R/cleanPacFIN.R
In nwfsc-assess/PacFIN.Utilities: Generate fishery composition data from PacFIN data for the NWFSC
Defines functions
cleanPacFIN
Documented in
cleanPacFIN
######################################################################
#
#' Filter PacFIN samples.
#'
#' @description
#' \code{cleanPacFIN} filters out unsuitable samples from data, and converts
#' fish lengths to cm. The original fields in the returned data are left untouched,
#' with the exception of SEX, which is modified so that unidentified fish are labeled
#' "U".
#'
#' \subsection{\code{\link{Workflow}}}{
#' If there are CalCOM samples to be integrated with PacFIN data, run \code{combineCalCOM}
#' first, otherwise run to \code{cleanPacFIN} as the first function in the workflow.
#' }
#'
#' @export
#'
#' @param Pdata a PacFIN dataset
#' @param only_USINPFC a logical value. FALSE by default.
#' @param keep_INPFC a set of INPFC areas. NULL by default.
#' @param remove_INPFC a set of INPFC areas. NULL by default.
#' @param badRecords a set of sample identifiers. NULL by default.
#' @param keep_gears A vector of character values specifying which gear types you want
#' to label as unique fleets. Order the vector the same way you want the fleets numbered.
#' @param keep_sample_type a set of sample types to retain. Default = c("", "M")
#' @param keep_sample_method a set of sample methods to retain. Default = "R"
#' @param keep_length_type a set of length types to retain.
#' There is no default value. Typically, users will want to retain
#' \code{c("", "F", "A")} at a minimum, but should also think about adding NA,
#' i.e., \code{c("", "F", "A", NA)}.
#' @param keep_missing_lengths a logical value. FALSE by default.
#' @param keep_CA default TRUE. CA data often have no sample type or method, or INPFC area.
#' @param CLEAN a logical value. Default is TRUE. If FALSE, return the original data unchanged,
#' but report what would have been removed. Additional columns of information
#' are added to the original data even if \code{CLEAN = FALSE}.
#' @template spp
#' @template verbose
#'
#' @return The input data filtered for desired areas and record types
#' specified, with added columns
#'
#' \tabular{ll}{
#' fishyr \tab initialized from SAMPLE_YEAR\cr
#' fleet \tab initialized to 1\cr
#' fishery \tab initialized to 1\cr
#' season \tab initialized to 1. Change using \code{\link{getSeason}}\cr
#' state \tab initialized from SOURCE_AGID. Change using \code{\link{getState}}\cr
#' lengthcm \tab floored cm from FORK_LENGTH when available, otherwise FISH_LENGTH\cr
#' geargroup \tab the gear group associated with each GRID, from http://pacfin.psmfs.org/pacfin_pub/data_rpts_pub/code_lists/gr.txt
#' }
#'
#'
#' @details
#'
#' \subsection{\strong{INPFC Area specification}}{
#'
#' The US INPFC areas are
#' c("VUS","CL","VN","COL","NC","SC","EU","CALCOM","CP","EK","MT","PS ")
#'
#' "CalCOM" is included because the combineCalCOM function
#' sets it, since CalCOM doesn't seem to record INPFC areas.
#'
#'
#' If \code{only_USINPFC} is TRUE, then only samples from the US INPFC areas will be retained.
#'
#' If a set of INPFC areas are specified in \code{keep_INPFC}, then only samples from
#' those areas will be retained.
#'
#' If \code{remove_INPFC} specifies a set of INPFC areas, samples from those areas
#' will be discarded.
#' }
#'
#' \subsection{\strong{Sample types and methods}}{
#'
#' SAMPLE_TYPEs may be (M=Market, R=Research, S=Special request, C=Commercial on-board).
#' Only samples of type M are generally used.
#'
#' SAMPLE_METHODs may be (R=Random, S=Stratified, N=Systematic, P=Purposive, X=Special).
#' Only samples collected in random sampling are generally used.
#' }
#'
#' \subsection{\strong{Furthermore}}{
#'
#' The values created as new columns are for use by other functions in this package.
