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User Guide - Newcastle University Staff Publishing

1. The plot below shows 2 groups one solid fill zone and a column style y axis q Af Jo 7 LE FAP rd IM d te ee pan il es lis a AAA AAA E AA 66 Stratigraphic diagrams User Guide C2 Global settings and defaults Global settings The default values of many of the parameters used to control the operation of C2 can be modified by the user by selecting Options from the Edit menu The six tabs in the Global options dialog box change the settings for User interface Global options Eq Default X sig digits in spreadsheet Default decimal places in spreadsheet Max decimal places in spreadsheet Dialog grid cell style colour DE Cancel Help FEE Reload ae Interface A Global Model A Graphs A symbols A Fonts nave rl User Guide C2 Global settings and defaults e 67 Global settings Global options Eq Case sensve comparisons Ts E sig digits in Cornell full output A E tems per line in Cornell full output A E Lancel Asi igts in Cornell condensed output 8 couplets per line in Cornell condensed otp 4 Help Default span for Lowess scatter plot smooth D45 o AA Interface A Global symbols A Fonts Dave If case sensitive comparisons is checked then comparisons between sample or variable codes when matching datasets or looking for duplicates 1s case sensitive The Show extended errors function reports extended errors if problems arise importing Excel
2. 1114 47 For variables you can sort by variable number code name or the data in any sample You can also sort variables by their weighted average of their sample number This is useful for species data that are in stratigraphic order sorting them in this way orders the species in terms of their occurrence in the core which provide a useful starting point for their order in a stratigraphic diagram Join merge datasets The join merge function allows you to join two datasets together row wise or column wise matching rows columns by number or code name Dataset jain Convert nulls to f Missing value code C Zetos Full outer join Replace exsting dataset Left outer join C Save as new dataset Inner join I Delete second dataset This function merges two datasets Dataset 1 is the currently open or viewed dataset Select dataset 2 in the top left combo box Joining by rows merges the two datasets by matching row numbers or codes Joining by columns merges the datasets by matching column names or numbers There are three options for the type of join which deal differently with non matching rows columns User Guide C2 Data manipulation e 19 Transform data 20 e Data manipulation Let us say we are merging 2 datasets by rows Full outer join will include all the rows from datasets 1 and 2 including rows in either dataset that are not matched in the other The empty cells in mismat
3. User Guide C2 Software for ecological and palaeoecological data analysis and visualisation User guide Version 1 5 Se AMI I Terry s Tia ee E Page 1 Please send comments bug reports to Stephen Juggins ncl ac uk Steve Juggins School of Geography Politics amp Sociology Newcastle University Newcastle upon Tyne NE1 7RU http www staff ncl ac uk stephen juggins University of Newcastle 2003 2007 Steve Juggins O 1991 2007 Contents User Guide C2 Introduction 7 Welcome to Cos aa 7 Prostate arica 8 COn paar lata 8 SUS cesicd CIALION ia laos 8 Getting started 9 ALI DO eae A O A Inte etal Se Te to 9 oporna datar dali 9 Selecting the worksheet table from an Excel spreadsheet or Database file 10 Duplic terow or columalabelsa td aia 10 Emp TOWS OF COI ta ia 11 Importins normaliscd dat ta ia 11 Importing CANOCO solution Hle rd da in 12 Viewin COIN dat A A A A IA 12 WAS WINS ada last a caco elas 12 Vi w Ine thelist of WallaDles ia lil 13 Miss ima A A A O a A e a aT 14 Panne daria 14 Spreadsheet proper a bd 14 Rename dataset 14 Delina adatas ala tc 15 Epone t CatASel xackise staal ltt accel Bled ct Suds a td ela cet Galak ta dr hills aac lala haa 15 AVI A dundee GDh ha art alla A 15 CPPS TT a EAT o dd 15 Closet Won pad das 15 Data manipulation 16 DAA Aids 16 A A a 16 Delete TOW So
4. 3 column form see Data Import there is now an additional checkbox on the File Export dialog that is enabled for spreadsheet database or comma tab delimited text files Zero data values can be included or excluded from the output Saving your work The C2 workspace can be saved by selecting Save from the file menu or clicking on the Save button on the main toolbar lad The single C2 file contains all the embedded datasets models graphs and reports in the Workspace Opening a C2 file A saved C2 file can be loaded into the workspace using the Open command on the File menu or by clicking on the Open button on the main toolbar La If there are existing unsaved objects in the workspace you will be given a chance to save them before opening a new C2 file Closing a workspace User Guide C2 An open workspace can be closed by selecting Close on the File menu or by clicking on the Close button on the main toolbar a If there are existing unsaved objects in the workspace you will be given a chance to save them before closing the workspace Getting started e 15 Data manipulation Data manipulation This section describes C2 s data editing and manipulation functions that can be useful in preparing data for subsequent numerical or graphical analysis Insert rows columns Select and view the appropriate dataset and choose insert rows or columns from the Data menu or click on the insert rows columns button on the data tool ba
5. igi i I i 4 A f F 1 i E i i 4 ar a m Bal Ls l a I Sj ii g E a a tee 1 z y x 1 o rE J Le i i 2 P hot Pax E ue i i l k if al Fink be E a od JE z Ovo he CA 1 yl Te ore Y 4 EE a ait iHa p Fat Ej Primas e E l A T a ksi A koar i ie MA i pp ir Lied hl E y D birri a mar E i E ri i E e E viy Ta CEDA Ae Ll e TFE TE pa T Par Habs oe Py run C2 has the following features Data manipulation Import export data to from Excel Access Lotus dBase Paradox Tilia Cornell condensed and full formats and comma or tab delimited text files Allows basic editing cut copy paste sorting transformation of data and merging of multiple datasets Data analysis Fits palaeoecological transfer functions or inference models to modern training sets of species and environmental data The following models are currently implemented Weighted averaging WA Partial least squares PLS Weighted averaging partial least squares WAPLS Introduction 7 Imbrie amp Kipp factor analysis a form of principal component analysis regression Correspondence analysis regression CAR Modern analogue technique k nearest neighbour MAT Maximum likelihood regression and calibration ML Options to delete variables and observations from the training set to transform the species or environmental data and to perform cross validation using leave one
6. izan F 3 63 33810 5751348 DES z 180 53 51754 ron Case a 31m 1301404 5 DB 14m zi 30 74 q EF 42 O ra 112 154 BABA Saw DAAN Faj 123 445774 OEA Cae User Guide C2 User Guide C2 Selecting the Variables tab at the bottom of the spreadsheet displays a list of variables for that model component together with the full explanatory name CBP CF Dect Biever Fe Edi Data Mer Wakes Ga window Help TETI cas hee BG Pom A IATA ote Damms TT API cep clo DetFeam oep LMiorialr Lidia fatinadsd pH by eee errar Sih fren dashing Mabel 1 Ge Ediiisd gH by se tv ga eh irio dg a Ayeni Geos JB Est maled pH i tered na ce derrite ih ire des iria J Cpecies cosiiciends T RAAT Cla Estiraisd 111 by pha ayer aging eras detras ee laica de rrrinicir FJ Atiak La Palomnarto E FE Model 2 Ba Giephe gt Ej Jaai R Model 01 Por Hale preven F The list of components is slightly different for each model For the training set all models list species coefficients sample estimates sample residuals and model performance If bootstrap cross validation is performed all models also list sample specific standard errors If a fossil dataset is also specified all models also list the reconstructions species diagnostics and reconstruction diagnostics If bootstrap cross validation 1s performed all models also list sample specific standard errors for the fossil samples A summary of the fitted model is als
7. left above or below the existing plot Choose Insert Copy to insert a copy of the existing graph Deleting an x y plot from a graph page To delete an x y plot right click the mouse over the plot and select Delete graph from the popup menu FP ogo m i Edit graph Delete graph a Insert new graph d d LED Insert copy i Copy Ctrl C Insert new graph page e pe E Duplicate graph page o Export to metafile 2 Delete ae Undoing redoing changes to x y plot Most modifications to a plot can be undone or redone by selecting undo redo from the Edit menu or clicking on the undo redo buttons on the main toolbar k cal Inserting a new graph page into a graph book To insert a new blank graph page into an existing graph book simply select Insert new graph page from the Graph menu or right click the mouse over an existing graph page and select Insert new graph page from the popup menu User Guide C2 Graphical tools 49 New graph pages are labelled Page 2 Page 3 etc and can be selected by clicking on the tab at the bottom of the graph window Page 1 APEZ If you want to use an existing graph as a template or starting point for a new plot you can Insert a duplicate This will create a copy of the selected graph page that can be further modified Deleting a graph page To delete a graph page simply select the page and choose Delete from the Edit menu or right click the mouse over the
8. lower error bars to be added subtracted from each data point Extras Graph properties i x Editing 4 curves Add x rererence Ine cL ae Apply f value of x reference line e Apply AAA Apply Class variable for symbol bar style eae Apply AA a seccmsssnansnanced Apply Variable for symbol bar colour Apply Start colour A Apoy End colour A Apply an Same as ficou pon Variable for bar widths Apoy Error bars _ Extras Apply all Undo Close Help Add a reference line vertical line to the plot at the specified x value Class variable class style changes the colour of bars or colour shape of symbols in a curve according to a 3 class integer variable Variable for symbol bar colour and start end colours changes the colour of bars symbols according to the value of a third quantitative variable Given a variable name and start end colour each point is coloured according to its position in the data range Variable for bar widths changes the width thickness of bars in stratigraphic plots Each sample can be sized to represent the depth or time it spans To use you need to insert into the dataset a variable that contains the width or thickness of each bar in the same units as you will use for the y axis Copying graph formats 58 e Stratigraphic diagrams Graphs for each variable can be individually edited via the Graph properties dialog box but in some cases it is easier to copy th
9. y Fegecen reler y Soeces cosHicaant 32 Data analysis User Guide C2 Re running a model Developing a transfer function often involves an iterative sequence of model fitting model diagnosis identification of outliers and re fitting To aid this process it is possible to open the Transfer function dialog box with the settings cross validation options transformations model options and variable or observation deletions of a previous model run To do this highlight the model in the Explorer tree view and choose re run model from the Analyse menu click on the Re run model button on the main toolbar En or right click on the model in the Explorer view and select Re run model from the pop up menu Deleting a model To delete a model highlight 1t in the Explorer tree view and choose Delete from the Edit menu click on the Delete button on the main toolbar A or right click on the model in the Explorer view and select Delete from the pop up menu Delete model El About to delete Model 01 Are you sure OK This operation cannot be undone Cancel M Delete associated graphs Help FEE e Delete associated report When you delete a model you are asked for confirmation and also get the chance to delete any auto generated graphs see below or Reports that are associated with that model Model diagnostic plots Diagnostic plots can be generated automatically for the training set analysis pressing the Plots button on the transf
