From ec5363115d00d5cb1c8f2417f11e9fe140d1bd5f Mon Sep 17 00:00:00 2001 From: kerim aydin Date: Fri, 31 May 2024 12:13:51 -0700 Subject: [PATCH] mysterious param.R not updating --- R/param.R | 1008 ++++++++++++++++++++++++++--------------------------- 1 file changed, 504 insertions(+), 504 deletions(-) diff --git a/R/param.R b/R/param.R index f746e54c..41e33fe3 100644 --- a/R/param.R +++ b/R/param.R @@ -1,504 +1,504 @@ -## Rpath functions for creating and checking parameter files - -#'Creates a shell for the Rpath.params object -#' -#'Creates a shell of the Rpath.params list object which contains the model, diet, -#'multistanza, and pedigree parameters. -#' -#'@family Rpath functions -#' -#'@param group Vector of group names. -#'@param type Numeric vector of group type. Living = 0, Producer = 1, Detritus = 2, -#' Fleet = 3. -#'@param stgroup Vector of multistanza group names. Include NA for non-stanza groups. -#' -#'@return Outputs a list object of Rpath parameters which are populated with values -#' of NA or logical default values. Values can then be filled in using -#' R. Use check.rpath.params() to ensure parameter files are filled out -#' correctly (NOTE: This does not ensure data is correct just that it is -#' in the right places). -#'@import data.table -#'@export -create.rpath.params <- function(group, type, stgroup = NA){ - #Need to define variables to eliminate check() note about no visible binding - Group <- DetInput <- V1 <- StGroupNum <- NULL - - Rpath.params <- list() - - pred.group <- group[which(type < 2)] - prey.group <- group[which(type < 3)] - det.group <- group[which(type == 2)] - fleet.group <- group[which(type == 3)] - - #Model parameters - model <- data.table(Group = group, - Type = type, - Biomass = as.numeric(NA), - PB = as.numeric(NA), - QB = as.numeric(NA), - EE = as.numeric(NA), - ProdCons = as.numeric(NA), - BioAcc = as.numeric(NA), - Unassim = as.numeric(NA), - DetInput = as.numeric(NA)) - - #Add detritial groups - for(i in 1:length(det.group)){ - model[Group %in% det.group, DetInput := 0] - model[, V1 := as.numeric(NA)] - setnames(model, "V1", det.group[i]) - } - - #Add fleets twice - Landings and Discards - for(i in 1:length(fleet.group)){ - model[, V1 := c(rep(0, length(group) - length(fleet.group)), - rep(NA, length(fleet.group)))] - setnames(model, "V1", fleet.group[i]) - } - for(i in 1:length(fleet.group)){ - model[, V1 := c(rep(0, length(group) - length(fleet.group)), - rep(NA, length(fleet.group)))] - setnames(model, "V1", paste(fleet.group[i], '.disc', sep = '')) - } - Rpath.params$model <- model - - #Diet matrix - diet <- data.table(Group = c(prey.group, 'Import')) - for(i in 1:length(pred.group)){ - diet[, V1 := as.numeric(NA)] - setnames(diet, "V1", pred.group[i]) - } - Rpath.params$diet <- diet - - #Multistanza parameters - if(length(stgroup) > 1){ - #Group Parameters - StanzaGroups <- unique(stgroup[!is.na(stgroup)]) - nstanzas <- as.vector(table(stgroup)[StanzaGroups]) - NStanzaGroups <- length(StanzaGroups) - Rpath.params$stanzas$NStanzaGroups <- NStanzaGroups - - stgroups <- data.table(StGroupNum = 1:NStanzaGroups, - StanzaGroup = StanzaGroups, - nstanzas = nstanzas, - VBGF_Ksp = NA, - VBGF_d = 0.66667, - Wmat = NA, - BAB = 0, - RecPower = 1) - - #Individual Stanza Parameters - ind.stanza.group <- model[!is.na(stgroup), Group] - ieco <- which(!is.na(stgroup)) - stindiv <- data.table(StGroupNum = rep(stgroups[, StGroupNum], - stgroups[, nstanzas]), - StanzaNum = as.integer(0), - GroupNum = ieco, - Group = ind.stanza.group, - First = NA, - Last = NA, - Z = NA, - Leading = NA) - - } else { - - Rpath.params$stanzas$NStanzaGroups <- 0 - - stgroups <- data.table(StGroupNum = NA, - StanzaGroup = NA, - nstanzas = NA, - VBGF_Ksp = NA, - VBGF_d = NA, - Wmat = NA, - RecPower = NA) - - stindiv <- data.table(StGroupNum = NA, - StanzaNum = NA, - GroupNum = NA, - Group = NA, - First = NA, - Last = NA, - Z = NA, - Leading = NA) - } - - Rpath.params$stanzas$stgroups <- stgroups - Rpath.params$stanzas$stindiv <- stindiv - - #Pedigree - pedigree <- data.table(Group = group, - Biomass = 1, - PB = 1, - QB = 1, - Diet = 1) - #Add fleet pedigree - for(i in 1:length(fleet.group)){ - pedigree[, V1 := 1] - setnames(pedigree, "V1", fleet.group[i]) - } - Rpath.params$pedigree <- pedigree - class(Rpath.params) <- 'Rpath.params' - return(Rpath.params) -} - - -#'Check Rpath parameter files -#' -#'Logical check that the parameter files are filled out correctly, i.e. data is entered where it