#' In particular, \code{fishyr} and \code{season} are useful if there are multiple
#' seasons (e.g., winter and summer, as in the petrale sole assessment), and the
#' year is adjusted so that "winter" occurs in one year, rather than across two.
#'
#' The \code{fleet}, \code{fishery}, and \code{state} columns are meant for use in
#' stratifying the data according to the particulars of an assessment.
#'
#' The \code{sink} command can be used to save the filtering report to a
#' file, in addition to printing it to the console.
#' }
#'
#' @seealso \code{\link{cleanAges}}, \code{\link{getState}}, \code{\link{getSeason}},
#' \code{\link{sink}}
#'
#' @author Andi Stephens
#
##############################################################################
cleanPacFIN = function( Pdata,
only_USINPFC = FALSE,
keep_INPFC = NULL,
remove_INPFC = NULL,
badRecords = NULL,
keep_gears = unique(Pdata$GRID)[order(unique(Pdata$GRID))],
keep_sample_type = c("", "M"),
keep_sample_method = "R",
keep_length_type,
keep_missing_lengths = FALSE,
keep_CA = TRUE,
CLEAN = TRUE,
spp = NULL,
verbose = TRUE) {
if (verbose) {
cat( "\nCleaning data\n\n" )
if (!CLEAN) {
cat("\nGenerating data report only. No data will be removed.\n")
}
}
# Define fishyr, fleet, fishery and season -- some assessments manipulate these.
if (verbose) {
cat("These values have been initialized for use when comps are generated.\n")
cat("Use Stratify and getSeason to reset them to appropriate values.\n\n")
}
# KFJ: only create columns if they do not exist or if they are not numeric
for ( i in c("fishery","season") ) {
if (!i %in% colnames(Pdata)) {
tmpcol = ncol(Pdata) + 1
tmp = rep(1, nrow(Pdata))
Pdata = cbind(Pdata, tmp)
names(Pdata)[tmpcol] = i
if (verbose) {cat("Pdata$",i," = 1\n")}
} # End if
} # End for
Pdata = getState(Pdata, CLEAN = CLEAN)
if (verbose) { cat("Pdata$state is initialized to Pdata$SOURCE_AGID\n") }
Pdata$fishyr = Pdata$SAMPLE_YEAR
if (verbose) { cat("Pdata$fishyr is initialized to Pdata$SAMPLE_YEAR\n") }
Pdata = getGearGroup(Pdata, spp = spp)
if (!"fleet" %in% colnames(Pdata)) Pdata[, "fleet"] <- match(Pdata$geargroup, keep_gears)
if (keep_CA) {
Pdata[Pdata$state == "CA" & is.na(Pdata$SAMPLE_TYPE), "SAMPLE_TYPE"] <- "M"
Pdata[Pdata$state == "CA" & is.na(Pdata$SAMPLE_METHOD), "SAMPLE_METHOD"] <- "R"
Pdata[Pdata$state == "CA" & is.na(Pdata$INPFC_AREA), "INPFC_AREA"] <- "CalCOM"
if (!is.null(keep_INPFC) & any(Pdata$INPFC_AREA == "CalCOM")) {
keep_INPFC <- c(keep_INPFC, "CalCOM")
if (verbose) { message("CalCOM was added to 'keep_INPFC' because 'keep_CA' is TRUE.") }
