sample_nhanes(), which simulates virtual pediatric populations (ages 2-17) with realistic body weight and/or height by MEC-weighted resampling of children from four NHANES releases (2013-2023), bundled as nhanes_peds. Resampling keeps each child's weight and height together; method = "smooth" adds correlated kernel noise for continuous values. compare_nhanes() and plot_nhanes() check the simulated population against the reference. A new vignette, vignette("nhanes", package = "pmxTools"), walks through them.Added cut_quantile(), which creates quantile-based bins for one or more continuous variables, with per-variable control over the number of groups.
Added datamap(), which plots individual dosing and observation records over time.
dgr_table() now takes fields as a named character vector mapping column names to display labels. The separate names argument is deprecated, but unnamed fields with names continues to work.
Added dependencies purrr and tidyr.
Fixed read_nm(), which passed the file extension to xml2::read_xml() as an encoding rather than appending it to the file name, and read the unresolved file name instead of the one located on disk. The directory argument and file names given without the .xml extension were therefore ignored, and macOS reported an Unsupported encoding: .xml warning (#36).
Removed the blanket stats and utils imports, which caused a replacing previous import 'stats::filter' by 'dplyr::filter' warning when the package was loaded (#36).
calc_derived() and the calc_derived_*() functions now return AUCtau and AUCtau_dose_normalized as plain numbers. PKNCA 0.12.1.9000 attaches a method attribute to the AUC it returns, which propagated into the derived-parameter list and broke comparisons against plain numeric values (#37).
Test snapshots are now committed, the CI workflows have been refreshed, and the documentation has been regenerated with roxygen2 8.1.0 (#36).
calc_derived() and the calc_derived_*() functions now work with vector inputs (#29).
plot_dist has been rewritten to adapt to ggplot2 4.0.0 changes, and to make it more intuitive to interpret
Dependency gghalves has been removed
Many fixes and updates to documentation
dgr_table() now provides geometric means by default
gm() now provides options to strip NA values (na.rm) and non-positive values (neg.rm) before computation.
Added NCA parameter estimation to calc_derived_1cpt(), calc_derived_2cpt() and calc_derived_3cpt(), if dose and other required information (e.g. tinf, dur, tau) is provided.
Added a warning about flip-flop kinetics and their potential effects on derived half-lives to calc_derived_1cpt(), calc_derived_2cpt(), and calc_derived_3cpt().
Added blq_trans() and blq_log_trans() for assistance with visualization of measurements below a limit of quantification.
Added a test for valid XML to read_nm().
Small fixes and enhancements to read_nmtable_single() and read_nm_multi_table() to ensure that stray text is properly handled while reading in NONMEM output files.
count_na() now throws a warning if NaN values are included in the NA count, and indicates how many of them there are.
Changed the significant digits functionality for 95% confidence intervals for get_theta(), get_omega() and get_sigma(), and all functions that apply these.
Replaced gridExtra with patchwork.
Numerous small fixes.
Removed some unnecessary dependencies.
Added many new unit tests, increasing test coverage considerably.
Fixed another error in sample_uncert() which was still crashing the function.
Added helper functions count_na(), dgr_table(), gcv(), fmt_signif().
Added distribution plotting function plot_dist().
sample_uncert() which was crashing the function.Added vignette describing PK curves.
Fixed a systematic error in calc_sd_1cmt_linear_oral_0_lag(), calc_ss_1cmt_linear_oral_0_lag(), calc_sd_2cmt_linear_oral_0_lag() which resulted in incorrect curves being plotted.
Rewrote plot_scm function to produce tree diagrams via DiagrammeR.
Fixed a rare bug in get_auc in which measurements from different individuals could be erroneously mixed.
Amended (or added) read_nm(), read_nm_all(), read_nmext(), read_nmcov(), read_nmtables() functions to allow reading of multiple NONMEM estimation steps.
Clarified documentation for calc_derived().
Now using xml2 to read NONMEM-generated XML files.
Fixed partial argument match warnings encountered during tests.
Add function for calculting geometric CV.