Add the logistic model

1 files changed, 13 insertions, 7 deletions

diff --git a/R/mkinmod.R b/R/mkinmod.R
index 491b3d0a..2805ef54 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2010-2015 Johannes Ranke {{{

+# Copyright (C) 2010-2015,2019 Johannes Ranke {{{

 # Contact: jranke@uni-bremen.de

 

 # This file is part of the R package mkin

@@ -42,8 +42,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
   parms <- vector()

   # }}}

 

-  # Do not return a coefficient matrix mat when FOMC, IORE, DFOP or HS is used for the parent {{{

-  if(spec[[1]]$type %in% c("FOMC", "IORE", "DFOP", "HS")) {

+  # Do not return a coefficient matrix mat when FOMC, IORE, DFOP, HS or logistic is used for the parent {{{

+  if(spec[[1]]$type %in% c("FOMC", "IORE", "DFOP", "HS", "logistic")) {

     mat = FALSE

   } else mat = TRUE

   #}}}

@@ -57,10 +57,10 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
     # Check the type component of the compartment specification {{{

     if(is.null(spec[[varname]]$type)) stop(

       "Every part of the model specification must be a list containing a type component")

-    if(!spec[[varname]]$type %in% c("SFO", "FOMC", "IORE", "DFOP", "HS", "SFORB")) stop(

-      "Available types are SFO, FOMC, IORE, DFOP, HS and SFORB only")

-    if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS") & match(varname, obs_vars) != 1) {

-        stop(paste("Types FOMC, DFOP and HS are only implemented for the first compartment,",

+    if(!spec[[varname]]$type %in% c("SFO", "FOMC", "IORE", "DFOP", "HS", "SFORB", "logistic")) stop(

+      "Available types are SFO, FOMC, IORE, DFOP, HS, SFORB and logistic only")

+    if(spec[[varname]]$type %in% c("FOMC", "DFOP", "HS", "logistic") & match(varname, obs_vars) != 1) {

+        stop(paste("Types FOMC, DFOP, HS and logistic are only implemented for the first compartment,",

                    "which is assumed to be the source compartment"))

     }

     #}}}

@@ -71,6 +71,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
       IORE = varname,

       DFOP = varname,

       HS = varname,

+      logistic = varname,

       SFORB = paste(varname, c("free", "bound"), sep = "_")

     )

     map[[varname]] <- new_boxes

@@ -141,6 +142,11 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
       decline_term <- paste(HS_decline, "*", box_1)

       parms <- c(parms, "k1", "k2", "tb")

     } #}}}

+    if(spec[[varname]]$type == "logistic") { # {{{ Add logistic decline term

+      # From p. 67 of the FOCUS kinetics report (2014)

+      decline_term <- paste("(k0 * kmax)/(k0 + (kmax - k0) * exp(-r * time)) *", box_1)

+      parms <- c(parms, "kmax", "k0", "r")

+    } #}}}

     # Add origin decline term to box 1 (usually the only box, unless type is SFORB)#{{{

     diffs[[box_1]] <- paste(diffs[[box_1]], "-", decline_term)#}}}

     if(spec[[varname]]$type == "SFORB") { # {{{ Add SFORB reversible binding terms