 2000 so the index for the current period is period 2000 period is the last dimension of the array and we do not want to modify other dimensions so we use for those dimensions mig_period MIG period 2000 Distribute total desired migrants by age and gender need num_migrants mig_period households have a 50 chance to be candidate for immigration Se eSmCanGearcaiee a Unior a OS apply alignment using the number of persons in each household aS a score so that households with more persons are tried first as this gives better results aligned align_abs num_persons need filter is_candidate link persons secondary_axis gender errors carry logit_regr logit_regr is a shortcut form to call logit_score and evaluate whether the event happened in a single function Thus the function returns a boolean True for individuals which are selected False for all others Its general form is aligned logit_regr expression filter conditions align proportions The align argument supports all the same formats than the proportions argument of align file
42. ce between her age and the average age of candidate men In a third step for each candidate woman in turn following the order set by difficult_match all candidate men which are still available are assigned a score and the man with the highest score is matched with that woman This score depends on his age his difference in age with the woman and the work status of the potential partners rank_matching New in version 0 9 rank_matching works in three steps 1 Set 1 is sorted by decreasing orderby1 2 Set 2 is sorted by decreasing orderby2 3 Individuals in the nth rank position in each list are matched together The function returns the id of the matched individual for each individual which was actually matched 1 for others If the two sets are of different sizes the surplus of the largest set is ignored generic setup rank_matching setlfilter boolean_expr set2filter boolean_expr orderbyl expression orberby2 expression 5 5 Built in Functions 33 LIAM2 User Guide Release 0 10 2 5 5 9 Lifecycle functions new new creates new individuals It can create individuals of the same entity eg a women gives birth or another entity eg a person s marriage creates a new houshold The function returns the id of the newly created individuals generic format new entity_name filter expr number value xset initial values of a selection of variables The first argument specifie
43. code and benefit from this optimisation there is a pure python fallback he needs to have cython and a C compiler installed other minor optimisations to groupby and alignments with take or leave filters slightly sped up initial data loading for very large datasets with a lot of historical data e choices arguments options and probabilities now accept expressions ie they can be computed at run time e improved the interactive console made the interactive console start in the last simulated period by default changed the behaviour of the entity command without argument to print the current entity the period command can now be called without argument to print the current period e added more explicit checks for bad input check for duplicate headers in alignment files check all arguments to groupby are valid instead of only the first one check for invalid keyword arguments to dump Q check for invalid keyword arguments to csv check the type of arguments to choice validate globals at load time to make sure the declared globals are actually present in the dataset e disallow strings for the score expression in the matching function 10 4 Change log 93 LIAM2 User Guide Release 0 10 2 improved the test coverage There is still a long way for full test coverage but the changes in this version is already a first step in the right direction automated many tests by using the new asse
44. d blue bars Note boxplot does not support the colors argument grid FalselTrue determine whether to display a grid in addition to axes ticks It defaults to True for bar and plot and to False for boxplot and stackplot Note pie does not support the grid argument maxticks limit the number of axes ticks It defaults to 20 for all charts except bar3d where it defaults to 10 Note pie does not support the maxticks argument bar charts New in version 0 8 bar can be used to draw bar charts It uses matplotlib pyplot bar and inherits all of its keyword arguments There are 3 ways to use it loyetia Alicl_ sxjore 5 4 4 par ilicl_ esgoreil EEPE 64 baie 2dlMexpaa en In the first two d_expr is an expression returning a one dimensional array for example an entity field or a groupby expression with only one dimension For example bar groupby agegroup would produce 42 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 800L 600l 400 200 0 5 10 15 20 25 30 35 40 45 50 60 70 80 90 agegroup If one passes several arrays expressions they will be stacked on each other bar groupby agegroup filter not gender groupby agegroup filter gender 5 7 Output 43 LIAM2 User Guide Release 0 10 2 800L 600l 400 0 5 10 15 20 25 30 35 40 45 50 60 70 80 90 agegroup Alternativ
45. declared return type of many random distributions which caused a problem if they were used with a filter or within an if expression This change also fixed cont_regr when both mult and filter arguments are used closes issue 153 10 4 6 Version 0 9 Released on 2015 02 03 New features e added support for most of the random number generators provided by Numpy which were not already supported by LIAM2 beta chisquare dirichlet exponential f gamma geometric hypergeometric laplace lognormal multivariate_normal noncentral_chisquare noncentral_f pareto power rayleigh stan dard_cauchy standard_exponential standard_gamma standard_normal standard_t triangular vonmises wald weibull zipf binomial logseries negative_binomial poisson and multinomial see the random func tions section for details Closes issue 137 added the rank_matching function as an alternative method to match two sets of individuals Based on pull request 136 from Alexis Eidelman added an optional algo argument to the matching function which can be set to either onebyone or byvalue onebyone is the current default and should give the same result as previous versions byvalue groups individuals by their value for all the variables involved in both the score and orderby expressions and match groups together Depending on whether all individuals have different com bination of values or not this can be
46. different than above even though we did not explicitly assign it a new value 3 5 4 processes Here you define the processes you will need in the model For details see the Processes section 3 6 simulation The simulation block includes the location of the datasets input output the number of periods and the start period It sets what processes defined in the entities block are simulated since some can be omitted and the order in which this is done Please note that even though in all our examples periods correspond to years the interpretation of the period is up to the modeller and can thus be an integer number representing anything a day a month a quarter or anything you can think of This is an important choice as it will impact the whole model Suppose that we have a model that starts in 2002 and has to simulate for 10 periods Furthermore suppose that we have two entities individuals and households The model starts by some initial processes defined in the init section that precede the actual prospective simulation of the model and that only apply to the observed dataset in 2001 or before These initial simulations can pertain to the level of the individual or the household Use the init block to calculate variables for the starting period The prospective part of the model starts by a number of sub processes setting the household size and composition Next two processes apply on the level of the individual changing
47. e so you might want to get used to typing the parentheses 5 3 2 Call To execute a function it has to be either 1 specified in the processes section of the simulation block of the model example entities person fields Ager aine processes ageing age age 1 simulation processes person ageing 2 called explicitly within an expression In that case the format is function_name If the function does not return any result or if the result is not interesting this comes down to processes myfunction anotherfunction but it can really be used anywhere within an expression whose result can be stored in a variable like any other expression 5 3 Functions 17 LIAM2 User Guide Release 0 10 2 variable_name expr function_name expr example entities person processes other_func show in other_func plus a b retim F 9 test_func show in test _func ther _func how back to test_func o s storing the result in a temporary variable three plus 1 2 show l 2 is three but the function call can happen anywhere within an expression s Row CU IL ae 2 2 2 ats o S a SH He simulation processes person test_func 5 3 3 Local temporary variables All fields declared in the fields section of the entity are stored in the output file Of
48. e 0 10 2 Fixes added log and exp to the list of available functions they were already implemented but not usable because of that fixed log_regr cont_regr and clip_regr which were comparing their result with 0 5 like logit_regr when there is no alignment fixed new function which created individuals correctly but in some cases returned values which did not correspond to the ids of the newly created individuals due to a bug in numpy 10 4 20 Version 0 2 Released on 2011 06 07 New features added support for retrospective simulation ie simulating periods for which we already have some data at the start of each simulated period if there is any data in the input file for that period it is merged with the result of the last simulated period If there is any conflict the data in the input file has priority added clone function which creates new individuals by copying all fields from their origin individuals except for the fields which are given a value manually added breakpoint function which launches the interactive console during a simulation Two more console commands are available in that mode s tep to execute the next process r esume to resume normal execution The breakpoint function takes an optional period argument so that it triggers only for that specific period added tsum function which sums an expression over the whole lifetime of individuals It returns an
49. e and has four sub processes The first sub process defines a local variable no_collar which will be used to select those that the function should apply to These are all the workers that do not have a value for collar The next three sub processes simulate the actual collar variable If one meets the above no_collar filter and has the lowest level of education 2 then one has a probability of about 83 6 men and 68 7 women of being a blue collar worker If one has education_level equal to 3 the probability of being a blue collar worker is lower 64 3 for men and 31 3 for women etc 5 5 7 Regressions logit_score The logit of a number p between 0 and 1 is given by the formula logit jo loge il ja Its inverse the logistic function has the interesting property that it can convert any real number into a probability logistic a 1 1 exp a The logit_score function is a logistic with a random part Ho guiums Corel a a Logusiee au a logase up where u is a random number from an uniform distribution 0 1 logit_score is very useful in behavioural equations A behavioural equation starts by creating a score that reflects the risk p i of an event occurring A typical usage is as follow score_variable if condition_l logit_score logit_expr_1 Tt i conca tion 7 logit_score logit_expr_2 FA However the nested structure can make things less readable
50. e command line Run main run h for details closes issue 173 Fixes e fixed the error message when using an unknown variable to be more explicit like it was in versions before 0 9 closes issue 167 e the output of the demonstration models is no longer included in the bundles closes issue 169 e made simulations which terminate in an error exit with the correct error code even without debug closes issue 174 10 4 3 Version 0 10 Released on 2015 06 15 New features implemented support for calling user defined functions previously called procedures from within user code optionally passing arguments to them and retrieving their return value As a consequence of this every mention of procedures in the documentation has been replaced by functions including the name of the procedures logging level which is now deprecated Closes issue 152 implemented while loops closes issue 151 added support for not storing some fields in the output file closes issue 58 added support for using the inf infinite constant Miscellaneous improvements e improved our error handling code to display the part of the line where the error occurred in more cases and to not strip the traceback error log of some important information in the cases where the line was already displayed configured the bundle editor Notepad to display some warning and error lines in red in the console log Additionally
51. e dump or groupby functions In the interactive console you can use any of those output functions to inspect the data interactively 36 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 5 7 1 show show evaluates expressions and prints the result to the console log Note that in the interactive console show is implicit on all commands so you do not need to use it show has the following signature show exprl expr2 expr3 example 1 show count age gt 18 show count not dead avg age filter not dead The first process will print out the number of persons of age 18 and older in the dataset The second one displays the number of living people and their average age example 2 Showt Counc gt count Average age avg age Age std dev std age gives Count 19944 Average age 42 7496991576 Age std dev 21 9815913417 Note that you can use the special character n to display the rest of the result on the next line example 3 Sshowt Councs count nAverage age avg age nAge std dev std age gives Count 19944 Average age 42 7496991576 Age std dev 21 9815913417 5 7 2 qshow qshow evaluates expressions and prints their results to the console log alongside the textual form of the expres sions If several expressions are given they are each printed on a separate line gsho
