diff --git a/R/diag_fleet_catch.R b/R/diag_fleet_catch.R index 77819d0..b0cb3d4 100644 --- a/R/diag_fleet_catch.R +++ b/R/diag_fleet_catch.R @@ -5,7 +5,7 @@ #' #' #'@param fgs A character string. Path to location of functional groups file. -#'@param fishery.file A character string. Path to the fishery definitions file. +#'@param fishery.prm A character string. Path to the fishery definitions file. #'@param bgm A character string. Path to the bgm file. #'@param catch.ref A data.frame containing reference catch by fleet data (species|fleet|polygon|ref.value) #'@param speciesCodes Character vector. A vector of Atlantis species codes in which to test for stability. @@ -33,7 +33,7 @@ #'@importFrom magrittr %>% diag_fleet_catch <- function(fgs, - fishery.file, + fishery.prm, catch.file, bgm, catch.ref, @@ -45,14 +45,14 @@ diag_fleet_catch <- function(fgs, boxes = atlantistools::convert_bgm(bgm)%>% dplyr::distinct(polygon,inside_lat,inside_long) - catch.fleet =atlantisprocessing::process_catch_fleet(fishery.prm = fishery.file, + catch.fleet =atlantisprocessing::process_catch_fleet(fishery.prm = fishery.prm, catch = catch.file, - groups.file = fgs.file) + groups.file = fgs) if(!is.null(speciesCodes)){ - fgs.df = read.csv(fgs.file,as.is =T) + fgs.df = read.csv(fgs,as.is =T) - spp.match = fgs$LongName[which(fgs$Code %in% speciesCodes)] + spp.match = fgs.df$LongName[which(fgs.df$Code %in% speciesCodes)] catch.fleet = catch.fleet %>% dplyr::filter(species %in% spp.match) diff --git a/man/diag_fleet_catch.Rd b/man/diag_fleet_catch.Rd index 8fb8823..cc6e0fe 100644 --- a/man/diag_fleet_catch.Rd +++ b/man/diag_fleet_catch.Rd @@ -6,7 +6,7 @@ \usage{ diag_fleet_catch( fgs, - fishery.file, + fishery.prm, catch.file, bgm, catch.ref, @@ -19,7 +19,7 @@ diag_fleet_catch( \arguments{ \item{fgs}{A character string. Path to location of functional groups file.} -\item{fishery.file}{A character string. Path to the fishery definitions file.} +\item{fishery.prm}{A character string. Path to the fishery definitions file.} \item{bgm}{A character string. Path to the bgm file.}