diff options
Diffstat (limited to 'R/plot.nlme.mmkin.R')
| -rw-r--r-- | R/plot.nlme.mmkin.R | 22 |
1 files changed, 17 insertions, 5 deletions
diff --git a/R/plot.nlme.mmkin.R b/R/plot.nlme.mmkin.R index ef6d100a..0f3ad715 100644 --- a/R/plot.nlme.mmkin.R +++ b/R/plot.nlme.mmkin.R @@ -11,6 +11,12 @@ #' @param standardized Should the residuals be standardized? This option #' is passed to \code{\link{mkinresplot}}, it only takes effect if #' `resplot = "time"`. +#' @param show_errmin Should the chi2 error level be shown on top of the plots +#' to the left? +#' @param errmin_var The variable for which the FOCUS chi2 error value should +#' be shown. +#' @param errmin_digits The number of significant digits for rounding the FOCUS +#' chi2 error percentage. #' @param cex Passed to the plot functions and \code{\link{mtext}}. #' @param rel.height.middle The relative height of the middle plot, if more #' than two rows of plots are shown. @@ -25,16 +31,19 @@ #' function(x) subset(x$data[c("name", "time", "value")], name == "parent")) #' f <- mmkin("SFO", ds, quiet = TRUE, cores = 1) #' #plot(f) # too many panels for pkgdown +#' plot(f[, 3:4]) #' library(nlme) #' f_nlme <- nlme(f) #' #' #plot(f_nlme) # too many panels for pkgdown -#' plot(f_nlme, 1:2) +#' plot(f_nlme, 3:4) #' @export plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), main = "auto", legends = 1, resplot = c("time", "errmod"), standardized = FALSE, + show_errmin = TRUE, + errmin_var = "All data", errmin_digits = 3, cex = 0.7, rel.height.middle = 0.9, ymax = "auto", ...) { @@ -79,13 +88,14 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), state_ini[names(odeini_optim)] <- odeini_optim odeparms <- fit_a$bparms.ode - odeparms[names(odeparms)] <- odeparms_optim + odeparms[names(odeparms_optim)] <- odeparms_optim mkinfit_call[["observed"]] <- ds[[a]] mkinfit_call[["parms.ini"]] <- odeparms mkinfit_call[["state.ini"]] <- state_ini - mkinfit_call[["control"]] <- list(iter.max = 1) + mkinfit_call[["control"]] <- list(iter.max = 0) + mkinfit_call[["quiet"]] <- TRUE res <- suppressWarnings(do.call("mkinfit", mkinfit_call)) return(res) @@ -94,9 +104,11 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), # Set dimensions with names and the class (mmkin) attributes(mmkin_nlme) <- attributes(x$mmkin_orig[, i]) - plot(mmkin_nlme[, i], main = main, legends = legends, + plot(mmkin_nlme, main = main, legends = legends, resplot = resplot, standardized = standardized, - show_errmin = FALSE, cex = cex, + show_errmin = show_errmin, + errmin_var = errmin_var, errmin_digits = errmin_digits, + cex = cex, rel.height.middle = rel.height.middle, ymax = ymax, ...) |