diff --git a/R/param.R b/R/param.R
index f746e54..41e33fe 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)
+    }
+  }
+}