is -#'expected. -#' -#'@family Rpath functions -#' -#'@inheritParams rpath -#' -#'@return Checks Rpath parameter files for consistency. An error message will be produced if one of -#' the logical checks fails. Checks include: -#' (NOTE: This does not ensure data is correct just that it is in the right places). -#'@import data.table -#'@export -#' -check.rpath.params <- function(Rpath.params){ - #Need to define variables to eliminate check() note about no visible binding - Type <- Group <- Biomass <- EE <- PB <- QB <- ProdCons <- BioAcc <- Unassim <- DetInput <- NULL - - w <- 0 #warning counter - #Check to make sure all types are represented - if(nrow(Rpath.params$model[Type == 0, ]) == 0){ - warning('Model must contain at least 1 consumer') - w <- w + 1 - } - if(nrow(Rpath.params$model[Type == 1, ]) == 0){ - warning('Model must contain a producer group') - w <- w + 1 - } - if(nrow(Rpath.params$model[Type == 2, ]) == 0){ - warning('Model must contain at least 1 detrital group') - w <- w + 1 - } - if(nrow(Rpath.params$model[Type == 3, ]) == 0){ - warning('Model must contain at least 1 fleet') - } - - #Check that there is the proper number of columns - n.groups <- nrow(Rpath.params$model) - n.living <- length(Rpath.params$model[Type <= 1, Group]) - n.dead <- length(Rpath.params$model[Type == 2, Group]) - n.fleet <- length(Rpath.params$model[Type == 3, Group]) - if(ncol(Rpath.params$model) != 10 + n.dead + 2 * n.fleet){ - warning('Model does not have the correct number of column. There should be 10 - columns plus one for each detrital group plus two for each fleet group - (landings and discards). Please double check your columns') - w <- w + 1 - } - - #Check that either biomass or EE is entered and not both - if(length(Rpath.params$model[is.na(Biomass) & is.na(EE) & Type < 2, Group]) > 0){ - warning(paste(Rpath.params$model[is.na(Biomass) & is.na(EE) & Type < 2, Group], - 'are missing both Biomass and EE...must enter one \n', sep = ' ')) - w <- w + 1 - } - if(length(Rpath.params$model[!is.na(Biomass) & !is.na(EE) & Type < 2, Group]) > 0){ - warning(paste(Rpath.params$model[!is.na(Biomass) & !is.na(EE) & Type < 2, Group], - 'have both Biomass and EE...Note that Rpath does not calculate BA - please enter a value for BA if appropriate \n', sep = ' ')) - w <- w + 1 - } - - #Check that Biomass / PB / QB / EE / ProdCons is not entered for types 3 - if(length(Rpath.params$model[Type == 3 & !is.na(Biomass), Group]) > 0){ - warning(paste(Rpath.params$model[Type == 3 & !is.na(Biomass), Group], - 'is a fleet and should not have a biomass...set to NA \n', - sep = ' ')) - w <- w + 1 - } - if(length(Rpath.params$model[Type == 3 & !is.na(PB), Group]) > 0){ - warning(paste(Rpath.params$model[Type == 3 & !is.na(PB), Group], - 'is a fleet and should not have a PB...set to NA \n', sep = ' ')) - w <- w + 1 - } - if(length(Rpath.params$model[Type > 1 & !is.na(QB), Group]) > 0){ - warning(paste(Rpath.params$model[Type > 1 & !is.na(QB), Group], - 'are not living and should not have a QB...set to NA \n', sep = ' ')) - w <- w + 1 - } - if(length(Rpath.params$model[Type > 1 & !is.na(EE), Group]) > 0){ - warning(paste(Rpath.params$model[Type > 1 & !is.na(EE), Group], - 'are not living and should not have a EE...set to NA \n', sep = ' ')) - w <- w + 1 - } - if(length(Rpath.params$model[Type > 1 & !is.na(ProdCons), Group]) > 0){ - warning(paste(Rpath.params$model[Type > 1 & !is.na(ProdCons), Group], - 'are not living and should not have a ProdCons...set to NA \n', - sep = ' ')) - w <- w + 1 - } - - #Check that types 0 and 1 have a PB unless QB and ProdCons are entered - if(length(Rpath.params$model[Type < 2 & is.na(PB), Group]) > 0){ - no.pb <- Rpath.params$model[Type < 2 & is.na(PB), Group] - if(length(Rpath.params$model[Group %in% no.pb & (is.na(QB) | is.na(ProdCons)), Group]) > 0){ - warning(paste(Rpath.params$model[Group %in% no.pb & (is.na(QB) | is.na(ProdCons)), Group], - 'are missing a PB without a QB and PQ...set to >= 0 \n', sep = ' ')) - w <- w + 1 - } - } - - #Check that consumers have a QB or ProdCons but not both unless missing PB - if(length(Rpath.params$model[is.na(QB) & is.na(ProdCons) & Type < 1, Group]) > 0){ - warning(paste(Rpath.params$model[is.na(QB) & is.na(ProdCons) & Type < 1, Group], - 'are missing both QB and ProdCons...must enter one \n', sep = ' ')) - w <- w + 1 - } - if(length(Rpath.params$model[!is.na(QB) & !is.na(ProdCons) & Type < 1, Group]) > 0){ - both <- Rpath.params$model[!is.na(QB) & !is.na(ProdCons) & Type < 1, Group] - if(length(Rpath.params$model[Group %in% both & !is.na(PB), Group]) > 0){ - warning(paste(Rpath.params$model[Group %in% both & !is.na(PB), Group], - 'have PB, QB, and ProdCons...only two should be entered \n', - sep = ' ')) - w <- w + 1 - } - } - - #Check that BioAcc / Unassim is NA for fleets and numeric for types < 3 - if(length(Rpath.params$model[Type == 3 & !is.na(BioAcc), Group]) > 0){ - warning(paste(Rpath.params$model[Type == 3 & !is.na(BioAcc), Group], - 'are fleets and should not have a BioAcc...set to NA \n', sep = ' ')) - w <- w + 1 - } - if(length(Rpath.params$model[Type == 3 & !is.na(Unassim), Group]) > 0){ - warning(paste(Rpath.params$model[Type == 3 & !is.na(Unassim), Group], - 'are fleets and should not have an Unassim...set to NA \n', sep = ' ')) - w <- w + 1 - } - if(length(Rpath.params$model[Type != 3 & is.na(BioAcc), Group]) > 0){ - warning(paste(Rpath.params$model[Type != 3 & is.na(BioAcc), Group], - 'must have a number for BioAcc...set to >= 0 \n', sep = ' ')) - w <- w + 1 - } - if(length(Rpath.params$model[Type != 3 & is.na(Unassim), Group]) > 0){ - warning(paste(Rpath.params$model[Type != 3 & is.na(Unassim), Group], - 'must have a number for Unassim...set to >= 0 \n', sep = ' ')) - w <- w + 1 - } - - #Check that only Type 2 has DetInput set - if(length(Rpath.params$model[Type != 2 & !is.na(DetInput), Group]) > 0){ - warning(paste(Rpath.params$model[Type != 2 & !is.na(DetInput), Group], - 'are not detritus...set DetInput to NA \n', sep = ' ')) - w <- w + 1 - } - if(length(Rpath.params$model[Type == 2 & is.na(DetInput), Group]) >0){ - warning(paste(Rpath.params$model[Type == 2 & is.na(DetInput), Group], - 'are detritus...set DetInput to 0 \n', sep = ' ')) - w <- w + 1 - } - - #Check detritus fate is numeric and sum to 1 - det.matrix <- Rpath.params$model[, 11:(10 + n.dead), with = F] - test.rows <- rowSums(det.matrix) - if(length(setdiff(which(Rpath.params$model[, Type] == 2), which(test.rows != 1))) > 0){ - warning(paste(Rpath.params$model[, Group][setdiff(which(Rpath.params$model[, Type] == 2), - which(test.rows != 1))], - 'detrital fate does not sum to 1 \n', sep = ' ')) - w <- w + 1 - } - if(length(which(is.na(det.matrix))) > 0){ - na.group <- which(is.na(det.matrix)) - for(i in 1:length(na.group)) while(na.group[i] > n.groups) na.group[i] <- - na.group[i] - n.groups - na.group <- unique(na.group) - warning(paste(Rpath.params$model[na.group, Group], - 'one or more detrital fates are NA...set to >= 0 \n', sep = ' ')) - w <- w + 1 - } - - #Check that landings and discards are numbers for type < 3 - fleet.matrix <- Rpath.params$model[1:(n.groups - n.fleet), (11 + n.dead):ncol(Rpath.params$model), - with = F] - if(length(which(is.na(fleet.matrix))) > 0){ - na.group <- which(is.na(fleet.matrix)) - for(i in 1:length(na.group)) while(na.group[i] > n.groups) na.group[i] <- - na.group[i] - n.groups - na.group <- unique(na.group) - warning(paste(Rpath.params$model[na.group, Group], - 'one or more catches are NA...set to >= 0 \n', sep = ' ')) - w <- w + 1 - } - - #Check that fleets aren't catching other fleets - fleet.matrix.2 <- Rpath.params$model[(n.groups - n.fleet + 1):n.groups, (11 + n.dead): - ncol(Rpath.params$model), with = F] - if(length(which(!is.na(fleet.matrix.2))) > 0){ - not.na.group <- which(!is.na(fleet.matrix.2)) - for(i in 1:length(not.na.group)){ - while(not.na.group[i] > n.fleet){ - not.na.group[i] <- not.na.group[i] - n.fleet - not.na.group <- unique(not.na.group) - } - } - warning(paste(Rpath.params$model[not.na.group + (n.groups - n.fleet), Group], - 'are catching another fleet...set to NA \n', sep = ' ')) - w <- w + 1 - } - - #Diet - #Check that columns sum to 1 - col.names <- names(Rpath.params$diet)[2:ncol(Rpath.params$diet)] - col.sums <- Rpath.params$diet[, lapply(.SD, sum, na.rm = T), .SDcols = col.names] - - #Check types (>0 & <=1 are primary producers) - types <- Rpath.params$model[Type < 2, Type] - dctype <- round(col.sums + types, 3) - if(length(which(dctype != 1)) > 0){ - for(i in 1:length(which(dctype != 1))){ - warning(paste(col.names[which(dctype != 1)][i], 'sum,', - col.sums[, which(dctype !