diff options
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | NEWS.md | 6 | ||||
| -rw-r--r-- | R/mkinerrplot.R | 3 | ||||
| -rw-r--r-- | R/plot.mkinfit.R | 9 | ||||
| -rw-r--r-- | R/plot.mmkin.R | 25 | ||||
| -rw-r--r-- | man/mkinerrplot.Rd | 4 | ||||
| -rw-r--r-- | man/plot.mkinfit.Rd | 5 | ||||
| -rw-r--r-- | man/plot.mmkin.Rd | 7 |
8 files changed, 41 insertions, 20 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index b95c33bd..bc8e61d6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data Version: 0.9.49.6 -Date: 2019-07-05 +Date: 2019-09-02 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de", comment = c(ORCID = "0000-0003-4371-6538")), @@ -1,4 +1,8 @@ -# mkin 0.9.49.6 (2019-07-08) +# mkin 0.9.49.6 (unreleased) + +- Support frameless plots ('frame = FALSE') + +- Support to suppress the chi2 error level ('show_errmin = FALSE') in 'plot.mmkin' - Update README and the introductory vignette diff --git a/R/mkinerrplot.R b/R/mkinerrplot.R index cc163922..6153a3c0 100644 --- a/R/mkinerrplot.R +++ b/R/mkinerrplot.R @@ -23,6 +23,7 @@ mkinerrplot <- function (object, xlab = "Predicted", ylab = "Squared residual", maxy = "auto", legend= TRUE, lpos = "topright", col_obs = "auto", pch_obs = "auto", + frame = TRUE, ...) { obs_vars_all <- as.character(unique(object$data$variable)) @@ -48,7 +49,7 @@ mkinerrplot <- function (object, plot(0, type = "n", xlab = xlab, ylab = ylab, xlim = xlim, - ylim = c(0, 1.2 * maxy), ...) + ylim = c(0, 1.2 * maxy), frame = frame, ...) for(obs_var in obs_vars){ residuals_plot <- subset(object$data, variable == obs_var, c("predicted", "residual")) diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R index df9888e7..2a82301f 100644 --- a/R/plot.mkinfit.R +++ b/R/plot.mkinfit.R @@ -31,7 +31,8 @@ plot.mkinfit <- function(x, fit = x, maxabs = "auto", sep_obs = FALSE, rel.height.middle = 0.9, lpos = "topright", inset = c(0.05, 0.05), - show_errmin = FALSE, errmin_digits = 3, ...) + show_errmin = FALSE, errmin_digits = 3, + frame = TRUE, ...) { if (add && show_residuals) stop("If adding to an existing plot we can not show residuals") if (add && show_errplot) stop("If adding to an existing plot we can not show the error model plot") @@ -138,7 +139,7 @@ plot.mkinfit <- function(x, fit = x, if (add == FALSE) { plot(0, type="n", xlim = xlim, ylim = ylim_row, - xlab = xlab, ylab = ylab, ...) + xlab = xlab, ylab = ylab, frame = frame, ...) } # Plot the data @@ -197,7 +198,7 @@ plot.mkinfit <- function(x, fit = x, plot(0, type="n", xlim = xlim, ylim = c(-1.2 * maxabs_row, 1.2 * maxabs_row), - xlab = xlab, ylab = "Residuals") + xlab = xlab, ylab = "Residuals", frame = frame) for(obs_var in row_obs_vars){ residuals_plot <- subset(fit$data, variable == obs_var, c("time", "residual")) points(residuals_plot, pch = pch_obs[obs_var], col = col_obs[obs_var]) @@ -208,7 +209,7 @@ plot.mkinfit <- function(x, fit = x, # Show error model plot if requested if (show_errplot) { mkinerrplot(fit, obs_vars = row_obs_vars, pch_obs = pch_obs[row_obs_vars], col_obs = col_obs[row_obs_vars], - legend = FALSE) + legend = FALSE, frame = frame) } } if (do_layout) par(oldpar, no.readonly = TRUE) diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R index c9d98718..ef80949c 100644 --- a/R/plot.mmkin.R +++ b/R/plot.mmkin.R @@ -18,6 +18,7 @@ plot.mmkin <- function(x, main = "auto", legends = 1, resplot = c("time", "errmod"), + show_errmin = TRUE, errmin_var = "All data", errmin_digits = 3, cex = 0.7, rel.height.middle = 0.9, ...) { n.m <- nrow(x) @@ -83,23 +84,27 @@ plot.mmkin <- function(x, main = "auto", legends = 1, datasets = colnames(x)[i.fit], none = "") - chi2 <- signif(100 * mkinerrmin(fit)[errmin_var, "err.min"], errmin_digits) - - # Use LateX if the current plotting device is tikz - if (names(dev.cur()) == "tikz output") { - chi2_text <- paste0(fit_name, " $\\chi^2$ error level = ", chi2, "\\%") - } else { - chi2_perc <- paste0(chi2, "%") - chi2_text <- bquote(.