10. 20 Zone column lett space mm 5 Zone column line style PPP Tome tont 12 pt Arial Variables AY axle Zones A Groups j Edil nde The box has seven columns of data for each zone The first two are depths ages etc for the zone top bottom The third column sets the zone style single line drawn at the top value lines at top and bottom values or a solid fill rectangle The forth and fifth set the line and fill style for the zone The sixth column gives the zone name and the seventh allows you to hide a zone The zone name is plotted in a column on the right of the diagram if the Zone column style is Show column Other options change the zone column width line style and font Ple Edt Wew gah Hep Er BET A ke Ago E DE O 2 E A Mo a Depi EN ESEESE ewe se eee ee i T l E a T A o ore i T T sranseatey CURE cs Stratigraphic diagrams 65 Adding groups Select the Groups tab on the Stratigraphic diagram options dialog box Stratigraphic diagram options Page 1 Group Firstgrapy Lastgraph Groupname Group 1 Group 2 Group 3 Group 4 Group 5 Group 6 Group T Group 8 Group 3 Group 10 Group 11 Group 12 Group 13 Group 14 Group 15 Show groupe E Group pen siyie Group Tort 12 pt Arial Mirman heaghi of croup test mm 40 Edi Unde Cae me For each simply group specify the start and end variables graphs and group name
11. 7 dd smooth Grruber_ ene GFEACCU G rubes 0 G pac L G pac A 5 G bulo TE G aequi Corbi i5 G duler a G infia cinn R Fis G crasT Si G mentu i 18 i kFozs P obig Pitobalicg 35 0 Smoothes are added to each selected variable as overlain curves You can remove the overlay delete or otherwise modify the curve as with any other data series Note The x and y data for the smooth are stored with the graph the y is simply a copy of the y axis variable currently selected for that graph If you change the y axis scaling you must also re create the smooth This is easily done by selecting the smooth in the Stratigraphic options dialog box and clicking Add smooth If the selected variable is a smooth it will be re created using the currently selected y axis variable Select the Zones tab on the Stratigraphic diagram options dialog box User Guide C2 User Guide C2 bx Stratigraphic diagram options Page 1 Zone Top Bottom Ste Line Fim Zonename Miej Zone 1 Coke lims 1 Zone 2 Double line Zone 3 Doubie lines J Zsa O T Doublieline Ei Tone 5 Double line Ex Zone 6 Double line ET imri Double line ify Zone 3 Double line EE Zone 9 Double line EE Zone 10 a Double line EN Zone 11 Double line Y Zone 12 Double line Y Zone 13 Doubs line ug Zone 14 oe e ae Zone 15 Double line Ld Show DOES E Zone column style Show column Zone columna with Conn
12. AAIE teste 56 EaD I e A A EE A E A OT A EAEE 57 RN 57 E aA E AE E A AE A OE AOS 58 COPY aPINa S A EAN T 58 Changing the y axis style and position ccccccccnnccnnnnnonononononnnonnnnnnnnononnnononnnnnnnnnnnnnnnnnnnnnnnos 59 Settins the y axis vanidoso ld di 59 Adding a secondary y axis aAA R EAE ETNE ie ini 60 Adding variables from a new dataset to the diagram occcccccccccnnnnnonononnnnnnnnnnnnnnnnnnnnnnnnnnnos 61 Removing variables from the diagraM occccccccnnnnnnnnonnnnnnnnnnnnnnnnnnnononononnnnnnnnnnnnnnnnnnnnnnnnnnnos 61 Changing the order of variables in the diagram cccccccccecececceeeeeseeseeeseeeeeceeeeeeeeeaeaas 61 Introduction e 4 User Guide C2 Overlay ine vanablesim a srap aega a Addin aA IOWESS MOM INGUIN ZONES Sonne a a N iwsanteedivaueteotones POCA COTO LIS irase neer E E tadsmanater Global settings and defaults CGlopDal se AOS ara dd id USES A ias AS A O A A an caradnca eases Models clan os ts o iaa Graph CLIO PP eo A A arate dee edness A E A EE A E A E E E S FON Saee EE E A NA A E T Acknowledgements ANCKMOWICUSCINGNUS ao a caca Appendix Importine data MOmMmExCe l oera a A EET E Introduction 71 71 72 05 Introduction Welcome to C2 User Guide C2 Version 1 5 2007 Welcome to C2 a Microsoft Windows program for the analysis and visualisation of ecological and palaeoenvironmental data My DH Bee e ap Ge Sake i Sark ond wae tad an dia 1515 ESB Te
13. CoMo isis 16 SOTO DY TOW SOF COMUNAS iodo 19 Jon IEE SS ALAS CUS io dis sare dasaas 19 PTAS CAC eis A O a eauactbennad 20 RAMS DOSE A Mare Me eterna A ciate 21 Duplicate dataseta a e eA a hea aatnoesnenes 21 Classifying da edu E Olea ncia sca dlestdadssesuacneeeaaeeesoages ZA Make classe ios rca ZA Edit CLASSES ii ios 22 Link dictionary da eleahaaanGlonadod nena aa atnoeesanees 23 PAIN OSE Sea 24 Descriptive statistics 25 Descriptive StatistiCS adc as wees Geass Soe se doen sta ob aed id ls 25 Data analysis 27 Introduction e 3 User Guide C2 esas O 27 WIG WS model Tess pia ae 28 Deleting observations or variables from a model cccccccccnnnnnonnnnnocncnnnnnnnnnnnnnos 30 Transforming species or environmental data and changing model options o 31 Exportine model TesulS rotonda irc 32 Converting model results into a data 32 Rie STN ek Mode lesson ooo E eniale 33 Derine a Mode raso co nictnndes A dci esa 33 Model Tae NOSE COS ai seso o ori i ciao cabos lao rencor dardos 33 Multivanate analysis 34 Graphical tools 37 Graphis OVET IEW aiai o A A it lolo ic 37 Ereatinesa new rapto id 37 C Fea a DO li ibi 37 Mods a Ky DIOL dci 39 A E A EA E E EE anaes eb EE E VEEE E T 39 Changing line and symbol Styles 0 40 SD tel aca O 41 AROS A E A 42 Layout enine a O N 43 EOC DIES ei er e meee oer a ee 44 A San ns asyocituda ses eocrse vation Neen gaat camanc toad E E E E we cetene ues 44 Plotting multiple datase
14. Descriptive statistics User Guide C2 Data analysis Transfer functions User Guide C2 Transfer function E Model biie 7 Model name Weighled Aveiaging pa bg Averaging Partial Least Squeres rasta aia Least Squares Imbne amp Kipp Factor Annales Regression Fae Principal Components Regression Training sel species data i Conespondence Analysis regression k2zcep 3 Modem Analog Technique IK22 cep Select variables Maamun Likekbood ENY cep i Ophir Sum55T i alidalic method Plots Nore aa Leave one out mul cross validation I gt sili 61 0 SETE pec obz n ide io oe 2 B fm Eny obs 61 E o Cancel Fost war Select the desired transfer function type choose a cross validation method and select the datasets to be used for the training set species data the training set environmental data and the environmental variable to be predicted You may also provide an optional fossil dataset under Supplementary data if you want to perform a reconstruction C2 will automatically generate a name for your transfer function in the sequence Model01 Model02 etc This name is used within the program to refer to the results of a particular model run You may also specify a separate model title to provide a more useful memory jogger name for a particular model The matrix of numbers under
15. The class style number field allows you to choose which symbol style to use for the current data series Variable for symbol bar colour and start end colours changes the colour of bars symbols according to the value of a third quantitative variable Given a variable name and start end colour each point is coloured according to its position in the data range Axes OF Data seres Add Copy Remove Labels Hide Add smooth iE Maxis title ee ee E Y axis title eG ae reer re ee Cee eee ads minimum value andes maximum value Y axis minimum value Y axis Maximum value A Log scale for x axis E ee Log scale for y axis eee ee en Equal scaling for x amp y axes ee eee Equal data ranges for x amp y axes Show x axis grid lines Show y axis grid lines A ee EE E A AA i RN Series A Symbols Ares M This tab allows you to Change the text used to label the axes Override the automatic calculation of axes limits Plot x or y axes on a log10 scale Scale the x and y axes equally that is one data unit on x one data unit on y Force the x and y axes to have the same data limits if the Equal scaling for x and y axis is also selected the length of the y axis will be adjusted accordingly Display x or y grid lines Change the length of the axes tick marks User Guide C2 Draw a horizontal line through the x or y axis origin zero data value Reverse the scale of the
16. and other spreadsheet database files Model settings Global options Eq Seed fr random number ne Number of bootstrap cycles MO Number of cross validation groups Cancel Permute samples in n fold leawe out BQ l WA use M2 in tolerance calculation Ex E Help Via missing tolerance method BH Wa replace missing tolerances method Minimum WAPLS number of components to extract 5 E PLS Standardize species data MA PCAR number of axes to extract ON E PEAR rotate axes L A E ee Reload PEAR use quadratic terms in regression Sets the defaults used in the various transfer function models 68 e Global settings and defaults User Guide C2 Graph settings x axis origin mm EEA E axis origin Gn a o Josi length men da Cancel axis lent 9s 0 Top margin mm 20 E Hep Botton mara en A 0 a ie al E 0 aaa ore 0 allow multiple inclusions in Stratigraphic diag O A E Moveable labels by default AAA Reload 4 eh Interface A Global A Model A Graphs Symbols A Fonts Save Sets the defaults for new graphs Allow multiple inclusions allows you to select and include a variable in a stratigraphic diagram more than once Symbols Global options x Defaut mb Style 1 Class O Style 1 Class 1 o Style 1 Class 2 o a Eo o C Style 1 Class 4 A Style 1 Class 5 E A Style 1 Class Bs Style 1 Class 7 E l Style 1 Class 8 2 style 1 Class 3 ae ee ee
17. class variable for symbol fine style OO Class style number ele GEN Dare E Symbol coeur variable Start colour M o SNNN E End colour AA EE MN 2 Series ASymbols A Axes A Layout A Error bars A Fonts Symbols are by default plotted using the size defined by the symbol chosen on the Series tab default 2 5mm The options here allow you to scale the size of a symbol according to the value of a 3 variable Z variable There are two ways to scale the points Z variable min max maps the symbol size linearly from the minimum to 42 e Graphical tools maximum values of the Z variable to the values in Min symbol size to Max symbol size in mm Constrained min max maps the symbol size linearly from the Min data value to Max data value to the values in Min symbol size to Max symbol size in mm Z variable min max scaling is useful for individual plots whereas Constrained min max is useful for retaining a consistent scaling across multiple plots The class variable allows you to specify an integer variable that defines the class or group membership for each data point Different groups of data are then plotted using different symbols The symbols used for plotting are defined in the global options Up to 10 different symbol class styles can be defined For example class style 1 may define circles of different colour for colour plots and Class style 2 may define different symbols of a single colour for B amp W plots
18. clicking on the dataset name or the Data node in the tree view or by right clicking on the spreadsheet and selecting Rename from the popup menu or with the dataset selected choosing Rename from the Data menu Rename dataset Eq Enter new name for dataset OK IK22 cep Cancel ae User Guide C2 Deleting a dataset Datasets may be removed from the workspace by selecting the dataset name in the Explorer Pane and selecting Delete from the Edit menu clicking on the delete button or pressing the delete key Deleting a dataset from the workspace cannot be undone so you will be asked for confirmation x About to delete IK22 cep 4re vou sure This operation cannot be undone concel_ Exporting a dataset Datasets can be exported in the following formats Access Excel Cornell condensed or full Tilia dBase Lotus Paradox or ASCII comma or tab delimited Click on the dataset in the tree view and select Export from the file menu or right click on the name and select Export from the popup menu When exporting to Access if a database already exists with the name given in the File Export dialog the table will be added to the existing database If the table name already exists in that database you will be asked to give a new name or overwrite the existing table If the database mdb file doesn t already exist it will be created as an Access 2000 database and a table added To save data in normalised form