}
} # End keep_CA
# Define legal areas. "CalCOM" is included because the combineCalCOM function
# sets it -- CalCOM doesn't seem to record INPFC areas.
USinpfc = c("VUS","CL","VN","COL","NC","SC","EU","CalCOM","CP","EK","MT","PS ")
# Fix Lengths. Use FISH_LENGTH if there is no FORK_LENGTH.
width2length <- convertlength_skate(Pdata, returntype = "estimated")
Pdata$length <- ifelse(Pdata$FISH_LENGTH_TYPE %in% c("", "A", "F", NA),
Pdata$FORK_LENGTH, NA)
if (all(Pdata$SPID %in% c("LSKT", "BSKT"))) {
Pdata$length <- ifelse(
# type "A" is associated with disc width for skates
"A" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "A",
width2length,
Pdata$length)
}
Pdata$length <- ifelse(
"D" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "D" &
Pdata$FORK_LENGTH != Pdata$FISH_LENGTH,
Pdata$FORK_LENGTH, Pdata$length)
Pdata$length <- ifelse(
# type "R" is associated with inter-spiracle width for skates (used by WDFW)
"R" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "R",
width2length,
Pdata$length)
Pdata$length <- ifelse(
"S" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "S",
Pdata$FISH_LENGTH,
Pdata$length)
Pdata$length <- ifelse(
"T" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "T",
Pdata$FISH_LENGTH,
Pdata$length)
Pdata$length <- ifelse(
"U" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "U",
ifelse(is.na(Pdata$FORK_LENGTH), Pdata$FISH_LENGTH, Pdata$FORK_LENGTH),
Pdata$length)
Pdata$length <- ifelse(
"" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "",
Pdata$FISH_LENGTH,
Pdata$length)
Pdata$length <- ifelse(
NA %in% keep_length_type & is.na(Pdata$FISH_LENGTH_TYPE),
ifelse(is.na(Pdata$FORK_LENGTH), Pdata$FISH_LENGTH, Pdata$FORK_LENGTH),
Pdata$length)
Pdata$length <- ifelse(Pdata$FISH_LENGTH_TYPE %in% keep_length_type,
Pdata$length, NA)
Pdata$length[Pdata$length == 0] <- NA
goodtypes <- c("", "A", "D", "F", "R", "S", "T", "U", NA)
if (any(!Pdata$FISH_LENGTH_TYPE %in% goodtypes)) {
stop("cleanPacFIN only knows how to accommodate the following FISH_LENGTH_TYPEs:\n",
paste(sprintf("'%s'", goodtypes), collapse = ", "), ".",
"\nPlease contact the package maintainer to add additional types.")
}
# Remove bad OR samples
if (verbose) {
message(
"Changing length and age to NA and -1 for ",
sum(Pdata$SAMPLE_NO %in% paste0("OR", badORnums)),
" special samples from OR."
)
}
Pdata$length[Pdata$SAMPLE_NO %in% paste0("OR", badORnums)] <- NA
Pdata[is.na(Pdata[, "EXP_WT"]) & Pdata[, "state"] == "OR", "length"] <- NA
Pdata[is.na(Pdata[, "SPECIES_WGT"]) & Pdata[, "state"] == "CA", "length"] <- NA
# Convert mm to cm
Pdata$lengthcm = floor(Pdata$length / 10)
# We don't want no stinkin' NAs!
Pdata$SEX[is.na(Pdata$SEX)] = "U"
Pdata$SEX[Pdata$SEX == 0 ] = "U"
# Fix Ages (originally in cleanAges)
# MH is checking with JW to see if there is a AGE_METHOD per age reader
if (!"FISH_AGE_YEARS_FINAL" %in% colnames(Pdata)) {
Pdata$FISH_AGE_YEARS_FINAL <- NA
}
if (!"age1" %in% colnames(Pdata)) Pdata$age1 <- NA
if (!"age2" %in% colnames(Pdata)) Pdata$age2 <- NA
if (!"age3" %in% colnames(Pdata)) Pdata$age3 <- NA
Pdata$age <- ifelse(!is.na(Pdata$FISH_AGE_YEARS_FINAL),
Pdata$FISH_AGE_YEARS_FINAL, Pdata$age1)
Pdata$age <- ifelse(!is.na(Pdata$age), Pdata$age, Pdata$age2)
Pdata$age <- ifelse(!is.na(Pdata$age), Pdata$age, Pdata$age3)
