BMEGUI3.0.0 User Manual - The University of North Carolina at
Contents
1. 29 Figure 16 The mean trend smoothing parameters and the Recalculate Mean Trend DOOI crete teeter eee enti eae ated i A A AAA a AR 31 Figure 17 Dialog Box 5 Space Time Covariance Analysis ccccsssssseeeeseeeeeeeeeeeeeees 33 Figure 18 Calculating experimental covariance by modifying the number of the lags 34 Figure 19 Calculating experimental covariance values by directly entering the lags and TE TO AA 36 Figure 20 Covariance model parameter gsettngg a 38 Figure 21 Automatic covariance model Dinge 39 Figure 22 Dialog Box 06 BME Esumatiom E 40 Ficute 257 BME EE 42 Figure 24 Estimation parameters for the BME spatial estmaton 43 Proure 2 List or BME eSiumation naps sai Raia O 44 Figure 26 Maps of BME mean estimates and BME error variances 46 Figure 27 BMEGUI box 6 showing BMEGUI generated maps and buttons for creating ArcGIS compatible and vector data file using BMEGUI output 11 0 000077 47 Figure 28 Enter name of the file to save as BMEGUI output a message after creating ArcGIS compatible ArcASCID file b and point layer csv files c 48 Figure 29 Estimation and Display Parameters used for the BME temporal estimation 49 Figure 30 List of estimated time series edegeggeeg it snsmntebwsivwsdapspranssandencdatetassdeeniswedabedvadasencs 50 Figure 31 The time series plot at a specific monitoring location 51 Figure 32 The2. Close Tab Show and Delete buttons and the message box to ON CNA CIC AN 32 Figure 33 Message showing the number of failed estimation points 53 Figure 34 Failed Estimation Points black dots on the estimation map 54 Figure 35 The message dialog box to confirm whether to quit BMEGUI 54 Figure 36 ArcGIS warning message saias tata NAAN ANA a a 56 Figure 37 The various message dialog boxes that display when data errors are detected AR cette ee 58 Figure 38 Error message due to an inappropriate new line character Figure 39 ConTEXT editor 1 Introduction 1 1 About BMEGUI BMEGUIL ss the software providing a Graphical Users Interface GUI to the Bayesian Maximum Entropy BME advanced functions of Space Time geostatistical analysis Using this software the user has access to an easy to use interface for the analysis of space time data BMEGUI version 3 0 0 uses BMElib 2 0b and python 2 5 1 2 Download and Installation To install BMEGUI go to the BMEGUI website at http www unc edu depts case BMEGUI and select version 3 0 0 from the list which gives you access to the installation package and installation manual Follow the instructions on the installation manual 1 3 Software Requirement BMEGUT uses the following software modules Before using the software you need to install all software modules GTK 2 10 11 s FreeType Py
3. These errors are detected when the user press the Next button on Dialog Box 1 BMEGUI displays the message dialog boxes shown in Error Reference source not found when errors are etected The user can select whether to accept the BMEGUI default error correction or to quit the application and correct the error manually The default error correction methods are listed below When BMEGUI detects that the same station ID is assigned to different geographic locations BMEGUI replaces these different locations with their unique spatial average When BMEGUI detects that different station IDs are assigned to the same location BMEGUI takes the alphanumerically smallest ID as the valid station ID and replaces all the other IDs with it When BMEGUI detects duplicated measurements i e measurements made at the same station ID geographic location and time BMEGUI takes the average of the duplicated values 57 fii BMEGUI 1 Station 24 assigned to different locations Error 1 of 1 Lon Lat bi Next 74 10153198 3994816971 f4 05590924 40 03955841 Bd Back l 4 II To correct this error BMEGUI will assign station 24 to new location 74 07875061 39 99386406 Accept Data Correction by BMEGUI Quit Application and Correct Data Manually DN BMEGUI jj Parameter has changed Delete all parameters and estimation files and continue using new parameters Quit Application and use
4. cay RI E d dt m Te ng T lag m mp3 Quit H Back Figure 31 The time series plot at a specific monitoring location 4 8 10 Show Close and Delete Maps or Time Series Plots The user can create maps or time series plots as many times as s he wants Every time the new map or plot is created BMEGUI automatically stores the estimation results Therefore the user can temporally close the map or plot and redraw the map or plot whenever s he needs it Moreover the user can also permanently delete the estimation result Error Reference source not found To close a map tab or a plot tab first click the selected map tab or plot tab Then click on the Close Tab button and the corresponding tab is hidden However the user cannot close the Map List tab or the Plot List tab To redraw the map or plot select the corresponding entry from the map list or plot list then click on the Show button that is located below the list To permanently delete the map or plot select the entry from the map list or plot list then click on the Delete button that is located below the list A message dialog box will appear select OK to close it 51 oo TODO MA Grid Color BME estimation 6 6 mag El ON l B Plot Map HELP Spatial Distribution Temporal Distribution Maps Estimated New Map MapID Map Time BME Parameters Plot ID Es
5. 076149803 Spatial Component Temporal Component E z Vas Plot Model Spatial Range spaceUnit Temporal Range timeU nit E emecut 2 Input the lags and Spatial Lag Figure 19 Calculating experimental covariance values by directly entering the lags and the lag tolerances 4 7 3 Covariance Model The user must select a space time covariance model that fits the experimental covariance values BMEGUI lets the user select that model among the large class of space time covariance models given by the following equation c r T KE Co Ca rT C4 7 36 where N is the number of covariance structures co 1s the variance contribution or sill of the i th covariance structure and c r and c i 7 are permissible functions representing the spatial and temporal components respectively of the i th covariance structure BMEGUI supports up to four structures 1 e N lt 4 The permissible covariance functions for the spatial components cr include the following A 3r Exponential Cri F exp rl o 2 e Gaussian c r oan d NA ri o 3 se Spheroidal car KA ei Holecos c r cos mr a el o Holesin c r mla and similar ones are available for the temporal component ct 7 Generally a and ay are called the spatial range and the temporal range respectively of the i th structure of the covariance function I
6. 1s used to calculate the space time distance The space Time distance is obtained as Spatial distance Space Time Metric Temporal distance NG Max Hard Data Point The maximum number of hard data values used in the estimation NG Max Soft Data Point The maximum number of soft data values used in the estimation KG Local Mean Order of the polynomial used to model the mean trend or drift along the spatial and temporal axes within the neighborhood of the estimation point The default setting 1s Zero which will use a mean trend of zero and corresponds to simple kriging Constant will use a constant local drift which corresponds to ordinary kriging applied locally around the estimation point Linear will use a local drift that varies linearly along the spatial and temporal axes Quadratic will use a polynomial of order 2 etc Generally Order gt 1 corresponds to universal kriging applied locally around the estimation point The values of these parameters are displayed in the BME parameters section in each tab BMEGUI automatically displays default BME parameters however the user can modify these parameters Error Reference source not found 41 DA BMEGUI BME estimation 6 6 E E Plot Map HELP Spatial Distribution Temporal Distribution Pr PATA EY Maps Estimated BME Parameters MapID Map Time Maximum Temporal Distance 4320 0000 Max Hard Dat
7. BMEGUI uses only Vall and Val2 column so user can put any garbage values in Val3 and Val4 columns In case of data type 3 BMEGUI uses only 3 columns so fourth column can have any garbage value However in case of data type equal 4 all columns are used in space time estimation 3 6 2 Example CSV Format of river network data The CSV file shown below corresponds to a river network consisting of three river reaches Each river reach is delineated with three points located along that river reach The CSV file contains two columns listing the X Y coordinates of the points delineated each river reach Each river reach is ended by a line with NaN values The last line has the X Y coordinates of the river network outlet 12 Figure 1 River network csv file and network plot 4 Getting Started with BMEGUI 4 1 Input File and Directory Dialog Box BMEGUI can be started by clicking on the BMEGUI shortcut on desktop BMEGUI pops up a window as shown below in figure 1 Wicome to BMEGUI BMEGUIT 3 0 0 BMElab www unc edu depts case BMElab Working Directory Data File Figure 2 Input file s and directory dialog box 13 You can provide the working directory and the data file to BMEGUI by clicking on the Select Working Directory and Select Data File buttons Leave the Use River Network unchecked in order to use the Euclidean metric This 1s the default settings wh
