diff options
Diffstat (limited to 'R')
| -rw-r--r-- | R/mkinfit.R | 6 | ||||
| -rw-r--r-- | R/multistart.R | 4 | ||||
| -rw-r--r-- | R/parplot.R | 19 | ||||
| -rw-r--r-- | R/plot.mixed.mmkin.R | 2 |
4 files changed, 20 insertions, 11 deletions
diff --git a/R/mkinfit.R b/R/mkinfit.R index c851fddb..52053685 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -21,7 +21,8 @@ utils::globalVariables(c("name", "time", "value")) #' "FOMC", "DFOP", "HS", "SFORB", "IORE"). If a shorthand name is given, a #' parent only degradation model is generated for the variable with the #' highest value in \code{observed}. -#' @param observed A dataframe with the observed data. The first column called +#' @param observed A dataframe or an object coercible to a dataframe +#' (e.g. a \code{tibble}) with the observed data. The first column called #' "name" must contain the name of the observed variable for each data point. #' The second column must contain the times of observation, named "time". #' The third column must be named "value" and contain the observed values. @@ -292,6 +293,9 @@ mkinfit <- function(mkinmod, observed, # Get the names of observed variables obs_vars <- names(mkinmod$spec) + # Coerce observed data to a dataframe + observed <- as.data.frame(observed) + # Subset observed data with names of observed data in the model and remove NA values observed <- subset(observed, name %in% obs_vars) observed <- subset(observed, !is.na(value)) diff --git a/R/multistart.R b/R/multistart.R index aeea2d81..4ba82a43 100644 --- a/R/multistart.R +++ b/R/multistart.R @@ -40,7 +40,7 @@ #' f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE) #' f_saem_full <- saem(f_mmkin) #' f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16) -#' parplot(f_saem_full_multi, lpos = "topleft") +#' parplot(f_saem_full_multi, lpos = "topleft", las = 2) #' illparms(f_saem_full) #' #' f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2") @@ -50,7 +50,7 @@ #' library(parallel) #' cl <- makePSOCKcluster(12) #' f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl) -#' parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2)) +#' parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2), las = 2) #' stopCluster(cl) #' } multistart <- function(object, n = 50, diff --git a/R/parplot.R b/R/parplot.R index 3da4b51a..a33112a5 100644 --- a/R/parplot.R +++ b/R/parplot.R @@ -35,9 +35,6 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA, scale = c("best", "median"), lpos = "bottomleft", main = "", ...) { - oldpar <- par(no.readonly = TRUE) - on.exit(par(oldpar, no.readonly = TRUE)) - orig <- attr(object, "orig") orig_parms <- parms(orig) start_degparms <- orig$mean_dp_start @@ -59,11 +56,10 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA, selected <- which(ll > llmin) selected_parms <- all_parms[selected, ] - par(las = 1) if (orig$transformations == "mkin") { degparm_names_transformed <- names(start_degparms) degparm_index <- which(names(orig_parms) %in% degparm_names_transformed) - orig_parms[degparm_names_transformed] <- backtransform_odeparms( + orig_degparms <- backtransform_odeparms( orig_parms[degparm_names_transformed], orig$mmkin[[1]]$mkinmod, transform_rates = orig$mmkin[[1]]$transform_rates, @@ -74,14 +70,17 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA, transform_fractions = orig$mmkin[[1]]$transform_fractions) degparm_names <- names(start_degparms) - names(orig_parms) <- c(degparm_names, names(orig_parms[-degparm_index])) + orig_parms_back <- orig_parms + orig_parms_back[degparm_index] <- orig_degparms + names(orig_parms_back)[degparm_index] <- degparm_names + orig_parms <- orig_parms_back selected_parms[, degparm_names_transformed] <- t(apply(selected_parms[, degparm_names_transformed], 1, backtransform_odeparms, orig$mmkin[[1]]$mkinmod, transform_rates = orig$mmkin[[1]]$transform_rates, transform_fractions = orig$mmkin[[1]]$transform_fractions)) - colnames(selected_parms)[1:length(degparm_names)] <- degparm_names + colnames(selected_parms)[degparm_index] <- degparm_names } start_errparms <- orig$so@model@error.init @@ -99,6 +98,12 @@ parplot.multistart.saem.mmkin <- function(object, llmin = -Inf, llquant = NA, # Boxplots of all scaled parameters selected_scaled_parms <- t(apply(selected_parms, 1, function(x) x / parm_scale)) + i_negative <- selected_scaled_parms <= 0 + parms_with_negative_scaled_values <- paste(names(which(apply(i_negative, 2, any))), collapse = ", ") + if (any(i_negative)) { + warning("There are negative values for ", parms_with_negative_scaled_values, " which are set to NA for plotting") + } + selected_scaled_parms[i_negative] <- NA boxplot(selected_scaled_parms, log = "y", main = main, , ylab = "Normalised parameters", ...) diff --git a/R/plot.mixed.mmkin.R b/R/plot.mixed.mmkin.R index d6c3d0de..f05f1110 100644 --- a/R/plot.mixed.mmkin.R +++ b/R/plot.mixed.mmkin.R @@ -93,7 +93,7 @@ plot.mixed.mmkin <- function(x, nrow.legend = ceiling((length(i) + 1) / ncol.legend), rel.height.legend = 0.02 + 0.07 * nrow.legend, rel.height.bottom = 1.1, - pch_ds = 1:length(i), + pch_ds = c(1:25, 33, 35:38, 40:41, 47:57, 60:90)[1:length(i)], col_ds = pch_ds + 1, lty_ds = col_ds, frame = TRUE, ... |