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[feat]: More fims plots runs test, follows #469 #473
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| #' Convert FIMS output to the standard output format | ||
| #' | ||
| #' Reshape the estimates from a FIMS model (`FIMS::get_estimates()`) into the | ||
| #' standardized long format returned by [convert_output()]. | ||
| #' | ||
| #' @param file A tibble returned by `FIMS::get_estimates()`, a `FIMSFit` | ||
| #' object, or the path to an .rds file containing either. | ||
| #' @param out_new The empty standard output data frame from | ||
| #' [convert_output()]. | ||
| #' @param start_year Number. First year of the model. FIMS reports years as | ||
| #' indices (`year_i`, 1 = first model year), which are converted to years as | ||
| #' `year_i + start_year - 1`. NULL keeps the indices. | ||
| #' | ||
| #' @returns A data frame with the columns of `out_new`. | ||
| #' | ||
| #' @details Each data point (index, landings, and age and length compositions) | ||
| #' is one row in FIMS, with the observed value in `observed` and the expected | ||
| #' value in `estimated`. These are split into two rows, labeled | ||
| #' "*_observed" and "*_predicted" as for other models (e.g., "index_observed" | ||
| #' and "index_predicted"). Observed rows hold the observation error in | ||
| #' `uncertainty` and the negative log-likelihood of the observation in | ||
| #' `likelihood`. FIMS reports the observation error as `log_sd`, the log of | ||
| #' its standard deviation. For lognormal data this standard deviation | ||
| #' (\eqn{\sigma}) is on the log scale, so it is converted to the coefficient | ||
| #' of variation of the observation, \eqn{\sqrt{\exp(\sigma^2) - 1}}, and | ||
| #' labeled "cv"; for other data `exp(log_sd)` is labeled "se". Observations | ||
| #' coded as missing (-999) are not observations and are not included. | ||
| #' Compositions are kept as counts, as reported by FIMS. | ||
| #' | ||
| #' All other estimates keep one row each, with the value in `estimate` and | ||
| #' its standard error in `uncertainty`. FIMS codes estimates that could not | ||
| #' be calculated as -999; these are NA. Rows in years after the last year of | ||
| #' data (e.g., spawning biomass at the start of the year after the model | ||
| #' ends) have `era` "fore"; other rows with a year have `era` "time". | ||
| #' | ||
| #' @noRd | ||
| conout_fims <- function(file, out_new, start_year = NULL) { | ||
| dat <- read_fims_estimates(file) | ||
| names(dat) <- tolower(names(dat)) | ||
| if (!all(c("label", "estimated") %in% names(dat))) { | ||
| cli::cli_abort(c( | ||
| "{.arg file} is not FIMS output.", | ||
| "i" = "Supply the output of {.code FIMS::get_estimates()} or a {.cls FIMSFit} object." | ||
| )) | ||
| } | ||
| col <- function(name) { | ||
| if (name %in% names(dat)) dat[[name]] else rep(NA, nrow(dat)) | ||
| } | ||
| year_i <- suppressWarnings(as.numeric(col("year_i"))) | ||
| if (is.null(start_year)) { | ||
| cli::cli_alert_info( | ||
| "FIMS reports years as indices (1 = first model year); use {.arg start_year} to convert them to years." | ||
| ) | ||
| year <- year_i | ||
| } else { | ||
| year <- year_i + start_year - 1 | ||
| } | ||
| observed <- suppressWarnings(as.numeric(col("observed"))) | ||
| observed[observed %in% -999] <- NA | ||
| # The last year of data; later years are after the model ends | ||
| data_years <- year_i[!is.na(observed)] | ||
| last_year <- if (length(data_years) > 0) max(data_years) else max(year_i, na.rm = TRUE) | ||
| era <- dplyr::case_when( | ||
| is.na(year_i) ~ NA_character_, | ||
| year_i > last_year ~ "fore", | ||
| TRUE ~ "time" | ||
| ) | ||