8. Distribution respectively BMEGUI displays the time series plot of the measurement values at each monitoring location on the Temporal Evolution tab and the spatial distribution plot of the measurement values at specific times on the Spatial Distribution tab 21 Station ID System ID Figure 9 Dialog Box 3 Exploratory Data Analysis 22 In the Aggregation Period section the user can temporarily aggregate the data using the user defined time periods On the Temporal Evolution tab the user can select different monitoring location of Interest based on their user defined station ID or system ID There are three methods to select the monitoring location Figure 9 Select the user defined station ID from the dropdown menu Input the system ID in the entry box Click on the Next or Back buttons When a new location is selected the plot of the time series of the data available for that location is automatically updated Temporal Evolution Spas ea vam H Click Next or Back button Station ID System ID x1e 7 2 99 Location or Stations Select Station ID from reem menu 012012 5 e wA Eflog ucglL ta Figure 9 Temporal Evolution tab Three methods to select the monitoring location Similarly on the spatial distribution tab the user can select specific times for which to crea
9. Error Reference source not ound DN EMEGUI BME estimation failed at 9 out of 300 estimation points Figure 33 Message showing the number of failed estimation points 53 Plot Map HELP Figure 34 Failed Estimation Points black dots on the estimation map 4 9 Quitting from BMEGUI Each dialog box has a Quit button to exit from BMEGUI When the user presses on the Quit button a message dialog box appears Error Reference source not found ress OK to confirm that you really want to quit 2 Are you sure you want to quit Figure 35 The message dialog box to confirm whether to quit BMEGUI 54 5 Interaction with ArcGIS 5 1 Details of ArcGIS Files As explained in 4 5 3 Error Reference source not found and 4 8 7 BMEGUI has unctions to create ArcGIS compatible ArcASCII asc and CSV cv files CSV files can be saved as data base dbf file using MS Access to make them ArcGIS compactible The followings are the list of files that can be created and used with MATLAB and ArcGIS for further analysis Point layer file csv file o Spatial distribution plot Dialog Box 3 Exploratory Analysis Data fields X Y T and Val o Spatial raw mean trend csv file Dialog Box 4 Mean Trend Analysis Data fields X Y and Val Raw mean trend o Spatial smoothed mean trend csv file Dialog Box 4 Mean Trend Analysis Data fields X Y and Val
10. dummy values Same as Value or dummy values Lower bound of the interval for the true value Upper bound of the interval for the true value Value3 Field Lower bound of the interval for the true value or dummy Upper bound of the interval for the true value or dummy Mean also called expectation of the true value Standard deviation of the true value around its mean Mean of the true value or dummy values Standard deviation of the true value around its mean or dummy values Soft Triangular data Data Type 3 Valuel Field Value2 Field Lower limit Upper limit Value3 Field Mode Value4 Field Data Type 4 Lower limit or dummy values og Soft Truncated Gaussian data 11 o Valuel Field Mean also called expectation of the true value o Value Field Standard deviation of the true value around its mean o Value3 Field Lower truncation point value o Value4 Field Upper truncation point value 3 6 1 Example CSV Format of hard and soft data Table 1 Hard and soft data in csv format 1 jm jo 74 0907 39 91373 1 21 Jo 741293 39 81845 40 12 i EI 741532 3979262 40 E 2 74 1604 39 82512 40 13 2 188 220 22 la 74114 39 99956 250 29 4 74 056 40 03956 270 33 4 If using hard and soft data then we have to have four data columns 1 e vall val2 val3 and val4 However BMEGUI uses only yellow colored columns It is clear that in case of 0 1 2 data types
11. s s gt 0 non negativity d s s Oif and only if s s identity d s S d s S symmetry 14 de S lt d s s d s s triangle inequality In order to use the river metric the user just need to check the Use River Network button and provide a file that describes the topology of the river network BMEGUI will then automatically use covariance models that are permissible for the river metric so that the analysis is mathematically sound The topology of a river network is represented by a directed tree of river reaches with zero width Such representation is adequate only for downstream combining stream networks with somewhat narrow reaches but may not be adequate for wider water bodies such as connected estuaries or lakes In order to construct this river topology BMEGUI needs a river network data file that delineates individual river reaches of the river network as well as the point corresponding to the outlet of this river network The river network must be such that there is single river reach at the downstream end of the river network and the outlet provided by the user must be the downstream end of that reach BMEGUI will then attempt to construct the river topology by starting from the outlet and finding each river reach that is connected to that outlet Every time BMEGUI encounters a point where the river divides into two confluent reaches BMEGUI will designate that point as a confluence poin
12. se BMEGUI temporal estimation file O O 2 O O File Name Name of the data file Plot ID yse This file 1s used to store the BME temporal estimation parameters and results Every time the user creates a new estimation plot the PlotID is increased by and a new file is created These files are used to redraw any plot on the plot list and restore the corresponding estimation parameters If the user permanently removes a plot from the plot list See 4 8 10 then BMEGUI removes the corresponding file from the workspace a Initial parameter files File Name Name of the data file py c This file 1s used to store initial parameters such as the number of bins of the histogram the name of the ArcGIS output files and other default parameters 59 7 Troubleshooting errors 7 1 Data Error file due to an inappropriate new line character When the data file having an inappropriate new line character is specified as the data file in BMEGUI BMEGUI displays the following error message Error Reference ource not found DN BMEGUI invalid literal for float sdsad Figure 38 Error message due to an inappropriate new line character This error might happen when the data file was imported from a Unix or Macintosh machine or when the data file was created by the writeGeoEAS function of BMElb To fix this problem use a text editor that is capable of modifying the erroneous new line character with t
13. set of vector coordinates 3 3 Required Data Fields Since BMEGUI deals with space time data the Data File must have at least four data columns namely the X field Y field T field and data value field The X field and Y field are used to specify the spatial coordinate Currently BMEGUI supports only two dimensional spatial coordinates The T field 1s used to describe the time when the measurement are taken The Data value field corresponds to actual measurement values X field Y field Spatial Coordinates i e longitude latitude e T field Time when the measurement are taken e Data value field Measurement values If the data is purely spatial 1 e no changes over time then the user still needs to prepare the T field using a fixed arbitrary value e indicating that all values were collected at the same time Conversely if data is purely temporal 1 e a time series then the user still needs to prepare the X field and Y field using some fixed arbitrary values 1 e indicating that all values were collected at the same spatial location In case you want to analyze water quality parameters in river stream s then you have to prepare another data file for river network coordinates BMEGUI will ask to provide such file 1f you click on Use River Network check button 3 4 Station ID and System ID In addition to the required data fields described in 3 3 the user may want to use a user defined station ID for ea
14. stationary which implies that the covariance between two space time points p s t and p s t is only a function of the spatial lag i e the spatial distance r lls s and time lag i e the time difference zc between these two space time points Hence the covariance c p p between points p and p can be written as c p p c r lls s t lt t 31 where r is the spatial lag and ris the temporal lag There are two steps in modeling the covariance First we need to estimate the covariance value for different spatial and temporal lags We call these estimated values the experimental covariance values Then we need to fit a permissible covariance model to the experimental covariance values In order to simplify the visual representation of the fitting of the covariance model c r 7 to the experimental covariance values Dialog Box 5 shows the 2 dimensional covariance function in terms of two distinct one dimensional plots The first plot is shown on the Spatial Component tab Error Reference source not found a and it is a plot of the ovariance c r 7 0 with respect to the spatial lag r for 7 0 The second plot is shown on the Temporal Component tab Error Reference source not found b and it is a plot f the covariance c r 0 7 with respect to the temporal lag 7 for r 0 On the Spatial Component tab the experimental values of c r 7 0 are estimated for a set of user defined spatial lags