19. dela cap ACTIA fies EHW tes CUIDA E Ey Hodes ACIIIA D Gape ACSA E Reports ADA E Model 0 ACOAAA Model 02 ACOTTA Model 05 ACTIBA ATS954 Fer le pre User Guide C2 mits 4 100 alt 3501 acmanthes barisna Achnanthes ineas ACen thes A Achnanithes caica Achmanthes minutissina var minutes ame ACA cria var pitii Acirenthes sustresce ver mino Achnanthes SUS kc ar heketea Achmanthes kryopbila var kryophia Achnanthe istenosinsts l Acmanites nodosa Acmarthes mangiias Achmeanthes ponspicus ver CONSPCUS Acari dores Arahe Naveda 4chmenihes fexeie var sipestis Po oie AC ranihes Saxons Achmsnthes suse Arana suckler Acirenihes pusila ver pusia Anmanthe doyma to diya Achiha onder Acranihes afec e gotics Achanihaa hyperborea Achmranihes pubalompides Saomeanthes proa var Getting started 13 Currently only Tilia files support full names for variables data imported from other types of file will have the full name initially set to the same text as the code name Long names can be subsequently linked in from a dictionary see below Missing values C2 understands missing values These should be coded as null in Tilia and 99 9 in other files before importing Missing values are shown as in the data windows C2 can handle missing values in the graphic routines it ignores them but missing values are not allowed in most of the numerical analyses Editing data
20. out n fold leave out or bootstrapping Performs environmental reconstructions using a secondary or fossil dataset with the ability to derive sample specific reconstruction errors under bootstrapping C2 can also generate summary descriptive statistics for a dataset and can fit principal component and correspondence analysis models Visualisation X Y scatter and line plots with options to control symbol and line styles axis scaling Scale symbol size according to a third variable Add x and y error bars as a fixed value or third variable Overlay multiple data series with different numbers of observations on same graph Interactively zoom data ranges and label data points Plot stratigraphic diagrams in a variety of styles bar line silhouette symbol Combine multiple datasets or multi proxy data with different numbers of observations in the same diagram Print print preview and copy graphics to clipboard Program limits The unlicensed free version of C2 is limited to datasets with less than 75 samples observation rows Please contact Steve Juggins to obtain a license and unlock code that removes this limitation Contact Please send comments bug reports to Stephen Juggins ncl ac uk Steve Juggins School of Geography Politics and Sociology Newcastle University Newcastle upon Tyne NE1 7RU UK http www staff ncl ac uk stephen juggins September 2007 University of Newcastle 2003 2007 Steve Juggin
21. page and select Delete from the popup menu Zooming the graph page The plots on a graph page can be scaled or zoomed by choosing a scaling pA factor in the zoom box on the main toolbar 100 The selected zoom factor applies to the screen display and printed version of the plot Fit wndow will scale the plot to fit the existing size of the graph window or printed page The plot may also be zoomed in or out using the zoom buttons Ha Zoomed to full size 100 by clicking the El button or zoomed to fit the current window by clicking the button Copying a graph page A graph page can be copied to the clipboard as an enhance Windows metafile by selecting Copy from the Edit menu or clicking the Copy button on the main toolbar The graph can then be pasted into Word Excel or your favourite graphics program for further editing Note you may need to experiment with Paste and Paste special and pasting as a Picture Metatfile or Enhanced Windows Metafile to achieve best results Export a graph page as a Windows metafile Printing a graph 50 e Graphical tools A graph page can be saved to disk as an Enhanced Windows Metafile by selecting Export from the file menu or right clicking over the graph and selecting Export to metafile from the pop up menu The metafile can then be imported into Word Excel or your favourite graphics program for further editing page A graph page can be printed or print previewed in the normal
22. the left to those most abundant at the base of the core on the right Simply select the variables to be sorted right click over the names and choose the sort direction 62 e Stratigraphic diagrams User Guide C2 Stratigraphic diagram options Page 1 RLGH til BROOM A Brachysira vitrea RLGH til FROOSD Fr aaa virescens va FLH til A Osa RLGH til PEOO2 A ona fibula RLGH til eevee Eunotia naedelil Mavyicula leptostriata Add o Brachysira brebissonii Refresh name Sort variables Top left gt tan a A Bottom left gt top right RLGH til T4004 4 Tabellaria quadrizeptata Sides var Si Overlaying variables in a graph To overlay a curve on the previous graph simply check the Overlay button Stratigraphic diagram options x pal Add vanables Jeet d 1 ETT BRODA Brachyora Yea t E T 2 RLGH Ai FROOSD Fragilaria virescens var exigua a i x C 3 RLOH I TAQ0IA Tabelaria tlocculosa tad OU U 4 Rl i dil Bea Parnnia tikata E f F 1 Note The x axis label is only shown for the first variable in the plot Adding a lowess smooth A locally weighted scatterplot smooth lowess for a data series can be added to an individual plot to highlight temporal rends Select the variable s to be smoothed in the Stratigraphic options dialog right click over the name and select Add amooth User Guide C2 Stratigraphic diagrams 63 Adding zones 64 e Stratigraphic diagrams 2 ll kFoss l Gogok 5 ire or
23. values Leave blank for auto calculation Reduce label crowding avoids overlapping labels The left and right margins set the margins which are used to calculate the spacing between graphs Log scale for x axis sets the x axis to be plotted using a log10 scale Reverse x axis does just that Rare taxa cut off value displays a symbol for values lower than the cut off rather than a bar Baseline origin value If this field is blank the baseline is drawn as the left hand y axis of the graph If a value is entered that lies between the minimum and maximum of the x axis it is used to position the baseline Bars silhouettes and horizontal lines are drawn as deviations from this baseline Hide symbols with zero values does just that User Guide C2 Stratigraphic diagrams e 55 56 e Stratigraphic diagrams Style Graph properties 3 ox Editing 4 curves Graph type Line Bar width mm 2 Bar style l Line graph line style E Silhouette style _ Show horizontal line L Horizontal lime style E Symbol style Mo symbol ande line style Show baseline El Baseline line style ande tick length mn 2 Show exaggeration line L Exaggeration multiplier 1 Exaggeration line style E Plot axes above data L Apply 4 Appl Appl Appl Appl Appl _Appl Appl _Appl _Appl Ape Appl Appl Appl Appl Appl Apply all Undo Close Help Graph type Choose from Bar Line Silhouette Symbol and Nu
24. variable for the x or y axis place the cursor in the field labelled Dataset amp variable for x axis or y axis data Click the Field Edit icon H to display the Dataset variable select dialog box Dataset A Ike Spec IRE by Navigate through datasets or model results and select a variable Click Apply or OK on the Graph options dialog box to display the graph Both x and y variables must have the same number of observations If either the x or y variable is left blank C2 will generate an index plot that is the sample number or index will be used for that variable in the plot User Guide C2 Dataset A variable for k ai dale Dali oor fied dea Mody 03 eee MA in iwah hps Dan p ol Hostel 03 1Estrides Ctr pH Pe Iny 6 0 tEsimates d an Model 04 ira 40 5 0 6 0 ro 3 0 Model 03 Estmates Otrs pH Modifying an x y plot Various properties of the x y plot can be modified using the Graph options dialog box To change a property of a graph click Edit graph button on the Graph toolbar int right click the mouse over the graph and choose Edit from the popup menu or double click the mouse over the graph Different graph properties of are grouped into different pages in the Graph options dialog box These are Series The Series tab contains options for defining the data series used in the plot That is setting the x and y axis vari
25. way Note that only horizontal tiling 1s supported any part of a graph extending above the top margin of the page will be truncated User Guide C2 Graphs that extend beyond the right hand page margin will be printed on multiple pages with an overlap specified in the Global options Using the Fit to window zooming 1s useful to scale a large plot or a graphpage containing multiple plots to a single printed page Refreshing the view Sometimes changes are made to the diagram or underlying data and the graph is not A eee To manually redraw the graph press F5 or click the Refresh button L on the graph toolbar Opening the graph in a new window It is sometime useful to open the graph in a separate window e g when working with the graph and inspecting editing the underlying data To open the graph in a separate window either click the 14 button on the graph tool bar or right click the graph book or graph page in the tree view and select Open graph in a new window from the pop up menu The new graph window has a restricted menu and tool bar limited to graph editing functions The window can be closed in the normal way or will be automatically closed when you exit from C2 7 ar je ee Af ee ee ee ee e o Brushing multiple graphs User Guide C2 oi 8 _ i E 3 LA T m i q ri Fi al A a y T i a E x Em Heki E a da F o TTA E E T p x raa
26. x or y axis Layout OR Apply Cancel Help Data seres Add Copy Remove Hide E A Graph x origin mm da Graph y origin mm ee eee ee eee Length of x axis mm ol Length of y axis mim ne eee Left margin ee ee eee Bottom margin eee eee Top margin Se eee te en ree Right margin A ee ee Y A ry Series A Symbols Axes Layout This tab controls the layout and positioning of the graph on the page The graph origin is the location of the bottom left hand corner of the x and y axes The margins are the areas outside the axes containing ticks and axes labels User Guide C2 Graphical tools e 43 Error bars Ok Cancel Data serlez Add Copy Remove Labels Hide Add smooth it Show x error bars L B error bar lower value A Beat UPPE snus eo bar lower variable o yg oaa E A variable smn E Show y error bars A AA E Yeerror bar lower vate Oyy E errar bar Upper value E Yeerror bar lower variable o ya E Y error bar upper variable ooo yaa E Error bar style Litio E Error bar tick length A S A ry Series A Symbols A Axes A Layout A Error bars X and y error bars can be added to a plot by either specifying a fixed value to be added subtracted from each data point or by specifying a variable whose value will be added subtracted from each data point Fonts OK Lancel Data seres Add Copy Remove Labels Hide Add smooth H
27. 0 5 44P030 yi 514448001 32O SWAPO 33 SWAPOR3 4 SWAPOGM 5 WAPO Note excluding variables or observations does not delete them from the original dataset it simply omits them from this model run The number of explicit and implicit deleted observations and variables is updated in the Summary list in the transfer function dialog box Explicit deletions are those variables or observations excluded by the user Implicit deletions are those variables or observations that would have no data once explicit deletions have been made For example if a user excludes 10 taxa from the training set but retains all observations and in doing so is left with an observation that now contains no taxa this observation has no data and becomes an implicit deletion Transforming species or environmental data and changing model options Species and or environmental data can be transformed and options for each model transfer function type can be changed by selecting Options in the Transfer function dialog box User Guide C2 Data analysis 31 Model options Eq Species transtormation Mo transformation Value of taj in logi Ola bx spec trans Value of h in logi0fa bx spec trans Env var transformation Value of ta in logi Ola bx env trans Value of h in log Ola bx env trans Use N2 intolerance calculations Replace missing tolerance values with Species data may be transformed to percentages proporti
