diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinfit.R | 33 | ||||
| -rw-r--r-- | R/mkinpredict.R | 22 |
2 files changed, 49 insertions, 6 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index cf58a7d..6e455e1 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -30,6 +30,7 @@ mkinfit <- function(mkinmod, observed, plot = FALSE, quiet = FALSE,
err = NULL, weight = "none", scaleVar = FALSE,
atol = 1e-6, n.outtimes = 100,
+ trace_parms = FALSE,
...)
{
# Get the names of the state variables in the model
@@ -112,7 +113,7 @@ mkinfit <- function(mkinmod, observed, assign("calls", calls+1, inherits=TRUE) # Increase the model solution counter
# Trace parameter values if quiet is off
- if(!quiet) cat(P, "\n")
+ if(trace_parms) cat(P, "\n")
# Time points at which observed data are available
# Make sure we include time 0, so initial values for state variables are for time 0
@@ -216,10 +217,12 @@ mkinfit <- function(mkinmod, observed, }
fit$errmin <- errmin
- # Calculate dissipation times DT50 and DT90 from parameters
+ # Calculate dissipation times DT50 and DT90 and, if necessary, formation fractions
+ # from optimised parameters
parms.all = backtransform_odeparms(c(fit$par, parms.fixed), mod_vars)
fit$distimes <- data.frame(DT50 = rep(NA, length(obs_vars)), DT90 = rep(NA, length(obs_vars)),
row.names = obs_vars)
+ fit$ff <- vector()
fit$SFORB <- vector()
for (obs_var in obs_vars) {
type = names(mkinmod$map[[obs_var]])[1]
@@ -230,7 +233,7 @@ mkinfit <- function(mkinmod, observed, DT90 = log(10)/k_tot
for (k_name in k_names)
{
- fit$ff[[sub("^k_", "", k_name)]] = parms.all[[k_name]] / k_tot
+ fit$ff[[sub("k_", "", k_name)]] = parms.all[[k_name]] / k_tot
}
}
if (type == "FOMC") {
@@ -290,10 +293,12 @@ mkinfit <- function(mkinmod, observed, f_90 <- function(t) (SFORB_fraction(t) - 0.1)^2
DT90.o <- optimize(f_90, c(0.01, max_DT))$minimum
if (abs(DT90.o - max_DT) < 0.01) DT90 = NA else DT90 = DT90.o
+
for (k_out_name in k_out_names)
{
- fit$ff[[sub("^k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output
+ fit$ff[[sub("k_", "", k_out_name)]] = parms.all[[k_out_name]] / k_1output
}
+
# Return the eigenvalues for comparison with DFOP rate constants
fit$SFORB[[paste(obs_var, "b1", sep="_")]] = b1
fit$SFORB[[paste(obs_var, "b2", sep="_")]] = b2
@@ -310,6 +315,7 @@ mkinfit <- function(mkinmod, observed, fit$atol <- atol
fit$parms.all <- parms.all # Return all backtransformed parameters for summary
fit$odeparms.final <- parms.all[mkinmod$parms] # Return ode parameters for further fitting
+ fit$date <- date()
class(fit) <- c("mkinfit", "modFit")
return(fit)
@@ -337,7 +343,12 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) { param <- cbind(param, se)
dimnames(param) <- list(pnames, c("Estimate", "Std. Error"))
- ans <- list(residuals = object$residuals,
+ ans <- list(
+ version = as.character(packageVersion("mkin")),
+ Rversion = paste(R.version$major, R.version$minor, sep="."),
+ date.fit = object$date,
+ date.summary = date(),
+ residuals = object$residuals,
residualVariance = resvar,
sigma = sqrt(resvar),
modVariance = modVariance,
@@ -354,6 +365,7 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) { ans$fixed <- object$fixed
ans$errmin <- object$errmin
ans$parms.all <- object$parms.all
+ ans$ff <- object$ff
if(distimes) ans$distimes <- object$distimes
if(length(object$SFORB) != 0) ans$SFORB <- object$SFORB
class(ans) <- c("summary.mkinfit", "summary.modFit")
@@ -362,6 +374,11 @@ summary.mkinfit <- function(object, data = TRUE, distimes = TRUE, ...) { # Expanded from print.summary.modFit
print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), ...) {
+ cat("mkin version: ", x$version, "\n")
+ cat("R version: ", x$Rversion, "\n")
+ cat("Date of fit: ", x$date.fit, "\n")
+ cat("Date of summary:", x$date.summary, "\n")
+
cat("\nEquations:\n")
print(noquote(as.character(x[["diffs"]])))
df <- x$df
@@ -393,6 +410,12 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), . print(x$distimes, digits=digits,...)
}
+ printff <- !is.null(x$ff)
+ if(printff){
+ cat("\nEstimated formation fractions:\n")
+ print(data.frame(ff = x$ff), digits=digits,...)
+ }
+
printSFORB <- !is.null(x$SFORB)
if(printSFORB){
cat("\nEstimated Eigenvalues of SFORB model(s):\n")
diff --git a/R/mkinpredict.R b/R/mkinpredict.R index 2b7e51d..be43b0e 100644 --- a/R/mkinpredict.R +++ b/R/mkinpredict.R @@ -1,3 +1,23 @@ +# $Id$ + +# Copyright (C) 2010-2012 Johannes Ranke +# Contact: jranke@uni-bremen.de + +# This file is part of the R package mkin + +# mkin 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/> + mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "deSolve", map_output = TRUE, atol = 1e-6, ...) { # Get the names of the state variables in the model @@ -35,7 +55,7 @@ mkinpredict <- function(mkinmod, odeparms, odeini, outtimes, solution_type = "de evalparse(parent.name), evalparse(paste("k", parent.name, "bound", sep="_")), evalparse(paste("k", sub("free", "bound", parent.name), "free", sep="_")), - evalparse(paste("k", parent.name, sep="_"))) + evalparse(paste("k", parent.name, "sink", sep="_"))) ) out <- cbind(outtimes, o) dimnames(out) <- list(outtimes, c("time", sub("_free", "", parent.name))) |