Merge pull request #64 from tamnva/joss_manuscript

fix: error in readAllOutVar.R causes program to stop

R/readAllOutVar.R

@@ -45,7 +45,7 @@ readAllOutVar <- function(workingFolder, numTimesteps){
   outVarFiles <- list.files(coreFolders[1], full.names = TRUE)
 
   output <- list()
-  for (ifolder in 1:length(coreFolder)){
+  for (ifolder in 1:length(coreFolders)){
     # Loop over each outVarfiles
     for (var in 1:length(outVarFiles)){
       # Read content of each file and store

README.md

@@ -1,6 +1,6 @@
 ## RSWAT <a href="https://github.com/tamnva/R-SWAT/tree/master/inst/R-SWAT/figures/RSWAT_logo.svg"><img src="inst/R-SWAT/figures/RSWAT_logo.svg" align="right" height="50" /></a>
 
-[![DOI](https://zenodo.org/badge/395115735.svg)](https://zenodo.org/badge/latestdoi/395115735) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/tamnva/R-SWAT/blob/master/LICENSE) [![Release](https://img.shields.io/github/release/tamnva/R-SWAT.svg?style=flat-square)](https://github.com/tamnva/R-SWAT/releases) [![R-CMD-check](https://github.com/tamnva/R-SWAT/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tamnva/R-SWAT/actions/workflows/R-CMD-check.yaml)
+[![DOI](https://zenodo.org/badge/395115735.svg)](https://zenodo.org/badge/latestdoi/395115735) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://github.com/tamnva/R-SWAT/blob/master/LICENSE) [![Release](https://img.shields.io/github/release/tamnva/R-SWAT.svg?style=flat-square)](https://github.com/tamnva/R-SWAT/releases) [![R-CMD-check](https://github.com/tamnva/R-SWAT/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tamnva/R-SWAT/actions/workflows/R-CMD-check.yaml) [![status](https://joss.theoj.org/papers/89a04bc6f9a2a2b08cbac33fcd91c0c6/status.svg)](https://joss.theoj.org/papers/89a04bc6f9a2a2b08cbac33fcd91c0c6)
 
 - This is an R package with a graphical user interface (GUI) for parallel parameter calibration, sensitivity, and uncertainty analyses with the Soil and Water Assessment Tool models (e.g., [SWAT](https://swat.tamu.edu/), [SWAT+](https://swat.tamu.edu/software/plus/), [SWAT-Carbon](https://sites.google.com/view/swat-carbon), and its other modified versions). 
 - RSWAT can also be used without the GUI, please see the RSWAT vignettes (see Quick Start section).

vignettes/run_SWATplus_with_given_parametersets.R → vignettes/run_SWATplus_user_parameters.R

@@ -51,8 +51,12 @@ knitr::opts_chunk$set(
 #     FileType = c("channel_sd_day.txt"),
 #     FileName = c("channel_sd_day.txt"),
 #     Column = c("48"),
-#     Reach = c("1")
+#     Reach = c("1") # E.g., for 100 reaches use: Reach = paste(as.character(c(1:100)), collapse  = ",")
 #   )
+#  # NOTE: if you want to extract for many reaches (e.g., for the first 100 reaches), create variable for th
+#  
+#  reach <- paste(as.character(c(1:100)), collapse  = ",")
+#  
 #  
 #  # 10. Date range for extraction (TODO: change this)
 #  dateRangeCali <- as.Date(c("2003-01-01", "2012-12-31"), format = "%Y-%m-%d")

vignettes/run_SWATplus_with_given_parametersets.Rmd → vignettes/run_SWATplus_user_parameters.Rmd

@@ -75,8 +75,12 @@ outputExtraction <- data.frame(
    FileType = c("channel_sd_day.txt"),
    FileName = c("channel_sd_day.txt"),
    Column = c("48"),
-   Reach = c("1")
+   Reach = c("1") # E.g., for 100 reaches use: Reach = paste(as.character(c(1:100)), collapse  = ",")
  )
+# NOTE: if you want to extract for many reaches (e.g., for the first 100 reaches), create variable for th
+
+reach <- paste(as.character(c(1:100)), collapse  = ",")
+
 
 # 10. Date range for extraction (TODO: change this)
 dateRangeCali <- as.Date(c("2003-01-01", "2012-12-31"), format = "%Y-%m-%d")

vignettes/run_SWATplus_with_given_parametersets.html → vignettes/run_SWATplus_user_parameters.html

