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Merge pull request #132 from pfmc-assessments/get_raw_comps
Add new function to calculate raw/unexpanded composition data
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,274 @@ | ||
| #' Calculate unexpanded/raw length or marginal age compositions | ||
| #' | ||
| #' @details | ||
| #' Creates a matrix of unexpanded (or raw) marginal length or age composition | ||
| #' data formatted for Stock Synthesis. The code will return composition data | ||
| #' for all sexes present in the data frame and no sex assignment is done for | ||
| #' unsexed fish. The function will create composition data for either | ||
| #' lengths or ages based on the comp_column_name. The function will return a | ||
| #' list of composition data based upon the sexes present in the data for a | ||
| #' two-sex model or all length/ages for single-sex model. | ||
| #' | ||
| #' @param data A data frame that includes columns of year, sex, and length/ages. The data | ||
| #' frame can be survey data pulled using pull_bio from the data warehouse or any data frame | ||
| #' that includes column names of sex, year, and the comp_column_name. The sex column is | ||
| #' expected to have sexes denoted by F, M, and U. | ||
| #' @param comp_bins A vector on length bins or age bins to create compositions across. The | ||
| #' composition data is formatted for Stock Synthesis. | ||
| #' @param comp_column_name The column name to create composition data for. This column can be | ||
| #' is used to determine whether to format the composition data for length or age | ||
| #' compositions by looking for either age (e.g., age_years, Age, best_age) or length | ||
| #' (e.g., Length, length, Length_cm) in the comp_column_name. Default Length_cm. | ||
| #' @param two_sex_comps Default TRUE. If TRUE composition data will be formatted for a | ||
| #' Stock Synthesis two-sex model and if FALSE composition data will be formatted for a | ||
| #' single-sex model. | ||
| #' @param fleet A fleet number to assign the composition data to based on the expected | ||
| #' format for Stock Synthesis. Default "Enter Fleet". | ||
| #' @param month Month the samples were collected based on the expected format for | ||
| #' Stock Synthesis to determine the length/age estimate to compare to. Default | ||
| #' "Enter Month". | ||
| #' @param partition Partition to assign the composition data based on the expected | ||
| #' format for Stock Synthesis. Partition of 0 indicates that the composition data | ||
| #' include all composition data, 1 for discarded composition data, and 2 for retained | ||
| #' fish only. Default of 0. | ||
| #' @param age_error Number of ageing error vector to apply to the age data based on | ||
| #' Stock Synthesis. Default "Enter Age Error Vector". | ||
| #' @param age_low Lower age bin for all age composition data based on the expected | ||
| #' format for Stock Synthesis. Default value of -1 which translates to the lowest age | ||
| #' bin. | ||
| #' @param age_high Upper age bin for all age composition data based on the expected | ||
| #' format for Stock Synthesis. Default value of -1 which translates to the highest | ||
| # age bin. | ||
| #' @template dir | ||
| #' @template printfolder | ||
| #' @template verbose | ||
| #' | ||
| #' @returns A list of length or marginal age compositions for sexed and | ||
| #' unsexed fish formatted for Stock Synthesis. | ||
| #' | ||
| #' @author Chantel Wetzel | ||