15. 00 205083 3 Macintosh CH only E readdata py TKB F l 2000 205083 O 18 74 0429694 33 64569470 2000 205063 D 15 75 1007902 2 33 53162613 2000 205083 0 71 20 74 224404265 33 6967711 000 205063 0 5 Sa 4d 01000520 33 8145913 2000 205063 2 1 AA ranana CH we e Saar aA o sara a Sr Figure 39 ConTEXT editor 6l
16. 05 RI Spabal Lag spaceUnit Covariance Model Number of covariance structures 1 4 1 Automatic Cov Fit Covariance Structure 1 Sill Variance 530 076149803 Spatial Component Temporal Component Yas Plot Model Spatial Range spaceUnit Temporal Range timeUnit mp3 Quit I Back bl Next Figure 18 Calculating experimental covariance by modifying the number of the lags 34 To directly enter the lags and their corresponding lag tolerances follow these steps Error Reference source not found 1 2 5 4 Click on the Edit Spatial Lags or Edit Temporal Lags buttons and then a dialog box will appear Input the lags values e g 0 0 0 019 0 038 0 057 0 076 0 094 0 113 0 132 0 151 0 170 and a corresponding number of lag tolerances e g 0 0 0 009 0 009 0 009 0 009 0 009 0 009 0 009 0 009 0 009 in the entry box Use commas to delimit values Click on OK The experimental covariance plot will be updated 35 mo ST Sos Space Time Covariance Analysis 5 6 Experimental Covariacne Number of Spatial Lags ho A Edit Spatial Lags 3 Recalculate Spatial Component Number of Temporal Lags 10 l ce Recalculate Temporal Component Spatial Component Temporal Component A3 Covanance Don 0 05 0 10 Spabal Lag spaceUnit Covariance Model Number of covariance structures 1 4 1 Covariance Structure 1 Silk Variance 530
17. 25 List of BME estimation maps AQ saa 4 8 5 BME Mask Map Grid and Color Setting As explained earlier to perform a BME spatial estimation the user needs to specify the BME parameters and the Estimation parameters BMEGUI produce BME mean and associated error variance plots and graph Quality of these graphs and plots can be 44 improved by selecting appropriate color and grids from drop down menu Further user can enhance plots by placing mask and boundary map on the BMEGUI plots by clicking on Mask and Map buttons 4 8 6 BMEGUI Home Page and Help Latest information on BMEGUI updates and new versions can be accessed on BMEGUI web page Click on HELP button seated on top right corner of BME Estimation screen last screen and then click on Home page to access BMEGUI web page You can also contact us if you have any questions suggestions and any other BMEGUI related issues To access the BMEGUI User Manual click on Help and then click on User Manual button 45 D emecut Efe x BME estimation 6 6 E baga or Plot ID 0002 Mean Plot ID DOC E MMA RR a bA Figure 26 Maps of BME mean estimates and BME error variances 46 4 8 7 Create Output Files Point Layer File and ArcASCII File As with the spatial distribution plot in Dialog Box 3 see 4 5 3 the user can also create ArcGIS compactible ArcASCII asc files from the maps created in Dialog Box 6 The user can al
18. 4 4 Dialog Box 2 Data Distribution 4 4 1 Basic Operation Dialog Box 2 Data Distribution shown in Error Reference source not found is used o check the statistical distribution of the data The Statistics section displays the basic statistics of the raw data and of the log transformed data The Histogram section displays the histogram of the raw and log transformed data By switching the tabs between Raw data and Log Data the user can switch histograms The user can also modify the settings for the log of negative and zero data values 17 Statistics Raw Data Log Data Mean 25 9172811607 283633302052 Set log of negative and zero data to Standard Deviation 27 3175245806 0 901238788138 ee eee ds Skewness 243917756423 0 26143645733 Ot O Kurtosis 747442170711 0 619760924886 Histogram Raw Data Log Data Statistics Raw Data Log Data Mean 25 9172811607 2 83633302052 Set log of negative and zero data to Standard Deviation 27 3175245806 0 901238 788138 Aes ee gs h Skewness 24391 77564253 0 26143645 33 Kurtosis 747442170711 0 619760924886 Aros Histogram Log Data Figure 6 Dialog Box 2 Data Distribution 18 4 4 2 Data Transformation Method Based on the basic statistics and the histogram the user can select the data transformation method used in the analysis In order to use log transformed data in the analysis the user must check the Use Log transformed
19. BMEGU13 0 0 User Manual BMEGUI3 0 0 Last Edited on 01 20 2012 BMElab Dept of Environmental Sciences and Engineering School of Public Health University of North Carolina Contents COMIC TUG Dre EE 2 l oi ee ee pn RR RN RR SR RR 6 lal About TEE 6 L2 Download and lista lla ee 6 E SO WC E UE E 6 2 e ehr MEG OD RA ARNO Meese cart Ue a 7 3 Woatar Pre pal dul Ova ANAKAN NESE 7 Jal Workspaceand Data EE 7 LEL Works Aka AA de SED Rd a dead 7 I2 Da mre nee Maer een nes 7 Is RIVER ING LW OR Eia da DR A CR RO di i 8 Oye E e EE 8 Hal CORA SON AA GA enn a LAGA 8 Na COV FORMAL cabin di salsa Eri insana ea al oi a menue tacit eats 8 3 2 3 CSV Format without Header Line for River Network 8 3 2 4 Shape File Format for River Network 1a 9 do Required Data Plak 9 34 station ID and System ID aNG ANAN 9 do MD ata Pale e ia CD NAA e 10 duel CCORA S EF OFM Al NAKAIN O beets nts 10 ore CON PO tries esis cence ale eer eee ete neil once esate NR 10 20 Hard Datacalid SOL Data suas sairia NANA NGA seuss wane teats 10 3 6 1 Example CSV Format of hard and soft data 00 nnneesseoeennessssssseerrssss 12 3 6 2 Example CSV Format of river network data 12 4 Getting Started with BMEGUL isama paa Ga haa Ga kala 13 4 1 Input File and Directory Dialog Box 13 4 2 Input River Network File River Metric ia 14 do _ Pialos Box Data Bataan a a a ai a 15 4al Basie DELANO E aha ia 15 14 32 Data File wit
20. Data check box otherwise the raw data i e not log transformed data is used Error Reference source not found DAN BMEGUI Data Distribution 2 6 Statistics Raw Data Log Data Mean 25 91 2811607 2 030633302052 Set log of negative a nd Tero data to Standard Deviation 27 3175245806 0 901238788138 Skewness 23917756423 0 26143645733 Kurtosis 747442170711 0 619760924886 log smallest positive value 25 log Histogram Log Data Histogram of Lom agents A agent log d taUnmit Use Log transformed Data Quit k Back HI Next Figure 7 Use Log transformed data If the user selects Use Log transformed Data then the histogram automatically switches to the Log Data tab Similarly 1f the user unselects this check box then the histogram automatically switches to the Raw Data tab 4 4 3 Log of Zero and Negative Value Setting BMEGUI provides two options for dealing with the log of zero and negative values It assigns for each zero or negative values a log value that is either 19 2 a The smallest strictly positive value divided by a user defined integer or The log of a user defined value The default setting is to use the smallest strictly positive value divided by 25 To change this setting follow the steps described below 1 Select the method you want to use by clicking on the corresponding radio button 2 Input the integer for the first option Error Reference sourc
21. Display Point X 100 No of Display Point Y 80 Ki Save Vector Data esw k gi Save Arc ASCI asc File O Use Mask A Close Tab EEN Display Failed Estimation Points mp3 Quit k Back Figure 24 Estimation parameters for the BME spatial estimation 4 8 4 BME Spatial Estimation As explained in 4 8 2 and 4 8 3 to perform a BME spatial estimation the user needs to specify the BME parameters and the Estimation parameters Once these parameters are set the user needs to click on the Estimate button on the Spatial Distribution tab to create the corresponding map Then two new tabs are displayed named PlotID xxxx Mean and PlotID xxxx Error and a new entry appears on the list in the Maps Estimated section Error Reference source not found User can also provide the mask file of area of estimation to BMEGUI This is an optional and BMEGUI doesn t consider any mask by default However mask file shape file with 43 shp extension should be contained only one single polygon BMEGUI complains if user provides a mask file containing multiple polygons poly lines polygons poly areas etc The map of the BME mean estimated values 1s plotted on the PlotID xxxx Mean tab and the map of BME error variance is plotted on the PlotID xxxx Error tab Maps are displayed by clicking on their corresponding tab Error Reference source not found he list in the Maps Est
22. FE emecur EES oad BME estimation 5 6 me Lo H Plot Map HELP Spatial Distribution Map List Maps Estimated New Map MapID Map Time BME Parameters PlotID Estimation Time Maximum Spatial Distance 0 34 Maximum Temporal Distance Space Time Metric o Max Hard Data Points Max Soft Data Points Local Mean Estimation Grid Estimation Time No of Est Points GI No of Est Point Y Include Data Points Include Voronoi Points East Max X 74 0437 West Min X North Max Y 40 South Min Y Display Grid 4 II F Display Failed Estimation Points New Plot PlotID Station ID BME Parameters Plot ID Station ID Maximum Spatial Distance Maximum Temporal Distance Space Time Metric 0 0008 Max Hard Data Pointe Max Soft Data Points 2o ical Ricci Estimation Parameters seo bo Ed Eid Paa Ka timeUnit to 4409 0 timeUnit Display Parameter Sealing Factor Display Failed Estimation Points Figure 22 Dialog Box 6 BME Estimation 40 4 8 2 BME Parameters The user needs to specify the following six BME estimation parameters to obtain BME estimated values both on Spatial Distribution tab and on Temporal Distribution tab K Maximum Spatial Distance The maximum spatial distance between an estimation location and data locations K Maximum Temporal Distance The maximum temporal lag between an estimation location and data locations K Space Time Metric A parameter that
