diff --git a/R/readAllOutVar.R b/R/readAllOutVar.R
index 18ee603..dfc501c 100644
--- a/R/readAllOutVar.R
+++ b/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
diff --git a/README.md b/README.md
index d20b830..a0aa976 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
## RSWAT 
-[](https://zenodo.org/badge/latestdoi/395115735) [](https://github.com/tamnva/R-SWAT/blob/master/LICENSE) [](https://github.com/tamnva/R-SWAT/releases) [](https://github.com/tamnva/R-SWAT/actions/workflows/R-CMD-check.yaml)
+[](https://zenodo.org/badge/latestdoi/395115735) [](https://github.com/tamnva/R-SWAT/blob/master/LICENSE) [](https://github.com/tamnva/R-SWAT/releases) [](https://github.com/tamnva/R-SWAT/actions/workflows/R-CMD-check.yaml) [](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).
diff --git a/vignettes/run_SWATplus_with_given_parametersets.R b/vignettes/run_SWATplus_user_parameters.R
similarity index 94%
rename from vignettes/run_SWATplus_with_given_parametersets.R
rename to vignettes/run_SWATplus_user_parameters.R
index deffa7c..1e499ea 100644
--- a/vignettes/run_SWATplus_with_given_parametersets.R
+++ b/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")
diff --git a/vignettes/run_SWATplus_with_given_parametersets.Rmd b/vignettes/run_SWATplus_user_parameters.Rmd
similarity index 95%
rename from vignettes/run_SWATplus_with_given_parametersets.Rmd
rename to vignettes/run_SWATplus_user_parameters.Rmd
index f101ffd..d9d7071 100644
--- a/vignettes/run_SWATplus_with_given_parametersets.Rmd
+++ b/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")
diff --git a/vignettes/run_SWATplus_with_given_parametersets.html b/vignettes/run_SWATplus_user_parameters.html
similarity index 93%
rename from vignettes/run_SWATplus_with_given_parametersets.html
rename to vignettes/run_SWATplus_user_parameters.html
index 77a5f43..76dcc89 100644
--- a/vignettes/run_SWATplus_with_given_parametersets.html
+++ b/vignettes/run_SWATplus_user_parameters.html
@@ -408,31 +408,35 @@ 3. Input configuration
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 = ",")
)
-
-# 10. Date range for extraction (TODO: change this)
-dateRangeCali <- as.Date(c("2003-01-01", "2012-12-31"), format = "%Y-%m-%d")
+# 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 = ",")
-# 11. Number of parallel runs (TODO: change this)
-ncores <- 2
-
-# 12. Generate parameter samples using Latin Hypercube Sampling (TODO: change this)
-parameterValue <- as.matrix(read.table(file = "C:/data/user_parameter_values.txt",
- header = TRUE, sep =""))
+
+# 10. Date range for extraction (TODO: change this)
+dateRangeCali <- as.Date(c("2003-01-01", "2012-12-31"), format = "%Y-%m-%d")
+
+# 11. Number of parallel runs (TODO: change this)
+ncores <- 2
-# Here is the content of my user_parameter_values.txt"
-#cn2.hru canmax.hru
-#0.10 1.5
-#-0.20 3.0
-#-0.10 0.2
-#0.22 1.0
-#
-
-# Remove the column names and number these parametersets from 1 to n. DONOT change this
-parameterValue <- cbind(c(1:nrow(parameterValue)),parameterValue)
-colnames(parameterValue) <- NULL
-rownames(parameterValue) <- NULL
+# 12. Generate parameter samples using Latin Hypercube Sampling (TODO: change this)
+parameterValue <- as.matrix(read.table(file = "C:/data/user_parameter_values.txt",
+ header = TRUE, sep =""))
+
+# Here is the content of my user_parameter_values.txt"
+#cn2.hru canmax.hru
+#0.10 1.5
+#-0.20 3.0
+#-0.10 0.2
+#0.22 1.0
+#
+
+# Remove the column names and number these parametersets from 1 to n. DONOT change this
+parameterValue <- cbind(c(1:nrow(parameterValue)),parameterValue)
+colnames(parameterValue) <- NULL
+rownames(parameterValue) <- NULL
4. Run SWAT+