52. e through a many2one link like in the num_kids_in_hh process This process computes for each person the number of children in the household of that person Note that the variable num_kids_in_hh could also have been simulated by just one process on the person level by using num_kids_in_hh household get persons count age lt 17 6 2 one2many 61 LIAM2 User Guide Release 0 10 2 62 Chapter 6 Links CHAPTER SEVEN IMPORTING OTHER MODELS A model file can optionally import an other model file s An import directive can take two forms import path filename yml or BEMO Onaiers pathi filenamel yml path2 filename2 yml Each file in the import section will be merged with the current file in the order it appears Merging means that fields links macros and processes from the imported file are added to the ones of the current file If there is a conflict something with the same name is defined for the same entity in both files the current file the model importing the other model takes priority This means one can override entity processes defined in imported files or add fields to an entity defined in the imported model Note that both the importing model and the imported model need not be complete valid models they do not need to include all required sub sections as long as the combined model is valid See the examples below example common yml
53. ead of just once greatly slowing down the function fixed accessing columns for the next to last period in the interactive console after a simulation it was either giving bad results or returning an error fixed all aggregate functions except grpcount grpsum and grpavg which worked on boolean expressions This is actually only remotely useful for grpgini and grpstd fixed groupby with both filter and expr arguments fixed groupby expr scalar fixed sumlink link scalar fixed new number fixed non aligned regressions with a filter it was ignored fixed the editor shortcuts to launch liam2 to work when the directory containing the model contains spaces fixed handling of comments in the first cell of a row in alignments files the entire row is ignored now fixed textual form of choice expressions when bins or choices are dynamic fixed using numpy 1 7 Experimental new features implemented optional periodicity for simulation processes 10 4 14 Version 0 5 1 Released on 2012 11 28 Miscellaneous improvements if there is only one entity defined in a model like in demoO1 yml and the interactive console is launched start directly in that entity instead of requiring the user to set it manually improved introduction comments in demo models display whether C extensions are used or not in versions use default_entity in demos from demo03 onward 10 4 Change log 91 LIAM2 User Guide Rel
54. ease 0 10 2 do not display python version in normal execution but only in versions use cx_freeze instead of py2exe to build executables for Windows so that we can use the same script to build executables across platforms and tweaked further our build script to minimise the executable size compressed as many files as possible in the 32 bit Windows bundle with UPX to make the archive yet smaller UPX does not support 64 bit executables yet improved our build system to automate much of the release process Fixes fixed the explore command fixed integer fields on 64 bit platforms other than Windows fixed demo06 WEMRA is an int now fixed demo01 introduction comment bad file name 10 4 15 Version 0 5 Released on 2012 10 25 New features added a way to import several files for the same entity A few comments are in order Each file can have different data points eg if you have historical data for some fields data going back to 1950 for some individuals and other fields going back to only 2000 the import mechanism will merge those data sets It can also optionally fill missing data points Currently it only supports filling with the previous value the value the individual had if any for that field in a previous period In the future we will add more ways to fill those by interpolating existing data Note that currently only data points which are entirely missing are filled not those which are
55. ed Copy the contents of the bundle in a directory on your disk let us call it BUNDLEPATH Run the Notepad Portable exe from the BUNDLEPATH Jeditor directory Open a model eg BUNDLEPATH Jexamples demo01 yml Press F6 to run the model A console window will open within the editor and display the status of the simulation After the simulation completes the console window becomes interactive Use this console to explore the results If you already quit the interactive console and want to explore the results with the interactive console again without re simulating the model you can press F7 Alternatively you can explore the results graphically by pressing F9 This will open both the input dataset and the result file if any with an hdf5 viewer ViTables Using your own data Prepare your data as CSV files The first row should contain the name of the fields You need at least two integer columns id and period though they do not necessarily need to be named like that in the csv file Create an import file as described in the Jmporting data section You can use BUNDLEPATH examples demo_import yml as an example Press F5 to convert your CSV files to hdf5 Use the newly created data file with your model LIAM2 User Guide Release 0 10 2 4 Chapter 2 Environment CHAPTER THREE MODEL DEFINITION To define the model we have to describe the different entities their fields the way the
56. ed precisions in the documentation of align based on Alexis Eidelman suggestions made a few more error messages a bit more useful by displaying the line where the error occurred sped up global array_expr give a hint to use assertNanEqual when it would make a failing assertEqual pass implemented global slice_expr eg MINR period period 2 When the slice bounds are arrays different for each individual and the slice length is not constant not the same for all individals it returns a special array with an extremely limited set of supported operations only aggregates on axis 1 are implemented include the documentation only in HTML Help format chm in the bundle pdf and normal html are still available as separate downloads on the website removed the predictor keyword support it now raises an exception instead of a warning adapted the release script since our move to git and converted it to Python Fixes fixed the syntax upgrade script by removing a special case for grpmin and grpmax as it was in fact not needed and caused problems when the expression being aggregated contained parentheses 10 4 10 Version 0 7 Released on 2013 06 18 New features implemented imports so that simulation files can be split and reused This can be used to simply split a large model file into smaller files or more interestingly to create simulation variants without having to duplicate the common parts This feature was ins
57. elloul pull request 161 e allow simulations with no processes section but an init section e reworked a few sections of the documentation e trying to set a value to an unknown variable in new clone produces a warning instead of being silently ignored or even crashing with debug Fixes e fixed end of simulation stats when simulating 0 periods closes issue 158 e allow overriding detected field types of period and id fields in import closes issue 154 e fixed autodump broken in 0 9 Note that it is currently incompatible with while loops and recursive user defined functions 10 4 Change log 81 LIAM2 User Guide Release 0 10 2 10 4 4 Version 0 9 1 1 Released on 2015 04 14 Fixes e fixed version number release 0 9 1 reports itself as 0 9 e fixed various small problems with the release script e made the 32b version use the exact same versions of third party packages as the 64b version 10 4 5 Version 0 9 1 Released on 2015 03 31 Fixes e Alignment under and overflows are displayed again even when debug is not set closes issue 155 e Always load all declared entities even if there is no process executed for them but produce a warning in that case This used to cause a problem if an entity had no process but was used through links closes issue 89 e Fixed dump when the filter is False a scalar for example in dump filter period 2100 closes issue 142 e Fixed the
58. ely one can pass an expression returning a two dimensional array in which case the first dimension will be stacked for each possible value of the first dimension there will be a bar part with a different color bar groupby eduach agegroup 44 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 800 600l 400 plot New in version 0 8 5 10 15 20 25 30 35 40 45 50 60 70 80 90 agegroup plot can be used to draw line plots It uses matplotlib pyplot plot and inherits all of its keyword arguments There are 4 ways to use it plot ld_expr plot ld_exprl plot 2d_expr plot ld_exprl o cl SEone2 5 56 D scyle scil lel sxor Sreyle STi2p ooo In the first two d_expr is an expression returning a one dimensional array for example an entity field or a groupby expression with only one dimension For example plot groupby age 5 7 Output 45 LIAM2 User Guide Release 0 10 2 200 100 50 O 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 age If one passes several expressions each will be plotted as a different line plot groupby age groupby age filter not gender groupby age filter gender 46 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 200 100 50 A ce IN N7 e O 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 age The third
59. ent data error message when loading an alignment file by changing the word ing and adding the path of the file with the error reorganised bundle files so that there is no confusion between directories for Notepad and those of liam2 tweaked Notepad configuration added explore command as F7 removed more unnecessary features Fixes disallowed using one2many links like many2one it was never intended this way and produced wrong re sults fixed groupby with a scalar expression it does not make much sense but it is better to return the result than to fail re enabled the code to show the expressions containing errors where possible in addition to the error mes sage This was accidentally removed in a previous version fixed usage to include the explore command 94 Chapter 10 Appendix LIAM2 User Guide Release 0 10 2 10 4 17 Version 0 4 Released on 2011 11 25 New features added grpgini function added grpmedian function implemented filter argument in grpsum implemented N dimensional alignment alignment can be done on more than two variables dimensions in the same file added keyword arguments to csv fname to allow defining the exact name of the csv file mode to allow appending to a csv file instead of overwriting it reworked csv function to support several arguments like show It also supports non table arguments added skip_shows simulation
60. file expr py and many others Expressions are the meat of the code The Expr class is the base class for all expressions in LIAM2 It defines all the basic operators on expressions arithmetic logical comparison but it should not be inherited from directly file exprbases py LIAM2 provides many different bases classes to inherit from when implementing a new function e NumexprFunction base class for functions which are implemented as is in numexpr eg abs log exp e CompoundExpression base class for expressions which can be expressed in terms of other liam expres sions eg min max zeroclip e EvaluableExpression base class for all other expressions those that do not exist in numexpr and cannot be expressed in terms of other liam2 expressions These expressions need to be pre evaluated and stored in a hidden temporary variable before being fed to numexpr and this is what EvaluableExpression does One should only inherit from this class directly if none of the below subclasses applies 1 NumpyFunction subclass for functions which are implemented as is in Numpy Should not be used directly NumpyCreateArray subclass for functions which create arrays out of nothing usually random functions NumpyChangeArray subclass for functions which take an array as input and give another array as output eg clip round NumpyAggregate subclass for aggregate functions eg count min max std median 2 Functio
61. files containing alignment data but by convention they usually use the following pattern start with the prefix al_ followed by the name of the endogenous variable and a suffix _m or _f depending on gender e filter an expression specifying which individuals to take into account for the alignment Note that if the align function is used inside an if expression its filter is adjusted accordingly anded with the filter of the if expression For example aligned if condition align score_exprl filenamel csv align score_expr2 filename2 csv is equivalent to alignedl align score_expril filenamel csv filter condition aligned2 align score_expr2 filename2 csv filter not condition aligned if condition alignedl aligned2 take an expression specifying individuals which should always be selected regardless of their score This argument should be used with care as those individuals will be selected unconditionally even if that means overflowing the number of individuals desired to satisfy the alignment Suppose that the alignment specifies that 10 individuals should experience a certain event and that there are 3 individuals who meet the conditions specified in the take Then these 3 individuals will be selected a priori irrespective of their score and the alignment process will select the remaining 7 candidates from the rest of the sample A softer alternative can be e