# Remove bad OR samples
Pdata$age[Pdata$SAMPLE_NO %in% paste0("OR", badORnums)] <- NA
Pdata$age[is.na(Pdata$age)] <- -1
Pdata[is.na(Pdata[, "EXP_WT"]) & Pdata[, "state"] == "OR", "age"] <- -1
Pdata[is.na(Pdata[, "SPECIES_WGT"]) & Pdata[, "state"] == "CA", "age"] <- -1
# Flag records without a SAMPLE_NO
Pdata$sample = Pdata$SAMPLE_NO
# KFJ: use more values than just NA, also only do if TRUE
# Andi: thanks!
flags <- c("NA", "Nan", "")
if (any(Pdata$sample %in% flags)) {
Pdata$sample[Pdata$sample %in% flags] <- "-1"
} # End if
Pdata$MALES_WGT[is.na(Pdata$MALES_NUM) & Pdata$MALES_WGT == 0] <- NA
Pdata$FEMALES_WGT[is.na(Pdata$FEMALES_NUM) & Pdata$FEMALES_WGT == 0] <- NA
Pdata$UNK_WT[is.na(Pdata$UNK_NUM) & Pdata$UNK_WT == 0] <- NA
# Remove records
Rec_summary = rep(0,9)
Rec_summary[1] = nrow(Pdata)
Rec_summary[8] = ifelse(only_USINPFC,
sum(!Pdata$INPFC_AREA %in% USinpfc), 0)
if (only_USINPFC == TRUE & CLEAN) { Pdata = Pdata[Pdata$INPFC_AREA %in% USinpfc,] }
Rec_summary[2] = ifelse(!is.null(keep_INPFC),
sum(!Pdata$INPFC_AREA %in% keep_INPFC), 0)
Rec_summary[9] = ifelse(!is.null(remove_INPFC),
sum(Pdata$INPFC_AREA %in% remove_INPFC), 0)
if (!is.null(keep_INPFC) & CLEAN) { Pdata = Pdata[Pdata$INPFC_AREA %in% keep_INPFC,] }
if (!is.null(remove_INPFC) & CLEAN) { Pdata = Pdata[!Pdata$INPFC_AREA %in% remove_INPFC,] }
Rec_summary[3] = sum(Pdata$sample %in% badRecords)
if (CLEAN) Pdata = Pdata[!Pdata$sample %in% badRecords,]
Rec_summary[4] = sum(!Pdata$SAMPLE_TYPE %in% keep_sample_type)
if (!is.null(keep_sample_type) & CLEAN) { Pdata = Pdata[Pdata$SAMPLE_TYPE %in% keep_sample_type,] }
Rec_summary[5] = sum(!Pdata$SAMPLE_METHOD %in% keep_sample_method)
if (!is.null(keep_sample_method) & CLEAN) { Pdata = Pdata[Pdata$SAMPLE_METHOD %in% keep_sample_method,] }
Rec_summary[6] = sum(Pdata$SAMPLE_NO == -1)
if (CLEAN) Pdata = Pdata[Pdata$SAMPLE_NO != -1,]
Rec_summary[7] = sum(is.na(Pdata$length))
if (!keep_missing_lengths & CLEAN) { Pdata = Pdata[!is.na(Pdata$length),] }
# Report removals
if (verbose) {
cat("\nRemoval Report\n\n")
cat("Records in input: ", Rec_summary[1], "\n")
cat("Records not in USINPFC ", Rec_summary[8], "\n")
cat("Records not in INPFC_AREA: ", Rec_summary[2], "\n")
cat("Records in bad INPFC_AREA: ", Rec_summary[9], "\n")
cat("Records in badRecords list: ", Rec_summary[3], "\n")
cat("Records with bad SAMPLE_TYPE ", Rec_summary[4], "\n")
cat("Records with bad SAMPLE_METHOD ", Rec_summary[5], "\n")
cat("Records with no SAMPLE_NO ", Rec_summary[6], "\n")
cat("Records with no usable length ", Rec_summary[7], "\n")
cat("Records remaining: ", nrow(Pdata), "\n\n")
if (!CLEAN) {
cat("\n\nReturning original data because CLEAN=FALSE\n\n")
}
}
return(Pdata)
} # End cleanPacFIN
nwfsc-assess/PacFIN.Utilities documentation built on Jan. 3, 2020, 10:28 p.m.
