diff --git a/NAMESPACE b/NAMESPACE
index 64384aa..e6bd129 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -33,6 +33,8 @@ export(updateCalibrationFile)
export(updateMultiFile)
export(updateSingleFile)
export(updatedFileContent)
+export(userObjFunction)
+export(userReadSwatOutput)
export(yearlyOutputLoc)
importFrom(doParallel,registerDoParallel)
importFrom(foreach,"%dopar%")
diff --git a/R/userObjFunction.R b/R/userObjFunction.R
new file mode 100644
index 0000000..f99cab7
--- /dev/null
+++ b/R/userObjFunction.R
@@ -0,0 +1,58 @@
+
+#' User-defined objective function
+#'
+#' @description
+#' This is a dummy function. There are countless number of objective functions,
+#' which RSWAT cannot include all of them in here. Instead, RSWAT only
+#' provides some of the most commonly used objective functions, such as the NSE,
+#' KGE, aBIAS, R2. User can implement their own objective function and replace
+#' this function. For more detail see RSWAT vignettes (user_objective_function).
+#'
+#' @examples
+#' \donttest{
+#' # Create example data of observed and simulated
+#' obs <- list()
+#' obs[[1]] <- runif(100)
+#' obs[[2]] <- runif(100)
+#'
+#' # Simulated data
+#' sim <- list()
+#' sim[[1]] <- runif(100)
+#' sim[[2]] <- runif(100)
+#'
+#' # Lets say now our objective function is the correlation R2 and the weight
+#' # for the first variable (obs[[1]]) is 1 and for the second variable is 2
+#'
+#' # Create a custom objective function for this task
+#' updatedUserObjFunction <- function(obs, sim){
+#'
+#' # Define output variable
+#' output <- list()
+#' output$perCriteria <- list()
+#'
+#' # R2 of the first variable
+#' output$perCriteria[[1]] <- cor(obs[[1]], sim[[1]])**2
+#'
+#' # R2 of the second variable
+#' output$perCriteria[[2]] <- cor(obs[[2]], sim[[2]])**2
+#'
+#' # Final objective function value (with different weights), must be with the name "output"
+#' output$overalPerCriteria <- (1 * output$perCriteria[[1]] + 2 * output$perCriteria[[2]])/3
+#'
+#' for (i in 1:length(output$perCriteria)){
+#' output$perCriteria[[i]] <- data.frame(userObjFunc = output$perCriteria[[i]])
+#' }
+#'
+#' return(output)
+#' }
+#'
+#' # Overwrite the userObjFunction with our updatedUserObjFunction
+#' environment(updatedUserObjFunction) <- asNamespace('RSWAT')
+#' assignInNamespace("userObjFunction", updatedUserObjFunction, ns = "RSWAT")
+#' }
+#'
+#' @export
+
+userObjFunction <- function(obs, sim){
+ output <- NA
+}
diff --git a/R/userReadSwatOutput.R b/R/userReadSwatOutput.R
new file mode 100644
index 0000000..a993740
--- /dev/null
+++ b/R/userReadSwatOutput.R
@@ -0,0 +1,18 @@
+
+#' User-defined output extraction
+#'
+#' @description
+#' This is a dummy function. As SWAT/SWAT+ have many outputs, RSWAT only provides
+#' some standard output extraction. Users want to extract other model outputs can
+#' implement their own function and replace this function. For more detail see
+#' RSWAT vignettes (userReadSwatOutput).
+#'
+#' @examples
+#'
+#' # Please see RSWAT vignettes for an example
+#'
+#' @export
+
+userReadSwatOutput <- function(){
+ output <- NA
+ }
diff --git a/inst/R-SWAT/HTML/helpCheckCurrentSimulation.html b/inst/R-SWAT/HTML/helpCheckCurrentSimulation.html
new file mode 100644
index 0000000..af32a34
--- /dev/null
+++ b/inst/R-SWAT/HTML/helpCheckCurrentSimulation.html
@@ -0,0 +1,10 @@
+
+
+
+
+
+
+You can only open this files when all SWAT simulations are finished. If SWAT is running on background, you can manually go to the working folder ./Output/CurrentSimulationReport.log and open it with any text editor (e.g., notepad)
+
+
+
diff --git a/inst/R-SWAT/HTML/helpOutputExtraction.html b/inst/R-SWAT/HTML/helpOutputExtraction.html
index 6bd6f2a..4e9e5c8 100644
--- a/inst/R-SWAT/HTML/helpOutputExtraction.html
+++ b/inst/R-SWAT/HTML/helpOutputExtraction.html
@@ -15,16 +15,15 @@ SWAT project
→ Input to the Column should be '7, 8', to the Reach should be
'1, 2 * 1, 2, 3 * 3'
-If you want to read from other files, please modified the source code file ./R/userReadSwatOutput.R, more information about this could be found in the Section 4 of R-SWAT wiki page https://github.com/tamnva/R-SWAT/wiki/R-SWAT-User-Manual
+If you want to read from other files, please create a "userReadSwatOutput.R" and load this file to RSWAT (by click the check box below this table. For detail on how to create this file, please see RSWAT vignettes "userReadSwatOutput".
Please check the tick box below (Display corresponding observed file names) to ensure that all numbers you enter here appear in the display table. The information from this text box is very important, as the observed data files should have the same name as listed in here
SWAT+ project
- Currently, R-SWAT can extract output from different channel files (e.g., channel_sd_day.txt, channel_sd_month.txt, and so on). The Column number indicates which columns in this output file you want to extract and the Reach number indicates which reaches you want to extract. For example, if you want to extract from column 48 and for reach numbers 1 and 2, and column 53 for reach numbers 1,2,3. You write in the Column '48, 53' and in the Reach '1, 2 * 1, 2, 3'
- IMPORTANT: Reach number is the "unit" in column 5 of the output file, you can see this when open the output file for in SWAT+ documentation https://swatplus.gitbook.io/io-docs/swat+-output-files/channel
-- You can also read from other files by modifying the source code file ./R/userReadSwatOutput.R
+- You can also read from other files by creating "userReadSwatOutput.R" file and load this file to RSWAT (by click the check box below this table. For detail on how to create this file, please see RSWAT vignettes "userReadSwatOutput".
-