| uncertainty <- dplyr::na_if(suppressWarnings(as.numeric(col("uncertainty"))), -999) | ||
| base <- data.frame( | ||
| module_name = as.character(col("module_name")), | ||
| label = as.character(dat$label), | ||
| era = era, | ||
| year = year, | ||
| initial = suppressWarnings(as.numeric(col("input"))), | ||
| estimate = dplyr::na_if(suppressWarnings(as.numeric(dat$estimated)), -999), | ||
| uncertainty = uncertainty, | ||
| uncertainty_label = ifelse(is.na(uncertainty), NA_character_, "se"), | ||
| likelihood = NA_real_, | ||
| fleet = as.character(col("fleet")), | ||
| age = suppressWarnings(as.numeric(col("age"))), | ||
| len_bins = suppressWarnings(as.numeric(col("length"))), | ||
| stringsAsFactors = FALSE | ||
| ) | ||
|
|
||
| # Data points: split into observed and predicted rows | ||
| stream <- dplyr::case_when( | ||
| grepl("^index_?expected$", base$label, ignore.case = TRUE) ~ "index", | ||
| grepl("^(catch|landings)_?expected$", base$label, ignore.case = TRUE) ~ "landings", | ||
| grepl("^age_?comp(osition)?_?expected$", base$label, ignore.case = TRUE) ~ "age_composition", | ||
| grepl("^length_?comp(osition)?_?expected$", base$label, ignore.case = TRUE) ~ "length_composition", | ||
| TRUE ~ NA_character_ | ||
| ) | ||
| # Fleets with data for a stream; expected values for other fleets (e.g., | ||
| # the expected index of a fishery without an index) keep their FIMS label | ||
| has_data <- stats::ave(!is.na(observed), stream, base$fleet, FUN = any) | ||
| is_data <- !is.na(stream) & has_data %in% TRUE | ||
| obs_rows <- base[is_data & !is.na(observed), , drop = FALSE] | ||
| if (nrow(obs_rows) > 0) { | ||
| is_obs <- is_data & !is.na(observed) | ||
| sigma <- exp(suppressWarnings(as.numeric(col("log_sd")))[is_obs]) | ||
| # A lognormal sigma is on the log scale; report the CV of the observation | ||
| lognormal <- grepl("^(d?lnorm|log_?normal)$", col("distribution")[is_obs], ignore.case = TRUE) | ||
| obs_rows$label <- paste0(stream[is_obs], "_observed") | ||
| obs_rows$estimate <- observed[is_obs] | ||
| obs_rows$uncertainty <- ifelse(lognormal, sqrt(exp(sigma^2) - 1), sigma) | ||
| obs_rows$uncertainty_label <- dplyr::case_when( | ||
| is.na(sigma) ~ NA_character_, | ||
| lognormal ~ "cv", | ||
| TRUE ~ "se" | ||
| ) | ||
| obs_rows$initial <- NA_real_ | ||
| # Stock Synthesis reports the negative log-likelihood of each observation | ||
| obs_rows$likelihood <- -suppressWarnings(as.numeric(col("likelihood")))[is_obs] | ||
| } | ||
| pred_rows <- base[is_data, , drop = FALSE] | ||
| pred_rows$label <- paste0(stream[is_data], "_predicted") | ||
| out <- rbind(base[!is_data, , drop = FALSE], obs_rows, pred_rows) | ||
|
|
||
| missing <- setdiff(names(out_new), names(out)) | ||
| out[missing] <- NA | ||
| out[, names(out_new)] | ||
| } | ||
|
|
||
| # The estimates of a FIMS model from get_estimates() output, a FIMSFit | ||
| # object, or an .rds file with either | ||
| read_fims_estimates <- function(file) { | ||
| if (is.character(file) && length(file) == 1) { | ||
| file <- readRDS(file) | ||
| } | ||
| if (inherits(file, "FIMSFit")) { | ||
| get_estimates <- tryCatch( | ||
| getExportedValue("FIMS", "get_estimates"), | ||
| error = function(e) { | ||
| cli::cli_abort("The {.pkg FIMS} package is needed to read a {.cls FIMSFit} object.") | ||
| } | ||
| ) | ||
| file <- get_estimates(file) | ||
| } | ||
| if (!is.data.frame(file)) { | ||
| cli::cli_abort("{.arg file} must be FIMS output from {.code FIMS::get_estimates()} or a {.cls FIMSFit} object.") | ||
| } | ||
| as.data.frame(file) | ||
| } |
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was devtools::document run when this was made? I don't see new documentation.