28. 5 A jz win 0 41 2 05 01041 ES 16 30 13 11 052 0 62 0 73 223 a 4 52 079 Dz 8 06 45 13 55 197 a 0 34 2651 2 2 01 1 12 oz BiT 3 24 123 135 133 o 18 87 133 5 85 odd 072 472 323 535 da 5 33 0 26 41 2 56 1912 045 0 55 Ore Burt 144 413 415 4357 042 8 51 0 0 Ez 0 a 205 2 05 17 49 54 1 77 4 06 038 17 1 77 342 A 4 64 JE 1233 0 4 3 82 fs A GES 1 561 3 61 4 ees Gata Cates ca Enu f takross BD y 1 Ifthe first leftmost column contains numbers this column will be interpreted as sample numbers and the second column will be interpreted as sample codes 2 If the first column contains alphanumeric codes this column will be interpreted as sample codes and the sample number will be set to the row number 3 Ifthe column after the sample codes ie second or third column depending on or 2 above contains alphanumeric data this column will be interpreted as sample names If the column after the sample codes contains numbers only it will be interpreted as data 4 All other columns will be interpreted as data Only numeric data is allowed text data will generate an error Empty cells are not allowed either fill them with zero if species data or 99 9 to indicate missing values 5 The first row should contain text not numeric labels for the variable codes 72 e Appendix User Guide C2 6 Spaces and the following characters should be avoided in the header row variable codes These characters will be replace
29. 8 21 Delete samples Delete variables Importing normalised data C2 also has support for reading writing normalised data that is data in 3 column form where column 1 is the sample code column 2 is the variable code and column 3 is the data value This is a more efficient and effective way of storing and manipulating species abundance data in a database such as Access Paradox or dBase When importing data if the data consists of only 3 columns and the first two contain alphanumeric data corresponding to sample code and variable codes C2 assumes this is in normalized form ie first column represents sample codes second column variable codes and third column data values If C2 finds data like this it will display the following dialog box and ask if you would like to cross tabulate ie convert to a rectangular matrix using the values in the first two columns as the row and column labels for the new dataset respectively Getting started 11 Crosstabulate 3 ox File ES pec has 3 columns would you like to Ves crosstabulate it Ho Fill empty cells with Treat sample and 1 AEREA eros variable codes Missing values as case sensitive Click Yes to crosstabulate and convert the normalised data into a full table or click No to import the data directly Importing CANOCO solution file CANOCO solution files may be imported using the File Open dialog enabling easy plotting of CANOCO o
30. Stratigraphic diagram options Paget a The next step is to add variables to the diagram Click the Add variables button and select a dataset and list of variables from the Dataset select variables dialog box User Guide C2 Stratigraphic diagrams 53 Dataset variable elec E Datasets SWAP TT 4 cap 174 SAP Er cep 174 ALGHAge til eu ALGHS pec ti 20 H Model 01 e Model 02 You can select multiple variables by control clicking ie holding down the Ctrl key while clicking The Advanced button also allows selection of multiple variables using N N2 and Max criteria Click OK and the selected variables will be added to the Stratigraphic diagram options dialog box Click Apply to update the diagram DOO OOOO ooo COMIC IE I 3 4 13 ad 1 oy 3 113 Sp es Sep Stour SS ee ee Se ee eg SS Se a J LJ a s ae IE mn GB Bas PL AnS a E a iE J mui ia Bean T da Pa Bas 1 an Modifying the appearance of individual graphs 54 e Stratigraphic diagrams The properties of a single graph can be modified by clicking the edit button next to the variable name To change the properties of more than one curve first select the rows to be modified in the list of variables by clicking on the row number and click the Edit button at the bottom left of dialog box Either action will display the Graph properties dialog box Alternatively you can double click the left mouse button over an individual graph to in
31. Summary list the total numbers of observations and variables in the species environment and fossil data For the number of observations and variables in the species data and the number of variables in the fossil data the Summary also lists the number of explicit deletions implicit deletions and number of active observations or variables 1e the number after any deletions See below under Deleting observations or variables for a definition of these terms Click Run to run the model A dialog box shows the progress of the model calculations When complete the model results are added to tree in the Explorer pane under Models and a summary is added under Reports Note any variables that occur in the fossil data but are missing from the training set are excluded from the reconstruction for all methods except Modern Analogue Technique For this method all taxa in the fossil dataset even if they Data analysis e 27 28 e Data analysis have been deleted from the training set are still used in the reconstructions For this method it is therefore important that the fossil data only contains species that should be included in the reconstruction Note also modern and fossil datasets are matched according to taxon codes This matching is case insensitive by default Go to Edit gt Options gt Global tab on the main menu to make matching case sensitive Viewing model results The various components of the fitted model are stored as separate
32. When initially opened in the viewer a dataset is in read only mode To edit the dataset click on the Edit button E on the data toolbar select Edit from the data menu or right click the mouse over the spreadsheet and select Edit from the popup menu The spreadsheet supports full editing including Excel like auto fill and cut copy and pasting of cells ranges rows columns or complete tables to Excel or other programs The spreadsheet also supports full undo redo although undo information is lost when the user moves to another view that is either selects the variable view or selects another item on the left hand tree view The spreadsheet does not currently support formulae any text pasted into cells will be converted to missing values Spreadsheet properties The zoom level of the spreadsheet can be changed using the drop down zoom box on the data tool bar by selecting a zoom factor on the View menu or by using the Ctrl scroll wheel function on a wheel mouse The number of decimal places displayed in the spreadsheet can be changed by clicking on the decimal increment decrement buttons on the data tool bar The default view displays numbers in a general view showing a maximum of 6 significant figures Click these buttons to change the view to a fixed number of decimal places To return to general format keep clicking the decimal decrement button Renaming a dataset 14 e Getting started Datasets can be renamed by right
33. ables the graph type line symbol or line symbol the line and symbol styles and the label style User Guide C2 Graphical tools 39 40 e Graphical tools lx Graph options g 1 Apply Close Data seres Add Copy Remove Labels Hide Add smooth Dataset amp variable for x axis data 12HEnvw SumssT Dataset amp variable for y axis data Graph type Line style Plotting symbol Label style Omit tram feedback labelling Unda Help ddd Changing line and symbol styles Click the Field Edit icon H in the Line style field to display the Line style dialog box Click the Field Edit icon in the Symbol style field to display the Symbol style dialog box User Guide C2 Symbol style Eq Symbol 21 Lok ice xl e Size 2 Outline style width li Style Solid Colour a Fill style f Ho fill Same az outline Choose colour Halo Show Size Halo draws a thin white line around the symbol This 1s useful when there are multiple overlapping symbols with a solid fill style Symbols The Symbols tab contains options for setting the symbol size and style used in bubble or coded scatter plots Graph options a xj Data series Add Copy Remove Close Hide Undo Help Z variable for symbol size a Size scaling method Z variable min me Min symbol size NAS E Max symbol size ONE E Min data value A E Max data value ES E
34. ansfer function dialog box The list box displays a list of variables included in the model together with the number of occurrences N the effective number of occurrences N2 and the maximum abundance Max for each variable Select variables A E N2 M 141 46 y 139 125 39 59 117 53 38 216 43 13 zJ EN 55 405 131 30 AS 207 BS 15 45 12 57 57 1 14 78 13 97 18 123 185 34 255 ao 11 41 Z 35 673 Help 13 248 24 24 Exclude the variables to be omitted from the model and click OK The Advanced button allows selection of variables by N N2 or Max xj Code Ho MH2 Pia ACIDE 30 126 234 ACOTA 124 4688 46 0 ACO14A 7 30 35 ACO14B 30 33 55 ACOT4Cc az 190 245 ACOA 11659 32 ACN SA 11 69 14 ACT SA 17 64 56 Acozds izi 31S 463 ATI A54 ee 133 13 ACT 234 23 50 8 0 AOZA nm 61 17 ATIS5A4 34 TB6 20 ACIS 7 47 10 D items highlighted User Guide C2 Select variables advanced options Eq SelectbyN 2 Select by N2 f2 Help Clear The Select samples option on the Transfer function dialog box similarly allows the exclusion of observations Select Samples Eg 1 51L8P001 2 SM APODZ 12 SAPO 2 3 Swe POS 13 SWAPO 3 4 SWARD 14 SWAPT 4 5 SWeAPOOE 15 SWAF E 5W4A4POD 16 SWAPOIE SAPO lf SwaPoi 6 SW APODB 18 SAPO E 19 Swi P009 19 SWARTS 10 SAPO O 20 SWAPOSD 211 SWAPO 1 el SWAPO de SWAPO22 23 SAPO 24 SwWAPO24 25 SWAPIZI 26 SAPO 27 SWAPozZ 28 oWAPOZE 29 SWAPS 3
35. as Inia o Y axis minimum D Y axis label font 10 pt Arial Y aude maximi Y axis label font angia 30 Y axis mejor fick interval Y as label position Side Y axis minor tick ratio 1 Y axis label horz offsea immi 15 Yate tick length ren 2 Weends label vertical offset mm O Drew y axi Values as Data values Width of y axis column imen huriber of decimal planes Fiohthand margin ern 25 ante values font E pi Arial Show secondary y axis _ Y axis values angie 0 Secondary y axis origin 15 Y axis line style o Primary ya variable Show right hand y axis Secondary y seds variabla Reverse y axis LI Mejor tick interval Show grid ines None Minor tek rabia 1 Grid line style Secondary y 505 minimum Y axis top space mm 1 Secondary y axis name Yawis bottom space mm 1 Y axis scaling Cost eset Y axis verisble An entry appears at the bottom under Y axis scaling for each dataset that is included in the diagram Click in the right hand field and select a dataset variable to be used as the y axis for all graphs based on the listed dataset Alternatively click the Auto find button to give a list of any variables starting with Age Chron or Depth that matches the dataset This process must be repeated for each listed dataset Different y axis variables can then be specified for different datasets Adding a secondary y axis To add a secondary axis select the y axis tab in the Stratigraphic diagram options dialog
