Loading NONMEM (NONlinear Mixed-Effect Modeling, < http://www.iconplc.com/innovation/solutions/nonmem/>) and PSN (Perl-speaks-NONMEM, < https://uupharmacometrics.github.io/PsN/>) output files to extract parameter estimates, provide visual predictive check (VPC) and goodness of fit (GOF) plots, and simulate with parameter uncertainty.
The functions have e.g. functionality for adding caption which also have been added to vpcfig2 and vpcfig3.
Using global package variable to specify the model folder instead of looking for the variable "model.path" holding the path to model files, the function set.model.path is used set the folder path.
vpcfig2: Added parameter param bin.idv to either use median of independent variable on x-axis (default), or to use midpoint of bins on x-axis.
vpcfig2: Added argument median.only to only display median (median.only=TRUE) or display both quantile (e.g. 5 and 95%) and median (median.only=FALSE, this is the default)
vpcfig3: Added ... parameter to vpcfig3 that are passed to loess.smooth
Update of systemNM for SCP
Bug fix for modload. Previuous version did not run when using model.path.
Fixed issue for vpc folders with multiple vpc_results and vpctab files (e.g. vpc_results-old1, vpctab-old1). Now only filesnames NOT containing "old" are loaded.
Added vpcfig3 for creating multiple VPC plots from one single PSN vpc output file
Added modload for loading model file and print on screen
Added stat_QQnorm for Quantile-Quantile plots with ggplot2
Added stat_QQCL for confidence intervals for Quantile-Quantile plots with ggplot2
Updated vpgfig2; now using geom_ribbon (instead of geom_polygon) for drawing model confidence intervals. This means x-axis limits can be set by e.g. xlim or scale_x_continuous. (Previous version using geom_polygon required using coord_cartesian for setting axis limits to avoid a corrupted VPC.)
Added model.path argument to vpcfig & vpcfig2, with similar use of model.path as in e.g. sumoR & extload
Add footnote extToTable to keep track if OMEGA and SIGMA are reported as variances or as standard-deviations
Updated covload to handle cov files with multiple tables from NONMEM model files with multiple $COV and/or multiple $EST.
Fixed column names for covload output
Updated help-page for vpcfig2 with advice for setting axis limits