feat: allow extracting results to csv files and behavioral parametersets

tamnva · Sep 1, 2024 · 10f03e0 · 10f03e0
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diff --git a/inst/R-SWAT/HTML/helpCheckSaveSimTocsv.html b/inst/R-SWAT/HTML/helpCheckSaveSimTocsv.html
@@ -0,0 +1,10 @@
+<!DOCTYPE html>
+<html>
+<head>
+</head>
+<body>
+
+<p>The time series of simulated variables will be saved to ".csv" files in the working folder (e.g., sim_variable_1.csv, sim_variable_2.csv, ...). The variable number => see "1. Define model outputs for extraction" => "Display corresponding observed file names" => "Variable number". The column names: sim_1,sim_2,sim_3,... correspond to simulated results with parameter set 1,2,3,...The number of rows is the number of timesteps => See "2. Select date range"(</p>
+
+</body>
+</html>
diff --git a/inst/R-SWAT/HTML/introduction.html b/inst/R-SWAT/HTML/introduction.html
@@ -3,19 +3,16 @@
 <p><span style="font-size: 16px; font-family: 'Arial Black',sans-serif;">About this app<br /></span></p>
 </div>
 <div>
-<div>
 <ul>
 <li style="font-size: 16px; font-family: 'Times New Roman'; margin: 0in 0in 8.0pt 0in;">This is an R package (RSWAT) with a graphical user interface for parallel parameter sensitivity, calibration, and uncertainty analysis with <a href="https://swat.tamu.edu/software/swat-executables/">SWAT</a>, <a href="https://swat.tamu.edu/software/plus/">SWAT+</a>, <a href="https://sites.google.com/view/swat-carbon">SWAT-Carbon</a> and other modified SWAT</li>
 <li style="font-size: 16px; font-family: 'Times New Roman'; margin: 0in 0in 8.0pt 0in;">The latest version of this app is always in the <a href="https://github.com/tamnva/R-SWAT/tree/development">development</a> branch. If you would like to contribute to the code, have any suggestions, want to report errors, and have scientific collaboration, please <a href="https://www.ufz.de/index.php?en=46415" target="_blank"><span style="color: blue;">contact me</span></a>. The best way to contact me is via the <a href="https://groups.google.com/g/R-SWAT" target="_blank"><span style="color: blue;">Google group</span></a> specially designed for this app. Tutorial videos can be found in <a href="https://www.youtube.com/channel/UCRK1rKFiNgYbG7qKWxAPtEQ" target="_blank"><span style="color: blue;">RSWAT YouTube channel.</span></a></li>
 <li style="font-size: 16px; font-family: 'Times New Roman'; margin: 0in 0in 8.0pt 0in;">The app will be continued to be developed to serve the SWAT community. If you would like to contribute to the development of this app, please let me know. Together we can make this app much better as my time &amp; R knowledge for this app are very limited.</li>
 </ul>
 </div>
-</div>
 <div>
 <p><span style="font-size: 16px; font-family: 'Arial Black',sans-serif;">Usage<br /></span></p>
 </div>
 <div>
-<div>
 <ul>
 <li style="font-size: 16px; font-family: 'Times New Roman'; margin: 0in 0in 8.0pt 0in;">Always follow the numbering scheme in this app, e.g., start with Tab 1. General setting &rarr; 2. Parameter sampling &rarr; 3. Run SWAT &rarr; 4. Evaluate outputs. On each Tab, different input fields are required. These fields are also numbered, describing each working step in order. Help is provided for each respective input field by clicking the "Help" icon on the right side.</li>
 </ul>
@@ -27,22 +24,23 @@
 <p><span style="font-size: 16px; font-family: 'Arial Black',sans-serif;">Citing RSWAT<br /></span></p>
 </div>
 <div>
-<div>
 <ul style="margin-bottom: 0in;" type="square">
 <li style="font-size: 16px; font-family: 'Times New Roman'; margin: 0in 0in 8.0pt 0in;">Nguyen, T. V., Dietrich, J., Dang, D. T., Tran, D. A., Doan, B. V., Sarrazin, F. J., Abbaspour, K., Srinivasan, R. (2022). An interactive graphical interface tool for parameter calibration, sensitivity analysis, uncertainty analysis, and visualization for the Soil and Water Assessment Tool. Environmental Modelling &amp; Software, 156, 105497. <a href="https://doi.org/10.1016/j.envsoft.2022.105497" target="_blank" rel="noopener">https://doi.org/10.1016/j.envsoft.2022.105497.</a></li>
 </ul>
 </div>
 </div>
-</div>
-</div>
 <div>
 <p><span style="font-size: 16px; font-family: 'Arial Black',sans-serif;">Contribution and Acknowledgement<br /></span></p>
 </div>
 <div>
-<div>
 <ul>
 <li style="font-size: 16px; font-family: 'Times New Roman'; margin: 0in 0in 8.0pt 0in;">This package was developed by <a href="https://www.ufz.de/index.php?en=46415" target="_blank">Dr. Tam V. Nguyen</a>, Department of Hydrogeology, Helmholtz Centre for Environmental Research - UFZ, Germany.</li>
 <li style="font-size: 16px; font-family: 'Times New Roman'; margin: 0in 0in 8.0pt 0in;">We thank reviewers of RSWAT papers, whose comments have helped to improve the quality of RSWAT. We thank RSWAT users for reporting bugs, suggestion on the app functionalities.</li>
 </ul>
 </div>
+<div>
+<p><span style="font-size: 16px; font-family: 'Arial Black',sans-serif;">Updates/News<br /></span></p>
 </div>
+<ul>
+<li style="font-size: 16px; font-family: 'Times New Roman'; margin: 0in 0in 8.0pt 0in;">Version 4.01: FEATURES: extract simulated results to .csv file, extract behavioral parametersets; FIX: RSWAT is interrupted when reading HRU information </li>
+</ul>
diff --git a/inst/R-SWAT/R/runSWATUI.R b/inst/R-SWAT/R/runSWATUI.R
@@ -126,7 +126,7 @@ runSwatUI <- function(id) {
       #-------------------------------------------------------------------------
       # 5. See simulation report
       #-------------------------------------------------------------------------
-      div( style = "margin-top: 15em",
+      div( style = "margin-top: 20em",
            column(width = 10,
                   HTML("<b>","5. See simulation report","</b>"),
            ),
@@ -140,19 +140,12 @@ runSwatUI <- function(id) {
                           class = NULL),
       ),
 