36. aset in spreadsheet view and select Classes gt Make classes from the Data menu Data manipulation e 21 22 e Data manipulation Make classes X Unclassified 0 Equal ranges Class 04667 0 Cancel Number of E classes Overwrite existing data Save as new variable Save as new dataset The Make classes dialog box accepts a single variable in the top right combo box and seeks to partition the individual data values into a number of groups Each class can have up to 20 groups although in practise we usually use a much smaller number Class method gives a number of choices for splitting the range of the selected variable The default is Even range nicely rounded intervals are formed based on the minimum and maximum values of the variable and the chosen number of classes Change the variable number of classes and click Refresh to update the grid showing the class boundaries and numbers of items in each group Any unclassified items ie with missing values or falling outside the class boundaries are placed in class 0 Other classification methods are Equal count and percentage boundaries at 0 5 10 20 50 100 useful for percentage species data and 10 user defined ranges These can be set and saved in the C2 configuration database for future use You can save an integer variable that lists the class membership of each item either overwriting the original variable a
37. box and select the variables used for the primary and second axes 60 e Stratigraphic diagrams User Guide C2 ie a e a gt a Pa wer e E ni a Ol i D on ES Foe P D T t q ae a mu ie e E ee E a Da iad x oe Pe gt E EA E EA A er amp A a rn sm ss ls ao sm es ooo o eos os f jka hi Fon E P p 5 E tt gt i E hos d 5 p la FP E FR 5 F h a z i P b i La y p E u n a E E gt p b w4 E Y 5 Ey 10 E eS a J Ci Lo T P p 1573 i 7 3 i l t i 50 1 15 A i lo E im P 7 1204 i i pp i i J 4 1353 ia a e po ES IELE o 20 0 o o O 0 0 o 0 0 a 20 The above diagram has a depth primary axis and a secondary axis showing samples ages Try adjusting the x origin and label offsets to produce an optimal layout Adding variables from a new dataset to the diagram Simply click the Add variables button and select the variables to be added Remember to set a variable for the y axis for the new dataset Removing variables from the diagram Variables can be deleted from the diagram by selecting the row for that variable by clicking on the row number and pressing the Delete button Alternatively variables can be temporarily hidden by checking the Hide checkbox in the variables list 4 RLGHSpectil FUOD2F Frustuliarhomboides war viridula RLGHSpec til ELO Eunotia naegeli 6 YRLGHA
38. ch is simply Model 01 02 etc and a user given title The internal name is used to identify the model within the program The user title can be more recognisable description of the model The internal name is generated by the program and is shown on the top right of the dialog box The user title is initially set to the same text as the internal model name but can be changed before the model is run To run the model first select the appropriate dataset in the dataset combo box All summary statistics are calculated for all variables by default Click Select variable to remove some from the analysis and deselect any summary statistics that you don t want Summaries can be calculated for the dataset as a whole or for groups of samples by specifying a Split by variable The split by variable must be an integer with group numbers indicating group membership for each sample in the dataset It must have the same number of rows as the dataset If you are splitting the data by group you can either have the output listed by variable or by group For the former the output lists the summaries for all the Descriptive statistics e 25 variables for group 1 then group 2 etc For the latter the list contains the summaries for variable 1 for the different groups then variable 2 etc The latter listing makes it easier to compare differences between groups for each variable The results of the model are added to the tree view under the model number 26 e
39. ched rows will be filled with missing values or zeros depending on what is selected in the convert nulls to box Left outer join will contain all the rows of dataset 1 regardless of whether they are matched in dataset 2 and only those rows in dataset 2 that are matched in dataset 1 Inner join only includes rows that are matched in both datasets Link the rows or columns by sample code or number By default alphanumeric comparisons are not case sensitive This behaviour can be changed in the global options Finally give a destination for the merged dataset either replace the original or save as anew dataset You also have the option to delete dataset 2 after th emerge Note by default code matching is case insensitive Go to Edit gt Options gt Global tab on the main menu to make matching case sensitive The transform function allows simple transformation of individual or groups of variables Choose Transform from the Data menu or click the Transform button on the data tool bar E Tran horin daka E DHiri GHcglob 4 Gitar Proparsons NA 3 GHpec A 5 Gkseccu LoglO fy kbA Bl Coma 19 GHbulo b Raters Suena spot 10 GHfaloo F Gipsa L Agwegate 11 Gitcabd Missing values 0 0 Helo 12 Harris Missing wakes gt mear 13 Hohn Add constant fr r A 14 Hsi kuia be corsi T Ya s 15 Giria enian usable ie shinni mean 115 GHtm L NULL abues lf Is Htim H f r 8 GHcras Af Win o 13 Gttecitu H p Replace vih mis
40. datasets under the model name in the tree view Selecting the node of a named model displays a summary of the fitted model in the Data Pane SWAP C2 Object Browser mmm O a eee ee ee ee e Pear Mig XxSBh E B Detasels a E SWAPTT4 ceap 19 Merch 2003 16 57 09 E CWw4Perny c p Peick Type Viskiled Averaging EE Models Trai yecies d AP 174 cop SEE Training sel environmental data SVAF er cop 5 Regiession coalficiens Environmental variable pH Ej Species coelficients Tola number of samples 174 ES Estimales Pumicer of samples in mode 1174 A Residuals Total number of variables 270 Perlormance Mumber of variables in model 279 E Model 2 Cross validation hone PS Graphs E Model 01 Selecting a model component displays the results for that component in a spreadsheet TOR EA ee EA ERE A A DWAF f 2 Dalaiada a 4 57 14 0661 EME bota w O Sea 3 35 12583 EFD 0555 El amp ED mc 1H 85 07 5 Ne DEJ amp Modes F 34 IHESA ro EEE EEH Medel 01 3 sn 313468 EA ir d Aethai ciosa a 2344 Iasi 54319 Liras 0 ESSAN 11 J15 52km oe Cae as E Estar 11 13 A TIE ro D 7 n47ar EJ Ardual iF J E E oe DES Petomante iH HSA 515 Odes E EE Model 2 Fe 135 1A A DRA Ey Graph a am 20743 225113 rar o EJ Apes 11 1 8114004 EFJ 00461401 5 Model 0 3 2H 155364 Bh 0150041 T 10 4 TEH are nl E 1334 aa igan Wista ani Sii E GETE DANG Pri 53M 11 714 Bese Lard aa 2165 10146 IT DAA A r 13 Hi A raja
41. e formats of an adjacent graph This function works in a similar way to the format painter in Word and Excel Select a graph whose format you want to copy and click the new Copy Format button Then just click other graphs to copy the format Click outside the graph area to end Double click the Copy Format button to select which attributes of the curve are copied graph style axis scaling etc The default is to copy all attributes User Guide C2 Changing the y axis style and position Various properties of the y axis can be changed by selecting the y axis tab in the Stratigraphic diagram options dialog box Stratigraphic diagram options x Origin mr y Origin imm Y axis lengh ren aos minii Y 2015 maximi Y axis major fick interval Y axis minor tick ratio aes tick lencih ren Drea y axis Values me hummer 01 decimal planes aks values font Y axis values angie Y axis line style Show right hand y axis Reverse y axis Show grid ines Grid line style Y axis op space mm Baseline extends to top space Top margin mn 50 W ends label Y axis label ford 10 pt Ariel Yaris label font angie 90 Y as label position Sida Y axis label horz offset immi 15 Y eds label vertical offset mm 0 Wih of y axis column men 0 Riohihand margin mm 23 Show secondary y axis Secondery y axis origin 15 Primary y az variable Secondary y 10 s variabla Mejor tick interval Minor tick rabia Secondary y ais Minimu
42. e te E Reload Style 1 Class 10 A ja interface A Global A Model j Sets the style of the default symbol and the symbols used in the 10 built in class styles with each class style having 21 distinct symbols User Guide C2 Global settings and defaults 69 Fonts Global options Eq x axis tithe font 12 pt Arial Y axis title font x axis label font Y axis label font raph title font Object label font Axez pen Baseline pen Curve pen Horizantal line Origin pen Smooth pen A Global A Model A Graphs A Symbols Sets the font and line styles 70 e Global settings and defaults User Guide C2 Acknowledgements Acknowledgements User Guide C2 C2 brings together the data analysis functions of several of my earlier DOS programs namely CALIBRATE WAPLS and MAT and integrates them with a range of graphical visualisation tools into a single program Some earlier code has been reused but C2 represents a re write of many of the graphical user interface and numerical routines I am very grateful to John Birks for providing the impetus and encouragement to tackle this project and to the Norwegian Research Council NORPAST project for financial support Acknowledgements 71 Appendix Importing data from Excel C2 can import data from Excel and Lotus spreadsheets dBase Paradox and Access databases and ASCII comma or tab delimited files To import correctly the data must be formatted according to cer
43. e worksheet table from an Excel spreadsheet or Database file If you import a dBase or Paradox file you will get a popup Select worksheet table dialog box asking you to select again the file from a list of similar files found in the directory If you are importing data from Excel or Access you will see the same dialog box but with a list of worksheets Excel or tables and queries Access found in the selected spreadsheet or database Select the appropriate file worksheet or table and click OK You can optionally specify a name to be given to the dataset when imported C2 will also list individual fields in the dataset Character fields are indicated with an asterisk The first character field will read as the sample or case code The second character field if there is one will be read as the same name Subsequent fields will be read as data These defaults can be changed using the radio buttons in the right hand pane Missing values can be imported as missing default or recoded as zero select worksheet table Paste numb Corres Valable code sneng iy Sif z values lo r impon as maes isk Spex rc Dala Eon DIOS Duplicate dataset names Each item of data in C2 is uniquely identified by its dataset or model output and row column names Dataset names must therefore be unique If you try to import a file with the same name as one already loaded the following dialog box will popup and give you the op
44. er function dialog box Model graph options Eq Obs vs inf WA Inv DS OK Obs vs int WW Cla DS Obs va inf WAT Inv DS Cancel Obs ve int WAT Cla DS Select all Select the desired plots on the Model graph options dialog box and click OK When the model is run the requested plots will be generated and added to Graphs folder in the tree view User Guide C2 Data analysis 33 seers MAA AA AAA AS Sl ri r F Fi 1 2 8 a Ta rap Tir em E se bizin E R i te L Pera ar ee eS et ni oe4 y F eman i T k F Rd La Fada E A Pip 4 e ldi N a bl rin TF a e a Ty a Ea ots EE bier i e ith E TE ES J T p i 1 sl El Micedein a Li il Fr Of 7 far A tete ee a A tae ot E TA d et Eo BL A i Ei in m C e Es a i 3 pr D ikii ed e Flia Bev heat iT ha a es eel Me J r fe ha ld ay repr tak er J j E E oe PE i E nel B boe B A 40 50 LE ha AG 45 Ll go rio 15 Kinda 1621 Exrrais Cta pe HA fd Redal es A 1n1i i t a z Ei a a E i i 4 b ji La 1 h E it jj E yl de am ip 4 Eas in y 7 a E E i i E 1e E 44 E a i a ao Ka i 8 a E Ei p ee EN a T 4 ce bs a Ah Ti X IE HE E ME e Pte A E a Hpi J ins E PA E pata of i i u ae 1 1E ma G A aif H LE L TT Ci FL P Aa pled F gt Dal Sa Diagnostic plots may also be created after a model has run by right clicking on
