CentreForHydrology · KevinShook · Jan 4, 2022 · Jan 4, 2022 · Jun 17, 2022
diff --git a/.Rbuildignore b/.Rbuildignore
diff --git a/.gitignore b/.gitignore
diff --git a/CRHMr.Rproj b/CRHMr.Rproj
diff --git a/CRHMr.pdf b/CRHMr.pdf
diff --git a/CRHMr_cheatsheet.pdf b/CRHMr_cheatsheet.pdf
diff --git a/CRHMr_release_notes.txt b/CRHMr_release_notes.txt
diff --git a/DESCRIPTION b/DESCRIPTION
diff --git a/LICENSE b/LICENSE
diff --git a/NAMESPACE b/NAMESPACE
diff --git a/R/BadLake7376.R b/R/BadLake7376.R
diff --git a/R/CRHM_summary.R b/R/CRHM_summary.R
diff --git a/R/CRHM_vars.R b/R/CRHM_vars.R
diff --git a/R/CRHMr-package.R b/R/CRHMr-package.R
diff --git a/R/GMToffset.R b/R/GMToffset.R
diff --git a/R/PcpFiltPosTh.R b/R/PcpFiltPosTh.R
diff --git a/R/addPrjHRU.R b/R/addPrjHRU.R
@@ -0,0 +1,258 @@
+#' Adds a specified HRU to .prj file
+#'
+#' @description Adds a single HRU to a .prj file. Note
+#' that this function is potentially destructive, so it's a good idea to have a backup copy
+#' of your \code{.prj} file \emph{before} running it!
+#' @param inputPrjFile Required. Name of the \code{.prj} file to read.
+#' @param numOldHRUs. Optional. If not specified (the default), the number of HRUs in the existing
+#' file will be read from the .prj file. If you are reading a REWGrp file, where the
+#' specified number of HRUs is actually the number of groups, then you should specify this
+#' value.
+#' @param addHRUnumber Required. Number of HRU to be inserted. All existing HRUs with numbers
+#' greater than or equal to this number will be incremented by one.
+#' @param addHRUname  Required. Name for the added HRU.
+#' @param copyHRUvalues Optional. If specified, values from this HRU will be used
+#' for the new HRU. Note that the value of this parameter refers to the the HRU numbers
+#' \emph{before} the addition of the new HRU. So it would be possible to have
+#' \code{addHRUnmber = 5}, and \code{copyHRUvalues = 5}. This would add a new HRU at
+#' position 5, and would set the parameters to be those of the existing HRU 5.
+#' @param outputPrjFile Optional. If omitted, the input \code{.prj} file will be overwritten.
+#' @param quiet Optional. Suppresses display of messages, except for errors. If you are calling
+#' this function in an \R script, you will usually leave \code{quiet=TRUE} (i.e. the default).
+#' If you are working interactively, you will probably want to set \code{quiet=FALSE}.
+#' @param logfile Optional. Name of the file to be used for logging the action. Normally not used
+#'
+#' @return If successful, returns \code{TRUE}. If unsuccessful, returns \code{FALSE}.
+#' @author Kevin Shook
+#' @seealso  \code{\link{deletePrjHRUs}}
+#' @export
+#' @examples \dontrun{
+#' result <- addPrjHRU("CRHM/Bad74_Frozen.prj", c(3, 5, 7)}
+#'
+addPrjHRUs <- function(inputPrjFile = NULL,
+                          numOldHRUs = NULL,
+                          addHRUnumber = NULL,
+                          addHRUname = NULL,
+                          copyHRUvalues = NULL,
+                          outputPrjFile = NULL,
+                          quiet = TRUE, logfile = "") {
+  # check parameters
+  if (is.null(inputPrjFile))
+    stop("Missing CRHM input .prj file name")
+
+  if (is.null(addHRUnumber))
+    stop("No HRU number specified")
+
+  if (is.null(addHRUname))
+    stop("No HRU name specified")
+
+  if (is.null(outputPrjFile))
+    outputPrjFile <- inputPrjFile
+
+  # get HRU names
+  oldHRUnames <- readPrjHRUnames(inputPrjFile)
+
+  # check to ensure that new HRU number is OK
+
+  if ((addHRUnumber < 1) | (addHRUnumber > (numOldHRUs+1)))
+    stop("Invalid HRU number specified")
+
+  # add names of selected HRU
+  newHRUnames <- append(oldHRUnames, addHRUname, after = addHRUnumber)
