Attempt of an overall model for an mmkin row

1 files changed, 58 insertions, 0 deletions

diff --git a/R/mxkin.R b/R/mxkin.R
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+#' 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
+}