45. ge th O O O AO f y y yy a Changing the order of variables in the diagram Variables are plotted in the order they appear in the variables list To change the order simply select the rows to be changed and drag them to their new position User Guide C2 Stratigraphic diagrams 61 E ar A E A MA RLGHSpec 1111405324 Navicula cocconeiformis RLGHSpec i ELIO Frustulia rhomboides var viridula Eunotia naegeli pH ALE HS Spec HTA 001 A Tabellaria flocculoza RLGHS pec til EDOO2B Eunotia pectinaliz var minor It is also possible to drag and drop individual graphs to change their order in a stratigraphic diagram Select one or more graphs by clicking shift click for range or dragging a box to intersect the desired graphs Selected graphs will now have a shaded border Now click and drag the selected graphs The cursor will change shape according to drop zone Drag to the top of the window to delete from diagram Drag to bottom to hide Drag over another graph to move selected graph s in front of selected Drag and drop over upper 1 3 of another graph to overlay You can also select a range of graphs in a stratigraphic diagram and right click the mouse to edit the selected graphs It is also possible to automatically sort variables in a stratigraphic plot according to their optima on the y axis This provides a rough rearrangement of taxa from those more abundant at the top of the core on
46. is Axes label font 10 pt Aa i Axes title fort q2pt Arial O E Graph title font 14 pi Arial O E Object label fort Bpi Aral OoOO OO r A Series A Symbols A Axes A Layout A Error bars A Fonts Change the font face style and size of the graph labels Plotting multiple datasets on the same graph An individual graph can contain multiple datasets each plotted in a different style In C2 each plotted dataset is known as a series To add additional data series simply click Add or Copy in the Graph options dialog box Add will add a new blank series with default options Copy will add a copy of the highlighted series The figure below shows an x y plot with two data series plotted with different symbols Damse E vabe for sota debe eM OP wire cam oH Detese E var atde dor y aos date SEPIA can AS Sta plo Ram Coda 40 50 6 0 7 0 60 A data series can be deleted by highlighting 1t and clicking remove Note you cannot delete the first data series each graph must contain at least one data series Zooming in on data in an x y plot The data range in an x y plot can be zoomed simply by dragging the mouse to select the zoomed range Zooming is incremental and can be undone ie zoomed out by clicking on the incremental Zoom out E or Zoom out to original range A buttons on the Graph toolbar Identifying and labelling data points in an x y plot User Guide C2 C2 supports two types of interactive label
47. ise takes an Excel file of names and records merges and uses this to modify a dataset The Excel file should contain alist of at least two columns the first column is the old variable code the second the new code An optional 3rd column may give the long name for any new variable codes C2 will then rename variables in a dataset from the codes in column to those in column 2 of the dictionary After renaming it will merge sum the data for any duplicate codes A Dictionaries ae Coxtemo WE DemoD atasii k xls ad CD atai atasets 0147 CODE DiatlodeN amesF orl Help Replace existing dataset Save as new dataset l amp KSpec_2 24 e Data manipulation User Guide C2 Descriptive statistics Descriptive statistics User Guide C2 C2 has a single function to calculate summary descriptive statistics for a dataset Such statistics are a useful starting point in analysing a new dataset To calculate descriptive statistics for a dataset choose Descriptive statistics from the Analyse menu Descriptive statistics xl Model name ha odel 06 Select variables El variablez selected Model title Dataset 22 cep Split by C E i Standard deviation List results by e Variable C Group Help Aun Cancel Output from this function is treated as a model result and will be added to the Model folder on the tree view Models in C2 have two names an internal name whi
48. labels Choose this by clicking the down arrow on the Enable graph bales button sh 2 a a a Default position a Moveable labels User Guide C2 The Enable graph labels button with change to blue text Now when a data point is left mouse clicked the cursor changes to a hand pen p v212 b at Move the mouse to where you want the label placed a left click again Click the data point again to remove the label Labels are drawn with the font specified in the Object label font field of the Fonts tab in the Graph option dialog box Labelling from a list To find specific data points in a graph it is sometimes useful to select the point from a list Click on the Label button on the Graph options dialog box and select the data points to be labelled from the check list Graph label Eq 1 4114 61 Ok O 2 v17 196 O 3 18 110 Lancel O 4 16 227 5 14 47 Help O 6 23 22 7 2 12 O 8 23 29 O 9 12 43 O dii 10 3 4 Select all 1 15 Veso El Deselect all If a symbol is specified for a point the label is drawn horizontally centred above the symbol If the symbol type is set to No symbol the label is drawn horizontally and vertically centred over the data point OO T P Pa ba cn oo La Pa Hiding data points in a plot To hide specific data points in a graph click on the the Hide button on the Graph options dialog box and select the data points to be hidden from the list Adding a
49. ling data tips and data labels Both types of labelling carry a computational overhead and will slow down the redrawing of the graph on screen For pages with a few graphs consisting of a few hundred data points this will not be noticeable but for multiple graphs with many thousands of points the delay may be significant For this reason labelling is disabled for the page when it is created Graphical tools e 45 46 e Graphical tools Interactive data tips To identify a data point make sure the Enable graph tips button on the Graph toolbar is selected Use the drop down selector to show graph tips or on the program status bar Hover the mouse over a data point and the sample code and x and y data values will appear on the graph or in the status bar C 207 i q a CL e eT JJ p s Al D 7 la 164 E J tn L 124 cu nei g T pz 4 a ba ot g 0 4 86 12 6 2 2 A 23 Model 02 Estimates Obs SumssT Data tips are available for both x y plots and stratigraphic diagrams Interactive data labels To permanently label a data point make sure the Enable graph labels button EA on the graph toolbar 1s selected There are two labelling styles The default is fixed position labels Clicking on a point will simply place a label above the data point REES amp es 4 11447 4 E p v t O 4 Click the point a second time to remove the label The second method is moveable
50. lowess smooth A locally weighted scatterplot smooth lowess for a data series can added to the plot to identify or highlight the relationship between the x and y variables Click the Add smooth button on the Graph options dialog box User Guide C2 Graphical tools 47 Enter parameters for lowess smooth Spar 0 45 Cancel 0 lterations har a robust amooth Help The two available options for the smooth are the span the proportion of data points used in the local regression at each data point and the number of iterations used in computing robust estimates of the local regressions 6 0 F 45 AR E 30 T 15 DIE 0 0 H Model 02 Residuals WWAPLS C1_UA i ar 3 0 Pi 4 4 5 5 0 O 4 0 0 S 10 15 ZU 25 aU Model 02 Residuals Obs SumssT The smooth is generated as an additional data series and can be deleted or modified using the functions in the Graph options dialog box Adding additional x y plots to a graph page A graph page can contain multiple x y plots To add additional plots right click the mouse over an existing plot The following popup menu will appear 48 e Graphical tools User Guide C2 tl ct E DaO a on 45 Ed pipa Cielo Gap r 5 lipii co h ij a a Copy mie AustSoe cap RUBER ae ried rr GaSb page e Tn Crago quant page Empor ho restates CHO AustEre Tma Choose Insert new graph to insert a new empty plot to the right
51. m Secondary y axis name sss bottom space mim Y axis scaling Dost et Y axis variable FLGH Hi Anto Tired Variables y aue Y A Y m Cose Hee X and y origin sets the position of the bottom left corner of the y axis relative to the bottom left corner of the window or printed page Y offset 1s the horizontal distance of the y axis label from the y axis The y axis can now be drawn as a column There is an option on the y axis properties to set the width of the column Zero draws a normal y axis any other number draws a column of that width You will have to find the best width to fit the labels by trial and error but 12mm is a good starting point Y axis labels can be plotted as values default or sample codes names using a new option on the y axis properties Note this only works when data points are plotted against sample numbers on the y axis 1e the default It will not label items correctly if a chronology variable is given for the y axis The rest of the options are self explanatory Setting the y axis variable By default each variable in the diagram is plotted against sample number on the y axis To change the y axis variable select the y axis tab on the Stratigraphic diagram options dialog box User Guide C2 Stratigraphic diagrams e 59 Stratigraphic diagram options Page 1 Origin man 20 Baseline extends to top space _ y Origin mini 20 Top margin men 50 Y axis engh men We Y
52. meric Most of the options on this page are self explanatory If a symbol is set in the Symbol style field it will be overlain on silhouette and line graphs Show horizontal line draws a horizontal line from the y axis to the data point in silhouette line and symbol graphs User Guide C2 Labels Graph properties E x Editing 4 curves X axis ttle fort Tp A san Apply x axis tle orientation degrees gE m x axis tle horizontal offset mm OOO App x axis ttle vertical offset mm FOO App Graph tile on right a App X axis values font Bot O App x axis subtitle font Saa li x axis subtitle vertical offset mm E OO App Rotation angle for x axis values OOOO App Draw x axis values attop OOOO Appl Display x axis values in exponential Mone Appl Skip first X axis value Qe App 7 Style A Labels Apply all Unda Close Help Specify an x axis sub title drawn under each plot and change the font face size and styles used to label the graphs X axis title offset gives the label offset from the top of the y axis Error bars Graph properties xl amp chnanthes minutissima var minubssina SHEN Sa SA AA Apoy A ApH UNO ETA ApH a e A LL es AN a A Soria rele o anes eae ADRI Erne kaiteen A Eiron etalinesstie ee App Tt as scaing A Ste A Labels A Error bars Apply all Close Help User Guide C2 Stratigraphic diagrams e 57 Supply either a fixed number or a variable for the upper
53. o listed under the Reports section of the left hand tree view This displays the model types datasets etc the model performance and a list of variables excluded from the transfer function or reconstruction Data analysis e 29 30 e Data analysis FAAP CF Object Browser TFT DA AA ES Dated ES peA cop E EM Motel Cn E Flegeention makiii lg Spaces coll ices I Eriak 5 Fenius Ej Perlamarce o OC Por Helga prap P Results for model Model 01 Hodal are Hodel type Date Species date F Earicomrental data i FaVirGomictel wer beh La E Teil untar GE senples 3 Hober of samples in pode I Total number cl variables Mite of varcdaoles in modeli 1405 bm Basie T gt FT Deshrinking regression coefficients Id Inversa daghi urii 2 Clarrical dali Model performance i Tal TA Jun bhii D itii z EZ 0 04723 i di Pia 6 ADA 4 Has Biss 0 25142 i Hodel 01 Weighted ivecsging 19 Haeeh 20052 16 57 00 APTA cep RAPE cep pa LTA 174 pee Evo WAL Ed MA blo WATOL bD 86 NATOL El E TAE L eas f isa 1 1994 2 2605 D SOIL 2 1461 4112 WA Cle MATOZ Ine MATOS Clu JELG 0 1373 6 1183 CD OFE D ASELO gt AESLO BLE E ALA 1 Lee D LETIS DD IFEI 5 15245 3 De Deleting observations or variables from a model By default all observations and variables in the training set are used to generate a transfer function To delete variables click the Select variables button on the Tr