+
+  # read in prj file and find end of parameters
+  prj <- readPrj(inputPrjFile)
+  start_line <- grep('hru_names', prj, fixed = TRUE)
+  # find end line
+  done <- FALSE
+  numvals <- 0
+  end_line <- start_line
+  while (!done) {
+    end_line <- end_line + 1
+    vals <- parseText(prj[end_line])
+    numvals <- numvals + length(vals)
+    if (numvals >= length(oldHRUnames))
+      done <- TRUE
+  }
+
+  replace_vals <- paste("'", stringr::str_c(newHRUnames,
+                                       collapse = "' '"), "'", sep = '')
+  prj[start_line + 1] <- replace_vals
+  changed_lines <- end_line - start_line
+  if (changed_lines > 1)
+    prj <- prj[-((start_line + 2):(end_line))]
+
+  writePrj(prj, outputPrjFile)
+
+  # set new dimensions - if REW_Grp not present
+  REW_Grp_found <- sum(str_detect(prj, "REW_Grp"))
+
+  if (REW_Grp_found > 0) {
+    old_dimensions <- readPrjDimensions(inputPrjFile)
+    num_old_HRUs <-  old_dimensions[1, 2]
+    new_dimensions <- old_dimensions[, 2]
+    new_dimensions[1] <- length(newHRUnames)
+    setPrjDimensions(inputPrjFile = outputPrjFile,
+                     dimensionVals = new_dimensions)
+  }
+
+
+
+  # get number of parameters to change
+  prj <- readPrj(inputPrjFile)
+  param_loc <- grep("Parameters:", prj, fixed = TRUE)
+  prj <- prj[(param_loc + 1):length(prj)]
+  parameter_lines <- grep("<", prj, fixed = TRUE)
+  num_parameters <- length(parameter_lines)
+
+  omit_parameters <- c("basin_area", "basin_name", "distrib_Route", "HRU_OBS",
+                       "obs_elev", "soil_withdrawal", "RUN_END", "RUN_ID",
+                       "RUN_START")
+
+  param_names <- prj[parameter_lines]
+
+  # extract parameter names from strings
+  param_names_alone <- stringr::str_split_fixed(param_names, fixed(" "), 3)
+  param_names_alone <- param_names_alone[, 2]
+
+  for (i in 1:num_parameters) {
+    param_name <- param_names[i]
+    param_name_alone <- param_names_alone[i]
+    if (!param_name_alone %in% omit_parameters) {
+       params <- readPrjParameters(inputPrjFile, paramName = param_name)
+       if (!is.null(copyHRUvalues))
+         new_params <- params[copyHRUvalues]
+       else
+         new_params <- 0
+
+       new_params <- append(params, new_params, after = addHRUnumber)
+       result <- replacePrjParameters(inputPrjFile = outputPrjFile,
+                        paramName = param_name,
+                        paramVals = new_params,
+                        oldParamCount = old_dimensions[1, 2],
+                        quiet = quiet)
+    }
+  }
+
+  # do matrix parameters
+
+  if (sum(stringr::str_detect(prj, "distrib_Route")) > 0) {
+    old_route_vals <- readPrjMatrix(inputPrjFile, "distrib_Route")
+    num_new_HRUs <- length(newHRUnames)
+    new_routevals <- matrix(nrow = num_new_HRUs, ncol = num_new_HRUs)
+
+   # add new row
+    new_routevals <- apply(old_route_vals, 1, append, values = 0, after = addHRUnumber)
+
+   # add new col
+    if (addHRUnumber == 1)
+      new_routevals <- cbind(0, old_route_vals)
+    else if(addHRUnumber >= num_old_HRUs)
+      new_routevals <- cbind(old_route_vals, 0)
+    else {
+      left <- new_routevals[, 1:(addHRUnumber - 1)]
+      right <- new_routevals[, addHRUnumber:ncol(new_routevals)]
+      new_routevals <- cbind(left, 0, right)
+    }
+
+
+
+    result <- setPrjMatrix(outputPrjFile, paramName = "distrib_Route",
+                 paramMatrix = new_routevals)
+
+  }
+
+  if (sum(stringr::str_detect(prj, "HRU_OBS")) > 0) {
+    old_obs_vals <- readPrjParameters(inputPrjFile, "HRU_OBS")
+    old_obs_vals <- matrix(old_obs_vals, nrow = (length(old_obs_vals) / numOldHRUs),
+                             ncol = numOldHRUs)
+