=1)[i], with = F], - 'is not 1...check DC or proportion of primary production')) - w <- w + 1 - } - } - - #Check number of columns - dietcol <- ncol(Rpath.params$diet) - if(dietcol != (n.living + 1)){ - warning(paste(dietcol, ' is the incorrect number of columns in diet matrix.', - 'There should be', n.living + 1)) - w <- w + 1 - } - - #Check that final row of diet is "Import" - if(!Rpath.params$diet[nrow(Rpath.params$diet), 1] == 'Import' & - !Rpath.params$diet[nrow(Rpath.params$diet), 1] == 'import'){ - - warning('Diet matrix is missing the import row. Please add "Import" as the - final row. All entries can be 0 or NA.') - w <- w + 1 - } - -if(w == 0){ - cat('Rpath parameter file is functional. \n') -} else { - cat('Rpath parameter file needs attention! \n') - } -} - -#'Read Rpath parameters from .csv files -#' -#'Creates an Rpath.param object from a series of .csv files. -#' -#'@family Rpath functions -#' -#'@param modfile file location of the flat file containing the model parameters. -#'@param dietfile file location of the flat file containing the diet parameters. -#'@param stanzagroupfile file location of the flat file containing the group parameters -#' for multistanza groups. If not specified a blank stanza list will be created. -#'@param stanzafile file location of the flat file containing the individual stanza -#' parameters for multistanza groups. If not specified a blank stanza list will -#' be created. -#'@param pedfile file location of the flat file containg the pedgigree parameters. -#'@return Outputs an Rpath.param object that can be used for Rpath and subsequently -#' Rsim. (NOTE: This does function does not ensure data is correct or in the -#' correct locations...run check.rpath.param to ensure the appropriate columns are -#' present). -#'@export -read.rpath.params <- function(modfile, dietfile, pedfile = NA, - stanzagroupfile = NA, stanzafile = NA){ - #Need to define variables to eliminate check() note about no visible binding - Type <- Group <- V1 <- NULL - - Rpath.params <- list() - Rpath.params$model <- as.data.table(read.csv(modfile, header = T)) - Rpath.params$diet <- as.data.table(read.csv(dietfile, header = T)) - - if(!is.na(stanzagroupfile)){ - stanzagroup <- as.data.table(read.csv(stanzagroupfile, header = T)) - Rpath.params$stanzas$NStanzaGroups <- nrow(stanzagroup) - Rpath.params$stanzas$stgroups <- stanzagroup - Rpath.params$stanzas$stindiv <- as.data.table(read.csv(stanzafile, - header = T)) - } else { - Rpath.params$stanzas$NStanzaGroups <- 0 - Rpath.params$stanzas$stgroups <- data.table(StGroupNum = NA, - StanzaGroup = NA, - nstanzas = NA, - VBGF_Ksp = NA, - VBGF_d = NA, - Wmat = NA, - RecPower = NA, - Wmat001 = NA, - Wmat50 = NA, - Amat001 = NA, - Amat50 = NA) - Rpath.params$stanzas$stindiv <- data.table(StGroupNum = NA, - StanzaNum = NA, - GroupNum = NA, - Group = NA, - First = NA, - Last = NA, - Z = NA, - Leading = NA) - } - if(!is.na(pedfile)){ - Rpath.params$pedigree <- as.data.table(read.csv(pedfile, header = T)) - } else { - Rpath.params$pedigree <- data.table(Group = Rpath.params$model$Group, - B = 1, - PB = 1, - QB = 1, - Diet = 1) - fleets <- as.character(Rpath.params$model[Type == 3, Group]) - for(i in 1:length(fleets)){ - Rpath.params$pedigree[, V1 := 1] - setnames(Rpath.params$pedigree, 'V1', fleets[i]) - } - } - class(Rpath.params) <- 'Rpath.params' - return(Rpath.params) -} - -#'Write Rpath parameters to .csv files -#' -#'Creates a series of .csv files from an Rpath.params object. -#' -#'@family Rpath functions -#' -#'@param Rpath.params R object containing the Rpath parameters. Most likely this -#' was created using create.rpath.params or read.rpath.params. -#'@param eco.name ecosystem name that will be included in all the file names. -#'@param path location for the output files. -#'@return Outputs a series of .csv files named by the provided eco.name and the -#' parameters they represent. For example the model parameters will be named -#' "eco.name_model.csv". -#'@export -write.rpath.params <- function(Rpath.params, eco.name, path = ''){ - - write.csv(Rpath.params$model, - file = file.path(path, paste(eco.name, '_model.csv', sep = '')), - row.names = F) - - write.csv(Rpath.params$diet, - file = file.path(path, paste(eco.name, '_diet.csv', sep = '')), - row.names = F) - - write.csv(Rpath.params$pedigree, - file = file.path(path, paste(eco.name, '_pedigree.csv', sep = '')), - row.names = F) - - #Multistanza parameters are in several different files - write.csv(Rpath.params$stanzas$stgroups, - file = file.path(path, paste(eco.name, '_stanza_groups.csv', sep = '')), - row.names = F) - - write.csv(Rpath.params$stanzas$stindiv, - file = file.path(path, paste(eco.name, '_stanzas.csv', sep = '')), - row.names = F) - - if(Rpath.params$stanzas$NStanzaGroups > 0){ - for(isp in 1:Rpath.params$stanzas$NStanzaGroups){ - write.csv(Rpath.params$stanzas$StGroup[[isp]], - file = file.path(path, paste(eco.name, '_', - Rpath.params$stanzas$stgroups$StanzaGroup[isp], - '.csv', sep = '')), row.names = F) - } - } -} +## Rpath functions for creating and checking parameter files + +#'Creates a shell for the Rpath.params object +#' +#'Creates a shell of the Rpath.params list object which contains the model, diet, +#'multistanza, and pedigree parameters. +#' +#'@family Rpath functions +#' +#'@param group Vector of group names. +#'@param type Numeric vector of group type. Living = 0, Producer = 1, Detritus = 2, +#' Fleet = 3. +#'@param stgroup Vector of multistanza group names. Include NA for non-stanza groups. +#' +#'@return Outputs a list object of Rpath parameters which are populated with values +#' of NA or logical default values. Values can then be filled in using +#' R. Use check.rpath.params() to ensure parameter files are filled out +#' correctly (NOTE: This does not ensure data is correct just that it is +#' in the right places). +#'@import data.table +#'@export +create.rpath.params <- function(group, type, stgroup = NA){ + #Need to define variables to eliminate check() note about no visible binding + Group <- DetInput <- V1 <- StGroupNum <- NULL + + Rpath.params <- list() + + pred.group <- group[which(type < 2)] + prey.group <- group[which(type < 3)] + det.group <- group[which(type == 2)] + fleet.group <- group[which(type == 3)] + + #Model parameters + model <- data.table(Group = group, + Type = type, + Biomass = as.numeric(NA), + PB = as.numeric(NA), + QB = as.numeric(NA), + EE = as.numeric(NA), + ProdCons = as.numeric(NA), + BioAcc = as.numeric(NA), + Unassim = as.numeric(NA), + DetInput = as.numeric(NA)) + + #Add detritial groups + for(i in 1:length(det.group)){ + model[Group %in% det.group, DetInput := 0] + model[, V1 := as.numeric(NA)] + setnames(model, "V1", det.group[i]) + } + + #Add fleets twice - Landings and Discards + for(i in 1:length(fleet.group)){ + model[, V1 := c(rep(0, length(group) - length(fleet.group)), + rep(NA, length(fleet.group)))] + setnames(model, "V1", fleet.group[i]) + } + for(i in 1:length(fleet.group)){ + model[, V1 := c(rep(0, length(group) - length(fleet.group)), + rep(NA, length(fleet.group)))] + setnames(model, "V1", paste(fleet.group[i], '.disc', sep = '')) + } + Rpath.params$model <- model + + #Diet matrix + diet <- data.table(Group = c(prey.group, 'Import')) + for(i in 1:length(pred.group)){ + diet[, V1 := as.numeric(NA)] + setnames(diet, "V1", pred.group[i]) + } + Rpath.params$diet <- diet + + #Multistanza parameters + if(length(stgroup) > 1){ + #Group Parameters + StanzaGroups <- unique(stgroup[!is.na(stgroup)]) + nstanzas <- as.vector(table(stgroup)[StanzaGroups]) + NStanzaGroups <- length(StanzaGroups) + Rpath.params$stanzas$NStanzaGroups <- NStanzaGroups + + stgroups <- data.table(StGroupNum = 1:NStanzaGroups, + StanzaGroup = StanzaGroups, + nstanzas = nstanzas, + VBGF_Ksp = NA, + VBGF_d = 0.66667, + Wmat = NA, + BAB = 0, + RecPower = 1) + + #Individual Stanza Parameters + ind.stanza.group <- model[!is.na(stgroup), Group] + ieco <- which(!is.na(stgroup)) + stindiv <- data.table(StGroupNum = rep(stgroups[, StGroupNum], + stgroups[, nstanzas]), + StanzaNum = as.integer(0), + GroupNum = ieco, + Group = ind.stanza.group, + First = NA, + Last = NA, + Z = NA, + Leading = NA) + + } else { + + Rpath.params$stanzas$NStanzaGroups <- 0 + + stgroups <- data.table(StGroupNum = NA, + StanzaGroup = NA, + nstanzas = NA, + VBGF_Ksp = NA, + VBGF_d = NA, + Wmat = NA, + RecPower = NA) + + stindiv <- data.table(StGroupNum = NA, + StanzaNum = NA, + GroupNum = NA, + Group = NA, + First = NA, + Last = NA, + Z = NA, + Leading = NA) + } + + Rpath.params$stanzas$stgroups <- stgroups + Rpath.params$stanzas$stindiv <- stindiv + + #Pedigree + pedigree <- data.table(Group = group, + Biomass = 1, + PB = 1, + QB = 1, + Diet = 1) + #Add fleet pedigree + for(i in 1:length(fleet.group)){ + pedigree[, V1 := 1] + setnames(pedigree, "V1", fleet.group[i]) + } + Rpath.params$pedigree <- pedigree + class(Rpath.params) <- 'Rpath.params' + return(Rpath.params) +} + + +#'Check Rpath parameter files +#' +#'Logical check that the parameter files are filled out correctly, i.e. data is entered where it is +#'expected. +#' +#'@family Rpath functions +#' +#'@inheritParams rpath +#' +#'@return Checks Rpath parameter files for consistency. An error message will be produced if one of +#' the logical checks