@@ -408,31 +408,35 @@ <h3>3. Input configuration</h3>
 <span id="cb1-44"><a href="#cb1-44" tabindex="-1"></a>   <span class="at">FileType =</span> <span class="fu">c</span>(<span class="st">&quot;channel_sd_day.txt&quot;</span>),</span>
 <span id="cb1-45"><a href="#cb1-45" tabindex="-1"></a>   <span class="at">FileName =</span> <span class="fu">c</span>(<span class="st">&quot;channel_sd_day.txt&quot;</span>),</span>
 <span id="cb1-46"><a href="#cb1-46" tabindex="-1"></a>   <span class="at">Column =</span> <span class="fu">c</span>(<span class="st">&quot;48&quot;</span>),</span>
-<span id="cb1-47"><a href="#cb1-47" tabindex="-1"></a>   <span class="at">Reach =</span> <span class="fu">c</span>(<span class="st">&quot;1&quot;</span>)</span>
+<span id="cb1-47"><a href="#cb1-47" tabindex="-1"></a>   <span class="at">Reach =</span> <span class="fu">c</span>(<span class="st">&quot;1&quot;</span>) <span class="co"># E.g., for 100 reaches use: Reach = paste(as.character(c(1:100)), collapse  = &quot;,&quot;)</span></span>
 <span id="cb1-48"><a href="#cb1-48" tabindex="-1"></a> )</span>
-<span id="cb1-49"><a href="#cb1-49" tabindex="-1"></a></span>
-<span id="cb1-50"><a href="#cb1-50" tabindex="-1"></a><span class="co"># 10. Date range for extraction (</span><span class="al">TODO</span><span class="co">: change this)</span></span>
-<span id="cb1-51"><a href="#cb1-51" tabindex="-1"></a>dateRangeCali <span class="ot">&lt;-</span> <span class="fu">as.Date</span>(<span class="fu">c</span>(<span class="st">&quot;2003-01-01&quot;</span>, <span class="st">&quot;2012-12-31&quot;</span>), <span class="at">format =</span> <span class="st">&quot;%Y-%m-%d&quot;</span>)</span>
+<span id="cb1-49"><a href="#cb1-49" tabindex="-1"></a><span class="co"># </span><span class="al">NOTE</span><span class="co">: if you want to extract for many reaches (e.g., for the first 100 reaches), create variable for th</span></span>
+<span id="cb1-50"><a href="#cb1-50" tabindex="-1"></a></span>
+<span id="cb1-51"><a href="#cb1-51" tabindex="-1"></a>reach <span class="ot">&lt;-</span> <span class="fu">paste</span>(<span class="fu">as.character</span>(<span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="dv">100</span>)), <span class="at">collapse  =</span> <span class="st">&quot;,&quot;</span>)</span>
 <span id="cb1-52"><a href="#cb1-52" tabindex="-1"></a></span>
-<span id="cb1-53"><a href="#cb1-53" tabindex="-1"></a><span class="co"># 11. Number of parallel runs  (</span><span class="al">TODO</span><span class="co">: change  this)</span></span>
-<span id="cb1-54"><a href="#cb1-54" tabindex="-1"></a>ncores <span class="ot">&lt;-</span> <span class="dv">2</span></span>
-<span id="cb1-55"><a href="#cb1-55" tabindex="-1"></a></span>
-<span id="cb1-56"><a href="#cb1-56" tabindex="-1"></a><span class="co"># 12.  Generate parameter samples using Latin Hypercube Sampling (</span><span class="al">TODO</span><span class="co">: change this)</span></span>
-<span id="cb1-57"><a href="#cb1-57" tabindex="-1"></a>parameterValue <span class="ot">&lt;-</span> <span class="fu">as.matrix</span>(<span class="fu">read.table</span>(<span class="at">file =</span> <span class="st">&quot;C:/data/user_parameter_values.txt&quot;</span>,</span>
-<span id="cb1-58"><a href="#cb1-58" tabindex="-1"></a>                                       <span class="at">header =</span> <span class="cn">TRUE</span>, <span class="at">sep =</span><span class="st">&quot;&quot;</span>))</span>
+<span id="cb1-53"><a href="#cb1-53" tabindex="-1"></a></span>
+<span id="cb1-54"><a href="#cb1-54" tabindex="-1"></a><span class="co"># 10. Date range for extraction (</span><span class="al">TODO</span><span class="co">: change this)</span></span>
+<span id="cb1-55"><a href="#cb1-55" tabindex="-1"></a>dateRangeCali <span class="ot">&lt;-</span> <span class="fu">as.Date</span>(<span class="fu">c</span>(<span class="st">&quot;2003-01-01&quot;</span>, <span class="st">&quot;2012-12-31&quot;</span>), <span class="at">format =</span> <span class="st">&quot;%Y-%m-%d&quot;</span>)</span>
+<span id="cb1-56"><a href="#cb1-56" tabindex="-1"></a></span>
+<span id="cb1-57"><a href="#cb1-57" tabindex="-1"></a><span class="co"># 11. Number of parallel runs  (</span><span class="al">TODO</span><span class="co">: change  this)</span></span>