54. ons square roots or log10 Environmental variables may be transformed to square roots or log 10 Invalid transformations e g square root of a negative number will result in an error Note log10 transformations are only applied to non zero values in the dataset Original zero values remain zero Any species transformations are also applied to fossil data if a dataset is given for the supplementary data The exact options displayed will vary according to the type of model Most are self explanatory Exporting model results Model results can be exported to an Excel file by either highlighting the model title in the tree view and selecting Export from the file menu or right click on the model in the tree view and select Export from the pop up menu Each model component is inserted into a separate worksheet of the Excel file and a copy of the model summary that is written to the Report is inserted into the first worksheet If you only want to export one table of results from the model you can either copy and paste it into Excel for example or you can convert the model component to a dataset and export the dataset Converting model results into a dataset Model results cannot be edited If you want to modify a results table or export it to a format other than Excel you first have to convert it to a dataset To do this right click on the component of interest and select Convert to dataset from the pop up menu Ei Mode i ES Model 01
55. ot options dialog to omit a series from triggering a hit this should provide a work around for most situations Used sensibly brushing can be very helpful for diagnosing models For example in a transfer function to diagnose outliers make a symbol or bar stratigraphic plot of dominant taxa in the training set and use e g pH as the chronology Open this is a separate window and selected a residual plot of the TF in the main window Turn brushing on and brush the outliers the corresponding samples in the stratigraphic plot will be highlighted identifying any unusual assemblages associated with the outliers lial Dig ue Se Cee a AAA A fe J om i Mri J 4 ious prr ee nr r r 4 L ir e 1 Je e Pal E Pam a art ji F Papl mepi 17 A oe E i J il i E Epa 3 2 i bani rnem bee a a hr mm Fo Pd mei ma E E Da 3 A Malulen A nt ammi aoe a or irha ME E ri E Fe rek eee Fi HH 45415 0 re 1 User Guide C2 Stratigraphic diagrams Creating a stratigraphic diagram Please read the previous section on creating a graph before attempting to create a stratigraphic diagram To create a graph book containing a stratigraphic diagram simply click the New graph book with stratigraphic diagram or select Insert new graph book gt Stratigraphic diagram from the Graph menu This will create an empty plot and display the Stratigraphic diagram options dialog box
56. r LJ LJ E f The dataset does not need to be in Edit mode to insert or delete rows columns You are given the option to insert one or more rows or columns before the row column of the currently active cell or at the end of the spreadsheet If there is no currently active cell this option will be disabled Insert rows columns Eq Number of rows columns to Inzert Ok il Cancel Fill wath f Missing values Zeros Insert at Et Before current C Atend You can either fill the new rows columns with zeros or missing values Delete rows columns 16 e Data manipulation Select and view the appropriate dataset and choose delete rows or columns from the Data menu or click on the delete rows columns button on the data tool bar gt Y If there are currently selected rows or columns you will be asked to confirm their deletion User Guide C2 User Guide C2 C2 E About to delete 2 columnss This operation cannot be undone concel_ If there are no currently selected rows or columns you will be asked to select some in the Delete samples variables dialog box Delete samples variables xl Please select variables for deletion ok f Delete items from selected dataset C Save as new dataset IK22 cep2 Help Save deleted as IK22 cep3 Select To select samples or variables for deletion click the Select button If you are deleting samples
57. rows you then get a chance to select the appropriate samples from the Select samples dialog box Move samples for deletion to the right hand list using the exclude button Select variables E A Code NH ON HO M2 Max 1 174 61 4 1 1 Pd Wir 196 B 1 2 3 118 110 E 12 q WIB 227 5 13 5 Wid d 15 23 E W23 22 7 31 7 We 12 4 1 4 B 12323 3 dE 12 43 3 51 10 AS 10 50 311 41573 14 52 12 2381 10 439 13 14238 11 47 na 1253 15 50 15 W2383 1 43 16 1255 18 Eb 17 A15234 156 El 18 165 18 40 19 22122 19 41 20 VIEH A EE 21 W432 23 104 22 i265 HF l 3 1419245 ce 61 O items highlighted Click OK when done The delete samples variables dialog box now shows that some samples are selected and the OK button is enabled You can now choose to delete the samples from the original dataset or create a new dataset consisting of the original minus the selected samples You also have the option to save the deleted samples as a new dataset Thus the delete samples variables function can also be used to split one dataset into two Data manipulation 17 18 e Data manipulation Delete samples variables xl Warning About to delete 10 samples OK Thiz action cannot be undone f Delete items from selected dataset C Save as new dataset IK22 cepe Help Save deleted az Jk22 cepa If you are deleting variables you are asked to select the variables for deletion from the Select variables dialog box This is similar to above except i
58. s 1991 2007 Suggested citation Juggins S 2007 C2 Version 1 5 User guide Software for ecological and palaeoecological data analysis and visualisation Newcastle University Newcastle upon Tyne UK 73pp User Guide C2 Introduction e 8 Getting started The C2 workspace A C2 file or document can be thought of as a workspace that may contain one or more different datasets the results of one or more analyses models one or more graphs and a summary text report or log of each analysis The tree view in the left pane of the Object Browser window shows a hierarchical view of each of the above C2 objects arkat Ce anc E 210 de LE La A A A A j e de ADO RARD EXCEL l ag E WEEE CoE Een aaa a E a EEF Ead paee Tp A oe I FARAH sra obs ar 1 Pad 1 amada be m1 lai i EEEE wa et ee A Poe Pei peu Fl Importing data C2 is able to import data in Tilia Cornell Excel dBase Lotus 123 Paradox Microsoft Access and comma or tab delimited text ASCII file See the Appendix for the rules for formatting data in spreadsheet or database formats before importing into C2 User Guide C2 Getting started 9 10 e Getting started To import a dataset into C2 select Open from the File menu or click on the File Open button on the main toolbar The default file type is C2 Select the appropriate file using the drop down list in the File Open dialog box Selecting th
59. s Also each graph may contain one or more data series Source data for graphs may be combined from different datasets in the workspace making it easy to plot raw data alongside model results or to merge plots from different datasets into a single stratigraphic diagram This section describes x y scatter and line plots Stratigraphic diagrams are described in the next section Creating a new Graphbook To create a new Graphbook containing a blank graphpage to the workspace by selecting New graph book from the Graphs menu or clicking the New graph book button on the main toolbar A new graph book will be added to the Explorer tree view Graph books are automatically named Graphbook 01 02 etc Graph pages are automatically named Page 1 Page 2 etc Creating an x y plot User Guide C2 To create a new Graphbook containing an X Y plot select New graph book gt XY Scatterplot from the Graph menu or clicking the New graph book with scatterplot button on the main toolbar e l A new graph book will be added to the Explorer tree view a Graphs a Graph books are automatically named Graphbook 01 02 etc Graph pages are automatically named Page 1 Page 2 etc The can be renamed using function ley F2 and given a description This will create an empty plot and display the Graph options dialog box Graphical tools e 37 38 e Graphical tools Graph options 1 00 0 00 0 00 1 00 To specify a
60. s a new variable in the existing dataset or to a new dataset Edit classes To use the Edit classes function first select a cell in the spreadsheet of the class variable you want to edit This must be an integer variable you will get an error if it is not an integer class variable Then right click the mouse and select Classes gt Edit classes from the popup menu or selected Classes gt Edit classes from the Data menu User Guide C2 Link dictionary User Guide C2 Edit classes 1218 Je Wie 33 17 165 H W19 310 35 16 19 36 4153154 7 419 308 39 4110 98 40 Y22219 41 16 33 42 122 204 43 20 167 44 1410 89 45 W12 79 46 4139216 4 1414 90 49 2180 72 43 1621 50 2180 76 lca Lao ars oot G G G O G a oa aoa The Edit classes dialog box shows on the left a list of classes and the number of items in each class Use the list boxes on the left to remove items from a class and to place them first into class O unclassified and then into a new class The Link dictionary function allows you to link a dictionary of species full names into a dataset To link a dictionary open the dataset in spreadsheet view and select Link dictionary from the Data menu The dataset can be in either data or variable view but it is more useful to have it in variable view Up to 10 dictionaries can be defined and saved in the C2 global settings database Click the new file icon to add a new dictionary to
61. s by on import User Guide C2 Appendix 73
62. s new variables in the original dataset or 3 Saved in a new dataset With 2 if only one variable is selected the text entered into the adjacent text box will be used as the new name If more than one variable is used the test will be used as a suffix to the original names Any missing values generated during the transformation e g by log of zero can be converted to missing values replaced with zeros or prevented by a warning Selecting transpose from the data menu simply transposes a dataset and its row column names and numbers This function can sometimes be useful to get around the 255 column limit in data imported from Excel Note that C2 has no such limit Duplicate dataset Classifying data User Guide C2 Selecting Duplicate dataset from the Data menu does just that This option can be useful to keep an original versions of a dataset in the Workspace prior to transformation or other editing of the copy There are two functions to help you make classes or groups from the data These functions are currently manual and should not be confused with numerical classification techniques like cluster analysis Their main use at the moment is to generate class or grouping variables for use in visualisations There are two class functions The first Make classes helps define groupings of samples or variables from the raw data The second Edit classes is a tool to edit an existing class variable Make classes Open a dat
63. sing values 2 G Bieri l l pm A vah H Pitty 4 Replace vath zeroa 22 Citrate E Ceara esti data OU Give gt ney variable B i y Move the variables to be transformed to the right hand list box using the include exclude buttons Then select a transformation Current methods are 1 Percentages all selected variables are transformed to percentage based on the sum of those selected 2 Proportions as for percentages 3 Log10 all selected variables are transformed to log base 10 according to the formula log10 ax b where a and b are entered in the edit boxes 4 Square root all selected variables are converted to square roots 5 Aggregate a single new variable is created by summing the selected variables 6 Missing values gt 0 0 Missing values are converted to zero 7 Missing gt mean Missing values are converted to the mean of the variable 8 Add constant the number entered in the A edit box is added to all values 9 Multiply by constant all values are multiplied by the number entered in the A edit box 10 Centre variable variables are centred ie their mean is subtracted 11 Centre and standardise Variables are centred and divided by their standard deviation 12 Absolute value values are converted to their absolute value User Guide C2 Transpose data 13 Change sign New variables created during the transformation can be 1 copied over the original 2 saved a