fails. Checks include: +#' (NOTE: This does not ensure data is correct just that it is in the right places). +#'@import data.table +#'@export +#' +check.rpath.params <- function(Rpath.params){ + #Need to define variables to eliminate check() note about no visible binding + Type <- Group <- Biomass <- EE <- PB <- QB <- ProdCons <- BioAcc <- Unassim <- DetInput <- NULL + + w <- 0 #warning counter + #Check to make sure all types are represented + if(nrow(Rpath.params$model[Type == 0, ]) == 0){ + warning('Model must contain at least 1 consumer') + w <- w + 1 + } + if(nrow(Rpath.params$model[Type == 1, ]) == 0){ + warning('Model must contain a producer group') + w <- w + 1 + } + if(nrow(Rpath.params$model[Type == 2, ]) == 0){ + warning('Model must contain at least 1 detrital group') + w <- w + 1 + } + if(nrow(Rpath.params$model[Type == 3, ]) == 0){ + warning('Model must contain at least 1 fleet') + } + + #Check that there is the proper number of columns + n.groups <- nrow(Rpath.params$model) + n.living <- length(Rpath.params$model[Type <= 1, Group]) + n.dead <- length(Rpath.params$model[Type == 2, Group]) + n.fleet <- length(Rpath.params$model[Type == 3, Group]) + if(ncol(Rpath.params$model) != 10 + n.dead + 2 * n.fleet){ + warning('Model does not have the correct number of column. There should be 10 + columns plus one for each detrital group plus two for each fleet group + (landings and discards). Please double check your columns') + w <- w + 1 + } + + #Check that either biomass or EE is entered and not both + if(length(Rpath.params$model[is.na(Biomass) & is.na(EE) & Type < 2, Group]) > 0){ + warning(paste(Rpath.params$model[is.na(Biomass) & is.na(EE) & Type < 2, Group], + 'are missing both Biomass and EE...must enter one \n', sep = ' ')) + w <- w + 1 + } + if(length(Rpath.params$model[!is.na(Biomass) & !is.na(EE) & Type < 2, Group]) > 0){ + warning(paste(Rpath.params$model[!is.na(Biomass) & !is.na(EE) & Type < 2, Group], + 'have both Biomass and EE...Note that Rpath does not calculate BA + please enter a value for BA if appropriate \n', sep = ' ')) + w <- w + 1 + } + + #Check that Biomass / PB / QB / EE / ProdCons is not entered for types 3 + if(length(Rpath.params$model[Type == 3 & !is.na(Biomass), Group]) > 0){ + warning(paste(Rpath.params$model[Type == 3 & !is.na(Biomass), Group], + 'is a fleet and should not have a biomass...set to NA \n', + sep = ' ')) + w <- w + 1 + } + if(length(Rpath.params$model[Type == 3 & !is.na(PB), Group]) > 0){ + warning(paste(Rpath.params$model[Type == 3 & !is.na(PB), Group], + 'is a fleet and should not have a PB...set to NA \n', sep = ' ')) + w <- w + 1 + } + if(length(Rpath.params$model[Type > 1 & !is.na(QB), Group]) > 0){ + warning(paste(Rpath.params$model[Type > 1 & !is.na(QB), Group], + 'are not living and should not have a QB...set to NA \n', sep = ' ')) + w <- w + 1 + } + if(length(Rpath.params$model[Type > 1 & !is.na(EE), Group]) > 0){ + warning(paste(Rpath.params$model[Type > 1 & !is.na(EE), Group], + 'are not living and should not have a EE...set to NA \n', sep = ' ')) + w <- w + 1 + } + if(length(Rpath.params$model[Type > 1 & !is.na(ProdCons), Group]) > 0){ + warning(paste(Rpath.params$model[Type > 1 & !is.na(ProdCons), Group], + 'are not living and should not have a ProdCons...set to NA \n', + sep = ' ')) + w <- w + 1 + } + + #Check that types 0 and 1 have a PB unless QB and ProdCons are entered + if(length(Rpath.params$model[Type < 2 & is.na(PB), Group]) > 0){ + no.pb <- Rpath.params$model[Type < 2 & is.na(PB), Group] + if(length(Rpath.params$model[Group %in% no.pb & (is.na(QB) | is.na(ProdCons)), Group]) > 0){ + warning(paste(Rpath.params$model[Group %in% no.pb & (is.na(QB) | is.na(ProdCons)), Group], + 'are missing a PB without a QB and PQ...set to >= 0 \n', sep = ' ')) + w <- w + 1 + } + } + + #Check that consumers have a QB or ProdCons but not both unless missing PB + if(length(Rpath.params$model[is.na(QB) & is.na(ProdCons) & Type < 1, Group]) > 0){ + warning(paste(Rpath.params$model[is.na(QB) & is.na(ProdCons) & Type < 1, Group], + 'are missing both QB and ProdCons...must enter one \n', sep = ' ')) + w <- w + 1 + } + if(length(Rpath.params$model[!is.na(QB) & !is.na(ProdCons) & Type < 1, Group]) > 0){ + both <- Rpath.params$model[!is.na(QB) & !is.na(ProdCons) & Type < 1, Group] + if(length(Rpath.params$model[Group %in% both & !is.na(PB), Group]) > 0){ + warning(paste(Rpath.params$model[Group %in% both & !is.na(PB), Group], + 'have PB, QB, and ProdCons...only two