Another overhaul of analytical solutions

Still in preparation for analytical solutions of coupled models

1 files changed, 3 insertions, 40 deletions

diff --git a/R/mkinmod.R b/R/mkinmod.R
index f52baa4f..21551861 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -101,7 +101,7 @@
 #' }
 #'
 #' @export mkinmod
-mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)
+mkinmod <- function(..., use_of_ff = "max", speclist = NULL, quiet = FALSE, verbose = FALSE)
 {
   if (is.null(speclist)) spec <- list(...)
   else spec <- speclist
@@ -421,45 +421,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
   }
   # }}}
 
-  # Attach a degradation function if an analytical solution is available {{{
-  parent_type = spec[[1]]$type
-  parent_name = names(spec)[[1]]
-  if (length(spec) == 1) {
-    odeparm_map <- switch(parent_type,
-      SFO = c(
-        k = if(use_of_ff == "min") paste("k", parent_name, "sink", sep = "_")
-          else  paste("k", parent_name, sep = "_")),
-      FOMC = c(alpha = "alpha", beta = "beta"),
-      IORE = c(
-        k__iore = if(use_of_ff == "min") paste("k__iore", parent_name, "sink", sep = "_")
-          else paste("k__iore", parent_name, sep = "_"),
-        N = paste("N", parent_name, sep = "_")),
-      DFOP = c(k1 = "k1", k2 = "k2", g = "g"),
-      HS = c(k1 = "k1", k2 = "k2", tb = "tb"),
-      SFORB = c(
-        k_12 = paste("k", parent_name, "free_bound", sep = "_"),
-        k_21 = paste("k", parent_name, "bound_free", sep = "_"),
-        k_1output = paste("k", parent_name, "free_sink", sep = "_")),
-      logistic = c(kmax = "kmax", k0 = "k0", r = "r")
-    )
-    odeparm_rev_map <- names(odeparm_map)
-    names(odeparm_rev_map) <- odeparm_map
-
-    model$deg_func <- function(odeini, odeparms, outtimes) {
-      parent_func <- getFromNamespace(paste0(parent_type, ".solution"), "mkin")
-      odeparm_list <- as.list(odeparms)
-      names(odeparm_list) <- odeparm_rev_map[names(odeparm_list)]
-
-      values <- do.call(parent_func,
-        args = c(
-          list(t = outtimes, parent_0 = odeini[1]),
-          odeparm_list))
-      out <- data.frame(outtimes, values)
-      names(out) <- c("time", parent_name)
-      return(out)
-    }
-  }
-  # }}}
+  # Attach a degradation function if an analytical solution is available
+  model$deg_func <- create_deg_func(spec, use_of_ff)
 
   class(model) <- "mkinmod"
   return(model)