-      column(width = 5,
+      column(width = 10,
              checkboxInput('checkCurrentSimulation',
                            'Open file CurrentSimulationReport.log',
                            value = FALSE, width = NULL),
       ),
 
-      column(width = 5,
-             checkboxInput('checkDisplayParameterSet',
-                           'Display all parameter sets',
-                           value = FALSE, width = NULL),
-      ),
-
-
       conditionalPanel(
         condition = "input.checkCurrentSimulation == 1",
         column(width = 10,
@@ -161,12 +154,32 @@ runSwatUI <- function(id) {
         ),
       ),
 
+      column(width = 10,
+             checkboxInput('checkDisplayParameterSet',
+                           'Display all parameter sets',
+                           value = FALSE, width = NULL),
+      ),
+
       conditionalPanel(
         condition = "input.checkDisplayParameterSet == 1",
         column(width = 10,
                dataTableOutput("tableDisplayParameterSet"),
         ),
       ),
+
+      # Check box display all simulation results
+      column(width = 10,
+             checkboxInput("checkSaveSimTocsv",
+                           "Save simulated results as .csv files"),
+      ),
+
+      column(width = 1,
+             actionButton("helpCheckSaveSimTocsv",
+                          "Help",
+                          buttonType = "default",
+                          style="background-color: none; border-color: none",
+                          class = NULL),
+      ),
       #-------------------------------------------------------------------------
 
     )

diff --git a/inst/R-SWAT/R/utilities.R b/inst/R-SWAT/R/utilities.R
@@ -1,4 +1,3 @@
-
 #-------------------------------------------------------------------------------
 # Binding list object (with 3 levels of list)
 # ------------------------------------------------------------------------------

diff --git a/inst/R-SWAT/server.R b/inst/R-SWAT/server.R
@@ -615,8 +615,11 @@ server <- function(input, output, session) {
 