62. gender age 1 e the result of a groupby can be used in expressions This can be used for example to compute alignment targets on the fly e implemented explore on data files h5 so that one can for example explore the input dataset e added skip_na defaults to True argument to all aggregate functions to specify whether or not missing values nan for float expressions 1 for integer expressions should be ignored e macros can now be used in the interactive console e added globals command in the interactive console to list the available globals 10 4 Change log 89 LIAM2 User Guide Release 0 10 2 e added qshow command to show an expression textual form in addition to its value Example qshow grpavg age will display grpavg age 38 5277057298 e added optional pvalues argument to groupby to manually provide the axis values to compute the expression on instead of having groupby compute the combination of all the unique values present in the dataset for each column Miscellaneous improvements for users e improved the documentation in part thanks to the corrections and suggestions from Alexis Eidelman e added a known issues section to the documentation e grpmin and grpmax ignore missing values nan and 1 by default like other aggregate functions e grpavg ignore 1 values for integer expressions like other aggregate functions e m
63. groupby agegroup x colors Ee el Ma 5 7 Output 49 LIAM2 User Guide Release 0 10 2 0 5 10 15 20 25 30 35 40 45 50 60 70 80 90 agegroup stackplot New in version 0 8 stackplot can be used to draw stacked line plots It uses matplotlib pyplot stackplot and inherits all of its keyword arguments There are two ways to use it Stackplor Mdlexprily ss tdmiexpe2 7 stackplot 2d_expr Example stackplot groupby eduach age 50 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 200 150 100 50 0 O 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 age pie charts New in version 0 8 pie can be used to draw pie charts It uses matplotlib pyplot pie and inherits all of its keyword arguments It should be used like this jon ilicl_esgoreil 46 5 Where d_expr is an expression returning a one dimensional array for example an entity field or a groupby expression with only one dimension Examples pie groupby eduach pie groupby eduach explode 0 1 0 O labels Lower secondary Upper secondary Tertiary 5 7 Output 51 LIAM2 User Guide Release 0 10 2 eduach Tertiary Lower secondary Upper secondary 52 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 scatter plots New in version 0 8 scatter can be used to draw scatter plots It uses matplot
64. hange log 87 LIAM2 User Guide Release 0 10 2 Fixes e fixed using non scalar values eg fields as indices of n dimensional arrays and generally made indexing n dimensional arrays more robust e fixed choice which did not refuse to run when the sum of probability is 1 and the error is gt le 6 as it should This was the case in past versions but the test was accidentally removed in version 0 5 e fixed choice to warn when the sum of probabilities is gt 1 and the error is lt le 6 Previously it only warned if the sum was lt 1 10 4 13 Version 0 6 Released on 2013 03 15 New features e globals handling has been vastly improved multiple tables one can now define several tables in globals and not only the periodic table These should be imported in the import file and declared in the simulation file in the exact same way that periodic globals are Their usage within a simulation is a bit different though whereas periodic global variables can be used without prefixing others globals need to be prefixed with the name of their table For example if one has declared a global table named othertable othertable fields INEPT RD re FLOATFIELD float its fields can be used like this my_variable othertable INTFIELD 10 These other global tables need not contain a PERIOD column When using such a table LIAM2 will not automatically subtract t
65. he base period from the index which means that to access a particular row you have to use its row index 0 based n dimensional globals in addition to tables globals can now be n dimensional arrays The file format for those should be the same than alignment files They should be declared like this MYARRAY type float globals can now be used in all situations instead of only in simple expressions and only for the current period Namely it makes globals available in link functions temporal functions lag value_for_period matching new and in all the different flavours of the interactive console e alignment has been vastly improved align_abs is a new function with the same arguments than align which can be used to align to absolute numbers per category instead of proportions Combined with other improvements in this release this allows maximum flexibility for computing alignment targets on the fly see below align on a linked entity a k a immigration additionally to the arguments of align align_abs has also an optional link argument which makes it work on the linked entities The link argument must a one2many link For example it can be used to take as many household s as necessary trying to get as close as possible to a particular distribution of persons When the link argument is in effect the function uses the Chenard algorithm In this form align_abs also supports
66. he case of leave conditions for those who satisfy the filter of the alignment but for which a score is not explicitly specified the subsequent processes Next come four if conditions separating the various behavioural equations to the sub sample they pertain to The first two conditions pertain to men and respectively describe the probability of keeping a job and getting a job The next two conditions describe the same transitions but for women The last sub process describes the alignment process itself Alignment is applied to individuals between the age of 15 and 65 The input files of the alignment process are al_p_inwork_m csv and al_p_inwork_f csv The alignment process uses as input the scores simulated previously and the information in the alignment files and sets the boolean variable work No take or leave conditions are used in this case align_abs align_abs is equivalent to align except that it aligns to absolute numbers instead of proportions It also supports a few additional arguments to work on a linked entity The general form of align_abs is align_abs score need filter conditions take conditions leave conditions xpressions expressions possible _values pvalues ieicevel_joveverol Guo icone Wretonuvavel Neiohe ues Y 5 link link_name secondary_axis column_name errors default carry age 3 In addition to all the arguments supported b
67. help for details changed the syntax for all one2many link functions xxxlink link_name should now be link_name xxx For example countlink persons should now be persons count The old syntax is still valid but it is deprecated it will be removed in a later version As for aggregate functions one can upgrade its models automatically with the upgrade command the period argument of value_for_period can now be a scalar expression it must have the same value for all individuals when the output directory does not exist LIAM2 will now try to create it when debug mode is on print the position in the random sequence before and after operations which use random numbers entities are loaded stored for each period in alphabetical order instead of randomly This has no influence on the results but produces nicer log files 86 Chapter 10 Appendix LIAM2 User Guide Release 0 10 2 e deprecated the predictor keyword If you need several processes to write to the same variable you should use procedures instead Fixes using invalid indexes in global arrays do not crash anymore if they are properly enclosed in an if expres sion For example if you have an array by_age with values for indices from 0 to 99 the following code will now work as expected if age lt 50 by_age age 50 0 5 Periodic globals are unaffected they always return missing when out of bound
68. her models section 3 4 globals globals are variables aka parameters that do not relate to any particular entity defined in the model They can be used in expressions in any entity LIAM2 currently supports two kinds of globals tables and multi dimensional arrays Both kinds need to be declared in the simulation file as follow globals mytable fields MYINTFIELD int MYFLOATFIELD float MYARRAY type float Please see the g obals usage section for how to use them in you expressions Globals can be loaded from either csv files during the simulation or from the HDF5 input file along with the entities data In the later case they need to be imported as explained in the Jmporting data section before they can be used If globals need to be loaded from csv files during the simulation the path to the files need to be given like globals mytable path mytable csv fields NENE LD ae MYFLOATFIELD float MYARRAY path path to myarray csv type float If no path is specified the globals are assumed to be in the HDF5 file There are globals with a special status periodic globals Those globals have a different value for each period periodic is thus a reserved word and is always a table so the fields keyword can be omitted for that table For example the retirement age for women in Belgium has been gradually increasing from 61 in 1997 to 65 in 2009 A global variab
69. if you have many different conditions In that case one would prefer the following longer form process_name initialise the score Co score_variable 1 first condition 26 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 IES CO Cisemvic niple mente SO Clb tenet logit_score logit_expr_1 score_variable second condition SS COGCmyaiadalollc ase te eoOmcsukeahonunarr logit_score logit_expr_2 score_variable other conditions In a first sub process a variable score_variable is set equal to 1 because this makes it highly unlikely that the event will happen to those not included in the conditions for which the logit is applied Next subject to conditions condition_1 and condition_2 this score risk is simulated on the basis of estimated logits Note that by specifying the endogenous variable score_variable without any transformation in the else conditions of the if functions makes sure that the score variable is not manipulated by a sub process it does not pertain to When the score is known it can be either used as is event_happened uniform lt score_variable or in combination with an alignment see below align Now that we have computed a score risk for an event happening we might want to use alignment so the number of events occuring per category matches a proportion defined externaly There are different ways to choose which
70. import variant2 yml entities person processes use the alternate ageing function ageing age age 1 agegroup if age lt 50 Gy ey jeseblover eveje s Siy 10 trunc age 10 This last example could also be achieved by importing both variant1 yml and variant2 yml Notice that the order of imports is important since it determines the result of conflicts between variants For example in variant4 yml below the process list will be the one from variant2 and the output will go in variant2 h5 example variant4 yml 64 Chapter 7 Importing other models LIAM2 User Guide Release 0 10 2 import welica eioe JL iN variant2 yml 65 LIAM2 User Guide Release 0 10 2 66 Chapter 7 Importing other models CHAPTER EIGHT IMPORTING DATA 8 1 data files As of now you can only import CSV files LIAM2 currently supports two kinds of data files tables and multi dimensional arrays table files are used for entities data and optionally for globals They should have one column per field and their first row should contain the name of the fields These names should not contain any special character accents etc For entities data you need at least two integer columns id and period though they do not necessarily need to be named like that in the csv file array files are used for other external data alignment data for example They are arrays of any nu
71. ing output False in its definition Note that local temporary variables within functions do not need to be declared The only case where you want to use output False is when you need a variable that is accessible in several functions but not stored in the output file Warning All fields used in lag expressions must be in the output file example entities person fields ages int agegroup type int initialdata False temporary type int output False 3 5 2 links Individuals can be linked with each other or with individuals of other entities for example mothers are linked to their children partners are linked to each other and persons belong to households For details see the Links section 3 5 3 macros Macros are a way to make the code easier to read and maintain They are defined on the entity level Macros are re evaluated wherever they appear An usual convention is to use capital letters to define macros example entities person fields aee ine macros ISCHILD age lt 18 processes test_macros show before ISCHILD age age 1 hoy Watter TSCENLLD simulation processes person test_macros 8 Chapter 3 Model Definition LIAM2 User Guide Release 0 10 2 The above example does e show displays whether each person is a child e age the age is changed e show displays again whether each person is a child This value is