should be entered \n', + sep = ' ')) + w <- w + 1 + } + } + + #Check that BioAcc / Unassim is NA for fleets and numeric for types < 3 + if(length(Rpath.params$model[Type == 3 & !is.na(BioAcc), Group]) > 0){ + warning(paste(Rpath.params$model[Type == 3 & !is.na(BioAcc), Group], + 'are fleets and should not have a BioAcc...set to NA \n', sep = ' ')) + w <- w + 1 + } + if(length(Rpath.params$model[Type == 3 & !is.na(Unassim), Group]) > 0){ + warning(paste(Rpath.params$model[Type == 3 & !is.na(Unassim), Group], + 'are fleets and should not have an Unassim...set to NA \n', sep = ' ')) + w <- w + 1 + } + if(length(Rpath.params$model[Type != 3 & is.na(BioAcc), Group]) > 0){ + warning(paste(Rpath.params$model[Type != 3 & is.na(BioAcc), Group], + 'must have a number for BioAcc...set to >= 0 \n', sep = ' ')) + w <- w + 1 + } + if(length(Rpath.params$model[Type != 3 & is.na(Unassim), Group]) > 0){ + warning(paste(Rpath.params$model[Type != 3 & is.na(Unassim), Group], + 'must have a number for Unassim...set to >= 0 \n', sep = ' ')) + w <- w + 1 + } + + #Check that only Type 2 has DetInput set + if(length(Rpath.params$model[Type != 2 & !is.na(DetInput), Group]) > 0){ + warning(paste(Rpath.params$model[Type != 2 & !is.na(DetInput), Group], + 'are not detritus...set DetInput to NA \n', sep = ' ')) + w <- w + 1 + } + if(length(Rpath.params$model[Type == 2 & is.na(DetInput), Group]) >0){ + warning(paste(Rpath.params$model[Type == 2 & is.na(DetInput), Group], + 'are detritus...set DetInput to 0 \n', sep = ' ')) + w <- w + 1 + } + + #Check detritus fate is numeric and sum to 1 + det.matrix <- Rpath.params$model[, 11:(10 + n.dead), with = F] + test.rows <- rowSums(det.matrix) + if(length(setdiff(which(Rpath.params$model[, Type] == 2), which(test.rows != 1))) > 0){ + warning(paste(Rpath.params$model[, Group][setdiff(which(Rpath.params$model[, Type] == 2), + which(test.rows != 1))], + 'detrital fate does not sum to 1 \n', sep = ' ')) + w <- w + 1 + } + if(length(which(is.na(det.matrix))) > 0){ + na.group <- which(is.na(det.matrix)) + for(i in 1:length(na.group)) while(na.group[i] > n.groups) na.group[i] <- + na.group[i] - n.groups + na.group <- unique(na.group) + warning(paste(Rpath.params$model[na.group, Group], + 'one or more detrital fates are NA...set to >= 0 \n', sep = ' ')) + w <- w + 1 + } + + #Check that landings and discards are numbers for type < 3 + fleet.matrix <- Rpath.params$model[1:(n.groups - n.fleet), (11 + n.dead):ncol(Rpath.params$model), + with = F] + if(length(which(is.na(fleet.matrix))) > 0){ + na.group <- which(is.na(fleet.matrix)) + for(i in 1:length(na.group)) while(na.group[i] > n.groups) na.group[i] <- + na.group[i] - n.groups + na.group <- unique(na.group) + warning(paste(Rpath.params$model[na.group, Group], + 'one or more catches are NA...set to >= 0 \n', sep = ' ')) + w <- w + 1 + } + + #Check that fleets aren't catching other fleets + fleet.matrix.2 <- Rpath.params$model[(n.groups - n.fleet + 1):n.groups, (11 + n.dead): + ncol(Rpath.params$model), with = F] + if(length(which(!is.na(fleet.matrix.2))) > 0){ + not.na.group <- which(!is.na(fleet.matrix.2)) + for(i in 1:length(not.na.group)){ + while(not.na.group[i] > n.fleet){ + not.na.group[i] <- not.na.group[i] - n.fleet + not.na.group <- unique(not.na.group) + } + } + warning(paste(Rpath.params$model[not.na.group + (n.groups - n.fleet), Group], + 'are catching another fleet...set to NA \n', sep = ' ')) + w <- w + 1 + } + + #Diet + #Check that columns sum to 1 + col.names <- names(Rpath.params$diet)[2:ncol(Rpath.params$diet)] + col.sums <- Rpath.params$diet[, lapply(.SD, sum, na.rm = T), .SDcols = col.names] + + #Check types (>0 & <=1 are primary producers) + types <- Rpath.params$model[Type < 2, Type] + dctype <- round(col.sums + types, 3) + if(length(which(dctype != 1)) > 0){ + for(i in 1:length(which(dctype != 1))){ + warning(paste(col.names[which(dctype != 1)][i], 'sum,', + col.sums[, which(dctype !