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diff --git a/R/mixed.mmkin.R b/R/mixed.mmkin.R new file mode 100644 index 00000000..6fe5130d --- /dev/null +++ b/R/mixed.mmkin.R @@ -0,0 +1,101 @@ +#' Create a mixed effects model from an mmkin row object +#' +#' @param object An [mmkin] row object +#' @param method The method to be used +#' @param \dots Currently not used +#' @examples +#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) +#' n_biphasic <- 8 +#' err_1 = list(const = 1, prop = 0.07) +#' +#' DFOP_SFO <- mkinmod( +#' parent = mkinsub("DFOP", "m1"), +#' m1 = mkinsub("SFO"), +#' quiet = TRUE) +#' +#' set.seed(123456) +#' log_sd <- 0.3 +#' syn_biphasic_parms <- as.matrix(data.frame( +#' k1 = rlnorm(n_biphasic, log(0.05), log_sd), +#' k2 = rlnorm(n_biphasic, log(0.01), log_sd), +#' g = plogis(rnorm(n_biphasic, 0, log_sd)), +#' f_parent_to_m1 = plogis(rnorm(n_biphasic, 0, log_sd)), +#' k_m1 = rlnorm(n_biphasic, log(0.002), log_sd))) +#' +#' ds_biphasic_mean <- lapply(1:n_biphasic, +#' function(i) { +#' mkinpredict(DFOP_SFO, syn_biphasic_parms[i, ], +#' c(parent = 100, m1 = 0), sampling_times) +#' } +#' ) +#' +#' set.seed(123456L) +#' ds_biphasic <- lapply(ds_biphasic_mean, function(ds) { +#' add_err(ds, +#' sdfunc = function(value) sqrt(err_1$const^2 + value^2 * err_1$prop^2), +#' n = 1, secondary = "m1")[[1]] +#' }) +#' +#' \dontrun{ +#' f_mmkin <- mmkin(list("DFOP-SFO" = DFOP_SFO), ds_biphasic, error_model = "tc", quiet = TRUE) +#' +#' f_mixed <- mixed(f_mmkin) +#' print(f_mixed) +#' plot(f_mixed) +#' } +#' @export +mixed <- function(object, ...) { + UseMethod("mixed") +} + +#' @export +#' @rdname mixed +mixed.mmkin <- function(object, method = c("none"), ...) { + if (nrow(object) > 1) stop("Only row objects allowed") + + method <- match.arg(method) + if (method == "default") method = c("naive", "nlme") + + ds_names <- colnames(object) + res <- list(mmkin = object, mkinmod = object[[1]]$mkinmod) + + if (method[1] == "none") { + ds_list <- lapply(object, + function(x) x$data[c("variable", "time", "observed", "predicted", "residual")]) + + names(ds_list) <- ds_names + res$data <- purrr::map_dfr(ds_list, function(x) x, .id = "ds") + names(res$data)[1:4] <- c("ds", "name", "time", "value") + res$data$name <- as.character(res$data$name) + res$data$ds <- ordered(res$data$ds, levels = unique(res$data$ds)) + standardized <- unlist(lapply(object, residuals, standardized = TRUE)) + res$data$std <- res$data$residual / standardized + res$data$standardized <- standardized + + class(res) <- c("mixed.mmkin") + return(res) + } +} + +#' @export +#' @rdname mixed +#' @param x A mixed.mmkin object to print +#' @param digits Number of digits to use for printing. +print.mixed.mmkin <- function(x, digits = max(3, getOption("digits") - 3), ...) { + cat("Kinetic model fitted by nonlinear regression to each dataset" ) + cat("\nStructural model:\n") + diffs <- x$mmkin[[1]]$mkinmod$diffs + nice_diffs <- gsub("^(d.*) =", "\\1/dt =", diffs) + writeLines(strwrap(nice_diffs, exdent = 11)) + cat("\nData:\n") + cat(nrow(x$data), "observations of", + length(unique(x$data$name)), "variable(s) grouped in", + length(unique(x$data$ds)), "datasets\n\n") + + print(x$mmkin) + + cat("\nMean fitted parameters:\n") + print(mean_degparms(x$mmkin)) + + invisible(x) +} |