72. ith the same rank matching For each individual in set 1 following the order given by the orderby argument the function computes the score of all unmatched individuals in set 2 and takes the highest scoring one The function returns the id of the matched individual for each individual which was actually matched 1 for others If the two sets are of different sizes the surplus of the largest set is ignored generic setup matching setlfilter boolean_expr set2filter boolean_expr score coefl fieldl coef2 other field2 orderby expr expression or EDtM pool_size int None by default algo onebyone byvalue onebyone by default Arguments e setlfilter and set2filter specify the boolean filters which provide the two sets to match score is an expression to assign a value to each individual of set 2 given a particular individual in set 1 In the score expression the fields of the set 1 individual can be used normally while the fields of its possible partners from set 2 can be used by prefixing them by other e orderby defines the order in which the individuals of the first set are matched It can be either an expression or the EDtM string If it is an expression individuals in set 1 will by sorted by its decreasing values If set to EDtM Euclidean Distance to the Mean individuals will be sorted by decreasing distance to an hypothetical mean individual measured o
73. ix LIAM2 User Guide Release 0 10 2 e The behaviour when an assertion fails is configurable through the assertions option in the simulation block This option can take three values raise interrupt the simulation this is the default warn display a warning message skip do not run the assertion at all e added commands to the console entities prints the list of available entities periods prints the list of available periods for the current entity e added new command line arguments to override paths specified in the simulation file input path override the input path input file override the input file output path override the output path output file override the output file e added versions command line argument to display versions of all the libraries used Miscellaneous improvements e performance optimisations fields which are used in lag expressions are cached stored in memory to avoid fetching them from disk This considerably speeds up lag expressions at the expense of a bit more memory used implemented a few internal functions in Cython to get C level performance This considerably speeds up alignment and groupby expressions especially when the number of alignment categories the number of possible combinations of values for the variables used to partition is high The down side is that if someone wants to recreate liam2 binaries from the source
74. le iesiolles ail s 2 s cos a Asl o aS or ass could be rewritten as cma il ar 2Z ar son T asl gegilt iis a GSA ap Asis 10 2 Code architecture This document is meant for people who want to know more about the internals of LIAM2 for example to add or modify some functionality One should already be familiar with how the program is used on the user side 10 2 1 Concepts Here is a brief description of the most important concepts to understand the code of LIAM2 as well as where those concepts are implemented Simulation file simulation py The Simulation class takes care of loading the simulation file it delegates much of the work to entities prepares the data source and simulates each period in turn runs each process in turn Entity file entities py The Entity class stores all there is to know about each entity fields links processes and data It serves as a glue class between everything data processes 76 Chapter 10 Appendix LIAM2 User Guide Release 0 10 2 Process file process py The Process class stores users processes The most common kind of process is the Assignment which computes the value of an expression and optionally stores the result in a variable Another very common process is the Function previously known as procedures which runs a list of processes in order and optionally takes arguments and return a value Expressions
75. le WEMRA has therefore been included globals periodic 6 Chapter 3 Model Definition LIAM2 User Guide Release 0 10 2 PERIOD is an implicit column of the periodic table WEMRA float 3 5 entities Each entity has a unique identifier and a set of attributes fields You can use different entities in one model You can define the interaction between members of the same entity eg between partners or among different entities eg a person and its household using links The processes section describe how the entities behave The order in which they are declared is not important In the simulation block you define if and when they have to be executed this allows to simulate processes of different entities in the order you want In LIAM2 entities are declared as follows entities entity namel fields optional section can be omitted fields definition links optional section can be omitted links definition mE rROSK optional section can be omitted macros definition processes optional section can be omitted processes definition entity name2 As a reminder indentation and the use of are important 3 5 1 fields The fields hold the information of each member in the entity That information is global in a run of the model Every process defined in that entity can use and change the value LIAM2 handles three types of fields e bool boolea
76. lent to aligned_m align 0 0 al_p_dead_m csv filter gender aligned_f align 0 0 al_p_dead_f csv filter not gender aligned if gender aligned_m aligned_f One might wonder what happens if an explicit filter is used in addition to the contextual filter Both filters are combined using and as for example aligned if gender align 0 0 al_p_dead_m csv filter age gt 10 glillatcin 10 al p dees ic sir which is in fact evaluated as aligned_m align 0 0 al_p_dead_m csv filter gender and age gt 10 aligned_f align 0 0 al_p_dead_f csv filter not gender aligned if gender aligned_m aligned_f What is the inconsistency anyway This contextual filter propagation is implemented for new align logit_regr matching and some but not all aggregate functions Specifically it is implemented for sum and gini but not for other aggregate functions count avg min max std median and percentile This situation needs to be changed but I am unsure in which way implementing it for all aggregate functions or not contextutal filter for any aggregate function or any function at all While this features feels natural for new align and logit_regr it feels out of place for aggregate functions because it means we work at both the individual level and at the aggregate levels in the same expression or in more technical terms we work with both
77. lgorithm also scales better O N1g N2g instead of O N1 N2 where N1g and N2g are the number of combination of values in each set and N1 and N2 are the number of individuals in each set Note the byvalue algorithm is only available if the C extensions are installed Warning The results of the two algorithms are NOT exactly the same hence the switch cannot be done lightly from one to another if comparing simulation results with those of an earlier version of LIAM2 lt 0 9 is of importance New in version 0 9 example marriage to_couple not in_couple and age gt 18 and age lt 90 avg_age_males_to_couple avg age filter to_couple and MALE arere ematen sisi Omecouple sand EEMALE abs age avg_age_males_to_couple nan partner_id if to_couple matching setlfilter FEMALE set2filter MALE orderby difficult_match score 0 4893 other age 0 0131 other age ss 2 0 0001 other age 3 0 0467 x other age age 0 0189 x other age age x 2 0 0003 other age age x 3 0 9087 other work and not work 1 3286 not other work and work 0 6549 other work and work partner_id The code above shows an application First we decided that all persons between 18 and 90 years old who are not part of a couple are candidate for marriage Next for each candidate women the variable difficult_match is the differen
78. lib pyplot scatter and inherits all of its keyword arguments It should be used like this Scatter 6 Spore WEP oe m Where both x_expr and y_expr are expressions returning one dimensional arrays for example an entity field or a groupby expression with only one dimension Optional keyword arguments include among others see above link e c to set the color of each circle A color will be assigned for each different value of this argument e s to set the surface of each circle mutually exclusive with the r argument e r to set the radius of each circle r expr is equivalent to s pi expr 2 It is mutually exclusive with the s argument The r argument is specific to liam2 Examples salary 10000 uniform x 50000 area 3 1415 4 1 5 children count x 2 scatter age salary c eduach s area alpha 0 5s grid True scatter normal normal c age r 2 xx eduach 70000 60000 50000 30000 10000 20 0 20 40 60 80 100 5 7 Output 53 LIAM2 User Guide Release 0 10 2 boxplot New in version 0 8 boxplot can be used to draw box plots It uses matplotlib pyplot boxplot and inherits all of its keyword arguments There are two ways to use it loyepgoulore ilclexgoreil ilclesgoie2 46 boxplot 2d_expr Examples boxplot age gender age not gender boxplot groupby eduach expr age filter eduach 1
79. ll df Federal X Planning Bureau Economic analyses and forecasts LIAM2 User Guide Release 0 10 2 G Bryon G Dekkers G de Menten June 24 2015 9 CONTENTS Introduction 1 1 About LIAM 2 244 iaca ea 4884424 40 fb caw eee ewe ene PEPE SE es 1 2 About microsimulation sa dcp dk asm ego Al a ay Bede gy hae Gh ws Se a aA es a 13 About tisside aye oe Ga aS a Oa eee es ae a a Environment 2 1 LIAM bundle 22 2 24 c4 44 626414 25 bh bk Seed wba Ee Sha 22 Getting Slatted z sees Sky aces OR ESSE eR A ee eV Sle ee Bs 23 Usine yournowmdalan 44 2 22 0 eas CP EEE OR we a BA tet ear e e Model Definition Sill Comments z peoa i Bh Set Bak ts Bee eS BS ee Se ts Bi ee ee A Be 3 2 iGeneraliStructinre me Soci oe oa wo ee ee ee a ee SS oe Oe ee ol 3 3 IMPO sa pe gods ho AG RD hh Se AS Ba Sa A Bae Ba BB oe eS SA slobalS 4 cic 8 a et bea Ee bee ELA ee wed eee eh eed ES 3 3 Sentities 442 oak bed eh SHG Se hee HES RE SARS ESE ES 3 6 SIMULANOM 4000 6 4 YOR ee SR ee A ee Re LR eS A Running a model simulation Processes Sill EXpressions see Gob Ce oe ee wal RRM Ea he a eee Be Ge Ge ate 32 ASPENS s pei Ae aed ee eae GE MS Ba REE Sete we Ee ek Ad 533 FUMCHONS 04556 88 Pads ea eR Pee S PRR Pe Po ee eee eS SA globals 2 ce abe a eR BHP Oe REE PER SSPE TSS Ree ee hae A X Builtsim Functions se y hae aot a ee eee ee we BM Ae SY EY a eee E A 9 6 While loopse 04 6 ge HAR ae oe oR ES EOS Be BM REE ADS
80. llows Luxembourg and other countries at answering policy related questions about pensions and social transfers in the longer term trough microsimulation models The project received funding from both the European Community Programme for Employment and Social Solidar ity PROGRESS 2007 2013 under the Grant VS 2009 0569 and the General Inspectorate for Social Security IGSS of Luxembourg The PROGRESS programme was created by the European Commission to financially support the implementation of the objectives of the European Union in the employment social affairs and equal opportunities areas For more information see http ec europa eu progress 10 5 Credits 99 LIAM2 User Guide Release 0 10 2 100 Chapter 10 Appendix abs 20 aggregate functions 20 align 27 align_abs 30 alignment 26 all 21 any 21 assertEqual 56 assertions 56 assertTrue 56 avg 21 bar 42 bar charts 42 beta 23 binomial 23 boxplot 54 breakpoint 56 builtin functions 20 bundle 2 charts 41 chisquare 23 choice 25 clip 20 clone 35 comments 5 conditional function 20 count 21 csv 37 debugging 55 dirichlet 23 dump 39 duration 22 entities 7 exp 20 exponential 23 expressions 15 f 23 fields 7 function call 17 function declaration 16 gamma 23 geometric 23 INDEX gini 21 globals declaration 6 globals usage 19 groupby 39 gumbel 22 23 hdf5 79 hypergeometric
81. lt WRONG show back from old age backfromoldage In this example isold and backfromoldage are local variables They can only be used in the function where they are defined Because we are trying to use the local variable isold in another function in this example LIAM will refuse to run complaining that isold is not defined 5 3 4 Actions In LIAM2 there are a few builtin functions which do not return any value but have other effects We call those actions Since they do not need a variable to store their result we simply processes function_name action_expression example processes death dead age gt 150 remove dead 5 4 globals Globals can be used in expressions in any entity LIAM2 currently supports two kinds of globals tables and multi dimensional arrays They both declared see the g obals section before they can be used Globals tables come in two variety those with a PERIOD column and those without The fields in a globals table with a PERIOD column can be used like normal entity fields except they need to be prefixed by the name of their table myvariable mytable MYINTIFIELD 10 the value for MYINTFIELD is in fact the value MYINTFIELD has for the period currently being evaluated There is a special case for the periodic table its fields do not need to be prefixed by periodic but they can be if desired retirement_age if ge
82. many target person field household_id person fields age int income float household ad 3 int iL alinles household type manyZone target household field household_id e persons is the link from the household to its members e household is the link form a person to his her household To access the information stored in the linked individuals through a one2many link you have to use aggregate methods on the link link_name method_name arguments For example persons avg age one2many links support the following methods count sum avg minQ and max See link methods for details example entities household fields mem Chilerens slag links 60 Chapter 6 Links LIAM2 User Guide Release 0 10 2 link from a household to its members persons type one2many target person field household_id processes num_children persons count age lt 17 person fields aE aleve Ineisalacilcl_akels alae ERSE link form a person to his her household household type many2one target household field household_id processes num_kids_in_hh household num_children The num_children process once called will compute the number of persons aged 17 or less in each household and store the result in the num_children field of the household Afterwards that variable can be used like any other variable for exampl
