diff --git a/R/utils.R b/R/utils.R index adedd17a..fa21e55e 100644 --- a/R/utils.R +++ b/R/utils.R @@ -611,52 +611,6 @@ get_fitted_time <- function(x) { x$fitted_time } -update_version <- function(object) { - if (object$version < "0.4.3") { - cli::cli_abort("`update_version()` only works with models fit with version 0.4.3 or later.") - } - if (!"fitted_time" %in% names(object)) { # < 0.4.3.9004 - object$fitted_time <- sort(unique(object$data[[object$time]])) - - et <- object$extra_time - o <- object$tmb_obj$env$data$offset_i - real_data_n <- length(o) - length(et) - o <- o[seq(1, real_data_n)] - object$offset <- o - - y <- object$response - y <- y[seq(1, real_data_n), , drop = FALSE] - object$response <- y - - d <- object$data - d[["__fake_data__"]] <- d[["__weight_sdmTMB__"]] <- - d[["__sdmTMB_offset__"]] <- d[["__dcens_upr__"]] <- NULL - d <- d[seq(1, real_data_n), , drop = FALSE] - object$data <- d - } - - # add gengamma_Q - p <- object$tmb_obj$env$parList() - if (!"gengamma_Q" %in% names(p)) { - p$gengamma_Q <- 1 # not defined at 0 - ee <- object$tmb_obj$env - map <- object$tmb_map - map$gengamma_Q <- factor(NA) - object$tmb_obj <- TMB::MakeADFun( - data = ee$data, - parameters = p, - map = map, - random = ee$random, - silent = ee$silent, - DLL = "sdmTMB" - ) - object$tmb_obj$fn(object$model$par) - object$tmb_obj$env$last.par.best <- ee$last.par.best - object$tmb_map <- map - } - object -} - reload_model <- function(object) { if ("parlist" %in% names(object)) { # tinyVAST does this to be extra sure... I've found one case where it was needed