+    if (!is.null(copyHRUvalues))
+      copy_col <- old_obs_vals[, copyHRUvalues]
+    else
+      copy_col <- rep.int(1, numOldHRUs)
+
+
+    if (addHRUnumber < num_old_HRUs) {
+      new_obs_vals <- cbind(copy_col, old_obs_vals)
+    } else if(addHRUnumber >= num_old_HRUs) {
+        new_obs_vals <- cbind(old_obs_vals, copy_col)
+    }   else {
+         left <- old_obs_vals[, 1:(addHRUnumber - 1)]
+         right <- new_routevals[, addHRUnumber:ncol(new_routevals)]
+         new_obs_vals <- cbind(left, copy_col, right)
+    }
+
+
+
+
+    result <- replacePrjParameters(inputPrjFile = outputPrjFile,
+                     paramName = "HRU_OBS",
+                     paramVals = new_obs_vals,
+                     oldParamCount = numOldHRUs)
+  }
+
+  if (sum(stringr::str_detect(prj, "obs_elev")) > 0) {
+    old_elev_vals <- readPrjParameters(inputPrjFile, "obs_elev")
+    old_elev_vals <- matrix(old_elev_vals, nrow = length(old_elev_vals) / length(oldHRUnames),
+                           ncol = length(oldHRUnames))
+
+    if (!is.null(copyHRUvalues))
+      copy_col <- old_elev_vals[, copyHRUvalues]
+    else
+      copy_col <- rep.int(-1, length(oldHRUnames))
+
+    if (addHRUnumber < num_old_HRUs) {
+      new_obs_elev_vals <- cbind(copy_col, old_elev_vals)
+    } else if(addHRUnumber >= num_old_HRUs) {
+      new_obs_elev_vals <- cbind(old_elev_vals, copy_col)
+    } else {
+      left <- old_obs_vals[, 1:(addHRUnumber - 1)]
+      right <- old_routevals[, addHRUnumber:ncol(new_routevals)]
+      new_obs_elev_vals <- cbind(left, copy_col, right)
+    }
+
+
+
+    result <- replacePrjParameters(inputPrjFile = outputPrjFile,
+                     paramName = "obs_elev",
+                     paramVals = new_obs_elev_vals,
+                     oldParamCount = numOldHRUs)
+
+  }
+
+  if (sum(stringr::str_detect(prj, "soil_withdrawal")) > 0) {
+    old_withdraw_vals <- readPrjParameters(inputPrjFile, "soil_withdrawal")
+    old_withdraw_vals <- matrix(old_withdraw_vals, nrow = length(old_withdraw_vals) / length(oldHRUnames),
+                            ncol = length(oldHRUnames))
+
+    if (!is.null(copyHRUvalues))
+      copy_col <- old_withdraw_vals[, copyHRUvalues]
+    else
+      copy_col <- rep.int(-1, length(oldHRUnames))
+
+
+    if (addHRUnumber < num_old_HRUs) {
+      new_withdraw_vals <- cbind(copy_col, old_withdraw_vals)
+    } else if(addHRUnumber >= num_old_HRUs) {
+        new_withdraw_vals <- cbind(old_withdraw_vals, copy_col)
+    } else {
+        left <- old_withdraw_vals[, 1:(addHRUnumber - 1)]
+        right <- old_withdraw_vals[, addHRUnumber:ncol(old_withdraw_vals)]
+        new_withdraw_vals <- cbind(left, copy_col, right)
+    }
+
+
+    result <- replacePrjParameters(inputPrjFile = outputPrjFile,
+                     paramName = "soil_withdrawal",
+                     paramVals = new_withdraw_vals,
+                     oldParamCount = numOldHRUs)
+  }
+
+  # log action
+  comment <- paste('deletePrjHRUs input file: ', inputPrjFile,
+                   ' output file:', outputPrjFile)
+
+  result <- logAction(comment, logfile)
+  return(result)
+}
diff --git a/R/aggDataframe.R b/R/aggDataframe.R
diff --git a/R/appendObs.R b/R/appendObs.R
diff --git a/R/assembleObs.R b/R/assembleObs.R
diff --git a/R/automatePrj.R b/R/automatePrj.R
diff --git a/R/basinWaterBalancePlot.R b/R/basinWaterBalancePlot.R
diff --git a/R/changeEatoRH.R b/R/changeEatoRH.R
diff --git a/R/changeRHtoEa.R b/R/changeRHtoEa.R
diff --git a/R/createObsDataframe.R b/R/createObsDataframe.R
diff --git a/R/cumulDailyWater.R b/R/cumulDailyWater.R
diff --git a/R/cumulativeDischargePlot.R b/R/cumulativeDischargePlot.R
diff --git a/R/dailyByHourlyP.R b/R/dailyByHourlyP.R