83. mber of dimensions of a single homogeneous type The first row should contain the dimension names one dimension by cell The second row should contain the possible values for the last dimension Each subsequent row should start by the values for the first dimensions then the actual data example gender work civilstate i 2 S 4 False False Hails L912 695 1222 False True 432 Ase Bil 87 True False ATOL Zales Tae 1079 True True 369 155 IOL 16 This is the same format that groupby generates except for totals 8 2 description file To import CSV files you need to create a description file Those description files have the following general format out pur i lt pathmoehdiitomitble gt tes compression is optional compression type can be zlib bzip2 or lzo level is a digit from 1 to 9 and is optional defaults to 5 Examples of valid compression strings are zlib 1z0 1 bzip2 9 You should experiment to see which compression scheme if any offers the best trade off for your dataset compression lt type gt lt level gt globals are entirely optional globals periodic Pathe lt pachmo te timle gt esi if the csv file is transposed each field is on a row instead of 67 LIAM2 User Guide Release 0 10 2 a column and the field names are in the first column instead of the first row you can use transpo
84. much faster than matching each individual in turn It is highly encouraged to use this option as it is much faster in most cases and it scales better O N1g N2g instead of O N1 N2 where N1g and N2g are the number of combination of values in each set and N1 and N2 are the number of individuals in each set However the results are NOT exactly the same than in previous versions even though they are both correct This means that simulation results will 82 Chapter 10 Appendix LIAM2 User Guide Release 0 10 2 be harder to compare against simulation results obtained using previous versions This will be the new default value for version 0 10 Please also note that this new option is only available if the C extensions are installed In our test models on actual data this version ran from 50 faster to 3x faster This code is based on the optimized_matching work from pull request 144 by Alexis Eidelman added the possibility to automatically generate an order in matching by using the special value EDtM for its orderby argument Based on pull request 136 from Alexis Eidelman added an optional pool_size argument to matching If used the best match for an individual is looked for in a random subset of size pool_size Based on pull request 136 from Alexis Eidelman Miscellaneous improvements updated bundled dependencies to their latest version The numpy upgrade to version 1 9 brings some per formance improvements in variou
85. n True or False e int integer e float real number There are two implicit fields that do not have to be defined e id the unique identifier of the item e period the current period in the run of the program example entities person fields period and id are implicit isis INNE gender bool 1 single 2 married 3 cohabitant 4 divorced 5 widowed iwallsigatcas Lnr 3 5 entities 7 LIAM2 User Guide Release 0 10 2 petma Log alighe earnings float This example defines the entity person Each person has an age gender civil state and possibly a partner We use the field civilstate to store the marital status which can take one of several predefined values Field names must be unique per entity i e several entities may have a field with the same name By default all declared fields are supposed to be present in the input file because they are observed or computed elsewhere and their value can be found in the supplied data set and the value for all declared fields will be stored for each period in the output file However in practice there are often some fields which are not present in the input file They will need to be calculated later by the model and you need to tell LIAM2 that the field is missing by using initialdata False in the definition for that field see the agegroup variable in the example below One can have a field not stored in the output file by us
86. n all the variables of set 1 used in the score expression In short unusual individuals will be matched first e The optional pool_size argument specifies the size of the subset of set 2 to use as candidates If used it should be a positive integer In that case the best match for each individual of set 1 will be searched for in a random subset of size pool_size instead of in all unmatched individuals in set 2 This may be closer to actual marriage where people do not meet every single potential partner When the remaining number of candidates in set 2 is lower than pool_size the match is looked for among all remaining candidates New in version 0 9 e The optional algo argument specifies the algorithm to use It can be set to either onebyone or byvalue onebyone is the current default and should give the same result than with LIAM2 versions lt 0 9 byvalue groups individuals by their value for all the variables involved in both the score and orderby expressions and match groups together Depending on whether all individuals in each set have many different combinations of values or not this is usually much faster than matching each individual in 1 sum variable mean variable 2 var variable 32 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 turn It is thus highly encouraged to use this option if possible It will become the default value in a future version This a
87. n file ie local_path name_of_the_entity csv e if the fields section is omitted all columns of the csv file will be imported and their type will be detected automatically e if compression is omitted the output will not be compressed Note that if an entity section is entirely empty you need to use the special code simplest example output simplest h5 entities household person This will try to load all the fields of the household and person entities in household csv and person csv in the same directory than the description file simple example output simple h5 globals periodic path input globals csv entities household path input household csv person path input person csv This will try to load all the fields of the household and person entities in household csv and person csv in the input sub directory of the directory where the description file is 8 2 description file 69 LIAM2 User Guide Release 0 10 2 example 3 output example3 h5 globals periodic path input globals_transposed csv transposed True entities household path input household csv person path input person csv fields GioKSs8 tinie gender bool workstate int alwallkeiesneers TAE paene Log Ne oldnames gender male This will load all the fields of the household entity in household csv and lo
88. nExpr subclass for functions eg trunc lag duration FilteredExpression subclass for functions which have a filter argument and need to support con textual filters eg align sum avg gini LIAM2 current expressions are implemented in the following files actions py actions are expressions which do not have any result that can be stored in variables but have side effects Examples include csv show remove breakpoint alignment py handles align and align_abs functions align_link py the core algorithm an implementation of Chenard s for align_abs link exprmisc py all expressions which are not defined in another file groupby py handles groupby links py contains all link related code e the Link class stores the definition of links e the LinkGet class handles ManyToOne links e one class for each method of OneToMany links Count Sum Avg Min and Max matching py handles the matching functions matching and rank_matching 10 2 Code architecture 77 LIAM2 User Guide Release 0 10 2 regressions py handles all the regression functions logit_score logit_regr cont_regr clip_regr log_regr tfunc py handles all time related functions value_for_period lag duration tavg and tsum Context file context py A context is a data structure used to keep track of contextual information what is the current entity what is the current period what is the current dataset
89. name percentage list of values Evaluation whether the event happens is done differently whether the align argument is used or not If alignment is used logit_regr is equivalent to aligned align logit_score expression proportions filter conditions Without align argument the condition for the event occurring is p i gt 0 5 which means that in this form logit_regr is equivalent to aligned if conditions logit_score expression gt 0 5 False example n tongiveipirti ogiri reg 0M0 filter FEMALE and age gt 15 and age lt 50 alretal a oaen ES 5 5 Built in Functions 31 LIAM2 User Guide Release 0 10 2 other regressions e Continuous expr normal 0 1 mult error_var cont_regr expr filter None mult 0 0 er ror_var None e Clipped continuous always positive clip_regr expr filter None mult 0 0 error_var None e Log continuous exponential of continuous log_regr expr filter None mult 0 0 error_var None 5 5 8 Matching functions The goal of matching functions is to match individuals from a set with individuals from another set for example to select spouses for marriage There are many different algorithms to do so LIAM2 currently implements two matching takes the highest scoring individual in set 2 for each individual in set1 while rank_matching sorts both sets by their own ordering expression and match individuals w
90. nder 65 WEMRA workstate if age gt retirement_age 9 workstate This changes the workstate of the individual to retired 9 if the age is higher than the required retirement age in that year Another way to use globals from a table with a PERIOD column is to specify explicitly for which period you want them to be evaluated This is done by using tablename FIELDNAME period_expr where period_expr can be any expression yielding a valid period value Here are a few artificial examples 5 4 globals 19 LIAM2 User Guide Release 0 10 2 women_retirement_age_in_2010 WEMRA 2010 women_retirement_age_in_previous_period WEMRA period 1 a possibly different value for each woman women_retirement_age_when_60 WEMRA year_of_birth 60 Globals tables without a PERIOD column can only be used with the second syntax and the row index 0 based must be given explicitly LIAM2 does not automatically compute it by subtracting the base period from the index Globals arrays can simply be used like a normal field myvariable MYARRAY x 2 5 5 Built in Functions 5 5 1 conditional function One of the most used function in LIAM2 is the conditional function It evaluates a condition and depending on its value returns the result of one expression or another Its general format is if condition_expression expression_if_true expression_if_false example
91. old_composition function is re executed 3 6 2 init Every process specified here is only executed in the last period before start period start_period 1 You can use it to calculate initialise variables derived from observed data This section is optional it can be entirely omitted 3 6 3 input The initial observed data is read from the file specified in the input entry Specifying the path is optional If it is omitted it defaults to the directory where the simulation file is located The hdf5 file format can be browsed with vitables http vitables org or another hdf5 browser available on the net 3 6 4 output The simulation result is stored in the file specified in the output entry Only the variables defined at the entity level are stored Temporary local variables are not saved The output file contains values for each period and each field and each item Specifying the path is optional If it is omitted it defaults to the directory where the simulation file is located 3 6 5 start_period Defines the first period integer to be simulated It should be consistent use the same scale time unit with the period column in the input data 3 6 6 periods Defines the number of periods integer to be simulated 3 6 7 random_seed Defines the starting point integer of the pseudo random generator This section is optional This can be useful if you want to have several runs of a simulation use the same random
92. on model as long as it use cross sectional ageing ie all individuals are simulated at the same time for one period then for the next period etc 1 1 1 License LIAM2 is licensed under the GNU General Public License GPL version 3 This means you can freely use copy modify and redistribute this software provided you follow a few conditions See the license text for details 1 1 2 Staying informed You can get notified of new versions and other LIAM2 related announcements by either using our website RSS feed or subscribing to the LIAM2 announce mailing list on Google Groups 1 1 3 Credits The software is primarily being developed at the Federal Planning Bureau Belgium with testing and funding by CEPS INSTEAD Luxembourg and IGSS Luxembourg and funding from the European Commission See the credits page for details 1 2 About microsimulation Microsimulation is a modelling technique that operates at the level of individual units such as persons house holds vehicles or firms Each unit has a set of associated attributes e g a person has an associated age sex and employment status In the case of discrete time dynamic models a set of rules intended to represent individual preferences are applied to these units at each time step leading to simulated changes in state and possibly be haviour These rules may be deterministic probability 1 such as ageing or stochastic probability lt 1 such as the chance of dying ma