23. Smoothed mean trend o BME mean estimate and error variance at estimation grid points Dialog Box 6 BME Estimation Data fields X Y Mean BME mean estimate and Var BME error variance o BME mean estimate and error variance at display grid points Dialog Box 6 BME Estimation File name bmeRst Plot ID lyr Data fields X Y Mean and Var ArcASCII asc file o BME mean estimate Dialog Box 6 BME Estimation o BME error variance Dialog Box 6 BME Estimation 5 2 Coordinate System of ArcGIS Files BMEGUI does not define a coordinate system for any of the ArcGIS files created Therefore when you add layer file or raster file created by BMEGUI in ArcGIS the 55 following warning message will be displayed Error Reference source not found he user can define a spatial coordinate system by using ArcGIS tools 4 Unknown Spatial Reference D The following data sources you added are missing spatial reference information This data can be drawn in ArcMap but cannot be projected BMEmeanVarlimeS00MeanArcASCll asc Figure 36 ArcGIS warning message 56 6 Advanced Topics 6 1 Data Error Handling BMEGUI can detect and automatically modify the following data errors 1 The same station ID is assigned to the different geographic locations 2 Different station IDs are assigned to the same geographic location 3 Duplicated measurements BMEGUI detects and corrects the error in the order listed above
24. Unit Data Unit Name of Data mp Quit pil Next spaceUnit timeUnit dataUnit agenta Figure 4 Dialog Box 1 Data Field 4 3 2 Data File with Soft data As explained in 0 BMEGUI supports space time analysis using soft data in addition to hard data To use soft data the user needs to specify which columns of the data file 16 correspond to the data type field the valuel field the value2 field the value3 field and the value4 field The procedure 1s as follow 1 Check the Use Datatype check box then drop down boxes for Data Type Valuel Field Value2 Field Value3 Field and Value4 Field will appear Error Reference source not found 2 Select the appropriate data columns for Data Type Valuel Field Value2 Field Value3 Field and Value4 Field 3 Click Next to move to the second dialog box DN BMEGUI Data Field 1 6 Working Directory Data File Working Directory C Users jat Desktop AAAAAA Data File 9 C Users jat Desktop AmmoniaData_NJDatalype csv X Field Y Field Time Field ID Lon el Lat el Time e Automatic ID e Use Datatype Data Type Valuel Field Value Field Values Field Valued Field DataType el Ammonia Varl Ammonia e Ware el Unit Name Space Unit Time Unit Data Unit Name of Data spaceUnit timeUnit dataUnit agenta Figure 5 Dialog Box 1 Data Field To use the soft data check the Use Datatype check box
25. a Points 10 Local Mean BME Parameters Maximum Spatial Distance 0 3401 Maximum Temporal Distance 4320 0000 Space Time Metric 0 0008 Max Hard Data Points 10 North Max Y 40 0733 South Min Y 39 6889 al Display Grd E Show No of Display Point X 100 No of Display Point Y EN em Save Arc ASCI asc File F A Use Mask M Close Tab Figure 23 BME Parameters d Je m 4 8 3 Estimation Parameters Spatial Distribution In order to obtain maps of BME estimates the user needs to specify the Estimation Grid parameters and the Display Grid parameters To obtain a map first BMEGUI creates an Estimation Grid consisting of estimation nodes distributed across space within a user defined rectangle area and calculates the BME estimates at these estimation nodes Then BMEGUI creates a Display Grid consisting of nodes distributed over a fine regular grid within the defined rectangle area and linearly interpolates the BME estimates at estimation nodes onto the display regular grid This two step process speeds up the creation of the map In the Estimation Grid section the user can specify the following parameters Error eference source not found K Estimation Time The time of interest for which to produce the BME map There is no default value for this field NG Number of Estimation Points X and Y The number of estimation grid points along t
26. an Trend Mean Trend Smoothing Parameter Search Radius Smoothing Range Spatial Mean Trend 01134 spaceUnit 0 0378 spaceUnit Temporal Mean Trend 1440 0000 timeUnit 480 0000 timeUnit C3 Recalculate Mean Trend Temporal Mean Trend Spatial Mean Trend Raw Spatial Mean Trend Smoothed HE Display Time Temporal Mean Trend timeUnit timeUnit ye Redraw 36 Default agentXjdataUnit 2000 2500 Time omeUnit goe TI Ha JI Hu Figure 16 The mean trend smoothing parameters and the Recalculate Mean Trend button 4 6 3 Create Point Layer File Similarly to with the spatial distribution plot in Dialog Box 3 see section 4 5 3 the user can create a point layer file of the raw and smoothed spatial mean trend To create this point layer file click on the Create Point Layer button Then a message box will appear asking for file name and directory name where file has to save After user provide file name and directory and click on OK button another message box will appear saying the name of the point layer file has been created 4 7 Dialog Box 5 Space Time Covariance Analysis 4 7 1 Basic Operation Dialog box 5 Space Time Covariance Analysis shown in Error Reference source not ound is used to calculate the spatial and temporal components of the covariance of the data or of its residual if the mean trend was removed from the data The data or its residual are assumed to be homogeneous and
27. analysis Model mean trend and remove it from data Mean Trend Mean Trend Smoothing Parameter Search Radius Smoothing Range Spatial Mean Trend 0 1134 spaceUnit 0 0378 spaceUnit Temporal Mean Trend 1440 0000 timeUnit 480 0000 timeUnit Ka Recalculate Mean Trend Temporal Mean Trend Spatial Mean Trend Raw Spatial Mean Trend Smoothed Spatial mean trend Smoothed dataUnit Extent of Display Area North spaceUnit South spaceUnit East spaceUnit spaceUnit Dee Redraw 36 Default spacelUnit JADE 7406 e z spaceUnit gf Create Point Layer File mp3 Quit 4 Back H Next Figure 14 Dialog Box 4 Mean Trend Analysis A global mean trend 1s a function of space and time that describes consistent patterns in the data 1 e 1t describes where or when the data seems to be consistently higher or consistently lower than the mean The word global emphasizes that this trend applies globally to the whole space time domain encompassing all the available data Dialog Box 4 displays the global mean trend and the user must decide whether this global trend should be used in further analysis If the global mean trend is used then it 1s removed from the data yielding residual values e data minus global trend that are then used in the ensuing analysis e for the covariance analysis and BME estimation Hence the goal of the global mean trend should be to prod
28. ay Failed Estimation Point 111 52 ao Quittine rom DMEGUL unter 54 3 LG a a AGC G S eiaa AA 55 Se Dekor Ane E 55 52 Coordinate System or ArcGIS Eeer 55 O Nee WK e ne 57 ol Ge Mandihhe seee 57 6 2 BMEGUI Parameter File and Estimation bles 58 Ser Keier EE 60 7 1 Data Error file due to an inappropriate new line character 60 List of Figures Figure 1 River network csv file and network plot erre 13 Figure 2 Input file s and directory dialog box 13 Figure 3 A Euclidian distances and b river distances a 14 Fisure 4 Dialog Box Data Field mama AGA 16 Figure 5 Dialog Box 1 Data Field To use the soft data check the Use Datatype CHECK DO Xaar SEDES 17 Figure o Dialos Box 2 Data Distr i DU OM ss siga do ag NANANA 18 Ficure 7 Use Los transtormed DAN ass as NIAN AA N 19 Figure 8 Settings for the log of negative and zero data values awww 20 Figure 9 Dialog Box 3 Exploratory Data Analys 22 Figure 10 Spatial Distribution tab Methods to select specific times 23 Figure 11 Example of data aggregation with 10 time unit aggregation period 1 raw dataand C yat ores EE 24 Foure BA AS Cre oa Ore Ee 23 Figure 13 The Create Point Layer button and the message box 26 Figure 14 Dialog Box 4 Mean Trend Analysis ii a aaa aaaasnsssssssssssssns Zi Figure 15 Calculating the global mean trend and removing it from the data
29. ch monitoring location site The station ID is a unique identification alphanumeric string that 1s used to identify monitoring locations in various plots of the BMEGUI as well as in its drop down lists 1n the third and sixth dialog boxes Alphanumeric values 0 9 a z and A Z can be used for station ID To enter user defined station IDs the user has to prepare an additional station ID column in the Data File If the Data File does not have a station ID column then BMEGUI creates the system ID The system ID is automatically assigned to each monitoring location in order to help the user select one specific monitoring location from the lists in the third and sixth dialog boxes The system ID is a sequential number starting from one 3 5 Data File Example 3 5 1 GeoEAS Format Tetrachloroethene micrograms per liter in New Jersey LONGITUDE LATITUDE NUMDAYS YEAR DATATYPE VALI VAL2 74 5278 40 5594 880 2001 O 0 01 0 01 74 7781 40 2217 376 2000 O 0 01 0 01 3 5 2 CSV Format LONGITUDE LATITUDE NUMDAYS YEAR DATATYPE VAL1 VAL2 74 5278 40 5594 880 2001 0 0 01 0 01 74 7781 40 2217 376 2000 0 0 01 0 01 3 6 Hard Data and Soft Data Hard data correspond to measurements without errors or with errors that are small enough to be 1gnored Soft data correspond to measurements with an associated uncertainty for example data with appreciable measurement errors The uncertainty associated with soft data 1s described by mea