+<span id="cb1-58"><a href="#cb1-58" tabindex="-1"></a>ncores <span class="ot">&lt;-</span> <span class="dv">2</span></span>
 <span id="cb1-59"><a href="#cb1-59" tabindex="-1"></a></span>
-<span id="cb1-60"><a href="#cb1-60" tabindex="-1"></a><span class="co"># Here is the content of my user_parameter_values.txt&quot;</span></span>
-<span id="cb1-61"><a href="#cb1-61" tabindex="-1"></a><span class="co">#cn2.hru         canmax.hru</span></span>
-<span id="cb1-62"><a href="#cb1-62" tabindex="-1"></a><span class="co">#0.10            1.5</span></span>
-<span id="cb1-63"><a href="#cb1-63" tabindex="-1"></a><span class="co">#-0.20           3.0</span></span>
-<span id="cb1-64"><a href="#cb1-64" tabindex="-1"></a><span class="co">#-0.10           0.2</span></span>
-<span id="cb1-65"><a href="#cb1-65" tabindex="-1"></a><span class="co">#0.22            1.0</span></span>
-<span id="cb1-66"><a href="#cb1-66" tabindex="-1"></a><span class="co">#</span></span>
-<span id="cb1-67"><a href="#cb1-67" tabindex="-1"></a></span>
-<span id="cb1-68"><a href="#cb1-68" tabindex="-1"></a><span class="co"># Remove the column names and number these parametersets from 1 to n. DONOT change this</span></span>
-<span id="cb1-69"><a href="#cb1-69" tabindex="-1"></a>parameterValue <span class="ot">&lt;-</span> <span class="fu">cbind</span>(<span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="fu">nrow</span>(parameterValue)),parameterValue)</span>
-<span id="cb1-70"><a href="#cb1-70" tabindex="-1"></a><span class="fu">colnames</span>(parameterValue) <span class="ot">&lt;-</span> <span class="cn">NULL</span></span>
-<span id="cb1-71"><a href="#cb1-71" tabindex="-1"></a><span class="fu">rownames</span>(parameterValue) <span class="ot">&lt;-</span> <span class="cn">NULL</span></span></code></pre></div>
+<span id="cb1-60"><a href="#cb1-60" tabindex="-1"></a><span class="co"># 12.  Generate parameter samples using Latin Hypercube Sampling (</span><span class="al">TODO</span><span class="co">: change this)</span></span>
+<span id="cb1-61"><a href="#cb1-61" tabindex="-1"></a>parameterValue <span class="ot">&lt;-</span> <span class="fu">as.matrix</span>(<span class="fu">read.table</span>(<span class="at">file =</span> <span class="st">&quot;C:/data/user_parameter_values.txt&quot;</span>,</span>
+<span id="cb1-62"><a href="#cb1-62" tabindex="-1"></a>                                       <span class="at">header =</span> <span class="cn">TRUE</span>, <span class="at">sep =</span><span class="st">&quot;&quot;</span>))</span>
+<span id="cb1-63"><a href="#cb1-63" tabindex="-1"></a></span>
+<span id="cb1-64"><a href="#cb1-64" tabindex="-1"></a><span class="co"># Here is the content of my user_parameter_values.txt&quot;</span></span>
+<span id="cb1-65"><a href="#cb1-65" tabindex="-1"></a><span class="co">#cn2.hru         canmax.hru</span></span>
+<span id="cb1-66"><a href="#cb1-66" tabindex="-1"></a><span class="co">#0.10            1.5</span></span>
+<span id="cb1-67"><a href="#cb1-67" tabindex="-1"></a><span class="co">#-0.20           3.0</span></span>
+<span id="cb1-68"><a href="#cb1-68" tabindex="-1"></a><span class="co">#-0.10           0.2</span></span>
+<span id="cb1-69"><a href="#cb1-69" tabindex="-1"></a><span class="co">#0.22            1.0</span></span>
+<span id="cb1-70"><a href="#cb1-70" tabindex="-1"></a><span class="co">#</span></span>
+<span id="cb1-71"><a href="#cb1-71" tabindex="-1"></a></span>
+<span id="cb1-72"><a href="#cb1-72" tabindex="-1"></a><span class="co"># Remove the column names and number these parametersets from 1 to n. DONOT change this</span></span>
+<span id="cb1-73"><a href="#cb1-73" tabindex="-1"></a>parameterValue <span class="ot">&lt;-</span> <span class="fu">cbind</span>(<span class="fu">c</span>(<span class="dv">1</span><span class="sc">:</span><span class="fu">nrow</span>(parameterValue)),parameterValue)</span>
+<span id="cb1-74"><a href="#cb1-74" tabindex="-1"></a><span class="fu">colnames</span>(parameterValue) <span class="ot">&lt;-</span> <span class="cn">NULL</span></span>
+<span id="cb1-75"><a href="#cb1-75" tabindex="-1"></a><span class="fu">rownames</span>(parameterValue) <span class="ot">&lt;-</span> <span class="cn">NULL</span></span></code></pre></div>
 </div>
 <div id="run-swat" class="section level3">
 <h3>4. Run SWAT+</h3>