93. operor I pro coEdOM 2 song WROD _Cjoit Cm _im Note that both the list of options and their probabilities are between s The options can be of any numeric type A simple example of a process using a choice expression is the simulation of the gender of newborns 51 males and 49 females as such gender choice True False 0 51 0 49 In the current version of LIAM2 it is not possible to combine a choice with alignment Here is a more complex example of a process using choice Suppose we want to simulate the work status blue collar worker or white collar worker for all working individuals We want to assign 1 or 2 to their collar variable based on their sex and level of education education_level 2 3 4 We could write our process as follow 5 5 Built in Functions 25 LIAM2 User Guide Release 0 10 2 collar_process no_collar WORKING and collar 1 collar if no_collar and education_level 2 if gender EloOnkeSe li Lily O 836 O 164 EMonca il 2 Os637 OoS13 collar collar if no_collar and education_level 3 if gender EMoOeS li Ally O 64S 1 O 6483 Elnoskee lil Zip O 313 1 O 313 Yep collar collar if no_collar and education_level 4 if gender ElnoOeSa lil Lily O 082 1 0 082 CnoskeSs il 2iyh O 039 1 O 0S9 collar The function collar_process has collar as the key endogenous variabl
94. oses issue 147 fixed computing most expressions involving arrays with more than one dimension It only worked if all the arrays involved were based on the same source array which was the case in our tests assertEqual fails gracefully when comparing two arrays with different shapes fixed global fields colliding with fields with the same name from other global tables fixed expressions like aie Geleer ear ellicia s6 aecaylSsealael sas False and made all if expr GLOBAL scalar_value expressions faster in the process fixed a rare problem with some expressions using scalars returned by aggregate functions 10 4 Change log 83 LIAM2 User Guide Release 0 10 2 10 4 7 Version 0 8 2 Released on 2014 10 02 New features e allow loading globals from csv files directly instead of having them in the input HDF file One can mix both approaches have some globals in the input HDF file while other globals in csv files This makes it more practical in case you have a relatively stable input dataset for entities but need to change the globals often or have several variants with different globals See the globals section for details This closes issue 30 e added a new simulation option category logging This is the new home for the existing timings option and for a new level option which allows to sets the verbosity of logging to one of periods procedures this is
95. ousehold_id clone clone is very similar to new but is intended for cases where most or all variables describing the new individual should be copied from his its parent origin instead of being set to missing With clone you cannot specify what kind of entity you want to create as it is always the same as the origin item However similarly to new clone also allows fields to be specified manually by any expression evaluated on the parent origin Put differently a new with no fields mentioned will result in a new item of which the initial values of the fields are all set to missing and have to be filled through simulation on the contrary a clone with no fields mentioned will result in a new item that is an exact copy of the origin except for its id number which is always set automatically example make_twins clone filter new_born and is_twin gender choice True False 0 51 0 49 remove remove removes items from an entity dataset With this command you can remove obsolete items eg dead persons empty households thereby ensuring they are not simulated anymore This will also save some memory and in some cases improve simulation speed The function below simulates whether an individual survives or not and what happens in the latter case dead_function decide who dies dead if gender logit_regr 0 0 align al_p_dead_m csv logit_regr 0 0 align al_p_dead_f csv change the ci
96. pired by some code from Alexis Eidelman For details see the Importing other models section added new logit and logistic functions They were previously used internally but not available to modellers 10 4 Change log 85 LIAM2 User Guide Release 0 10 2 added two new debugging features autodump and autodiff autodump will dump all non scalar variables including temporaries at the end of each procedure in a separate hdf5 file It can be used stand alone for debugging or in combination with autodiff Autodiff will gather all variables at the end of each procedure and compare them with the values stored previously by autodump in another run of the model or a variant of it This can be used to precisely compare two versions variants of a model and see exactly where they start to differ added new assert functions assertIsClose to check that two results are almost equal tolerating small value differences for ex ample due to rounding differences assertEquiv to check that two results are equal tolerating differences in shape though they must be compatible assertNanEqual to check that two arrays are equal even in the presence of nans because normally nan nan added a new timings option to hide timings from the simulation log so that two simulation logs are more easily comparable for example with diff tools like WinMerge added a menu entry in notepad to run a simulation in deb
97. processes need to be executed Processes are usually grouped in functions 5 1 Expressions LIAM2 at its core compute expressions Expressions are any combination of variables operators constants globals and functions which explain how to compute a value Expression syntax looks like many other programming languages gt gt gt denotes an interactive prompt gt gt gt 1 2 3 z gt 1 5 2 2 0 0 5 8 0 Od Numeric constants with a fractional part e g 3 0 1 6 have type float others e g 1 2 20 have type int Operations with mixed types int and float return floats gt gt gt 4 0 5 amp 25 Parentheses can be used for grouping For example ser 26 5 0 5 A 3 0 LIAM2 supports many common operators e Arithmetic operators exponent modulo Note An integer divided by an integer returns a float For example 1 2 will evaluate to 0 5 instead of 0 as in many programming languages If you are only interested in the integer part of that result for example if you know the result has no decimal part you can use the trunc function SSS imine S 7 2 1 e Comparison operators lt lt gt gt e Boolean operators and or not Note Starting with version 0 6 you do not need to use parentheses when you mix boolean operators with other operators age gt 10 and age lt 20 15
98. rite it like below bad example wrong_repeat_while_below_1 score age max age while score lt 1 lt this line is WRONG scones scone Omi show score However that would result in this error ValueError The truth value of an array with more than one element is ambiguous Use a any or a all The solution is to follow the advice in the error message and use any in this case example 2 repeat_while_below_1 score age max age while any score lt 1 score score 0 1 show score This will repeat the code until all individuals have reached the target but individuals who reached it early will continue to be updated and it might not be what is needed If that is the case one has to explicitly only update the individuals which are not done yet example 3 repeat_while_below_1 score age max age while any score lt 1 SSC One wei Ss Core L S Core r Or IMS COTE show score 5 7 Output LIAM2 produces simulation output in three ways First of all by default the simulated datasets are stored in hdf5 format These can be accessed at the end of the run You can use several tools to inspect the data You can display information during the simulation in the console log using the show function You can write that same information to csv files using the csv function You can produce tabular data by using th
99. rrying giving birth or moving within a given time period The aim of such simulations is to give insight about both the overall aggregate change of some characteristics and most importantly the way these changes are distributed in the population that is being modelled The methodology is often used to design and evaluate public policies that are affected by earlier events and choices as is the case for pensions or education LIAM2 User Guide Release 0 10 2 1 3 About this guide This guide will help you develop dynamic microsimulation models using LIAM2 Please note that it describes version 0 10 of LIAM2 but both the software package and this manual are work in progress and are therefore subject to change 2 Chapter 1 Introduction 2 1 CHAPTER TWO ENVIRONMENT LIAM2 bundle The bundle includes 2 2 2 3 The executable for Windows A text editor Notepad pre configured to work with LIAM2 models Notepad is a free and open source text editor that is available at http sourceforge net projects notepad plus We pre configured it so that you can import csv files and run your models directly from within the editor by simply pressing F5 or F6 respectively See below for more information The documentation in HTML Help format chm You can find pdf and html versions on our website A demonstration model with a synthetic data set of 20 200 persons grouped in 14 700 households Getting Start
100. rtions functions added more tests only copy declared globals to the output file and do not create a globals node at all if there is no declared global manually close input and output files when an error happens during initialisation so that the user only sees the real error message globals can be entirely missing from the input file if they are not used in the simulation file made the usual code clean ups Fixes fixed typo in the code outputting durations hourss instead of hours fixed a bug which prevented to define constants without quoting them in some cases fixed a crash when all groups were empty in a groupby xxx expr grpcount percent True fixed aggregate functions grpmin grpmax grpstd grpmedian and grppercentile to accept a scalar as argu ment even though it is not very useful to do that fixed a bug which prevented to use a simulation output file as input in some cases 10 4 16 Version 0 4 1 Released on 2011 12 02 Miscellaneous improvements validate both import and simulation files i e detect bad structure and invalid and missing keywords improved error messages both during import and the simulation by stripping any information that is not useful to the user For some messages we only have a line number and column left this is not ideal but should be better than before The technical details are written to a file error log instead improved incoherent alignm
101. s fixed link expressions which span 3 or more different entities fixed using show on a scalar created by summing a global array fixed the progress bar of matching when the number of individuals is different in the two sets 10 4 11 Version 0 6 2 Released on 2013 05 21 Fixes e fixed storing a copy of a declared field without any modification in a temporary backup variable The temporary variable was not a copy but an alias to the same data so if the field was modified afterwards the temporary variable was also modified implicitly As an example the following code failed before the fix age is a field backup age modify age this also modified backup age age 1 failed because backup was equal to age assertEqual age backup 1 J Ss 0 Ss i ss This only affected assignment of pure fields not expressions nor temporary variables for example the following code worked fine because backup stores an expression not a simple field backup age 1 age age 1 assertEqual age backup 1 and this code worked too because temp is a temporary variable not a field temp age 1 backup temp temp temp 1 assertEqual temp backup 1 10 4 12 Version 0 6 1 Released on 2013 03 27 Miscellaneous improvements e when importing an nd array skip cells with only spaces in addition to empty cells 10 4 C
102. s areas our test simulation runs approximately 15 faster overall large internal refactoring itis now easier to define new functions there is much less code to write all arguments to all functions can now be expressions Closes issue 5 cleaner variable scopes Eliminates a whole class of potential problems when using two fields with the same name but a different entity via a link in the same expression Closes issue 41 cache some internal structure so that it is not recomputed over and over which improves overall performance by a few percents in some cases especially when computing many small expressions as is often the case in one by one matching which improved in our tests by 10 20 remove can now be called without filter argument it removes all individuals better and more consistent error messages when calling functions with incorrect arguments too few too many use input path as the base directory for loading csv globals those using an explicit path instead of using the directory of the HDF input file nicer string representation of some expressions this only affects qshow and groupby the versions command line argument now also shows versions for optional dependencies if present improved many tests especially the ones for matching Fixes fixed the view command to launch ViTables via F9 for example in the 64 bit bundle This was a regression in 0 8 2 Cl
103. s the entity in which the individuals will be created eg person household Then one should use one of either the filter or the number argument e filter specifies which individuals of the current entity will serve as the origin for the new individuals for persons that would translate to who is giving birth but the function can of course be used for any kind of entity e number specifies how many individuals need to be created In this version those new individuals do not have an origin so they can copy value from it Any subsequent argument specifies values for fields of the new individuals Any field which is not specified there will receive the missing value corresponding to the type of the field nan for floats 1 for integers and False for booleans Those extra arguments can be given constants but also any expression possibly using links random functions Those expressions are evaluated in the context of the origin individuals For example you could write mother_age age which would set the field mother_age on the new children to the age of their mother example 1 Joyal sete loys oO _ealwe_ioalssciag Ihoeplic sege 0 0 filter not gender and age gt 15 and age lt 50 align al_p_birth csv new person filter to_give_birth mother_id id father_id partner id household_id household_id partener Ta ian age 0 civilstate SINGLE gender choice True F