30. different working space Figure 37 The various message dialog boxes that display when data errors are detected 6 2 BMEGUI Parameter File and Estimation Files As explained in 3 1 1 when analyzing a specific Data File BMEGUI uses the Workspace directory to store transient files during BME analysis The followings are name and description of the parameter file and estimation files that are be automatically created by BMEGUI during the analysis se BMEGUI parameter file o File Name Name of the Data File ysp 58 O This file 1s used to store the all estimation parameters and the intermediary results including the mean trend and covariance models generated prior to the BME estimation results produced on BME Estimation screen The information stored in this file 1s used to reproduce previously obtained intermediary results when the user restarts BMEGUI and specifies the same Workspace and Data File ze BMEGUI spatial estimation files O O File Name Name of the data file Plot ID yme This file is used to store the BME spatial estimation parameters and results Every time the user creates a new estimation map the PlotID 1s increased by 1 and a new file is created These files are used to redraw any map on the map list and restore the corresponding estimation parameters If the user permanently removes a map from the map list See 4 8 10 then BMEGUI removes the corresponding file from the workspace
31. e aggregated and the button will be deactivated Error Reference source not found 4 4 To go back to the non aggregated data uncheck the box Aggregate data every 24 Aggregation Period Ee EE ee Aggregation Period DO Jia Mres ot Aggregation Period pente caso om Aggregation Period pares date every 7 Jam Rm Create Point Layer 74 16 74 14 74 12 74 10 74 08 74 06 Figure 12 Data aggregation 4 5 3 Create Point Layer File The user can create ArcGIS MATLAB and other software compactible output file BMEGUI pop ups a window asking file and directory names where data files have to be saved Such file is saved by BMEGUI as CSV csv file regardless of extension supplied by users 25 Aggregate data every 90 timeUnit Data Aggregated Temporal Evolution 5patial Distribution Data attime 0 0 H timeUnit Ed Back bill Ned Spatial Distribution at 0 0 time Unit dataUnit Ki Create Point Layer spaceUnit CSV Point File esw JJ SpatialDist csv has been created Figure 13 The Create Point Layer button and the message box 4 6 Dialog Box 4 Mean Trend Analysis 4 6 1 Basic Operation Dialog Box 4 Mean Trend Analysis shown in Error Reference source not found llows the users to explore whether the data exhibits a global trend across space and time 26 D BMEGUI Mean Trend Analysis 4 6 Skip mean trend
32. e not found a or Input the number for the second option Error Reference source not found b 3 Click on the Redraw button then the basic statistics and the histogram will be updated a Option 1 uses the smallest positive value divided by a user defined integer Set log of negative and zero data to logfsmallest positive value Ole b Option 2uses the log of a user defined number Set log of negative and zero data to logfsmallest positive value D logf 0 001 Figure 8 Settings for the log of negative and zero data values 4 4 4 Soft Data in Histogram Since the soft data are defined in terms of their probability density function PDF i e either the uniform or Gaussian PDF the data have to be hardened before calculating their basic statistics and plotting the histogram BMEGUI converts the soft data into hard data using the following method Soft uniform data Mid point of lower and upper bound so Soft Gaussian data Mean value Hardened values are also used in the following steps Explanatory data analysis 2 Mean trend estimation 2 a Experimental covariance calculation 20 4 5 Dialog Box 3 Exploratory Data Analysis 4 5 1 Basic Operation Dialog Box 3 Exploratory Data Analysis shown in Error Reference source not ound is used to conduct the exploratory data analysis This dialog box has two tabs labeled Temporal Evolution and Spatial
33. eparated from the next river reach by a line containing two NaN values A line with two NaN values is added at the end of the last reach followed by a last line containing the X and Y coordinate of the river outlet The river outlet coordinate must correspond to the coordinate of the downstream most point of the river network 3 2 Data Format As explained in 3 1 2 GeoEAS format and CSV format are supported in BMEGUI The details of each data format are listed below 3 2 1 GeoEAS Format GeoEAS format data must be prepared in the following manner Ist line File description 2nd line Number of data column 3rd line to 3 number in 2nd line line Name of data column Tab separated data File extension txt 3 2 2 CSV Format CSV format data must be prepared in the following manner vw Ist line Comma separated data column name o Comma separated data 2 o File extension csv 3 2 3 CSV Format without Header Line for River Network CSV format data for river network must be prepared in the following manner 2 No data column name no header 2 a Comma separated data oa Last line should have river stream outlet coordinates NA File extension csv 3 2 4 Shape File Format for River Network A shapefile stores nontopological geometry and attribute information for the spatial features in a data set The geometry for a feature is stored as a shape comprising a
34. he X axis and Y axis K Area of Estimation Grid Boundaries of the rectangle where the estimation grid is created The user can specify the following four boundaries East Max X West Min X North Max Y and South Min Y 42 In addition the user can include to the estimation grid all the monitoring locations as well as the set of Voronoi points constructed from these monitoring locations Adding these points will increase the computation time but it will lead to maps with finer spatial details To include these points check the Include Data Points box or Include Voronoi Points box in Estimation Grid section In the Display Grid section the user can specify the number of display grid points along the X axis and Y axis Error Reference source not found A regular grid is hen constructed using these settings m BMEGUI Estimation Grid Estimation Time No of Est Points 09 No of Est Point Y Spatial Distribi Include Data Points Include Voronoi Points _ East Max X 74 0437 West Min X 74 1810 Maps Estimates Map D Map Time BME Diet ID Estimation Time May 0 3401 Maximum Temporal Distance 4320 0000 fic 0 0008 Max Hard Data Points 10 Gata Points 2 Local Mean Zero sl Estimation Grid Display Grid No of Display Point x No of Display Point Y 74 0437 West Min X 74 1810 Max Y 40 0733 South Min Y 39 6889 III Ka Gase EI Beete No of
35. he correct new line character for Windows For example you may use the Con TEXT text editor http www contexteditor org as follow 1 Open the data file using context From the Tools menu navigate to Convert Text To and select DOS CRLF Error Reference source not found 3 Save the file 60 ConTEXT C Documents and Settingstakita E5EML500 2AMy DocumentsABMElabiENVRA 6 BUIWsUAW AENVRA C File Edit View Format Project Tools Options Window Help Ae Haaa g Record Macro Ctrl F8 d Se G amp 8 Text files E ENVRE8hwk7Part3 tet Play Macro Fa File Panel Me bo 10 15 20 25 3 35 40 File Explorer User Command 1 F3 data in ppm except 9 means censul Chip Documents ProjecthE pidProject User Command 3 Fid tude degree ea Er E E ke E User Command 3 Fil de ienee Mame User Command 4 Fiz of sample decimal year dee Shell Execute Ctrl F12 pp 2000081 6 03 7021785 33 15746952 2000 0962 4 20000816 nongrid csv Compare 6912253 33 891716 2000 0962 2 20000861F cay Statistics 2622568 33 75009853 2000 0962 1 0000918 cew 8018116 33 38815942 2000 0962 5 1 E Set Highlighter i ei cams431 cb4 avrg 2000081 0429694 33 64569478 2000 0962 1 el came431_cb4_avra 2000081 Convert Text To te DOS CRLF aa ae Ej camm431 cbd avg 2000081 326 510 EB F Unicode aoe l Bees Ges eh e RE UNIX LF only 2000 205083 1 md gridreader pyc AED 0
36. ht SOU dadaanin 16 4 4 Dialog Box 2 Data Distribution 17 ACN BSC Opo a NEN AA AA NN AA Nad Ne teas 17 442 Data Transformation Method NANANA NAIBA KUNING 19 4 4 3 Log of Zero and Negative Value Setting a 19 Add HO Data ti TIMO aa ai Ea a a 20 4 5 Dialog Box 3 Exploratory Data Analveats t errar 21 Boek BANG Pera EE 21 As EE A Gere ANO eege 23 AD Greate Pomt ayer Fin raided AA AA AA NAA AN 23 4 6 Dialog Box 4 Mean Trend Analys 26 AO Basic RE e EE 26 4 6 2 Calculate Mean Trend Using User defined PDarameterg 30 Ao Create Pomt Layer ENG erecta ia RA RANA ANAK 31 4 7 Dialog Box 5 Space Time Covariance Analysis 31 2 E BASCOP TAO AA AA a aired 31 4 7 2 Calculate Experimental Covartance 34 Aah Covance MO aiii ANA BANANA GAAN BANANA 36 4 7 4 Automatic Covariance Model fitting a 38 ds Dialog BOX O casa saia asica dana adia nba dor due bi a doi 39 do BASIC OPCAO ria a dd o taste Pb o etree 39 TS 2 BME EE EE 4 4 8 3 Estimation Parameters Spatial Distribution a 42 4 54 BME Spatial ESTIMA eege ee ia 43 4 8 5 BME Mask Map Grid and Color Setting a 44 490 BMEGUIL Home Pace and Help aa hahaah 45 4 8 7 Create Output Files Point Layer File and ArcA SCH File 47 4 8 8 Estimation Parameters Temporal Distribution 48 18 9 BME Temporal Estima On uainiada AA a ENS ates 49 4 8 10 Show Close and Delete Maps or Time Series Plot 51 4 8 11 Hide and Displ