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Defines functions cleanPacFIN
Documented in cleanPacFIN
######################################################################
#
#' Filter PacFIN samples.
#'
#' @description
#' \code{cleanPacFIN} filters out unsuitable samples from data, and converts
#' fish lengths to cm. The original fields in the returned data are left untouched,
#' with the exception of SEX, which is modified so that unidentified fish are labeled
#' "U".
#'
#' \subsection{\code{\link{Workflow}}}{
#' If there are CalCOM samples to be integrated with PacFIN data, run \code{combineCalCOM}
#' first, otherwise run to \code{cleanPacFIN} as the first function in the workflow.
#' }
#'
#' @export
#'
#' @param Pdata a PacFIN dataset
#' @param only_USINPFC a logical value. FALSE by default.
#' @param keep_INPFC a set of INPFC areas. NULL by default.
#' @param remove_INPFC a set of INPFC areas. NULL by default.
#' @param badRecords a set of sample identifiers. NULL by default.
#' @param keep_gears A vector of character values specifying which gear types you want
#' to label as unique fleets. Order the vector the same way you want the fleets numbered.
#' @param keep_sample_type a set of sample types to retain. Default = c("", "M")
#' @param keep_sample_method a set of sample methods to retain. Default = "R"
#' @param keep_length_type a set of length types to retain.
#' There is no default value. Typically, users will want to retain
#' \code{c("", "F", "A")} at a minimum, but should also think about adding NA,
#' i.e., \code{c("", "F", "A", NA)}.
#' @param keep_missing_lengths a logical value. FALSE by default.
#' @param keep_CA default TRUE. CA data often have no sample type or method, or INPFC area.
#' @param CLEAN a logical value. Default is TRUE. If FALSE, return the original data unchanged,
#' but report what would have been removed. Additional columns of information
#' are added to the original data even if \code{CLEAN = FALSE}.
#' @template spp
#' @template verbose
#'
#' @return The input data filtered for desired areas and record types
#' specified, with added columns
#'
#' \tabular{ll}{
#' fishyr \tab initialized from SAMPLE_YEAR\cr
#' fleet \tab initialized to 1\cr
#' fishery \tab initialized to 1\cr
#' season \tab initialized to 1. Change using \code{\link{getSeason}}\cr
#' state \tab initialized from SOURCE_AGID. Change using \code{\link{getState}}\cr
#' lengthcm \tab floored cm from FORK_LENGTH when available, otherwise FISH_LENGTH\cr
#' geargroup \tab the gear group associated with each GRID, from http://pacfin.psmfs.org/pacfin_pub/data_rpts_pub/code_lists/gr.txt
#' }
#'
#'
#' @details
#'
#' \subsection{\strong{INPFC Area specification}}{
#'
#' The US INPFC areas are
#' c("VUS","CL","VN","COL","NC","SC","EU","CALCOM","CP","EK","MT","PS ")
#'
#' "CalCOM" is included because the combineCalCOM function
#' sets it, since CalCOM doesn't seem to record INPFC areas.
#'
#'
#' If \code{only_USINPFC} is TRUE, then only samples from the US INPFC areas will be retained.
#'
#' If a set of INPFC areas are specified in \code{keep_INPFC}, then only samples from
#' those areas will be retained.
#'
#' If \code{remove_INPFC} specifies a set of INPFC areas, samples from those areas
#' will be discarded.
#' }
#'
#' \subsection{\strong{Sample types and methods}}{
#'
#' SAMPLE_TYPEs may be (M=Market, R=Research, S=Special request, C=Commercial on-board).
#' Only samples of type M are generally used.
#'
#' SAMPLE_METHODs may be (R=Random, S=Stratified, N=Systematic, P=Purposive, X=Special).
#' Only samples collected in random sampling are generally used.
#' }
#'
#' \subsection{\strong{Furthermore}}{
#'
#' The values created as new columns are for use by other functions in this package.