diff --git a/R/dateToDatetime.R b/R/dateToDatetime.R
diff --git a/R/datetimeToDate.R b/R/datetimeToDate.R
diff --git a/R/deDupe.R b/R/deDupe.R
diff --git a/R/deletePrjHRUs.R b/R/deletePrjHRUs.R
diff --git a/R/deleteSpikes.R b/R/deleteSpikes.R
diff --git a/R/deltaStorage.R b/R/deltaStorage.R
diff --git a/R/distributeInst.R b/R/distributeInst.R
diff --git a/R/distributeMean.R b/R/distributeMean.R
diff --git a/R/distributeP.R b/R/distributeP.R
diff --git a/R/distributeQli.R b/R/distributeQli.R
diff --git a/R/distributeQsi.R b/R/distributeQsi.R
diff --git a/R/doubleMass.R b/R/doubleMass.R
diff --git a/R/extendObs.R b/R/extendObs.R
diff --git a/R/findDupes.R b/R/findDupes.R
diff --git a/R/findGaps.R b/R/findGaps.R
diff --git a/R/findSpikes.R b/R/findSpikes.R
diff --git a/R/hruGroupWaterSummary.R b/R/hruGroupWaterSummary.R
diff --git a/R/hydroYear.R b/R/hydroYear.R
diff --git a/R/hydrograph.R b/R/hydrograph.R
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diff --git a/R/plotTempsByYear.R b/R/plotTempsByYear.R
diff --git a/R/prjDimensions.R b/R/prjDimensions.R
diff --git a/R/qair2ea.R b/R/qair2ea.R
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diff --git a/R/readOutputUnits.R b/R/readOutputUnits.R
diff --git a/R/readPrj.R b/R/readPrj.R
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diff --git a/R/readPrjHRUnames.R b/R/readPrjHRUnames.R
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diff --git a/R/ribbonPlotAirTemps.R b/R/ribbonPlotAirTemps.R
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diff --git a/R/simpleMaxSolar.R b/R/simpleMaxSolar.R
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diff --git a/R/wetland_h_s.R b/R/wetland_h_s.R
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diff --git a/R/yearlyPeaks.R b/R/yearlyPeaks.R
diff --git a/R/zeroMissingPrecip.R b/R/zeroMissingPrecip.R
diff --git a/README.md b/README.md
diff --git a/data/CRHMr.RData b/data/CRHMr.RData
diff --git a/inst/CITATION b/inst/CITATION
diff --git a/man/BadLake7376.Rd b/man/BadLake7376.Rd
diff --git a/man/CRHM_summary.Rd b/man/CRHM_summary.Rd
diff --git a/man/CRHM_vars.Rd b/man/CRHM_vars.Rd
diff --git a/man/CRHMr-package.Rd b/man/CRHMr-package.Rd
diff --git a/man/GMToffset.Rd b/man/GMToffset.Rd
diff --git a/man/PcpFiltPosTh.Rd b/man/PcpFiltPosTh.Rd
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diff --git a/man/basinWaterBalancePlot.Rd b/man/basinWaterBalancePlot.Rd
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diff --git a/man/convertDPtoRH.Rd b/man/convertDPtoRH.Rd
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diff --git a/man/cumsumDataframe.Rd b/man/cumsumDataframe.Rd
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diff --git a/man/deDupe.Rd b/man/deDupe.Rd
diff --git a/man/deletePrjHRUs.Rd b/man/deletePrjHRUs.Rd
diff --git a/man/deleteSpikes.Rd b/man/deleteSpikes.Rd
diff --git a/man/deltaStorage.Rd b/man/deltaStorage.Rd
diff --git a/man/distributeInst.Rd b/man/distributeInst.Rd
diff --git a/man/distributeMean.Rd b/man/distributeMean.Rd
diff --git a/man/distributeP.Rd b/man/distributeP.Rd
diff --git a/man/distributeQli.Rd b/man/distributeQli.Rd
diff --git a/man/distributeQsi.Rd b/man/distributeQsi.Rd
diff --git a/man/doubleMass.Rd b/man/doubleMass.Rd
diff --git a/man/emissivity.Rd b/man/emissivity.Rd
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diff --git a/man/fakeDatetime.Rd b/man/fakeDatetime.Rd
diff --git a/man/fakeDatetimeHydroyear.Rd b/man/fakeDatetimeHydroyear.Rd
diff --git a/man/findDupes.Rd b/man/findDupes.Rd
diff --git a/man/findGaps.Rd b/man/findGaps.Rd
diff --git a/man/findSpikes.Rd b/man/findSpikes.Rd
diff --git a/man/hruGroupWaterSummary.Rd b/man/hruGroupWaterSummary.Rd
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