104. se True You do not need to specify anything if the file is not transposed transposed True fields are optional fields PERIOD is implicit lt fieldl_name gt lt fieldl_type gt lt field2_name gt lt field2_type gt if not specified all fields are imported other_table same options than for periodic path fields transpose other_array path lt path_of_file gt csv typ lt field_type gt entities lt entityl_name gt path lt path_to_entityl_data gt csv defaults to False if not present transposed True if you want to manually select the fields to be used and or specify their types you can do so in the following section If you want to use all the fields present in the csv file you can simply omit this section The field types will be automatically detected fields period and id are implicit lt fieldl_name gt lt fieldl_type gt lt field2_name gt lt field2_type gt if you want to keep your csv files intact but use different names in your simulation than in the csv files you can specify name changes her oldnames lt fieldX_newname gt lt fieldY_newname gt lt fieldxX_oldname gt lt fieldy_oldname gt another option to specify nam oldnames in case of conflicts newnames lt fieldxX_oldname gt lt fieldy_oldname gt changes takes precedence ov lt fieldxX_newname gt lt fieldY_newname gt if you want
105. set to the special value corresponding to missing for the field type i e False for booleans 1 for integers and nan for floats This will probably change in the future As a consequence of this new feature it is now possible to import liam1 files using the normal import file syntax added an optional default_entity key to the simulation block of simulation files so that the interactive console starts directly in that entity added function to compute the Nth percentile grppercentile expr percent filter implemented an optional filter argument for many functions The behaviour is different depending on the kind of function for functions that change an existing variable clip and round the value for filtered individuals is not modified for functions which create a new variable uniform normal and randint the value for filtered individuals is the missing value corresponding with the type of the column 1 for randintQ nan for uniform and normal for aggregate functions grpmin grpmax grpstd grpmedian and grppercentile the aggregate is computed over the individuals who satisfy the filter added new functions for testing assertTrue and assertEqual assertTrue expr evaluates its expression argument and check that it is True assertEqual expr1 expr2 evaluates its two expressions and check that they are equal 92 Chapter 10 Append
106. tate expr count age gt 80 civilstate eee 3 4 toral Saa O 150 BS HUT The expr argument will usually be used with an aggregate function but it also supports normal expressions in which case the values for each individual will be displayed in a list This feature should only be used with care and usually in combination with a strong filter to avoid producing extremely large tables which would take forever to display groupby agegroup_civilstate gender expr id filter id lt 20 agegroup_civilstate gender False True total 0 0 1 4 6 2 3 5 VW O L4a 623 5 7 5 ie 10 12 1S ih TS ie 10 12 9 ai 13 10 Ea aS 1E Lis 17 Ws Fila ae ig 15 17 19 voral oO 2 4 6 amp io 23 5 7 L a 4 G amp IO az ile 2 da le 181 ii abs 15 17 1G 18 23 57 9 1i AL S 13 15 iy ig or groupby civilstate gender expr age filter id gt 100 and id lt 110 Civilstate gender False True total 46 ami AG ay Ai 46 47 46 47 47 Ami PAS Aol 47 45 46 al Lel Li 46 corel 45 47 47 26 46 427 27 425 46 46 47 47 46 46 47 427 425 46 5 7 6 charts New in version 0 8 LIAMZ2 has some charting capabilities courtesy of matplotlib They are available both during a simulation and in the interactive console Each of the following functions is designed around the function of the same name in 5 7 Output 41 LIAM2 User Guide Release 0 10 2
107. ten you need a variable only to store an intermediate result during the computation of another variable In LIAM2 you can create a temporary variable at any point in the simulation by simply having an assignment to an undeclared variable Temporary variables defined computed within a function are local to that function they are only valid within that function and their value will be discarded at the end of the function example person fields period and id are implicit ages Ime agegroup int processes ageing age age 1 agedivl0 trunc age 10 agegroup agedivlO 10 In this example agediv10 is a temporary local variable In this particular case we could have bypassed the temporary variable but when a model contains very long expressions it is often more readable to split it using temporary variables Also if some long expression occurs several times it is often more efficient to express it and compute it only once and store its result in a temporary variable If you want to pass variables between functions you have to make them global by defining them in the fields section bad example person fields age int 18 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 processes ageing age age 1 isolog ege gt 150 isold is a local variable show isold asold rejuvenation Sagen age l backfromoldage isold and age lt 150
108. ter id lt 10 gives ael age partner ag gender 0 2 False 1 86 WAL False 2 16 True 3 LO i False 4 2i all False 5 89 92 True 6 8 61 True 7 65 29 False 8 38 35 True 9 48 52 True 5 7 5 groupby groupby aka pivot table group all individuals by their value for the given expressions and optionally compute an expression for each group using the expr argument If no expression is given it will compute the number of individuals in that group A filter can be specified to limit the individuals taken into account 5 7 Output 39 LIAM2 User Guide Release 0 10 2 general format groupby exprl expr2 expr3 expr expression filter filterexpression percent True pvalues possible_values example Show groupby trunc age 10 gender gives trunc age 10 gender False True total 0 818 803 162i L 800 800 1600 2 Ale 1197 2396 3 1598 1598 SANS 4 1697 1696 3393 5 1496 1491 2987 6 INEO 1182 DSS YT 684 671 1355 8 369 SIST 726 9 T0 147 PEN total 10002 9942 19944 example show groupby inwork gender gives inwork gender False True total False GLO 5587 LL7TS7 True SESA 4355 STE7 corce 10002 S942 TJA example show groupby inwork gender percent True gives inwork gender False True total ralse 30 9
109. th individuals of other entities for example mothers are linked to their children partners are linked to each other and persons belong to households A typical link declaration has the following form name type lt type gt target lt entity gt field lt name of link field gt LIAM2 uses integer fields to establish the link between entities Those integer fields contain the id number of the linked individual For link fields 1 is a special value meaning the link points to nothing eg a person has no partner Other negative values should never be used whatever the reason for link fields LIAM2 allows two types of links many2one and one2many 6 1 many2one A many2one link links an individual of the entity to one other individual in the same eg a person to his her mother or another entity eg a person to its household This allows the modeller to use information stored in the linked entities entities person icaLellsg Sages smite aAMCGCies i oat Motier ree mE tarner Lei Lmt pertoer Lels int EESE mother type many2one target person field mother_id father type many2one target person field father_id partner type manyZone target person field partner_id BOGS siSesr age age 1 mother_age mother ag parents_income mother income father income To access a field of a linked individual possibly of the same entity you use link_name field_name
110. the age and agegroup Finally mortality and fertility are simulated Seeing that this changes the numbers of individuals in households the process establishing the household size and composition is again used example simulation aLiguLic optional household household_composition person agegroup processes household household_composition person age agegroup death birth household household composition impute path liam2 optional file base h5 SULpULS path liam2 optional file simulation hd5 start_period 2015 periods 10 skip_shows False optional random_seed 5235 optional assertions warn optional 3 6 simulation 9 LIAM2 User Guide Release 0 10 2 default_entity person optional logging optional timings True optional level functions optional autodump False optional autodiff False optional 3 6 1 processes This block defines which processes are executed and in what order They will be executed for each period starting from start_period for periods times Since processes are defined on a specific entities they change the values of items of that entity you have to specify the entity before each list of process Note that you can execute the same process more than once during a simulation and that you can alternate between entities in the simulation of a period In the example you see that after death and birth the househ
111. the newly created individuals is now 1 instead of 0 for parents which are not in the filter fixed some expressions crashing when used within a lag fixed the progress bar to display correctly even when there are only very few iterations 10 4 21 Version 0 1 First semi public release released on 201 1 02 24 10 5 Credits LIAM2 is the result of ongoing collaboration between individual researchers from the Federal Planning Bureau FPB in Belgium CEPS INSTEAD and the General Inspectorate of Social Security Inspection G n rale de la S curit Sociale IGSS in Luxembourg The software package is primarily being developed at the Federal Planning Bureau by Ga tan de Menten and Geert Bryon Testing and model development is done by Rapha l Desmet and Gijs Dekkers FPB Philippe Li geois and Fr deric Berger CEPS INSTEAD and Raymond Wagener IGSS Finally Cathal O Donoghue shared the source code of the first version of LIAM which the FPB used in the AIM project Dekkers et al 2010 LIAM was initially the result of the MiDaL project December 2009 November 2011 Towards the develop ment of a dynamic Microsimulation toolbox LIAM II and the complementary implementation of administra tive Data needed for dynamic microsimulation of pensions in Luxembourg The general objective of the project 98 Chapter 10 Appendix LIAM2 User Guide Release 0 10 2 was to develop an advanced analysis tool that a
112. tion True for all Returns True if all individuals who satisfy the optional condition2 also satisfy condition1 False otherwise Note that all condition 1 filter condition2 is equivalent to all conditionl and condition2 or not condition2 e any condition1 filter condition2 is condition True for any Returns True if any individual who satisfy the optional condition2 also satisfy condition1 False otherwise Note that any condition 1 filter condition2 is equivalent to any condition1 and condition2 5 5 4 link methods one2many links e link count filter counts the number of related individuals link sum exprl filter compute the sum of an expression over the related individuals e link avg exprl filter compute the average of an expression over the related individuals link min exprl filter compute the minimum of an expression over the related individuals e link max expr filter compute the maximum of an expression over the related individuals example entities household fields period and id are implicit 5 5 Built in Functions 21 LIAM2 User Guide Release 0 10 2 nb_persons type int initialdata False Tinks persons type one2many target person field household_id processes household_composition nb_persons persons count nb_children persons count age lt 18 total_income persons sum income avg_age persons avg age
113. two extra arguments 88 Chapter 10 Appendix LIAM2 User Guide Release 0 10 2 x secondary_axis name of an axis which will influence rel_need when the subtotal for that axis is exceeded See total_by_sex in Chenard secondary_axis must be one of the alignment columns errors if set to carry the error for a period difference between the number of individuals aligned and the target for each category is stored and added to the target for the next period renamed the probabilities argument of align to proportions the proportions argument of align is now much more versatile as all the following are now ac cepted x a single scalar for aligning with a constant proportion a list of scalars for aligning with constant proportions per category this used to be the only supported format for this argument an expression returning a single scalar an expression returning an n dimensional array expressions and possible_values will be retrieved from that array so you can simply use align score array_expr x a list of expressions returning scalars exprl expr2 a string in which case it is treated as a filename The fname argument is still provided for backward compatibility added an optional frac_need argument to align to control how fractional needs are handled It can take any of three values uniform default cutoff