       # If this is a SWAT project
       if (globalVariable$SWATProject & globalVariable$TxtInOutSWAT){
+
         # Get HRU information (land use, slope, soil, sub)
-        globalVariable$HRUinfo <<- getHruInfo(globalVariable$TxtInOutFolder)
+        spsComps::shinyCatch(
+          globalVariable$HRUinfo <<- getHruInfo(globalVariable$TxtInOutFolder),
+          blocking_level = "error")
 
         # Get unique soil, land use, slope, max number of subbasins
         uniqueSoil <- unique(globalVariable$HRUinfo$soil)
@@ -1059,11 +1062,17 @@ server <- function(input, output, session) {
                           "formatted as follows:","\n",
                           "   First row: Name of the parameters","\n",
                           "   From the second row: Parameter value", "\n",
-                          "   Leave one row empty at the end of the file", "\n",
                           " ", "\n",
                           "   As many column as the number of parameters","\n",
+                          "   Columns are seperated by one or more spaces or tabs","\n",
                           "   The order of parameters in these columns follows ",
                           "the order of the parameters in the above Table", "\n",
+                          " ", "\n",
+                          "Example (content of myParameterFile.txt)", "\n",
+                          " ", "\n",
+                          "   GW_DELAY.gw  CN2.mgt   SOL_K.sol    ALPHA_BF.gw  ESCO.hru    SURLAG.hru  CH_K2.rte     SURLAG.bsn", "\n",
+                          "   228.03       0.05     -0.21         0.07         0.80        0.14        0.41          3.39", "\n",
+                          "   96.27       -0.12      0.17         0.35         0.66        0.34        0.03          3.00", "\n",
                          sep = "")
 
     } else if (input$samplingApproach == 'Sensi_(from_userDefined_package)'){
@@ -1414,6 +1423,21 @@ server <- function(input, output, session) {
       easyClose = TRUE
     ))
   })
+
+  # ****************************************************************************
+  # Help button helpCheckSaveSimTocsv
+  # ****************************************************************************
+  observe({
+    req(input$helpCheckSaveSimTocsv)
+
+    showModal(modalDialog(
+      title = "Help: Save simulated results as .csv files",
+      HTML(readLines(file.path(HTMLdir,"HTML",
+                               "helpCheckSaveSimTocsv.html"),warn=FALSE)),
+      easyClose = TRUE
+    ))
+  })
+
   # ****************************************************************************
   # Run SWAT
   # ****************************************************************************
@@ -1825,6 +1849,15 @@ server <- function(input, output, session) {
                              min = 1,
                              max = globalVariable$nOutputVar,
                              step = 1)
+
+           # Update select variable number
+           updateSliderInput(session = session,
+                             "showSimResultsVariable",
+                             "Select variable",
+                             value = 1,
+                             min = 1,
+                             max = globalVariable$nOutputVar,
+                             step = 1)
         }
 
       } else {
@@ -1889,6 +1922,42 @@ server <- function(input, output, session) {
   })
 
 
+  # ****************************************************************************
+  # Display simulated results
+  # ****************************************************************************
+  observe({
+    req(input$checkSaveSimTocsv)
+    # Display observed data in table
+    spsComps::shinyCatch(
+      if (TRUE){
+        # Get simulated data
+        for (var in 1:globalVariable$nOutputVar){
+
+          data <- c()
+          for (core in 1:globalVariable$ncores){
+            data <- rbind(data, read.csv(file = file.path(globalVariable$workingFolder,
+                                              "Output",
+                                              paste0("Core_", core),
+                                              paste0("out_var_", var, ".txt")),
+                             header = FALSE))
+          }
+          # Convert to data frame
+          data <- matrix(data$V1, ncol = nrow(globalVariable$parameterValue), byrow = FALSE)
+          colnames(data) <- paste0("sim_", data[1,])
+
+          fileName <- file.path(globalVariable$workingFolder,
+                                paste0("sim_variable_", var, ".csv"))
+          write.csv(data[-c(1),], file = fileName,
+                    quote = FALSE, row.names = FALSE)
+
+          message(paste0("Simulated output variable ", var, " was saved as: ", fileName))
+        }
+      },
+      blocking_level = "error"
+    )
+  })
+
+
   # ****************************************************************************
   # Display parameter sets used for simulations
   # ****************************************************************************