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authorJohannes Ranke <jranke@uni-bremen.de>2018-09-18 15:15:55 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2018-09-18 15:15:55 +0200
commit850aa313ba60c7b784d96cfdc8d4c22f2beb661a (patch)
tree1244a42d1e8a47a096a43d4c14634f3fe32e8778 /R
parenta2246bef55eb74f3ad608c28dc3b759af32a41b9 (diff)
Make mkinpredict generic and write a method for fits
Diffstat (limited to 'R')
-rw-r--r--R/mkinpredict.R77
1 files changed, 52 insertions, 25 deletions
diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index 994af703..8e0823a8 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2010-2015 Johannes Ranke
+# Copyright (C) 2010-2016,2018 Johannes Ranke
# Some lines in this code are copyright (C) 2013 Eurofins Regulatory AG
# Contact: jranke@uni-bremen.de
@@ -17,14 +17,28 @@
# You should have received a copy of the GNU General Public License along with
# this program. If not, see <http://www.gnu.org/licenses/>
-mkinpredict <- function(mkinmod, odeparms, odeini,
- outtimes, solution_type = "deSolve",
- use_compiled = "auto",
- method.ode = "lsoda", atol = 1e-8, rtol = 1e-10,
- map_output = TRUE, ...) {
+mkinpredict <- function(x, odeparms, odeini,
+ outtimes = seq(0, 120, by = 0.1),
+ solution_type = "deSolve",
+ use_compiled = "auto",
+ method.ode = "lsoda", atol = 1e-8, rtol = 1e-10,
+ map_output = TRUE, ...)
+{
+ UseMethod("mkinpredict", x)
+}
+
+mkinpredict.mkinmod <- function(x,
+ odeparms = c(k_parent_sink = 0.1),
+ odeini = c(parent = 100),
+ outtimes = seq(0, 120, by = 0.1),
+ solution_type = "deSolve",
+ use_compiled = "auto",
+ method.ode = "lsoda", atol = 1e-8, rtol = 1e-10,
+ map_output = TRUE, ...)
+{
# Get the names of the state variables in the model
- mod_vars <- names(mkinmod$diffs)
+ mod_vars <- names(x$diffs)
# Order the inital values for state variables if they are named
if (!is.null(names(odeini))) {
@@ -40,22 +54,22 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
# Create a function calculating the differentials specified by the model
# if necessary
if (solution_type == "analytical") {
- parent.type = names(mkinmod$map[[1]])[1]
- parent.name = names(mkinmod$diffs)[[1]]
+ parent.type = names(x$map[[1]])[1]
+ parent.name = names(x$diffs)[[1]]
o <- switch(parent.type,
SFO = SFO.solution(outtimes,
evalparse(parent.name),
- ifelse(mkinmod$use_of_ff == "min",
- evalparse(paste("k", parent.name, "sink", sep="_")),
- evalparse(paste("k", parent.name, sep="_")))),
+ ifelse(x$use_of_ff == "min",
+ evalparse(paste("k", parent.name, "sink", sep="_")),
+ evalparse(paste("k", parent.name, sep="_")))),
FOMC = FOMC.solution(outtimes,
evalparse(parent.name),
evalparse("alpha"), evalparse("beta")),
IORE = IORE.solution(outtimes,
evalparse(parent.name),
- ifelse(mkinmod$use_of_ff == "min",
- evalparse(paste("k__iore", parent.name, "sink", sep="_")),
- evalparse(paste("k__iore", parent.name, sep="_"))),
+ ifelse(x$use_of_ff == "min",
+ evalparse(paste("k__iore", parent.name, "sink", sep="_")),
+ evalparse(paste("k__iore", parent.name, sep="_"))),
evalparse("N_parent")),
DFOP = DFOP.solution(outtimes,
evalparse(parent.name),
@@ -75,7 +89,7 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
names(out) <- c("time", sub("_free", "", parent.name))
}
if (solution_type == "eigen") {
- coefmat.num <- matrix(sapply(as.vector(mkinmod$coefmat), evalparse),
+ coefmat.num <- matrix(sapply(as.vector(x$coefmat), evalparse),
nrow = length(mod_vars))
e <- eigen(coefmat.num)
c <- solve(e$vectors, odeini)
@@ -88,14 +102,14 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
names(out) <- c("time", mod_vars)
}
if (solution_type == "deSolve") {
- if (!is.null(mkinmod$cf) & use_compiled[1] != FALSE) {
+ if (!is.null(x$cf) & use_compiled[1] != FALSE) {
out <- ode(
y = odeini,
times = outtimes,
func = "func",
initfunc = "initpar",
- dllname = getDynLib(mkinmod$cf)[["name"]],
- parms = odeparms[mkinmod$parms], # Order matters when using compiled models
+ dllname = getDynLib(x$cf)[["name"]],
+ parms = odeparms[x$parms], # Order matters when using compiled models
method = method.ode,
atol = atol,
rtol = rtol,
@@ -106,11 +120,11 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
time <- t
diffs <- vector()
- for (box in names(mkinmod$diffs))
+ for (box in names(x$diffs))
{
diffname <- paste("d", box, sep="_")
diffs[diffname] <- with(as.list(c(time, state, parms)),
- eval(parse(text=mkinmod$diffs[[box]])))
+ eval(parse(text=x$diffs[[box]])))
}
return(list(c(diffs)))
}
@@ -127,17 +141,17 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
}
if (sum(is.na(out)) > 0) {
stop("Differential equations were not integrated for all output times because\n",
- "NaN values occurred in output from ode()")
+ "NaN values occurred in output from ode()")
}
}
if (map_output) {
# Output transformation for models with unobserved compartments like SFORB
out_mapped <- data.frame(time = out[,"time"])
- for (var in names(mkinmod$map)) {
- if((length(mkinmod$map[[var]]) == 1) || solution_type == "analytical") {
+ for (var in names(x$map)) {
+ if((length(x$map[[var]]) == 1) || solution_type == "analytical") {
out_mapped[var] <- out[, var]
} else {
- out_mapped[var] <- rowSums(out[, mkinmod$map[[var]]])
+ out_mapped[var] <- rowSums(out[, x$map[[var]]])
}
}
return(out_mapped)
@@ -145,3 +159,16 @@ mkinpredict <- function(mkinmod, odeparms, odeini,
return(out)
}
}
+
+mkinpredict.mkinfit <- function(x,
+ odeparms = x$bparms.ode,
+ odeini = x$bparms.state,
+ outtimes = seq(0, 120, by = 0.1),
+ solution_type = "deSolve",
+ use_compiled = "auto",
+ method.ode = "lsoda", atol = 1e-8, rtol = 1e-10,
+ map_output = TRUE, ...)
+{
+ mkinpredict(x$mkinmod, odeparms, odeini, outtimes, solution_type, use_compiled,
+ method.ode, atol, rtol, map_output, ...)
+}

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