#' In particular, \code{fishyr} and \code{season} are useful if there are multiple
#' seasons (e.g., winter and summer, as in the petrale sole assessment), and the
#' year is adjusted so that "winter" occurs in one year, rather than across two.
#'
#' The \code{fleet}, \code{fishery}, and \code{state} columns are meant for use in
#' stratifying the data according to the particulars of an assessment.
#'
#' The \code{sink} command can be used to save the filtering report to a
#' file, in addition to printing it to the console.
#' }
#'
#' @seealso \code{\link{cleanAges}}, \code{\link{getState}}, \code{\link{getSeason}},
#' \code{\link{sink}}
#'
#' @author Andi Stephens
#
##############################################################################
cleanPacFIN = function( Pdata,
only_USINPFC = FALSE,
keep_INPFC = NULL,
remove_INPFC = NULL,
badRecords = NULL,
keep_gears = unique(Pdata$GRID)[order(unique(Pdata$GRID))],
keep_sample_type = c("", "M"),
keep_sample_method = "R",
keep_length_type,
keep_missing_lengths = FALSE,
keep_CA = TRUE,
CLEAN = TRUE,
spp = NULL,
verbose = TRUE) {
if (verbose) {
cat( "\nCleaning data\n\n" )
if (!CLEAN) {
cat("\nGenerating data report only. No data will be removed.\n")
}
}
# Define fishyr, fleet, fishery and season -- some assessments manipulate these.
if (verbose) {
cat("These values have been initialized for use when comps are generated.\n")
cat("Use Stratify and getSeason to reset them to appropriate values.\n\n")
}
# KFJ: only create columns if they do not exist or if they are not numeric
for ( i in c("fishery","season") ) {
if (!i %in% colnames(Pdata)) {
tmpcol = ncol(Pdata) + 1
tmp = rep(1, nrow(Pdata))
Pdata = cbind(Pdata, tmp)
names(Pdata)[tmpcol] = i
if (verbose) {cat("Pdata$",i," = 1\n")}
} # End if
} # End for
Pdata = getState(Pdata, CLEAN = CLEAN)
if (verbose) { cat("Pdata$state is initialized to Pdata$SOURCE_AGID\n") }
Pdata$fishyr = Pdata$SAMPLE_YEAR
if (verbose) { cat("Pdata$fishyr is initialized to Pdata$SAMPLE_YEAR\n") }
Pdata = getGearGroup(Pdata, spp = spp)
if (!"fleet" %in% colnames(Pdata)) Pdata[, "fleet"] <- match(Pdata$geargroup, keep_gears)
if (keep_CA) {
Pdata[Pdata$state == "CA" & is.na(Pdata$SAMPLE_TYPE), "SAMPLE_TYPE"] <- "M"
Pdata[Pdata$state == "CA" & is.na(Pdata$SAMPLE_METHOD), "SAMPLE_METHOD"] <- "R"
Pdata[Pdata$state == "CA" & is.na(Pdata$INPFC_AREA), "INPFC_AREA"] <- "CalCOM"
if (!is.null(keep_INPFC) & any(Pdata$INPFC_AREA == "CalCOM")) {
keep_INPFC <- c(keep_INPFC, "CalCOM")
if (verbose) { message("CalCOM was added to 'keep_INPFC' because 'keep_CA' is TRUE.") }
