diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/add_err.R | 48 | ||||
| -rw-r--r-- | R/plot.mmkin.R | 15 |
2 files changed, 56 insertions, 7 deletions
diff --git a/R/add_err.R b/R/add_err.R new file mode 100644 index 00000000..0995e634 --- /dev/null +++ b/R/add_err.R @@ -0,0 +1,48 @@ +# Copyright (C) 2015-2016 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/> + +add_err = function(prediction, sdfunc, + n = 1000, LOD = 0.1, reps = 2, + digits = 1, seed = NA) +{ + if (!is.na(seed)) set.seed(seed) + + # The output of mkinpredict is in wide format + d_long = mkin_wide_to_long(prediction, time = "time") + + # Set up the list to be returned + d_return = list() + + # Generate datasets one by one in a loop + for (i in 1:n) { + d_rep = data.frame(lapply(d_long, rep, each = 2)) + d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value)) + + d_rep[d_rep$time == 0 & d_rep$name %in% c("M1", "M2"), "value"] <- 0 + + # Set values below the LOD to NA + d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value)) + + # Round the values for convenience + d_NA$value <- round(d_NA$value, digits) + + d_return[[i]] <- d_NA + } + + return(d_return) +} diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R index 02bf4d6e..7b54be4b 100644 --- a/R/plot.mmkin.R +++ b/R/plot.mmkin.R @@ -20,12 +20,17 @@ plot.mmkin <- function(x, main = "auto", legends = 1, errmin_var = "All data", e cex = 0.7, rel.height.middle = 0.9, ...) { n.m <- nrow(x) n.d <- ncol(x) + + # We can handle either a row (different models, same dataset) + # or a column (same model, different datasets) if (n.m > 1 & n.d > 1) stop("Please select fits either for one model or for one dataset") if (n.m == 1 & n.d == 1) loop_over = "none" if (n.m > 1) loop_over <- "models" if (n.d > 1) loop_over <- "datasets" n.fits <- length(x) + # Set the main plot titles from the names of the models or the datasets + # Will be integer indexes if no other names are present in the mmkin object if (main == "auto") { main = switch(loop_over, none = paste(rownames(x), colnames(x)), @@ -34,11 +39,13 @@ plot.mmkin <- function(x, main = "auto", legends = 1, errmin_var = "All data", e } oldpar <- par(no.readonly = TRUE) + + # Set relative plot heights, so the first and the last plot are the norm + # and the middle plots (if n.fits >2) are smaller by rel.height.middle rel.heights <- if (n.fits > 2) c(1, rep(rel.height.middle, n.fits - 2), 1) else rep(1, n.fits) layout(matrix(1:(2 * n.fits), n.fits, 2, byrow = TRUE), heights = rel.heights) - #par(mfrow = c(n.fits, 2)) par(mar = c(3.0, 4.1, 4.1, 2.1)) # Reduce bottom margin by 2.1 - hides x axis legend par(cex = cex) @@ -48,12 +55,6 @@ plot.mmkin <- function(x, main = "auto", legends = 1, errmin_var = "All data", e # reduced plot height, therefore we need rel.height.middle in the layout par(mar = c(3.0, 4.1, 2.1, 2.1)) } - if (i.fit == n.fits) { - # Reduce top margin by 2 after the first plot as we have no main title, - # plot height remains about constant - par(mar = c(5.1, 4.1, 2.1, 2.1)) - - } fit <- x[[i.fit]] plot(fit, legend = legends == i.fit, ...) |