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| -rw-r--r-- | R/memkin.R | 133 | ||||
| -rw-r--r-- | R/mxkin.R | 58 |
2 files changed, 133 insertions, 58 deletions
diff --git a/R/memkin.R b/R/memkin.R new file mode 100644 index 00000000..68837d86 --- /dev/null +++ b/R/memkin.R @@ -0,0 +1,133 @@ +#' Estimation of parameter distributions from mmkin row objects +#' +#' This function sets up and attempts to fit a mixed effects model to +#' an mmkin row object which is essentially a list of mkinfit objects +#' that have been obtained by fitting the same model to a list of +#' datasets. +#' +#' @param object An mmkin row object containing several fits of the same model to different datasets +#' @param ... Additional arguments passed to \code{\link{nlme}} +#' @importFrom nlme nlme +#' @return A fitted object of class 'memkin' +#' @examples +#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) +#' m_SFO <- mkinmod(parent = mkinsub("SFO")) +#' d_SFO_1 <- mkinpredict(m_SFO, +#' c(k_parent_sink = 0.1), +#' c(parent = 98), sampling_times) +#' d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time") +#' d_SFO_2 <- mkinpredict(m_SFO, +#' c(k_parent_sink = 0.05), +#' c(parent = 102), sampling_times) +#' d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time") +#' d_SFO_3 <- mkinpredict(m_SFO, +#' c(k_parent_sink = 0.02), +#' c(parent = 103), sampling_times) +#' d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time") +#' +#' d1 <- add_err(d_SFO_1, function(value) 3, n = 1) +#' d2 <- add_err(d_SFO_2, function(value) 2, n = 1) +#' d3 <- add_err(d_SFO_3, function(value) 4, n = 1) +#' ds <- c(d1 = d1, d2 = d2, d3 = d3) +#' +#' f <- mmkin("SFO", ds) +#' x <- memkin(f) +#' +#' @export +memkin <- function(object, ...) { + if (nrow(object) > 1) stop("Only row objects allowed") + ds_names <- colnames(object) + + p_mat_start_trans <- sapply(object, parms, transformed = TRUE) + colnames(p_mat_start_trans) <- ds_names + + p_names_mean_function <- setdiff(rownames(p_mat_start_trans), names(object[[1]]$errparms)) + p_start_mean_function <- apply(p_mat_start_trans[p_names_mean_function, ], 1, mean) + + ds_list <- lapply(object, function(x) x$data[c("time", "variable", "observed")]) + names(ds_list) <- ds_names + ds_nlme <- purrr::map_dfr(ds_list, function(x) x, .id = "ds") + ds_nlme_grouped <- groupedData(observed ~ time | ds, ds_nlme) + + mkin_model <- object[[1]]$mkinmod + + # Inspired by https://stackoverflow.com/a/12983961/3805440 + # and https://stackoverflow.com/a/26280789/3805440 + model_function_alist <- replicate(length(p_names_mean_function) + 2, substitute()) + names(model_function_alist) <- c("name", "time", p_names_mean_function) + + + + model_function_body <- quote({ + arg_frame <- as.data.frame(as.list((environment()))) + res <- parent_0 * exp( - exp(log_k_parent_sink) * time) + dump(c("arg_frame", "res"), file = "out_1.txt", append = TRUE) + return(res) + }) + model_function <- as.function(c(model_function_alist, model_function_body)) + f_nlme <- eval(parse(text = nlme_call_text)) + + model_function_body <- quote({ + arg_frame <- as.data.frame(as.list((environment()))) + + res_frame <- arg_frame[1:2] + + parm_frame <- arg_frame[-(1:2)] + parms_unique <- unique(parm_frame) + + n_unique <- nrow(parms_unique) + + times_ds <- list() + names_ds <- list() + for (i in 1:n_unique) { + times_ds[[i]] <- + arg_frame[which(arg_frame[[3]] == parms_unique[i, 1]), "time"] + names_ds[[i]] <- + arg_frame[which(arg_frame[[3]] == parms_unique[i, 1]), "name"] + } + + res_list <- lapply(1:n_unique, function(x) { + parms <- unlist(parms_unique[x, , drop = TRUE]) + odeini_parm_names <- grep('_0$', names(parms), value = TRUE) + odeparm_names <- setdiff(names(parms), odeini_parm_names) + odeini <- parms[odeini_parm_names] + names(odeini) <- gsub('_0$', '', odeini_parm_names) + odeparms <- backtransform_odeparms(parms[odeparm_names], mkin_model) # TBD rates/fractions + out_wide <- mkinpredict(mkin_model, odeparms = odeparms, + solution_type = "analytical", + odeini = odeini, outtimes = unique(times_ds[[x]])) + out_array <- out_wide[, -1, drop = FALSE] + rownames(out_array) <- as.character(unique(times_ds[[x]])) + out_times <- as.character(times_ds[[x]]) + out_names <- names_ds[[x]] + out_values <- mapply(function(times, names) out_array[times, names], + out_times, out_names) + return(as.numeric(out_values)) + }) + res <- unlist(res_list) + #dump(c("arg_frame", "res"), file = "out_2.txt", append = TRUE) + return(res) + }) + model_function <- as.function(c(model_function_alist, model_function_body)) + debug(model_function) + f_nlme <- eval(parse(text = nlme_call_text)) + + undebug(model_function) + + model_function(c(0, 0, 100), parent_0 = 100, log_k_parent_sink = log(0.1)) + + nlme_call_text <- paste0( + "nlme(observed ~ model_function(variable, time, ", + paste(p_names_mean_function, collapse = ", "), "),\n", + " data = ds_nlme_grouped,\n", + " fixed = ", paste(p_names_mean_function, collapse = " + "), " ~ 1,\n", + " random = pdDiag(", paste(p_names_mean_function, collapse = " + "), " ~ 1),\n", + #" start = c(parent_0 = 100, log_k_parent_sink = log(0.1)), verbose = TRUE)\n") + #" start = p_start_mean_function)\n") + " start = p_start_mean_function, verbose = TRUE)\n") + cat(nlme_call_text) + + f_nlme <- eval(parse(text = nlme_call_text)) + + return(f_nlme) +} diff --git a/R/mxkin.R b/R/mxkin.R deleted file mode 100644 index ae7563df..00000000 --- a/R/mxkin.R +++ /dev/null @@ -1,58 +0,0 @@ -#' Estimation of parameter distributions from mmkin objects -#' -#' @param object An mmkin row object containing several fits of the same model to different datasets -#' @return A fitted object of class 'mrkin' -#' @examples -#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) - -m_SFO <- mkinmod(parent = mkinsub("SFO")) -d_SFO_1 <- mkinpredict(m_SFO, - c(k_parent_sink = 0.1), - c(parent = 98), sampling_times) -d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time") -d_SFO_2 <- mkinpredict(m_SFO, - c(k_parent_sink = 0.05), - c(parent = 102), sampling_times) -d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time") -d_SFO_3 <- mkinpredict(m_SFO, - c(k_parent_sink = 0.02), - c(parent = 103), sampling_times) -d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time") - -d1 <- add_err(d_SFO_1, function(value) 3, n = 1) -d2 <- add_err(d_SFO_2, function(value) 2, n = 1) -d3 <- add_err(d_SFO_3, function(value) 4, n = 1) -ds <- c(d1 = d1, d2 = d2, d3 = d3) - -f <- mmkin("SFO", ds) -x <- mrkin(f) -as.numeric(x) - -#' -#' @export -mrkin <- function(object) { - if (nrow(object) > 1) stop("Only row objects allowed") - n_d <- ncol(object) - p_names <- names(parms(object[[1, 1]])) - p_names_trans <- names(parms(object[[1, 1]])) - - p_mat_start_trans <- sapply(object, parms, transformed = TRUE) - colnames(p_mat_start_trans) <- colnames(object) - p_mat_attr_trans <- attributes(p_mat_start_trans) - - p_dist_names <- p_names[grepl("^log_", p_names)] - p_free_names <- p_names[!grepl("^log_", p_names)] - - cost <- function(P) { - p_cost_mat <- P - attributes(P) <- p_mat_attr_trans - - ll_ds <- 0 - for (i_d in 1:n_d) { - - } - - } - - p_mat_start -} |