Version 0.7.0 - improved transformation of layered data

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: simplaceUtil
 Title: Provides Utility Functions and ShinyApps to work with the modeling framework 'SIMPLACE'
-Version: 0.6.9
-Date: 2024-07-10
+Version: 0.7.0
+Date: 2025-02-21
 Authors@R: 
     person("Gunther", "Krauss", , "[email protected]", role = c("aut", "cre"))
 Description: Provides Utility Functions and ShinyApps to work with the modeling framework 'SIMPLACE'. It visualises components of a solution, runs simulations and displays results.
@@ -25,4 +25,4 @@ VignetteBuilder: knitr
 Suggests:
     knitr, rmarkdown, rsvg, DiagrammeRsvg
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -13,6 +13,7 @@ export(createCodeStubsForSimVariables)
 export(createResourceStubsFromCsv)
 export(createResourceStubsFromXml)
 export(enhanceFunctionWithBoundaries)
+export(enhanceFunctionWithPenalty)
 export(fetchDescriptionFromWebsite)
 export(fetchSimComponentlistFromWebsite)
 export(fetchSimVariablesFromWebsite)

NEWS

@@ -1,3 +1,8 @@
+Version 0.7.0
+* transformLayeredData can take now arbitrary separator
+* transformLayeredData now works on variable names that contain the separator multiple times
+
+
 Version 0.6.9
 * output filenames vector named by output ids
 * enhance functions to return penalty values when parameters outside boundaries

R/csvoutput_helper.R

@@ -1,16 +1,22 @@
 #' Transform layered output data in long format
 #'
 #' @param data dataframe
+#' @param sep character that separates layer number from variable name (default "_")
+#' @return dataframe in long format
 #' @export
-transformLayeredData <- function(data)
+transformLayeredData <- function(data, sep="_")
 {
-  if(any(grepl("[a-zA-Z]+_[0-9]+",names(data))))
+  if(sep %in% c(".","|","+","-","*","(",")","[","]")) {
+    sep = paste0("\\",sep)
+  }
+  pattern <- paste0("([a-zA-Z_0-9 .]+)",sep,"([0-9]+)")
+  if(sep!="" && any(grepl(pattern,names(data))))
   {
     tidyr::pivot_longer(
       data,
-      dplyr::matches("[a-zA-Z]+_[0-9]+"),
+      dplyr::matches(pattern),
       names_to = c(".value","layer"),
-      names_pattern ="([a-zA-Z_]+)_([0-9]+)$",
+      names_pattern =pattern,
       names_transform = list(layer=as.integer)
     )
   }

R/optim_helper.R

@@ -49,3 +49,57 @@ enhanceFunctionWithBoundaries <- function(fun, l_bound, u_bound,
     }
   }
 }
+
+#' Modifies function to return a penalised value for parameters outside boundaries
+#'
+#' The method takes a function as well as values for lower and upper boundaries
+#' and returns a modified function. The modified function returns the value of
+#' the original function when the parameters are within boundaries and a penalised
+#' function otherwise.
+#'
+#' Optionally an own function can be supplied to calculate the penalised value.
+#' The function must take two arguments: the original value and the distance
+#' of the parameter to the boundaries.
+#'
+#' Additionally an own distance function can be supplied, that has to take three
+#' arguments: the parameter, the lower boundaries and the upper boundaries.
+#'
+#' A main use case of this method are optimisation / calibration tasks. If the
+#' optimisation method and the function to optimise are both ignorant to boundaries
+#' one can turn the function into a boundary sensitive one.
+#'
+#' @param fun function to be modified
+#' @param l_bound vector with lower boundary values
+#' @param u_bound vector with upper boundary values
+#' @param penalty_fun function taking value and distance and returns
+#'   value modified value depending on distance
+#' @param distance_fun function that takes x, l_bound and u_bound and computes
+#'   the distance of x to the boundaries
+#' @param ... arguments passed to original function
+#' @param param_pos argument position of the parameter
+#' @return a modified function that changes value when parameter outside bounds
+#' @export
+#' @examples
+#' sqr_bd <- enhanceFunctionWithPenalty(\(x) x^2, .1, 10)
+#' sqr_bd(-1)
+#' sqr_bd(1)
+#' sqr_bd(11)
+#'
+enhanceFunctionWithPenalty <- function(fun, l_bound, u_bound,
+                                  penalty_fun= function(value, distance) (value+distance) * exp(1000*distance),
+                                  distance_fun = function(x,l,u) {max(0, (l-x)/(u-l), (x -u)/(u-l))},
+                                  param_pos=1,
+                                  ...) {
+  function(...) {
+    x <-  ...elt(param_pos)
+    invalid <- !all(l_bound <= x & x <= u_bound)
+    if(invalid) {
+      d <- distance_fun(x,l_bound, u_bound)
+      penalty_fun(fun(...),d)
+    }
+    else {
+      fun(...)
+    }
+  }
+}
+

R/plotting.R

@@ -105,19 +105,21 @@ plotScalarOutput <- function (data, column_x, columns_y,
 #' @param datecol column name for date (default CURRENT.DATE)
 #' @param nrow number of panel rows when plotting multiple simulation ids
 #' @param ncol number of panels in a row when plotting multiple simulation ids
+#' @param sep character that separates layer number from variable name (default "_")
 #' @export
 #' @importFrom rlang .data
 plotLayeredOutput <- function(data, column, simulationid = NULL,
                               date_from=NULL, date_to=NULL,
                               datecol="CURRENT.DATE",
                               nrow=NULL,
-                              ncol=NULL)
+                              ncol=NULL,
+                              sep="-")
 {
 
   data <- subsetDataForPlot(data, simulationid, date_from, date_to, datecol)
   if(nrow(data)>0 && !is.null(column) && !is.na(column))
   {
-    dt <- transformLayeredData(data)
+    dt <- transformLayeredData(data, sep)
     if(nrow(dt)>0 && column %in% names(dt) && "layer" %in% names(dt))
     {
       ggplot2::ggplot(dt,

vignettes/simplaceUtil.Rmd

@@ -188,7 +188,7 @@ graph <- solutionToGraph(solfile)
 DiagrammeR::render_graph(graph)
 ```
 ```{r echo=FALSE, out.width="100%"}
-includeGraphic(graph,"graph")
+try(includeGraphic(graph,"graph"))
 ```
 
 We can restrict the graph to specific component types and the neighborhood of
@@ -202,7 +202,7 @@ subgraph <- getNeighborhood(graph, c("SlimWater","SlimRoots"),
 DiagrammeR::render_graph(subgraph)
 ```
 ```{r echo=FALSE, out.width="100%"}
-includeGraphic(subgraph,"subgraph")
+try(includeGraphic(subgraph,"subgraph"))
 ```