}
} # End keep_CA
# Define legal areas. "CalCOM" is included because the combineCalCOM function
# sets it -- CalCOM doesn't seem to record INPFC areas.
USinpfc = c("VUS","CL","VN","COL","NC","SC","EU","CalCOM","CP","EK","MT","PS ")
# Fix Lengths. Use FISH_LENGTH if there is no FORK_LENGTH.
width2length <- convertlength_skate(Pdata, returntype = "estimated")
Pdata$length <- ifelse(Pdata$FISH_LENGTH_TYPE %in% c("", "A", "F", NA),
Pdata$FORK_LENGTH, NA)
if (all(Pdata$SPID %in% c("LSKT", "BSKT"))) {
Pdata$length <- ifelse(
# type "A" is associated with disc width for skates
"A" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "A",
width2length,
Pdata$length)
}
Pdata$length <- ifelse(
"D" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "D" &
Pdata$FORK_LENGTH != Pdata$FISH_LENGTH,
Pdata$FORK_LENGTH, Pdata$length)
Pdata$length <- ifelse(
# type "R" is associated with inter-spiracle width for skates (used by WDFW)
"R" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "R",
width2length,
Pdata$length)
Pdata$length <- ifelse(
"S" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "S",
Pdata$FISH_LENGTH,
Pdata$length)
Pdata$length <- ifelse(
"T" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "T",
Pdata$FISH_LENGTH,
Pdata$length)
Pdata$length <- ifelse(
"U" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "U",
ifelse(is.na(Pdata$FORK_LENGTH), Pdata$FISH_LENGTH, Pdata$FORK_LENGTH),
Pdata$length)
Pdata$length <- ifelse(
"" %in% keep_length_type & Pdata$FISH_LENGTH_TYPE == "",
Pdata$FISH_LENGTH,
Pdata$length)
Pdata$length <- ifelse(
NA %in% keep_length_type & is.na(Pdata$FISH_LENGTH_TYPE),
ifelse(is.na(Pdata$FORK_LENGTH), Pdata$FISH_LENGTH, Pdata$FORK_LENGTH),
Pdata$length)
Pdata$length <- ifelse(Pdata$FISH_LENGTH_TYPE %in% keep_length_type,
Pdata$length, NA)
Pdata$length[Pdata$length == 0] <- NA
goodtypes <- c("", "A", "D", "F", "R", "S", "T", "U", NA)
if (any(!Pdata$FISH_LENGTH_TYPE %in% goodtypes)) {
stop("cleanPacFIN only knows how to accommodate the following FISH_LENGTH_TYPEs:\n",
paste(sprintf("'%s'", goodtypes), collapse = ", "), ".",
"\nPlease contact the package maintainer to add additional types.")
}
# Remove bad OR samples
if (verbose) {
message(
"Changing length and age to NA and -1 for ",
sum(Pdata$SAMPLE_NO %in% paste0("OR", badORnums)),
" special samples from OR."
)
}
Pdata$length[Pdata$SAMPLE_NO %in% paste0("OR", badORnums)] <- NA
Pdata[is.na(Pdata[, "EXP_WT"]) & Pdata[, "state"] == "OR", "length"] <- NA
Pdata[is.na(Pdata[, "SPECIES_WGT"]) & Pdata[, "state"] == "CA", "length"] <- NA
# Convert mm to cm
Pdata$lengthcm = floor(Pdata$length / 10)
# We don't want no stinkin' NAs!
Pdata$SEX[is.na(Pdata$SEX)] = "U"
Pdata$SEX[Pdata$SEX == 0 ] = "U"
# Fix Ages (originally in cleanAges)
# MH is checking with JW to see if there is a AGE_METHOD per age reader
if (!"FISH_AGE_YEARS_FINAL" %in% colnames(Pdata)) {
Pdata$FISH_AGE_YEARS_FINAL <- NA
}
if (!"age1" %in% colnames(Pdata)) Pdata$age1 <- NA
if (!"age2" %in% colnames(Pdata)) Pdata$age2 <- NA
if (!"age3" %in% colnames(Pdata)) Pdata$age3 <- NA
Pdata$age <- ifelse(!is.na(Pdata$FISH_AGE_YEARS_FINAL),
Pdata$FISH_AGE_YEARS_FINAL, Pdata$age1)
Pdata$age <- ifelse(!is.na(Pdata$age), Pdata$age, Pdata$age2)
Pdata$age <- ifelse(!is.na(Pdata$age), Pdata$age, Pdata$age3)