37. ich calculates the straight line distance between points 4 2 Input River Network File River Metric Most geostatistical studies use the Euclidean or across land metric to calculate the distance between points However the choice of the distance metric 1s critical because the distance metric affects correlation functions such as the covariance as well as the selection of the estimation neighborhood Recent studies have shown that when dealing with water quality parameters measured along a river it may be better to use the river metric This will result in BME maps that are more accurate and realistic than those obtained using an Euclidean distance Using the river metric the distance between two points is calculated by finding the shortest path between these points along the river as opposed to a straight line distance Hence the river metric leads to distances that are always greater than that obtained with the Euclidean metric with an increase in distance that captures the topology of the river network A Euclidian distances and b river distances Figure 3 A Euclidian distances and b river distances Note that Euclidean distance and isotropic river distance both meet the qualifications of a metric therefore the term metric and distance are used interchangeably in this document The term metric 1s used to describe a distance that meets the following criteria for spatial points s and s d
38. imated section displays all the estimated maps and each entry on the list shows the Plot ID and Estimation Time of a given map 1 Click on the 2 Two new tabs appears with the Estimate estimated map Mean and the button corresponding variance Error Spatial Distribution Temporal Distribution Map List Plot ID 0001 Mean Plot ID 0001 Error Maps Estimated New Map ms Color n HELP cool e ON C Plot Map Spatial Distribution Tefnporal Distribution 3 A new entry corresponding to Map List Plot ID 0001 Mean Plot ID 0001 Error th ese tw om ap s app ears on th e Maps Estimated ewt A pH F Maps Estimated list MapID Map Time BME Parameti E aaa Maps Estimated Plot ID Estimr fion Time Maximum Spatial Distance 0 34 0001 400 0 Space Time Metric 0 00 Map ID Map Time Max Soft Data Points 2 gt z Plot ID Estimation Time Estimation Grid 0001 400 0 J Estimation Time 400 No of Est Points X 20 No of Est Point 1 15 Include Data Points T Include Voronoi Points E East Max X 74 028 West Min X 74 438 North Max Y 40 108 4 Enter mask file al m Ji Display Grid No of Display Point x 700 DS Vee Mack ap Save Vector Data csv 5 Estimate Sn Save Arc ASCI asc File Use Mask C Users jat Desktop Desktop May2011 NewlerseyRiverDOeric mask StudyArea_ShapeFile M Close Tab EEN Hide Failed Estimation Point Figure
39. ints E a Save Vector Data csv East Manx 32 a Save Arc ASCII asc File Mont Max Y No of Display Point X No of Display Point Y ogee Save Vector Data esw sip Save Arc ASCI asc File A Use Mask X Close Tab e Hide Failed Estimation Point Figure 27 BMEGUI box 6 showing BMEGUI generated maps and buttons for creating ArcGIS compatible and vector data file using BMEGUI output 47 Save in folder BMEGUIS Files Browse for other folders fi BMEGUI EM BMEGUI Arc ASCI asc files BMEmeanVarlimes00MeanArcASCl asc BIMEmeanVarT ime500VarArcA5CILasc have been created CSV Point File c5v k y BIMEmeanVartime500PL csv has been created Figure 28 Enter name of the file to save as BMEGUI output a message after creating ArcGIS compatible ArcA SCH file b and point layer csv files c 4 8 8 Estimation Parameters Temporal Distribution In order to obtain the time series plot at specific monitoring locations the user needs to specify the Estimation Parameters and Display Parameters Error Reference ource not found In Estimation Parameter section the user can specify the following parameters KG Station ID ID specifying the monitoring station where the time series needs to be obtained Select the appropriate station ID from the drop down list 48 K Estimation Period User defined estimation period of the time series There is only one para
40. lays the BME mean estimates and the green dotted line shows the lower and upper bounds of the 69 confidence interval which corresponds to the BME mean estimate 1 standard deviation under the assumption of a Gaussian distribution The blue dots show the hard data while the red triangles and squares show the hardened soft interval and soft Gaussian data 49 respectively BMEGUI also displays the shape 1 e either interval or Gaussian of the PDF describing the soft datum at each soft data point Plot List displays all the estimated time series plots and each entry on the list shows 1ts Plot ID and Station ID Plot List and new tab for a time series plot Spatial Distribution Temporal Distrik Plot List Plot ID 0001 Plot ID 0002 Plot List H DI BMEGUI BME estimation Res o A Di Plot List Plot ID 0001 Plot ID 00 e i Plot ELP BME Parameters E Maximum Spatial Distance PlotID Station ID Space Time Metric 00008 Max Soft Data Points PlotID Station ID 0001 10 Estimation Parameters Station ID 24 104 Estimation Period From Dis Parameter Scaling Factor H II I Ps Hide Failed Estimation Point Figure 30 List of estimated time series 50 DA BMEGUI racing Color Grid BME estimation 5 6 E MI Plot Ma HELP ON e L D cool BME Mean Estimate at Station 1
41. meter in the Display Parameter section This parameter is called the Scaling Factor and it is only used for cosmetic effect This parameter changes the aspect ratio used to display the Gaussian soft data overlaid on the time series plot The default setting of this parameter is 0 1 D BMEGUI Sa Color Grid BME estimation 6 6 Glo E F Plot Map HELP cool Temporal Distribution Station ID 001 1 v 1 Estimation Period From 5 0 days to 1707 0 Station ID DO E 1 J Estimation Period From 1 0 timeUnit to 4409 0 timeUnit Saling Factor Display Parameter II C E Show EI Delete Scaling Factor AS Close Tab 25 Hide Failed Estimation Point Figure 29 Estimation and Display Parameters used for the BME temporal estimation 4 8 9 BME Temporal Estimation As explained in 4 8 2 and 4 8 8 the user needs to specify the BME parameters and the Estimation parameters to perform a BME temporal estimation Once these parameters have been set the user needs to click on the Estimate button on the Temporal Distribution tab to perform the estimation Then a new tab labeled PlotID xxxx is displayed and the corresponding entry appears on the list in the Plot List section Error Reference source not found A plot of the time series is displayed when clicking on the tab Error Reference source ot found corresponding to a specific PlotID The blue solid line disp
42. ns of a statistical distribution for example uniform Gaussian etc BMEGUI supports the following five data types Hard data Soft data with uniform distribution Soft data with Gaussian distribution Soft data with Triangular distribution Soft data with truncated Gaussian distribution When using the default settings BMEGUI assumes that the data file only contains hard data and in that case it uses only the fields described so far 1 e the X field the Y field the T field the optional ID field and the Data field containing the hard data values 10 However when using a combination of hard and soft data then BMEGUI requires that the Data field be replaced by the following five fields The Data type field the Valuel field the Value2 field the Value3 field and the Value4 field The Data type field is used to specify the type of data The Valuel Value2 Value3 and Value4 fields are used to describe the data as follow 8 9 O O O O O 2 O O O O 2 O O O O O O O O O O NA O o Hard data Data Type O Valuel Field Value2 Field Value3 Field Value4 Field Soft uniform data Data Type 1 Valuel Held Value2 Field values Value4 Field values o Soft Gaussian data Data Type 2 Valuel Field Value2 Field Value3 Field Value4 Field The true value e g a measurement without error Same as Value 1 Same as Value or
43. omposite covariance model of space time separable models may be best suitable and fit model which can be done as described in previous section 38 DA BMEGUI o Bo x e Space Time Covariance Analysis 5 6 Experimental Covariacne Number of Spatial Lags 10 4 Edit Spatial Lags Gi Recalculate Spatial Component Number of Temporal Lags 10 4 Edit Temporal Lags C Recalculate Temporal Component Spatial Component Temporal Component Spatial component 0 10 Spabal Lag spaceUnit Covariance Model Number of covariance structures 1 4 1 Covariance Structure 1 Sill 489 29 Variance 530 076149803 Spatial Component exponentiall Temporal Component exponentialC Yas Plot Model Spatial Range 0 18043 spaceUnit Temporal Range 223 71 timeUnit Figure 21 Automatic covariance model fitting 4 8 Dialog Box 6 4 8 1 Basic Operation Dialog Box 6 BME Estimation shown in Error Reference source not found is used o calculate BME estimated values Dialog Box 6 has two tabs the Spatial Distribution tab and the Temporal Distribution tab The Spatial Distribution tab is used to create maps of the BME mean estimates and the BME error variance at specific times of interest The Temporal Distribution tab is used to create plots also called time series of the BME mean estimate and BME error variance as a function of time for specific monitoring locations of interest 39
