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Merge pull request #69 from tamnva/joss_manuscript
feat: add more vignettes and update help
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| #' 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 | ||
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| userObjFunction <- function(obs, sim){ | ||
| output <- NA | ||
| } |
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| #' 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 | ||
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| userReadSwatOutput <- function(){ | ||
| output <- NA | ||
| } |
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| <!DOCTYPE html> | ||
| <html> | ||
| <head> | ||
| </head> | ||
| <body> | ||
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| <p>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)</p> | ||
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| </body> | ||
| </html> |
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| <!DOCTYPE html> | ||
| <html> | ||
| <head> | ||
| </head> | ||
| <body> | ||
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| <p>When you click this button, all settings are saved to the file 'RSWATObject.rds' in the working directory folder. The parameter sets are generated and SWAT are run in parallel. Running can take time, R is busy while calling SWAT on the background therefore, it might not response to any anything. Don't turn of R. You can check the current simulation status in the file ./Output/CurrentSimulationReport.log You still go to step 4 and click the 'Open file CurrentSimulationReport.log'. When all simulations are finished, you will see a table appear</p> | ||
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| </body> | ||
| </html> |
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