| #' @export | ||
| #' | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' bio <- pull_bio( | ||
| #' common_name = "lingcod", | ||
| #' survey = "NWFSC.Combo" | ||
| #' ) | ||
| #' | ||
| #' length_comps <- get_raw_comps( | ||
| #' data = bio, | ||
| #' comp_bins = seq(20, 70, 4) | ||
| #' ) | ||
| #' | ||
| #' age_comps <- get_raw_comps( | ||
| #' data = bio, | ||
| #' comp_bins = 1:20, | ||
| #' comp_column_name = "Age" | ||
| #' ) | ||
| #' | ||
| #' } | ||
| #' | ||
| get_raw_comps <- function( | ||
| data, | ||
| comp_bins, | ||
| comp_column_name = "Length_cm", | ||
| two_sex_comps = TRUE, | ||
| fleet = "Enter Fleet", | ||
| month = "Enter Month", | ||
| partition = 0, | ||
| age_error = "Enter Age Error Vector", | ||
| age_low = -1, | ||
| age_high = -1, | ||
| dir = NULL, | ||
| printfolder = "forSS3", | ||
| verbose = TRUE) | ||
| { | ||
|
|
||
| plotdir <- file.path(dir, printfolder) | ||
| check_dir(dir = plotdir, verbose = verbose) | ||
|
|
||
| colnames(data) <- tolower(colnames(data)) | ||
| comp_column_name <- tolower(comp_column_name) | ||
|
|
||
| vars <- c("year", "sex") | ||
| if(sum(vars %in% colnames(data)) != 2){ | ||
| stop("Data frame does not contain a column name year and/or sex. | ||
| \n The columns names can be either upper or lower case.") | ||
| } | ||
|
|
||
| if(!comp_column_name %in% colnames(data)){ | ||
| stop("Data frame does not contain a column name of comp_column_name. | ||
| \n The columns names can be either upper or lower case. ") | ||
| } | ||
|
|
||
| if (!two_sex_comps){ | ||
| data[, "sex"] <- "U" | ||
| } | ||
|
|
||
| # Check to see if user is doing ages or lengths | ||
| if(length(grep("age", comp_column_name)) > 0) { | ||
| comp_type <- "age" | ||
| } else { | ||
| comp_type <- "length" | ||
| } | ||
|
|
||
| keep <- !is.na(data[, comp_column_name]) | ||
| data <- data[keep, ] | ||
| bins <- c(comp_bins, Inf) | ||
| data$bin <- bins[findInterval(data[, comp_column_name], bins, all.inside = T)] | ||
|
|
||
| # if there are NA sexes replace them with U | ||
| if (sum(is.na(data[, "sex"])) > 0) { | ||
| data[is.na(data[, "sex"]), "sex"] <- "U" | ||
| } | ||
|
|
||
| # Create the comps | ||
| Results <- out <- NULL | ||
| for (y in sort(unique(data[, "year"]))) { | ||
| # Identify relevant rows | ||
| Which <- which(data[, "year"] == y & data[, "sex"] %in% c("F", "M")) | ||
| # Skip this year unless there are rows | ||
| if (length(Which) > 0) { | ||
| Row <- c(y, length(Which)) | ||
| # Loop across F then M | ||
| for (s in c("F", "M")) { | ||
| # Loop across length bins | ||
| for (l in comp_bins) | ||
| { | ||
| # Subset to relevant rows | ||
| if (l == min(bins)) { | ||
| Which2 <- Which[which(data[Which, "bin"] %in% l & data[Which, "sex"] == s)] | ||
| } | ||
| if (l != min(bins)) { | ||
| Which2 <- Which[which(data[Which, "bin"] == l & data[Which, "sex"] == s)] | ||
| } | ||
| if (l == max(bins)) { | ||
| Which2 <- Which[which(data[Which, "bin"] %in% c(l, Inf) & data[Which, "sex"] == s)] | ||
| } | ||
| # Sum to effective sample size by length_bin x Sex x Fleet x Year | ||
| if (length(Which2) == 0) Row <- c(Row, 0) | ||
| if (length(Which2) >= 1) Row <- c(Row, length(Which2)) | ||
| } | ||
| } | ||
| # Add to results matrix | ||
| Results <- rbind(Results, Row) | ||
| } # end Which loop | ||
| } # end year loop | ||
|
|
||
| if(!is.null(Results)){ | ||
| Results <- as.data.frame(Results) | ||
| tmp <- data.frame( | ||
| year = Results[, 1], | ||