114. ug mode Miscellaneous improvements improved the performance and memory usage by changing the internal memory layout Most operations are now faster new remove merging data for retrospective simulations and writing data at the end of each period are now slower In our model this translates to a peak memory usage 20 smaller and a 35 overall speed increase However if your model has a low processes variables ratio it may very well be slower overall with this version If it is your case please contact us changed the syntax for all aggregate functions grpxxx should now be xxx For example grp sum age should now be sum age The old syntax is still valid but it is deprecated it will be removed in a later version A special note for grpmin and grpmax which becomes min and max respectively even though those functions already existed The meaning is deduced from the number of non keyword arguments min expr1 expr2 minimum between expr and expr2 for each individual min expr aggregate minimum value of expr over all individuals min expr1 filter expr2 aggregate minimum value of expr over individuals satisfying the filter A tool to automatically upgrade models to the new syntax is provided In notepad you should use the LIAM2 upgrade model command in the Macro menu You can also run it via the command line main upgrade model yml output yml see main upgrade
115. used in cpartition pyx see https github com attractivechaos klib main py The main script It reads command line arguments and calls the corresponding code run import ex plore in simulation py run explore or importer py import partition py handles partitioning objects depending on the possible values of their columns utils py miscellaneous support functions standalone scripts diff_h5 py diff two liam2 files dropfields_h5 py copy a subset of a liam2 file excluding specified columns filter_h5 py copy a subset of a liam2 file all rows matching specified condition 78 Chapter 10 Appendix LIAM2 User Guide Release 0 10 2 merge_h5 py merge two liam files build scripts build_exe py generic script to make executables for standalones scripts setup py compile cython extensions to pyd and make an exe for the main liam2 executable using cx_Freeze 10 3 Technical choices 10 3 1 Python We use the Python language http www python org for the development of LIAM2 Python runs on Windows Linux Unix Mac OS X and has been ported to the Java and NET virtual machines Python is free to use even for commercial products because of its OSI approved open source license 10 3 2 HDF5 We store the used data in an hdf5 format http www hdfgroup org HDFS5 is a data model library and file format for storing and managing data It supports an unlimited variety of data types and is designed for flexible
116. vilstate of the suriving partner cCivilstate if partner dead 5 civilstate break the link to the dead partner partner_id if partner dead 1 partner_id remove the dead remove dead The first sub process dead simulates whether an individual is scheduled for death using again only a logistic stochastic variable and the age gender specific alignment process Next some links are updated for the surviving partner The sub process civilstate puts the variable of that name equal to 5 which means that one is a widow er for those individuals whose partner has been scheduled for death Also in that case the partner identification code is erased All other processes describing the heritage process should be included here Finally the remove command is called to removes the dead from the simulation dataset 5 6 While loops New in version 0 10 generic format while scalar_condition the_code_to_repeat 5 6 While loops 35 LIAM2 User Guide Release 0 10 2 Warning the condition must be a scalar expression that is it must have a single value for all individuals In other words the number of iterations is always the same for all individuals See examples below example 1 Count 205 ais i while i lt 5 show i abe al ap il Now let us suppose one wants to repeat a computation until some condition is met per individual One could intuitively w
117. vonmises mu kappa size None Draw samples from a von Mises distribution See numpy random vonmises for details New in version 0 9 wald mean scale size None Draw samples from a Wald or Inverse Gaussian distribution See numpy random wald for details New in version 0 9 weibull a size None Weibull distribution See numpy random weibull for details New in version 0 9 zipf a size None Draw samples from a Zipf distribution See numpy random zipf for details New in version 0 9 choice Monte Carlo or probabilistic simulation is a method for iteratively evaluating a deterministic model using sets of random numbers as inputs In microsimulation the technique is used to simulate changes of state dependent variables Take the simplest example suppose that we have an exogenous probability of an event happening P x 1 or not P x 0 Then draw a random number u from an uniform 0 1 distribution If for individual i ui lt P x 1 then xi 1 If not then xi 0 The expected occurrences of x after say 100 runs is then P x 1 100 and the expected value is 1xP 1 0xP 0 P 1 This type of simulation hinges on the confrontation between a random variable and an exogenous probability In LIAM2 such a probabilistic simulation is called a choice process Suppose i 1 n choice options each with a probability prob_option_i A choice expression then has the following form CHOLES ositsom i opscidom 2 saa Cisealom_im DOO
118. w usage is exactly the same than show example qshow count avg age std age will give Coume Or 19944 avg age 42 7496991576 std a age 21 9815913417 5 7 3 CSV The csv function writes values to csv files esv espri ESqe2 GMOS oop suffix file_suffix fname filename mode w 5 7 Output 37 LIAM2 User Guide Release 0 10 2 suffix fname and mode are optional arguments By default if neither fname nor suffix is used the name of the csv file is generated using the following pattern entity _ period csv example csv avg income will create one file for each simulated period Assuming start_period is 2002 and periods is 2 it will create two files person_2002 csv and person_2003 csv with the average income of the population for period 2002 and 2003 respectively Arguments e suffix allows to customize the name of the files easily When it is used the files are named using the following pattern entity _ period _ suffix csv example csv avg income suffix income would create person_2002_income csv and person_2003_income csv e fname allows defining the exact file name or pattern to use You can optionally use the entity and period key words to customize the name example csv avg income fn
119. when the error message contains a filename and or a line number this is currently too rare unfortunately it is now click able to jump directly at the file line defining a process outside of a function has been deprecated because it is ambiguous For example this code will now trigger a warning and will be an error in a future version entities person fields agegroup int processes agegroup 10 trunc age 10 simulation processes person agegroup 80 Chapter 10 Appendix LIAM2 User Guide Release 0 10 2 It should be replaced by or possibly moved into another existing function entities person fields agegroup int processes compute_agegroup agegroup 10 trunc age 10 simulation processes person compute_agegroup If this construct was used to have a temporary field ie the field was not declared in the fields section accessible from several functions like entities person processes tempfield 0 Tacl 8 tempfield count PUNGAS otherfield tempfield 1 One should now declare that field with output False instead EMTT ILOS person jEaLSILCKS tempfield type int initialdata False output False processes ramels tempfield count EUGA E otherfield tempfield 1 This closes issue 124 e made bcolz optional which is only useful for interpolating the dataset during import Thanks to Mahdi Ben J
120. xample count male and age gt 18 will produce the number of men in the sample who are eighteen years old or older Note count can be used without any argument count will return the total number of individuals in the sample for the current entity e sum expr filter condition skip_na True sum of an expression It computes the sum of any expression over all individuals of the current entity If a filter boolean condition is given it only takes into account the individuals satisfying the filter For example sum earnings will produce the sum of the earnings of all persons in the sample while sum earnings age gt 30 will produce the sum of the earnings of all persons in the sample who are 30 or older skip_na determines whether missing values nan are discarded before the computation or not It defaults to True Note sum and count are exactly equivalent if their only argument is a boolean variable eg count age gt 18 sum age gt 18 e avg expr filter condition skip_na True average std expr filter condition skip_na True standard deviation min expr filter condition skip_na True minimum max expr filter condition skip_na True maximum median expr filter condition skip_na True median percentile expr percent filter condition skip_na True percentile gini expr filter condition skip_na True gini all condition1 filter condition2 is condi
121. xtension nam In the examples below of the file without that would be p_age and p_work on the string we got value eval basename replac We then us toget iridio tpus files param p_age csv param p_work csv interpolate work previous_value the replace method pot uN N 8 3 importing the data Once you have your data as CSV files and created a description file you can import your data e If you are using the bundled editor simply open the description file and press F5 e If you are using the command line use BUNDLEPATH liam2 main import lt path_to_description_file gt 8 3 importing the data 71 LIAM2 User Guide Release 0 10 2 72 Chapter 8 Importing data CHAPTER NINE INDICES AND TABLES e genindex e search 73 LIAM2 User Guide Release 0 10 2 74 Chapter 9 Indices and tables CHAPTER TEN APPENDIX 10 1 Known issues 10 1 1 Contextual filter is inconsistent First what is a contextual filter It is the name we gave to the feature which propagates the filter of an if function to the True side of the function and the opposite filter to the False side So for example in aligned if gender align 0 0 al_p_dead_m csv aiem 0 val a cees ic si the gender filter is automatically propagated to the align functions Which means the above code is exactly equiva
122. y align align_abs also supports an optional link argument which makes it work on a linked entity Here is a description of the arguments specific to align_abs e link must be the name of a one2many link When the link argument is used the groups given by the alignment file or in the expressions argument are evaluated on the linked entity and the needs are expressed in terms of that linked entity When the link argument is in effect align_abs uses the Chenard algorithm This can be used for example to take as many households as necessary trying to get as close as possible to a particular distribution of persons e secondary_axis name of an axis which will influence rel_need when the subtotal for that axis is exceeded See total_by_sex in Chenard secondary_axis can only be used in combination with the link argument and it must be one of the alignment columns e errors if set to carry the error for a period difference between the number of individuals aligned and the target for each category is stored and added to the target for the next period In the current version of LIAM2 errors can only be used in combination with the link argument 30 Chapter 5 Processes LIAM2 User Guide Release 0 10 2 example test_align_link this is a function defined at the level of households num_persons persons count total_population sum num_persons MIG_PERCENT is a simple float periodic glo
123. y interact Jinks and how they behave over time processes LIAM2 model files use a dialect of the YAML format This format uses the level of indentation and colons characters to differenciate objects from sub objects 3 1 Comments Another particularity inherited from YAML is the use of the hash character to start comments which extend to the end of the line A comment may appear at the start of a line or following whitespace or a complete line of code but not within an expression Since comments are only meant to clarify code they are ignored by LIAM2 and may be omitted if typing in examples 3 2 General structure A LIAM2 model file has the following general structure import optional section can be entirely omitted globals optional section entities simulation Here is an example of what a trivial model looks like entities person fields period and id are implicit ages mE processes ageing age age 1 simulation processes person ageing input LIAM2 User Guide Release 0 10 2 file input h5 SUEpUL file output h5 Site cla lemeto Suet Clim OAS periods 10 3 3 import A model file can optionally import an other model file s This can be used to simply split a large model file into smaller files or more interestingly to create simulation variants without having to duplicate the common parts For details see the Importing ot
124. ze None Draw samples from the Dirichlet distribution See numpy random dirichlet for de tails New in version 0 9 exponential scale 1 0 size None Exponential distribution See numpy random exponential for details New in version 0 9 f dfnum dfden size None Draw samples from a F distribution See numpy random f for details New in version 0 9 gamma shape scale 1 0 size None Draw samples from a Gamma distribution See numpy random gamma for details New in version 0 9 geometric p size None Draw samples from the geometric distribution See numpy random geometric for de tails New in version 0 9 gumbel loc 0 0 scale 1 0 size None Gumbel distribution also known as the Smallest Extreme Value SEV distribution See numpy random gumbel for details New in version 0 8 1 hypergeometric ngood nbad nsample size None Draw samples from a Hypergeometric distribution See numpy random hypergeometric for details New in version 0 9 laplace loc 0 0 scale 1 0 size None Draw samples from the Laplace or double exponential distribution with specified location or mean and scale decay See numpy random laplace for details New in version 0 9 lognormal mean 0 0 sigma 1 0 size None Return samples drawn from a log normal distribution See numpy random lognormal for details New in version 0 9 5 5 Built in Functions 23 LIAM2 User Guide Release 0 10 2 logseries p size None Draw samples from

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