64. t a 1 1 r oH 7 La a m7 1 r a AAA A 1a i fe a METE qm aago DITE pa suja ri i as ie ai s amiini Co LES gt E li i al i ite tel a ji T ir a a Fi La Jl E E i A 51 E n Fy at ia bg x any j Fir Las A E H T 1 m E fi ta 17 ak E a de la 3 a i T HA 15 E EN ap ae oe 5 ODE f eee ey et ed Y Fee Stn mra Fi zj PP a LE j ihi mm Taing ere CEARR AE HTP Brushing allows you to identify points in multiple 3 scatter or stratigraphic plots Turn this function on off using the brush button and choose the brushing radius from the drop down menu Now just move the mouse over a graph to brush data points Selected mm radius 10mm rectangle Individual point Hmm radins 1 mm radius 2 mm rectangle Graphical tools e 51 52 e Graphical tools data will plot red default colour can be changed in Edit menu gt options Corresponding points in any other visible graph will also be highlighted even if open in a different window C2 links points in different graphs by row number If the data in two graphs are unrelated they will still get highlighted This can cause some problems for example if you have two series e g species scores and samples scores from a CA overlain C2 will highlight points from both series which is not very useful There is a new option on the first tab of the scatter pl
65. t also shows N number of occurrences N2 Hill s measure of effective number of occurrences and maximum value for each variable Select variables xi Code N N2 AA Saia O hii 1 Vie 4 1 1 E 117 196 15 12 3 118 110 E 12 E WI1B 227 z 1 3 5 1114 47 156 23 E Was 22 7 31 Fi We 12 4 1 4 B 2323 y dE Wi2 49 3 5 10 AS 10 50 di 41573 14 52 2 2381 10 43 13 1234 11 47 14 Wied 15 30 15 W23B3 12 43 16 125 18 Eb 17 A15234 156 El 19 Vip 18 40 19 422122 19 41 20 Wied 21 ES 21 W432 at 104 22 WB 7 El 2 119245 cz 61 Clicking on the Advanced button invokes the Advanced options dialog box allowing rapid selection using N N2 or maximum abundance criteria For example clicking on the max button below would select all variables with a maximum value of less than 1 0 This function can be used for example to quickly delete rare species from a dataset Select variables advanced options Eq Select by N 20 SelectbyN2 2 Help Select by Mas ll Swap Clear 4414 User Guide C2 Sorting by rows or columns Datasets can be easily sorted by rows or columns by clicking on the sort buttons on the data toolbar et AZ by opening the dataset and selecting Sort rows columns from the Data menu For samples you can sort the dataset by sample number sample code or any variable in the dataset in ascending or descending order Dataset sort xl Sort by Sample No Sample Code 1114 61 4171396 118410 WE ee
66. tain rules The example below shows data formatted in an Excel spreadsheet but the same rules apply to all the above formats Ey TELE ls f alojxj EA AA O a O eee OO eas L M m 14 Smpkk Guri aoh Gnber Gima Gssccu Gruber Gpal pac Ohio _ otako Grad Gara Gg 2 4 51 o o a a 1 1 SE sr 05 o o a a E gv 7 156 o o a a 1 1 9813 054 047 o a a 0 47 pHi ea o o ao a 0 o 5633 ITI 1 2 a a E ayga 0 a q 0 0 4 Fd 45 035 0 o A 0 a 0 11 o 011 0011 Bae 5 2 11 10 35 1 55 ara 0 0 0 0 i 55 E 16 E 1949 0 0 0 2 28 We 12 0 O O 2631 325 O 0 a 0 E wz 26 Ui Do u l 17 26 ALS 30 54 ii l l aaa 2 03 o T a a 1 1 184 12 73 15 06 O16 a a Ra o o a a 1 1 341 Boe 75T 0 3 a a 1201 57 3 5 0 14 0 57 a 0 14 o 1335 1345 734 0 43 a a ERDA 155 o ao a 1 o 1 cre 1555 0 a 0 53 BETREE 076 0 o o 0 0 22 40 255 0 075 a 15141253 i 0 0 41 055 15 EA oo ER Oat 106 0 Wood 04 o l u 150 4544 19 6 l 02 47 ji 2 56 06 0 135 u 0 2 0 56 11 53 13 5 19 36 oa 2 15 EILEAN o o 67 a 0 08 1 oe 17 46 13 25 1127 153 1 14 49 18 50 0145 o 4 36 a 0 13 o 200 1426 5 5 74 093 0 74 wz2122 ars 0 15 0 83 0 15 0 7 i OB Wit 25 53 065 a a 1016 41 112 0 35 15 15 0 12 5 36 o Dar 373 162 ads 112 3 73 4 32 T 04S 1512 185 6 56 057 os 1058 4415 14 59 57 1 71 YI 2 06 155 O 47 153 3 29 01038 12 ES Br a 2 05 2 05 Wiis 151 055 10 53 0 if 0 10104 23 465 2a 13 38 oca 0 76 15 71 1 42 2 18 0018 08 46 17 36 1475 255 2 74 128016011
67. the list and click the small button on the right hand side of the list to browse for the file A dictionary can be in Excel Paradox dBase or Lotus format It should be formatted so that the first field or column in the spreadsheet database contains the variable short code and the second field contains the full name The content of other fields is not important Matches between the dictionary and dataset codes are not case sensitive by default although this behaviour can be changed in the global settings Dictionary lookup Eq Dictionaries ny C tempDiatCodeN ames xls EA E Help Data manipulation e 23 Highlight the dictionary name and click OK and C2 will read the names from the dictionary and match them using the variable codes to the codes in the dataset This operation may take a few seconds if you have many names in the dictionary If you have more than one worksheet in an Excel file or table in an Access database you will be asked to select the appropriate sheet from a popup list Select worksheet table EK Pass Tran Select the sheet containing the dictionary and click OK When finished C2 will report how many names it found and matched Harmonise Harmonising a dataset is a way of renaming and merging variables taxa to match the names in another file This is useful to harmonise a biological dataset e g fossil material to match the taxonomic criteria used in a surface dataset Harmon
68. the model name in the tree view and selecting Create graphs from the pop up menu Multivariate analyses C2 currently has three types of ordination methods currently grouped under the Multivariate heading These are Principal components analysis Imbrie and Kipp Factor analysis and Correspondence analysis Imbrie and Kipp Factor analysis is really a PCA with standardisation by samples and varimax rotation but is included separately here for ease of use Select Multivariate from the Analyse menu Multivariate Tis a components an alu m Madel ttle Model name Imbne amp Fapp Factor Analysts Mode da A a Comespondence Analpsis Model 03 E Model 03 Primary daaa gy 5 wAP174 cop Summary gt Supplimentany datasets l Mum obs 174 0 thi 0 3 Upton a The Multivariate dialog box is very similar in style and operation to the Transfer function dialog box Choose the appropriate method any options graphs and press Run 34 e Data analysis User Guide C2 The resulting model output is added to the tree view and can be explored listed and exported as normal User Guide C2 Data analysis 35 Graphical tools Graphics overview C2 currently offers two types of graphics x y scatter line plots or stratigraphic plots Graphics are organised in graph books A graph book contains one or more pages and each page may contain one or more graph
69. tion to either overwrite the existing dataset or to choose a new name Dataset import xl Warning Dataset 1 22 cep already esists Replace existing dataset Cancel Import dataset as IK22 cep2 Help Duplicate row or column labels Each row and column of a dataset 1s identified by a row column number a unique short alphanumeric code and a long name C2 uses the short code the species sample code or Id to uniquely identify each row column of a dataset User Guide C2 User Guide C2 C2 will issue a warning if duplicate row or column codes are found and display a list of the duplicate codes together with the number of times each occurs in brackets You should edit the dataset to ensure that all codes are unique Duplicate samples variables found Warning Duplicate sample variable codes found OK Duplicate sample codes Duplicate variable codes Cancel 24 SWAPUS4 4 1 ACOOTA 2 of SwWwAP0SS 2 Help lt Empty rows or columns C2 checks the data on import for empty rows or columns That is rows or columns that are blank or contain all missing data You are given the chance to delete the empty samples or variables Empty columns may be the result of importing badly formatted data in Excel Samples variables with no data Warming Listed samples varnables have no data Samples with no data Varlables with no data Cancel fo W212 40 Wings 22 Wl2 bb Help 35 416 190 BO 1
70. ts on the same graph oooooonnnnncnnnnnnnnncnnnonononononnnnnnnnnnnnnnnnnnnnnnnnnn 45 Zooming in on data m an Y plot meinen a e E E aE e E 45 Identifying and labelling data points in an x y plot cccccconnoooooooonnnncnnnnnnnnnnnnnnnonnnnnnos 45 Interac ve data UPS A E N E 46 Interactive data labels is 46 kabelin tom alt S 47 Hidins data pont raple a a das 47 Addn AOWESS SMOOT a a a a EES 47 Adding additional x y plots to a graph page ooooooonnnnnccnnnnnnnnnnnnononnnnnnnnnnnnnnnnnnnnnnnnnnnnnanos 48 Deletine an x y plot froma raph Palit 49 Undoing redoing chances to xy Dl its 49 Inserting a new graph page into a graph book occcccccncccccnononnnnonnnnnnononnnnnnnnnononononnns 49 Detna rapi PASS aaa tos 50 ZOOMING UNE rap PACE urin Ar E O 50 Co opyine A Crap Patada 50 Export a graph page as a Windows metafile oocccccccnccccconnoonononnnnnnnnnnnnnnonononononannns 50 Prantnearotapa Pare airada a 50 Retes IMU Wile td lic 51 Opening the graph in a new WINdOW ooooonncccccncnnncnnnononononononnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnos 51 Brushi e multiple SrapOs ini aos 51 Stratigraphic diagrams 53 Creating stratigraphic diagrami sasseii ssshaidiabaadcadasiadcedaddelsadandadcasasadicstangelenbecselgabsatascuadeaak 53 Modifying the appearance of individual grapbs occccccnncncncnononnnononnnnnnnononnnnnnnnnonnnnnnos 54 PSE SSC A A Aoa santana E hia EAAS 55 Day E T E PERE En A T EA AT N
71. utput When imported the CANOCO solution is imported as a model with it s various components not as a dataset Viewing editing data Viewing a dataset File Edit View Data Analyse Graph Window Help 11 a Datasets Fl ES 1 amp ES pec H E RK Envy 3 Models Graphs Reports The tree view in the left hand pane of the C2 Object Browser gives a list of imported datasets in the Datasets folder Selecting a dataset name show summary information for that dataset Click on the Data node to show a spreadsheet view of the dataset in the right hand pane of the Object Browser 12 Getting started User Guide C2 E H ta o 4 E es er i ee Ed eee A ee S The listing shows the sample number a short unique sample code a long sample name and the data for each variable Datasets are added to the workspace in the order they are imported It is not possible to change the order Viewing the list of variables Select the Variables tab at the bottom of the spreadsheet to show a list of variables for the dataset listed by short code name and full long name ib ce C2 Object broeeser Fie bR Data Wew Analyse Graph window Help age ons gt Bo 420014 ACDO2A ACDOLA ACNES ACHIA ACEi achia ACO SC m SWiAParw cap pre Aut GEL E me gend ACHIA JH tmi Aeid A e ENH Garig es G gH ACTIA iS DPerE ARDIA m SWAP cep ATHA E 3 Shea ACTIA fee gunz ADT ce ES EN AUTO ES Tes
72. voke the Graph properties dialog box for that graph The various modifiable properties are listed under four tabs Clicking Apply changes the setting for that property clicking Apply all changes the settings for all the properties on that page User Guide C2 X axis scaling Graph properties q q E x Editing 4 curvez Data scaling Absolute O Apply x axis fixed length mm cenit Apply Maxis percentage scale factor A Appl Pec MMUT me Appl A MR O Oaa Appl X axis major tick interval jy Apply X axis minor tick ratio an Appl Number of decimal places ojja Appl Reduce label crowding rennet Apply Lett margin mm o App Right margin men eso Appl Log scale for x axis O App Reverse x axis 0 Da Appl Rare taxa cutoff vale ae Appl Baseline origin vale y Appl Hide symbols with Zero value a P AE pl r X axis sealing Apply all Undo Close Help Data scaling Absolute sets the length of the x axis of the selected graphs to be the value specified in the x axis fixed length field in mm Percentage scales the length of the x axis using the value in the x axis percentage scale factor field multiplied by the length of the x axis in data units For example if the graph plots data that ranges from 0 to 50 percent and the scale factor is 0 5 the x axis will be set to 50 0 5 25mm X axis minimum maximum tick interval tick ratio and number of decimal places override the automatic calculation of these

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