(fit_name) ~ chi^2 ~ "error level" == .(chi2_perc)) + if (show_errmin) { + chi2 <- signif(100 * mkinerrmin(fit)[errmin_var, "err.min"], errmin_digits) + + # Use LateX if the current plotting device is tikz + if (names(dev.cur()) == "tikz output") { + chi2_text <- paste0(fit_name, " $\\chi^2$ error level = ", chi2, "\\%") + } else { + chi2_perc <- paste0(chi2, "%") + chi2_text <- bquote(.(fit_name) ~ chi^2 ~ "error level" == .(chi2_perc)) + } + mtext(chi2_text, cex = cex, line = 0.4) } - mtext(chi2_text, cex = cex, line = 0.4) if (resplot == "time") { mkinresplot(fit, legend = FALSE, ...) } else { mkinerrplot(fit, legend = FALSE, ...) } - mtext(paste(fit_name, "residuals"), cex = cex, line = 0.4) + if (show_errmin) { + mtext(paste(fit_name, "residuals"), cex = cex, line = 0.4) + } } par(oldpar, no.readonly = TRUE) diff --git a/man/mkinerrplot.Rd b/man/mkinerrplot.Rd index 3b557b0a..37338d01 100644 --- a/man/mkinerrplot.Rd +++ b/man/mkinerrplot.Rd @@ -18,6 +18,7 @@ xlab = "Predicted", ylab = "Squared residual", maxy = "auto", legend= TRUE, lpos = "topright", col_obs = "auto", pch_obs = "auto", + frame = TRUE, ...) } \arguments{ @@ -54,6 +55,9 @@ \item{pch_obs}{ Symbols to be used for the observed variables. } + \item{frame}{ + Should a frame be drawn around the plots? + } \item{\dots}{ further arguments passed to \code{\link{plot}}. } diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index 5e20ad90..a4f47073 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -27,7 +27,7 @@ maxabs = "auto", sep_obs = FALSE, rel.height.middle = 0.9, lpos = "topright", inset = c(0.05, 0.05), - show_errmin = FALSE, errmin_digits = 3, \dots) + show_errmin = FALSE, errmin_digits = 3, frame = TRUE, \dots) plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, \dots) } \arguments{ @@ -105,6 +105,9 @@ plot_sep(fit, sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE, \dots) \item{errmin_digits}{ The number of significant digits for rounding the FOCUS chi2 error percentage. } + \item{frame}{ + Should a frame be drawn around the plots? + } \item{\dots}{ Further arguments passed to \code{\link{plot}}. } diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd index 44e5e4c7..90b92d27 100644 --- a/man/plot.mmkin.Rd +++ b/man/plot.mmkin.Rd @@ -13,8 +13,8 @@ } \usage{ \method{plot}{mmkin}(x, main = "auto", legends = 1, - resplot = c("time", "errmod"), errmin_var = "All data", errmin_digits = 3, - cex = 0.7, rel.height.middle = 0.9, ...) + resplot = c("time", "errmod"), show_errmin = TRUE, errmin_var = "All data", + errmin_digits = 3, cex = 0.7, rel.height.middle = 0.9, ...) } \arguments{ \item{x}{ @@ -31,6 +31,9 @@ or as squared residuals against predicted values, with the error model, using \code{\link{mkinerrplot}}. } + \item{show_errmin}{ + Should the chi2 error level be shown on top of the plots to the left? + } \item{errmin_var}{ The variable for which the FOCUS chi2 error value should be shown. } |