Make compiled FOMC and DFOP models work

- Many thanks @karlines for the hint in ccSolve#1 how to declare
  the time variable and for writing the ccSolve package in the first
  place
- Add tests for the compiled versions of the FOMC and DFOP models

1 files changed, 4 insertions, 5 deletions

diff --git a/R/mkinmod.R b/R/mkinmod.R
index e73c56c6..3fff0878 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -126,8 +126,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
       }

     } #}}}

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

-      # From p. 53 of the FOCUS kinetics report

-      decline_term <- paste("(alpha/beta) * ((time/beta) + 1)^-1 *", box_1)

+      # From p. 53 of the FOCUS kinetics report, without the power function so it works in C

+      decline_term <- paste("(alpha/beta) * 1/((time/beta) + 1) *", box_1)

       parms <- c(parms, "alpha", "beta")

     } #}}}

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

@@ -295,10 +295,9 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL)
       replacement <- paste0("* y[", i - 1, "]")

       diffs.C <- gsub(pattern, replacement, diffs.C)

     }

-    # Unfortunately, the models with time occuring in the diffs do not compile

-    if (sum(sapply(spec, function(x) x$type %in% c("SFO", "SFORB"))) == length(spec)) {

+    if (sum(sapply(spec, function(x) x$type %in% c("SFO", "FOMC", "DFOP", "SFORB"))) == length(spec)) {

       message("Compiling differential equation model from auto-generated C code...")

-      model$compiled <- compile.ode(diffs.C, language = "C", parms = parms)

+      model$compiled <- compile.ode(diffs.C, language = "C", parms = parms, declaration = "double time = *t;")

     }

   }

   # }}}