reomved rd files for functions no longer exported

R/calc_DK.R

@@ -1,11 +1,9 @@
 #' Calculate discard to kept ratio
 #'
 #' Use observer data to calculate the ratio of discards to kept by species.
-#' 
 #'
-# @inheritParams strat_prep
-#' @param na.keep Boolean. Logical value to indicate whether original strata names
-#'  should be retained.
+#' @inheritParams get_comland_data
+#' @param comData data frame. calculated from inside \code{get_comdisc_data}
 #'
 #' @return Returns a \code{comdiscData} data.table with one additional column labeled
 #'  with the value of \code{areaDescription}
@@ -15,49 +13,50 @@
 #'
 #' @importFrom magrittr "%>%"
 #'
-#'@family comdisc
+#' @family comdisc
 #'
-#' @export
+#' Internal function
+#' @noRd
+
 
 
 calc_DK <- function(comData, areaDescription, fleetDescription){
-  
+
   comdata <- data.table::copy(comData[[1]])
-  
+
   #Standardize column names
-  comdata <- data.table::setnames(comdata, c(areaDescription, fleetDescription), 
+  comdata <- data.table::setnames(comdata, c(areaDescription, fleetDescription),
                                       c('area', 'fleet'))
-  
+
   #sum catch by species/disposition/area/fleet
   ob.sums <- comdata[, sum(SPPLIVMT), by = c('YEAR', 'area', 'fleet', 'NESPP3',
                                                  'CATDISP')]
   #identify discards
   ob.discard <- ob.sums[CATDISP == 0, ]
-  
+
   setnames(ob.discard, "V1", "DISCARD")
   ob.discard[, CATDISP := NULL]
-  
+
   #Sum kept by area/fleet
   ob.kept <- ob.sums[CATDISP == 1, sum(V1), by = c('YEAR', 'area', 'fleet')]
-  
+
   setnames(ob.kept, "V1", "KEPT.ALL")
-  
+
   #Merge discards and kept
   dk <- merge(ob.kept, ob.discard, by = c('YEAR', 'area', 'fleet'))
-  
+
   #Calculate ratio
   dk[, DK := DISCARD / KEPT.ALL]
   #NAs result if divide by 0 so set DK to 1 (all discards)
   dk[is.na(DK), DK := 1.0]
-  
+
   #Remove extra columns
   dk[, c('KEPT.ALL', 'DISCARD') := NULL]
-  
+
   #Replace standard column names
   #Standardize column names
-  data.table::setnames(dk, c('area', 'fleet'), 
+  data.table::setnames(dk, c('area', 'fleet'),
                        c(areaDescription, fleetDescription))
-  
+
   return(dk[])
 }
-

R/calc_discards.R

@@ -1,34 +1,23 @@
-#' Calculate stratified mean
+#' Calculates total discard by species
 #'
-#' Calculates the stratified mean. Details of method found here ...
+#' Applies discard ratio to landings to obtain total discards by species
 #'
-#' @inheritParams strat_prep
-#' @inheritParams strat_mean
-#' @param tidy Boolean. Return output in long format (Default = F).
-#' @param returnPrepData Boolean. Return both \code{stratmeanData} and \code{prepData}
-#'   as a list object. The default (F) returns only the \code{stratmeanData} as a
-#'   \code{data.table}.
+#' @inheritParams get_comland_data
+#' @param comland Data frame. Internally calculated by \code{get_comdisc_data}
+#' @param dk dk. Need to find out
 #'
-#' @return
 #'
-#'@family survdat
+#' @return dk
+#'
+#'@family comdisc
 #'
 #' @examples
 #' \dontrun{
-#' # Pull data and apply conversion corrections
-#' data <- get_survdat_data(channel)
-#' # Calculate stratified mean for specific survey strata for the SPRING season
-#' calc_stratified_mean(surveyData=data$survdat, filterByArea=c(1220, 1240, 1260:1290,1360:1400),filterBySeason = "SPRING")
-#'
-#' # Calculate stratified mean for area defined by EPU regions, for all seasons ("SPRING", "FALL")
-#' # Read in EPU shapefile (loaded as part of the package)
-#' area <- sf::st_read(dsn = system.file("extdata","EPU.shp",package="survdat"),quiet=T)
-#' calc_stratified_mean(surveyData=data$survdat, areaPolygon=area, areaDescription="EPU", filterByArea="all",filterBySeason = "all")
-#'
 #' }
 #'
 #'
-#' @export
+#' Internal function
+#' @noRd
 
 
 calc_discards <- function(comland, dk, areaDescription, fleetDescription) {

R/soeAreas.R

@@ -0,0 +1,15 @@
+#' soeAreas:  Area Species,EPU designations
+#'
+#' Option to pass to \code{get_comland_data} if the user wishes define EPUs exclusively
+#'  by Stat areas and not to proportion the landings in these Statistical areas to EPUs
+#'
+#' @format A Data frame
+#' \describe{
+#'     \item{AREA}{Statistical Area}
+#'     \item{NESPP3}{Gulf of Maine EPU}
+#'     \item{MeanProp}{Proportion of Statistical area to attribute to EPU}
+#'     \item{EPU}{Ecological Production Unit}
+#'}
+#'
+#'
+"soeAreas"