| month = month, | ||
| fleet = fleet, | ||
| sex = 3, | ||
| partition = partition, | ||
| nsamp = Results[, 2] | ||
| ) | ||
| out <- cbind(tmp, Results[, -c(1:2)]) | ||
| colnames(out)[-c(1:6)] <- c( | ||
| paste(rep("F", each = length(comp_bins)), comp_bins, sep = ""), | ||
| paste(rep("M", each = length(comp_bins)), comp_bins, sep = "")) | ||
| } | ||
|
|
||
| # Create unsexed comps if present in the data | ||
| out_u <- NULL | ||
| if (length(data[data[, "sex"] == "U", "sex"]) > 0) { | ||
| Results <- NULL | ||
| for (y in sort(unique(data[, "year"]))) { | ||
| # Identify relevant rows | ||
| Which <- which(data[, "year"] == y & data[, "sex"] == "U") | ||
| # Skip this year unless there are rows | ||
| if (length(Which) > 0) { | ||
| # Format reference stuff | ||
| Row <- c(y, length(Which)) | ||
| # Loop across length bins | ||
| for (l in comp_bins) | ||
| { | ||
| # Subset to relevant rows | ||
| if (l == min(bins)) { | ||
| Which2 <- Which[which(data[Which, "bin"] %in% l)] | ||
| } | ||
| if (l != min(bins)) { | ||
| Which2 <- Which[which(data[Which, "bin"] == l)] | ||
| } | ||
| if (l == max(bins)) { | ||
| Which2 <- Which[which(data[Which, "bin"] %in% c(l, Inf))] | ||
| } | ||
| # Sum to effective sample size by length_bin x Sex x Fleet x Year | ||
| if (length(Which2) == 0) Row <- c(Row, 0) | ||
| if (length(Which2) >= 1) Row <- c(Row, length(Which2)) | ||
| } | ||
| # Add to results matrix | ||
| Results <- rbind(Results, Row) | ||
| } # end Which loop | ||
| } # end year loop | ||
| Results <- as.data.frame(Results) | ||
| tmp <- data.frame( | ||
| year = Results[, 1], | ||
| month = month, | ||
| fleet = fleet, | ||
| sex = 0, | ||
| partition = partition, | ||
| nsamp = Results[, 2] | ||
| ) | ||
|
|
||
| if (two_sex_comps){ | ||
| out_u <- cbind(tmp, Results[, -c(1:2)], 0 * Results[, -c(1:2)]) | ||
| } else { | ||
| out_u <- cbind(tmp, Results[, -c(1:2)]) | ||
| } | ||
| colnames(out_u)[-c(1:6)] <- paste(rep("U", each = length(comp_bins)), comp_bins, sep = "") | ||
| } | ||
|
|
||
| if (comp_type == "length") { | ||
| if (!is.null(out)) { | ||
| out_comps <- out | ||
| } else { | ||
| out_comps <- NULL | ||
| } | ||
| if (!is.null(out_u)) { | ||
| out_u_comps <- out_u | ||
| } | ||
| } | ||
|
|
||
| if (comp_type == "age") { | ||
| if (!is.null(out)) { | ||
| out_comps <- cbind(out[, 1:5], age_error, age_low, age_high, out[, 6:dim(out)[2]]) | ||
| } else { | ||
| out_comps <- NULL | ||
| } | ||
| if (!is.null(out_u)) { | ||
| out_u_comps <- cbind(out_u[, 1:5], age_error, age_low, age_high, out_u[, 6:dim(out_u)[2]]) | ||
| } | ||
| } | ||
|
|
||
| if (!is.null(dir)) { | ||
| if (!is.null(out_comps)) { | ||
| write.csv(out_comps, | ||
| file = file.path(plotdir, paste0(comp_type, "_raw_comps_sex_3_", comp_type, "_bins_", comp_bins[1], "-", max(comp_bins), ".csv")), | ||
| row.names = FALSE | ||
| ) | ||
| } | ||
| if (!is.null(out_u)) { | ||
| write.csv(out_u_comps, | ||
| file = file.path(plotdir, paste0(comp_type, "_raw_comps_sex_0_", comp_type, "_bins_", comp_bins[1], "-", max(comp_bins), ".csv")), | ||
| row.names = FALSE | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| comps <- list() | ||
| if (!is.null(out_comps)) { | ||
| rownames(out_comps) <- NULL | ||
| comps$sexed <- out_comps | ||
| } | ||
| if (!is.null(out_u)) { | ||
| rownames(out_u_comps) <- NULL | ||
| comps$unsexed <- out_u_comps | ||
| } | ||
|
|
||
| return(comps) | ||
|
|
||
| } |
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