44. ories of Workspace and Data File used in the analysis so that the user can verify these directories In the Data Field Setting section the user can select which data columns of the data file are used in the analysis As explained in 3 3 the data file must have at least four data columns corresponding the following fields X field Y field se T field Data value field The user can select the name of the data column for the X Field Y Field T Field and Data Field using the corresponding drop down menus In addition the user can select the data column for the station ID ID field The default setting of the ID field is Automatic ID which automatically assigns sequential ID to each measurement locations If the data file does not have a column specifying user defined IDs then use the default setting In the Unit Name section the user can directly input the unit for the spatial coordinate the time event and the measurement values as well as the name of the parameter being mapped The units and the name of the parameter being mapped are only used in the labels of the plots generated by the BMEGUI DN BMEGUI Data Field 1 6 Working Directory Data File Working Directory CA Users yatDesktop AAAAAA Data File 9 C Users jat Desktop AmmoniaData_NJDatalype csv X Field Y Field Time Field ID Lon el Lat Time Automatic ID el Use Datatype Data Field SitelD l Unit Name Space Unit Time
45. r plus minus a corresponding set of spatial lag tolerances dr For example if the spatial lags are r 3 6 and the corresponding spatial tolerances are dr 1 2 then the experimental covariances on the Spatial Component tab will be estimated for zl and r 3 1 i e using all pairs of points with a temporal lag of zero and a spatial lags between 2 and 4 and for 7 0 and r 6 2 i e using all pairs of points with a temporal lag of zero and a spatial lags between 4 and 8 Conversely on the Temporal Component tab the experimental values of c r 0 7 are estimated for a set of user defined temporal lags 7 plus minus a corresponding set of spatial lag tolerances dr The next section explains how to modify the spatial and temporal lags in Dialog Box 5 to calculate the experimental covariance values and the following section explains how to use Dialog Box 5 to fit the covariance model on to the experimental covariance values 32 fi secur Experimental TA Covarlacne ie int emp Lag Number of covariance structures 1 4 1 Automatic Cov Fit ance Sarason Experimental Covariacne Hp L tnzsggtes HRP Recaiculate spatiat Component Meos 0 W sse diniinan ENEE Number of covariance structures 1 4 11 Automatic Cov Fit Covariance Structure 1 a ince oong Kata imicompone TJ Temp componer Spatial onge spaceUnit Temporal Range Ld teint Figure 17 Dialog Bo
46. rresponding to the radius of the spatial neighborhood used select points for the spatial exponential filter The Spatial Smoothing Range corresponding to the range of the spatial exponential function Similarly there are two parameters which are used to control the temporal exponential filter used to smooth the raw temporal averages m in order to obtain the smoothed temporal trend ms The Temporal Search Radius corresponding to the radius of the temporal neighborhood used to select points for the temporal exponential filter 2 a The Temporal Smoothing Range corresponding to the range of the temporal exponential function To calculate the mean trend input these four parameters in the Mean Trend Smoothing Parameter section Then click on the Recalculate Mean Trend button The plots of smoothed temporal and spatial mean trends will be updated Error Reference source ot found In order to make the spatial or temporal trend smoother increase the corresponding two parameter values and recalculate the trend Conversely to obtain a trend that is less smooth 1 e that follows more closely the raw averages decrease the parameters values and recalculate the trend 30 fii BMEGUI Mean Trend Analysis 4 6 Mean Trend Smoothing Parameter i Search Radi Smoothing R _ Skip mean trend analysis om A ar a a Aa Spatial Mean Trend 2 0 Model mean trend and rafiow Temporal Mean Trend 2000 Me
47. so create a vector data file csv MATLAB and other software compatible of the BME mean estimate and error variance calculated at each node of the estimation grid Arc ASCII format Arc ASCII file format refers to a specific interchange format developed for ARC INFO raster s in ASCII format Arc ACSII format consists of a header that specifies the geographic domain and resolution followed by the actual grid cell values Usually the file extension 1s asc To create these ArcASCII files for a given map click on the corresponding entry from the list in the Maps Estimated section Then click on the Save ArcASCII asc File File button or the Save Vector Data csv button Then a message box will appear asking name of the file to be saved as shown Error Reference source not found a nd place where file has to be saved After saving file at user specified place BMEGUI pop ups message saying file s have been created as shown in figure 27 a and b fii BMEGUI BME estimation 6 6 Spatial Distribution Map List Plot ID 0002 Mean Plot ID 0002 Error Plot JD 0002 Mean Plot ID Map Time Map ID Map Time BME Parameters Estimation Time Plot ID Estimf tion Time Maximum Spatial Distance 0 3401 0002 4000 Space Time Metric 0 0008 0003 gon Max Soft Data Points 2 Estimation Grid Estimation Time 600 E Click one of these buttons No of Est Points X 20 E Include Data Po
48. t and will delineate the two upstream reaches up to their upstream confluence point The process is repeated up until all the upstream reaches have been identified When this process 1s finished BMEGUI will have reorganized the set of river reaches into a directed tree of downstream only combining reaches In practice there may be many problems associated with river networks BMEGUI tests for the following river network problems 1 Network outlet error a Network outlet not connected with the river network b Network outlet located at the end of multiple river reaches 2 Broken river network Missing links between river reaches leads to river reaches that are not connected to the outlet or simply put to a broken river network There may be many other types of problems in the river network that cannot be handled by BMEGUI The user is therefore advised to plot and visualize the river network in any GIS software and make any necessary correction needed to eliminate broken links in the river network See tutorial 7 for an example of a geostatistical analysis using a river network 4 3 Dialog Box 1 Data Field 4 3 1 Basic Operation Dialog Box 1 Data Field shown in Error Reference source not found is used to elect which data columns of the data file will be used in the analysis and to enter the units of these data columns as well as the name of parameter being mapped 15 The Working Directory Data File section shows the direct
49. t can be noted that each of the functions used for the spatial and temporal components take a value of 1 for a lag of zero 1 e c 0 1 and c 0 1 i 1 N Since by definition the variance of the covariance model also called the model variance is obtained by calculating the model covariance at a spatial and time lags of zero 1t follows that the model variance is given by 5 Co because c 0 1 and c4 0 1 i 1 N Since the model variance should represent the variance of the data then the user should select the sills co i 1 N such that their sum is approximately equal to the variance of the data In order to help with this constraint BMEGUI displays the variance of the data in Dialog Box 5 see Variance xxxx in Error Reference source not found To select and plot a covariance model follow these steps Error Reference source not ound 1 Input the number N of the covariance structures desired making sure that 1 lt N lt 4 2 Input the sill co of the i th covariance structure Keep in mind that the sum of the sills should be equal to the variance of the data which is displayed on the right side of the entry box 3 Select the functions used to model the spatial and temporal components of the i th covariance structure using the dropdown menus 4 Input the value for the spatial range and temporal range of the i th covariance Structure 3 5 Repeat steps from 2 to 4 for each covariance struct
50. te spatial plots of the available data using the dropdown menu or the Next or Back buttons Error Reference source not found Temporal EvgtGtion Spatial Distributia Click Next or Back button Select time point from dropdown menu Figure 10 Spatial Distribution tab Methods to select specific times 4 5 2 Data Aggregation In Dialog Box 3 the user can aggregate the data temporally using user defined aggregation time periods When the data is aggregated all the measurement values within 23 a given aggregation period are treated as 1f they are sampled at the same time Error eference source not found 1 Raw Data DEI i d e A m mE i d n HR RS O O O O O O O O O O O O DO O O A O LI 2 Ageregated Data 0 10 20 Figure 11 Example of data aggregation with 10 time unit aggregation period 1 raw data and 2 aggregated data The aggregated data is used to create the spatial distribution plots in Dialog Box 3 for mean trend analysis in Dialog Box 4 and to obtain the experimental covariance in Dialog Box 5 To aggregate the data follow the steps described below 1 Check the box Aggregate data every then the entry box Aggregate Data button will be activated Error Reference source not found 1 and 2 2 Enter the aggregation period Error Reference source not found 3 in the ntry box 3 Click the Aggregate Data button then the data will b
