diff options
Diffstat (limited to 'R/mkinmod.R')
| -rw-r--r-- | R/mkinmod.R | 93 |
1 files changed, 62 insertions, 31 deletions
diff --git a/R/mkinmod.R b/R/mkinmod.R index e865fa27..a0307003 100644 --- a/R/mkinmod.R +++ b/R/mkinmod.R @@ -36,8 +36,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) # differential equations (if supported), parameter names and a mapping from
# model variables to observed variables. If possible, a matrix representation
# of the differential equations is included
- # Compiling the functions from the C code generated below using the ccSolve package
- # only works if the implicit assumption about differential equations specified below
+ # Compiling the functions from the C code generated below only works if the
+ # implicit assumption about differential equations specified below
# is satisfied
parms <- vector()
# }}}
@@ -99,7 +99,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) # If sink is required, add first-order/IORE sink term
k_compound_sink <- paste("k", box_1, "sink", sep = "_")
if(spec[[varname]]$type == "IORE") {
- k_compound_sink <- paste("k.iore", box_1, "sink", sep = "_")
+ k_compound_sink <- paste("k__iore", box_1, "sink", sep = "_")
}
parms <- c(parms, k_compound_sink)
decline_term <- paste(k_compound_sink, "*", box_1)
@@ -114,7 +114,7 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) } else {
k_compound <- paste("k", box_1, sep = "_")
if(spec[[varname]]$type == "IORE") {
- k_compound <- paste("k.iore", box_1, sep = "_")
+ k_compound <- paste("k__iore", box_1, sep = "_")
}
parms <- c(parms, k_compound)
decline_term <- paste(k_compound, "*", box_1)
@@ -135,9 +135,10 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) decline_term <- paste("((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * time)) / (g * exp(-k1 * time) + (1 - g) * exp(-k2 * time))) *", box_1)
parms <- c(parms, "k1", "k2", "g")
} #}}}
+ HS_decline <- "ifelse(time <= tb, k1, k2)" # Used below for automatic translation to C
if(spec[[varname]]$type == "HS") { # {{{ Add HS decline term
# From p. 55 of the FOCUS kinetics report
- decline_term <- paste("ifelse(time <= tb, k1, k2)", "*", box_1)
+ decline_term <- paste(HS_decline, "*", box_1)
parms <- c(parms, "k1", "k2", "tb")
} #}}}
# Add origin decline term to box 1 (usually the only box, unless type is SFORB)#{{{
@@ -272,35 +273,65 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE) model$coefmat <- m
}#}}}
- # Create a function compiled from C code if more than one observed variable and ccSolve is available #{{{
- if (length(obs_vars) > 1 & requireNamespace("ccSolve", quietly = TRUE)) {
- diffs.C <- paste(diffs, collapse = ";\n")
- diffs.C <- paste0(diffs.C, ";")
- for (i in seq_along(diffs)) {
- obs_var <- names(diffs)[i]
+ # Create a function compiled from C code if more than one observed variable and gcc is available #{{{
+ if (length(obs_vars) > 1) {
+ if (Sys.which("gcc") != "") {
- # Replace d_... terms by f[i-1]
- # First line
- pattern <- paste0("^d_", obs_var)
- replacement <- paste0("\nf[", i - 1, "]")
- diffs.C <- gsub(pattern, replacement, diffs.C)
- # Other lines
- pattern <- paste0("\\nd_", obs_var)
- replacement <- paste0("\nf[", i - 1, "]")
- diffs.C <- gsub(pattern, replacement, diffs.C)
+ diffs.C <- paste(diffs, collapse = ";\n")
+ diffs.C <- paste0(diffs.C, ";")
+
+ # HS
+ diffs.C <- gsub(HS_decline, "(time <= tb ? k1 : k2)", diffs.C, fixed = TRUE)
+
+ for (i in seq_along(diffs)) {
+ state_var <- names(diffs)[i]
+
+ # IORE
+ if (state_var %in% obs_vars) {
+ if (spec[[state_var]]$type == "IORE") {
+ diffs.C <- gsub(paste0(state_var, "^N_", state_var),
+ paste0("pow(y[", i - 1, "], N_", state_var, ")"),
+ diffs.C, fixed = TRUE)
+ }
+ }
+
+ # Replace d_... terms by f[i-1]
+ # First line
+ pattern <- paste0("^d_", state_var)
+ replacement <- paste0("\nf[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+ # Other lines
+ pattern <- paste0("\\nd_", state_var)
+ replacement <- paste0("\nf[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+
+ # Replace names of observed variables by y[i],
+ # making the implicit assumption that the observed variables only occur after "* "
+ pattern <- paste0("\\* ", state_var)
+ replacement <- paste0("* y[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+ }
- # Replace names of observed variables by y[i],
- # making the implicit assumption that the observed variables only occur after "* "
- pattern <- paste0("\\* ", obs_var)
- replacement <- paste0("* y[", i - 1, "]")
- diffs.C <- gsub(pattern, replacement, diffs.C)
- }
- if (sum(sapply(spec, function(x) x$type %in%
- c("SFO", "FOMC", "DFOP", "SFORB"))) == length(spec)) {
if (!quiet) message("Compiling differential equation model from auto-generated C code...")
- model$compiled <- ccSolve::compile.ode(diffs.C, language = "C",
- parms = parms,
- declaration = "double time = *t;")
+
+ npar <- length(parms)
+
+ initpar_code <- paste0(
+ "static double parms [", npar, "];\n",
+ paste0("#define ", parms, " parms[", 0:(npar - 1), "]\n", collapse = ""),
+ "\n",
+ "void initpar(void (* odeparms)(int *, double *)) {\n",
+ " int N = ", npar, ";\n",
+ " odeparms(&N, parms);\n",
+ "}\n\n")
+
+ derivs_code <- paste0("double time = *t;\n", diffs.C)
+ derivs_sig <- signature(n = "integer", t = "numeric", y = "numeric",
+ f = "numeric", rpar = "numeric", ipar = "integer")
+
+ model$cf <- cfunction(list(func = derivs_sig), derivs_code,
+ otherdefs = initpar_code,
+ convention = ".C", language = "C")
}
}
# }}}
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