=1)[i], with = F], + 'is not 1...check DC or proportion of primary production')) + w <- w + 1 + } + } + + #Check number of columns + dietcol <- ncol(Rpath.params$diet) + if(dietcol != (n.living + 1)){ + warning(paste(dietcol, ' is the incorrect number of columns in diet matrix.', + 'There should be', n.living + 1)) + w <- w + 1 + } + + #Check that final row of diet is "Import" + if(!Rpath.params$diet[nrow(Rpath.params$diet), 1] == 'Import' & + !Rpath.params$diet[nrow(Rpath.params$diet), 1] == 'import'){ + + warning('Diet matrix is missing the import row. Please add "Import" as the + final row. All entries can be 0 or NA.') + w <- w + 1 + } + +if(w == 0){ + cat('Rpath parameter file is functional. \n') +} else { + cat('Rpath parameter file needs attention! \n') + } +} + +#'Read Rpath parameters from .csv files +#' +#'Creates an Rpath.param object from a series of .csv files. +#' +#'@family Rpath functions +#' +#'@param modfile file location of the flat file containing the model parameters. +#'@param dietfile file location of the flat file containing the diet parameters. +#'@param stanzagroupfile file location of the flat file containing the group parameters +#' for multistanza groups. If not specified a blank stanza list will be created. +#'@param stanzafile file location of the flat file containing the individual stanza +#' parameters for multistanza groups. If not specified a blank stanza list will +#' be created. +#'@param pedfile file location of the flat file containg the pedgigree parameters. +#'@return Outputs an Rpath.param object that can be used for Rpath and subsequently +#' Rsim. (NOTE: This does function does not ensure data is correct or in the +#' correct locations...run check.rpath.param to ensure the appropriate columns are +#' present). +#'@export +read.rpath.params <- function(modfile, dietfile, pedfile = NA, + stanzagroupfile = NA, stanzafile = NA){ + #Need to define variables to eliminate check() note about no visible binding + Type <- Group <- V1 <- NULL + + Rpath.params <- list() + Rpath.params$model <- as.data.table(read.csv(modfile, header = T)) + Rpath.params$diet <- as.data.table(read.csv(dietfile, header = T)) + + if(!is.na(stanzagroupfile)){ + stanzagroup <- as.data.table(read.csv(stanzagroupfile, header = T)) + Rpath.params$stanzas$NStanzaGroups <- nrow(stanzagroup) + Rpath.params$stanzas$stgroups <- stanzagroup + Rpath.params$stanzas$stindiv <- as.data.table(read.csv(stanzafile, + header = T)) + } else { + Rpath.params$stanzas$NStanzaGroups <- 0 + Rpath.params$stanzas$stgroups <- data.table(StGroupNum = NA, + StanzaGroup = NA, + nstanzas = NA, + VBGF_Ksp = NA, + VBGF_d = NA, + Wmat = NA, + RecPower = NA, + Wmat001 = NA, + Wmat50 = NA, + Amat001 = NA, + Amat50 = NA) + Rpath.params$stanzas$stindiv <- data.table(StGroupNum = NA, + StanzaNum = NA, + GroupNum = NA, + Group = NA, + First = NA, + Last = NA, + Z = NA, + Leading = NA) + } + if(!is.na(pedfile)){ + Rpath.params$pedigree <- as.data.table(read.csv(pedfile, header = T)) + } else { + Rpath.params$pedigree <- data.table(Group = Rpath.params$model$Group, + B = 1, + PB = 1, + QB = 1, + Diet = 1) + fleets <- as.character(Rpath.params$model[Type == 3, Group]) + for(i in 1:length(fleets)){ + Rpath.params$pedigree[, V1 := 1] + setnames(Rpath.params$pedigree, 'V1', fleets[i]) + } + } + class(Rpath.params) <- 'Rpath.params' + return(Rpath.params) +} + +#'Write Rpath parameters to .csv files +#' +#'Creates a series of .csv files from an Rpath.params object. +#' +#'@family Rpath functions +#' +#'@param Rpath.params R object containing the Rpath parameters. Most likely this +#' was created using create.rpath.params or read.rpath.params. +#'@param eco.name ecosystem name that will be included in all the file names. +#'@param path location for the output files. +#'@return Outputs a series of .csv files named by the provided eco.name and the +#' parameters they represent. For example the model parameters will be named +#' "eco.name_model.csv". +#'@export +write.rpath.params <- function(Rpath.params, eco.name, path = ''){ + + write.csv(Rpath.params$model, + file = file.path(path, paste(eco.name, '_model.csv', sep = '')), + row.names = F) + + write.csv(Rpath.params$diet, + file = file.path(path, paste(eco.name, '_diet.csv', sep = '')), + row.names = F) + + write.csv(Rpath.params$pedigree, + file = file.path(path, paste(eco.name, '_pedigree.csv', sep = '')), + row.names = F) + + #Multistanza parameters are in several different files + write.csv(Rpath.params$stanzas$stgroups, + file = file.path(path, paste(eco.name, '_stanza_groups.csv', sep = '')), + row.names = F) + + write.csv(Rpath.params$stanzas$stindiv, + file = file.path(path, paste(eco.name, '_stanzas.csv', sep = '')), + row.names = F) + + if(Rpath.params$stanzas$NStanzaGroups > 0){ + for(isp in 1:Rpath.params$stanzas$NStanzaGroups){ + write.csv(Rpath.params$stanzas$StGroup[[isp]], + file = file.path(path, paste(eco.name, '_', + Rpath.params$stanzas$stgroups$StanzaGroup[isp], + '.csv', sep = '')), row.names = F) + } + } +}