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authorJohannes Ranke <jranke@uni-bremen.de>2017-10-18 10:17:59 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2017-10-18 10:17:59 +0200
commitbe6d42ef636e8e1c9fdcfa6f8738ee10e885d75b (patch)
treeb676def6da66527c056e25fa5a127b97ca3a5560 /CakeOlsPlot.R
Version 1.4v1.4
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+#$Id: CakeOlsPlot.R 216 2011-07-05 14:35:03Z nelr $
+# Generates fitted curves so the GUI can plot them
+# Based on code in IRLSkinfit
+# Author: Rob Nelson (Tessella)
+# Modifications developed by Tessella Plc for Syngenta: Copyright (C) 2011 Syngenta
+# Tessella Project Reference: 6245
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.”
+
+CakeOlsPlot <- function(fit, xlim = range(fit$data$time), ...)
+{
+ cat("<PLOT MODEL START>\n")
+
+ solution = fit$solution
+ if ( is.null(solution) ) {
+ solution <- "deSolve"
+ }
+ atol = fit$atol
+ if ( is.null(atol) ) {
+ atol = 1.0e-6
+ }
+
+ fixed <- fit$fixed$value
+ names(fixed) <- rownames(fit$fixed)
+ parms.all <- c(fit$par, fixed)
+ ininames <- c(
+ rownames(subset(fit$start, type == "state")),
+ rownames(subset(fit$fixed, type == "state")))
+ odeini <- parms.all[ininames]
+ names(odeini) <- names(fit$diffs)
+
+ outtimes <- seq(0, xlim[2], length.out=101)
+
+ odenames <- c(
+ rownames(subset(fit$start, type == "deparm")),
+ rownames(subset(fit$fixed, type == "deparm")))
+ odeparms <- parms.all[odenames]
+
+ # Solve the system
+ evalparse <- function(string)
+ {
+ eval(parse(text=string), as.list(c(odeparms, odeini)))
+ }
+ if (solution == "analytical") {
+ parent.type = names(fit$map[[1]])[1]
+ parent.name = names(fit$diffs)[[1]]
+ o <- switch(parent.type,
+ SFO = SFO.solution(outtimes,
+ evalparse(parent.name),
+ evalparse(paste("k", parent.name, sep="_"))),
+ FOMC = FOMC.solution(outtimes,
+ evalparse(parent.name),
+ evalparse("alpha"), evalparse("beta")),
+ DFOP = DFOP.solution(outtimes,
+ evalparse(parent.name),
+ evalparse("k1"), evalparse("k2"),
+ evalparse("g")),
+ HS = HS.solution(outtimes,
+ evalparse(parent.name),
+ evalparse("k1"), evalparse("k2"),
+ evalparse("tb")),
+ SFORB = SFORB.solution(outtimes,
+ evalparse(parent.name),
+ evalparse(paste("k", parent.name, "free_bound", sep="_")),
+ evalparse(paste("k", parent.name, "bound_free", sep="_")),
+ evalparse(paste("k", parent.name, "free_sink", sep="_")))
+ )
+ out <- cbind(outtimes, o)
+ dimnames(out) <- list(outtimes, c("time", parent.name))
+ }
+ if (solution == "eigen") {
+ coefmat.num <- matrix(sapply(as.vector(fit$coefmat), evalparse),
+ nrow = length(odeini))
+ e <- eigen(coefmat.num)
+ c <- solve(e$vectors, odeini)
+ f.out <- function(t) {
+ e$vectors %*% diag(exp(e$values * t), nrow=length(odeini)) %*% c
+ }
+ o <- matrix(mapply(f.out, outtimes),
+ nrow = length(odeini), ncol = length(outtimes))
+ dimnames(o) <- list(names(odeini), NULL)
+ out <- cbind(time = outtimes, t(o))
+ }
+ if (solution == "deSolve") {
+ out <- ode(
+ y = odeini,
+ times = outtimes,
+ func = fit$mkindiff,
+ parms = odeparms,
+ atol = atol
+ )
+ }
+
+ # Output transformation for models with unobserved compartments like SFORB
+ out_transformed <- data.frame(time = out[,"time"])
+ for (var in names(fit$map)) {
+ if(length(fit$map[[var]]) == 1) {
+ out_transformed[var] <- out[, var]
+ } else {
+ out_transformed[var] <- rowSums(out[, fit$map[[var]]])
+ }
+ }
+ print(out_transformed)
+
+ cat("<PLOT MODEL END>\n")
+}

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