51. thon Libraries o PyCairo o PyGObject o PyGTK o NumPy o SciPy o Matplotlib o Pywin MATLAB Component Runtime MCR 2 Starting up BMEGUI BMEGUI can be started by clicking on the BMEGUI shortcut on desktop You can conduct the basic exploratory data analysis and Space Time geostatistical estimation for air water or any other media for any environmental agent 1 e arsenic in water SO in air etc You can create ArcASCII or Comma Separated Value CSV output data files for further processing BMEGUI output in ArcGIS MATLAB and or any other compactible software 3 Data Preparation 3 1 Workspace and Data File In order to use BMEGUI you need to specify two input parameters Workspace and Data File Workspace is a directory which is used to store all the files BMEGUI creates during the analysis Data File is a file containing the space time data available including the measurement values their space time coordinates and information on measurement errors You need another data file in case you are analyzing river metric 3 1 1 Workspace Workspace is used to store all the files BMEGUI creates during the analysis The followings are the list of the files stored in Workspace ge BMEGUI parameter files ysp so BMEGUI estimation files yme yse Initial parameter files py pyc During the analysis all the estimation parameters and results are stored in the Workspace If the user quits the BMEGUI and e
52. timation Time Maximum Spatial Distance 0 3401 Maximum Temporal Distance 4320 8 8 0002 400 0 Space Time Metric 0 0008 Max Hard Data Points 10 es E Max Soft Data Points 2 Local Mean pa Estimation Grid m nclude Voronoi Points El East Max X West Min X 74438 North Max Y 40 108 South Min Y 39 448 Dis Grid No of Display Point X 100 hilary Point Y SU X Close Tab da EEN Hide Failed Estimation Point Following plot will be deleted Plot Id 0002 Do you want to continue Figure 32 The Close Tab Show and Delete buttons and the message box to confirm the deletion 4 8 11 Hide and Display Failed Estimation Point If there are no data in the estimation neighborhood BME estimation returns a NaN value The BMEGUI automatically replace the BME estimation result with the average of all the data values The BME error variance is also replaced with the variance of all the data 52 values In order to inform the user about the failed estimation point the message dialog box telling the number of failed estimation points appears if there are failed estimation points Error Reference source not found In addition the failed estimation points re displayed as block dots on the map The user can hide display black dots by clicking the Hide or Display Failed Estimation Point button
53. uce residuals that are as homogeneous De without spatial trend and stationary i e without temporal trend or drift as possible As a default setting BMEGUI does not calculate the mean trend nor does it remove it from the data BMEGUI assumes that the global mean trend m s t where s denotes the spatial coordinate and f is time is a space time additive separable function i e that it has the following form M S t Mss S myidt where m S is the spatial component smoothed over space and m t is the temporal component smoothed over time also called the temporal drift BMEGUI first averages the measurements at each monitoring sites to obtain values for the raw spatial mean mg and then it applies an exponential spatial filter to these raw spatial mean values to obtain a spatial component m that is smoothed over space Conversely BMEGUI first 21 averages the measurements for each monitoring time event or each aggregated time periods if the data has been time aggregated to obtain values for the raw temporal mean m and then it applies an exponential temporal filter to these raw average values minus their overall average to obtain a temporal component ms that is smoothed over time This dialog box has three tabs namely the Temporal Mean Trend tab showing both the raw temporal average values m and the temporal trend component m smoothed over time the Spatial Mean Trend Raw tab showing the raw spatial average
54. ure 6 Click on the Plot Model button to plot the covariance model 7 The covariance model shown as a plain line should fit the experimental covariance values show as markers Repeat steps 1 to 6 until the covariance model fits well with the experimental covariance values 8 Click on the Clear Plot at any time during step 7 to clear the different models previously plotted E emecu Experimental Covariacne Number of Spatial Lags 10 Number of Temporal Lags 10 Spatia iene Ca Temporal Component Covanance Structure 1 Covariance Structure Silk BI Vanance 5300076149803 Spatial Component ponentislC e Temporal Component exponential 7 Spatial Ran 0 19 spaceUnit Temporal Ran 1100 umeUnit ge nge dou Mow fiber of covariance structures 1 4 2 Automatic Cov Fit Covanance Structure Covariance Structure 2 mag A Clear Plot Salk Bo Wanance 5300076149603 Spatial Component eponentialC D Temporal Component exponentislC Spatial Range 019 spacelnit Temporal Range 1100 Figure 20 Covariance model parameter settings 4 7 4 Automatic Covariance Model fitting You can also fit covariance model by clicking on Automatic Cov Fit button as in figure 22 below However automatic fitting may not be a good fit for a specific problem since BMEGUI fits a single covariance model rather than a composite model In many situations c
55. values m and the Spatial Mean Trend Smoothed tab showing the spatial mean trend component ms smoothed over space To calculate the mean trend using the method described above and remove it from the data click on the Model mean trend and remove it from the data radio button Then BMEGUI calculates the mean trend using the default parameter Error Reference ource not found 28 Model mean trend and remove it from data Mean Trend Mean Trend Smoothing Parameter Search Radius Smoothing Range Spatial Mean Trend 0 1134 spaceUnit 0 0378 spaceUnit Temporal Mean Trend 1440 0000 timeUnit 480 0000 timeUnit C23 Recalculate Mean Trend Temporal Mean Trend Spatial Mean Trend Raw Spatial Mean Trend Smoothed If emecu Mean Trend Analysis 4 6 Skip mean trend analysis Model mean trend and remove it from data Mean Trend Mean Trdqd Smoothing Parameter Search Radius Smoothing Range Spatial Mean Tre 01 Temporal Mean edi ET O Skip mean trend analysis BEER Default Figure 15 Calculating the global mean trend and removing it from the data 29 4 6 2 Calculate Mean Trend Using User defined Parameters The user can calculate the global mean trend using user defined parameters There are two parameters which are used to control the spatial exponential filter used to smooth the raw spatial averages m in order to obtain the smoothed spatial trend mss 2 The Spatial Search Radius co
56. x 5 Space Time Covariance Analysis 33 4 7 2 Calculate Experimental Covariance There are two methods to set the spatial and temporal lags used to calculate the experimental covariance values One is to simply set the number of lags used in which case BMELIB uses equidistant lags and a constant identical lag tolerance for each lag By default BMEGUI automatically calculates the experimental covariance using 10 equidistance lags The other method is to enter each lag and corresponding lag tolerance individually which offers the flexibility that the lags need not be equidistant To modify the number of the lags follow these steps Error Reference source not ound 1 Input the number of the spatial or temporal lags you would like to use in the entry box In this case BMELIB sets equidistant spatial lags from O to half of the maximum distance between data points and equidistant temporal lags from O to half of the maximum time difference between data points 2 Click on the Recalculate Spatial Component or Recalculate Temporal Component buttons 3 The experimental covariance plot will be updated DN BMEGUI Space Time Covariance Analysis 5 6 Experimental Covariacne Number of Spatial Lags Lo 4 Edit Spatial Lags Gi Recalculate Spatial Component Number of Temporal Lags 10 4 Edit Temporal Lags Recalculate Temporal Component Click the Recalculate Spatial Component button Input the number of lags 0
57. xecutes it again using the same Workspace and Data File then all the estimation parameter settings and results that were saved are automatically used If the user modifies the estimation parameters during the second analysis then all the stored parameters and results obtained in the first analysis are erased and overwritten for the current analysis When that happens the BMEGUI pops up a dialog box to ask the user 1f they would like to overwrite the earlier results or not 3 1 2 Data File Data File is a file containing the space time data available including the measurement values their space time coordinates and information on measurement errors Currently BMEGUI supports following two data formats GeoEAS format 2 Comma Separated Value CSV format with header 7 The GeoEAS format is the default file format for BMElib packages BMElib users are able to use the data file prepared for BMElib without any modification 3 1 3 River Network File A river network file is a file containing the x y e g longitude and latitude coordinates of points defining river reaches Currently BMEGUI supports river network files that have one of the following two data formats ArcGIS shape file shp format Coma Separated Value CSV format without header A river network file in csv format contains two columns providing the X and Y e g longitude and latitude coordinates of points delineating river reaches Each river reach is s
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