# Remove bad OR samples
Pdata$age[Pdata$SAMPLE_NO %in% paste0("OR", badORnums)] <- NA
Pdata$age[is.na(Pdata$age)] <- -1
Pdata[is.na(Pdata[, "EXP_WT"]) & Pdata[, "state"] == "OR", "age"] <- -1
Pdata[is.na(Pdata[, "SPECIES_WGT"]) & Pdata[, "state"] == "CA", "age"] <- -1
# Flag records without a SAMPLE_NO
Pdata$sample = Pdata$SAMPLE_NO
# KFJ: use more values than just NA, also only do if TRUE
# Andi: thanks!
flags <- c("NA", "Nan", "")
if (any(Pdata$sample %in% flags)) {
Pdata$sample[Pdata$sample %in% flags] <- "-1"
} # End if
Pdata$MALES_WGT[is.na(Pdata$MALES_NUM) & Pdata$MALES_WGT == 0] <- NA
Pdata$FEMALES_WGT[is.na(Pdata$FEMALES_NUM) & Pdata$FEMALES_WGT == 0] <- NA
Pdata$UNK_WT[is.na(Pdata$UNK_NUM) & Pdata$UNK_WT == 0] <- NA
# Remove records
Rec_summary = rep(0,9)
Rec_summary[1] = nrow(Pdata)
Rec_summary[8] = ifelse(only_USINPFC,
sum(!Pdata$INPFC_AREA %in% USinpfc), 0)
if (only_USINPFC == TRUE & CLEAN) { Pdata = Pdata[Pdata$INPFC_AREA %in% USinpfc,] }
Rec_summary[2] = ifelse(!is.null(keep_INPFC),
sum(!Pdata$INPFC_AREA %in% keep_INPFC), 0)
Rec_summary[9] = ifelse(!is.null(remove_INPFC),
sum(Pdata$INPFC_AREA %in% remove_INPFC), 0)
if (!is.null(keep_INPFC) & CLEAN) { Pdata = Pdata[Pdata$INPFC_AREA %in% keep_INPFC,] }
if (!is.null(remove_INPFC) & CLEAN) { Pdata = Pdata[!Pdata$INPFC_AREA %in% remove_INPFC,] }
Rec_summary[3] = sum(Pdata$sample %in% badRecords)
if (CLEAN) Pdata = Pdata[!Pdata$sample %in% badRecords,]
Rec_summary[4] = sum(!Pdata$SAMPLE_TYPE %in% keep_sample_type)
if (!is.null(keep_sample_type) & CLEAN) { Pdata = Pdata[Pdata$SAMPLE_TYPE %in% keep_sample_type,] }
Rec_summary[5] = sum(!Pdata$SAMPLE_METHOD %in% keep_sample_method)
if (!is.null(keep_sample_method) & CLEAN) { Pdata = Pdata[Pdata$SAMPLE_METHOD %in% keep_sample_method,] }
Rec_summary[6] = sum(Pdata$SAMPLE_NO == -1)
if (CLEAN) Pdata = Pdata[Pdata$SAMPLE_NO != -1,]
Rec_summary[7] = sum(is.na(Pdata$length))
if (!keep_missing_lengths & CLEAN) { Pdata = Pdata[!is.na(Pdata$length),] }
# Report removals
if (verbose) {
cat("\nRemoval Report\n\n")
cat("Records in input: ", Rec_summary[1], "\n")
cat("Records not in USINPFC ", Rec_summary[8], "\n")
cat("Records not in INPFC_AREA: ", Rec_summary[2], "\n")
cat("Records in bad INPFC_AREA: ", Rec_summary[9], "\n")
cat("Records in badRecords list: ", Rec_summary[3], "\n")
cat("Records with bad SAMPLE_TYPE ", Rec_summary[4], "\n")
cat("Records with bad SAMPLE_METHOD ", Rec_summary[5], "\n")
cat("Records with no SAMPLE_NO ", Rec_summary[6], "\n")
cat("Records with no usable length ", Rec_summary[7], "\n")
cat("Records remaining: ", nrow(Pdata), "\n\n")
if (!CLEAN) {
cat("\n\nReturning original data because CLEAN=FALSE\n\n")
}
}
return(Pdata)
} # End cleanPacFIN
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