SumOut() bug fix: the line RunFolders <- MatchEnd(Folders, RunExt) previously assigned the logical vector returned by MatchEnd() to RunFolders instead of using it as a mask to subset Folders. This caused strsplit() inside GetModelNames() to fail with "non-character argument" whenever any run folders were present. Now RunFolders <- Folders[MatchEnd(Folders, RunExt)].
SumOut() default RunExt changed from ".R75" to ".R76" to match NONMEM 7.6 (the current production release). Users on NONMEM 7.5 should pass RunExt = ".R75" explicitly.
SumOut() now warns and returns invisible(NULL) when no matching run folders are found, instead of erroring on a zero-length loop.
GetProbVal() bug fix: grep(Tag, PROB) returns integer(0) when the requested tag (e.g. "P:" or "F:") is absent — for example when the $PROB record is longer than 80 characters and NM-TRAN truncates it inside the FCON file, dropping the tag. The previous if (Loc > 0) test raised "argument is of length zero". The test was changed to if (length(Loc) > 0 && Loc[1] > 0), returning an empty string when the tag is absent.
man/SumOut.Rd updated to reflect the new default RunExt and a richer description of the return value.
MatchEnd() bug fix: replaced for (i in 1:n) with for (i in seq_len(n)) so that calling on an empty character vector no longer iterates over c(1, 0) and tries to read NA elements.
Regression tests added in tests/testthat/test-utils_data.R covering the SumOut() empty-folder, GetProbVal() missing-tag, and MatchEnd() empty-input cases.
report_ebe() (S5 “ETA vs Categorical Variables”) bug fix: when the number of ETAs times the number of categorical covariates produced a panel grid too dense for boxplot margins, plot.new() raised “figure margins too large” and the PDF was truncated mid-page. The categorical-covariate panels are now split across multiple PDF pages (cap of ~35 panels per page, configurable through the internal MAX_CELLS_PER_PAGE constant), with page numbers appended to the panel title when more than one page is produced.
General-purpose helpers for NONMEM dataset construction added (build_nm_dataset, build_dose_records, build_obs_records).
Time-varying covariate merge by LOCF/LOCB: locf_value, merge_cov_locf.
Datetime parsers: parse_dtc, dat2_time_to_posix.
Coding helpers: code_sex, code_race.
Cockcroft-Gault CRCL: crcl_cg, add_crcl_cg.
Mass to molar unit conversion: nm_to_molar.
Post-run processing of NONMEM output with PDF diagnostic reports merged from nma package.
8 report types: OFV, Parameters, Predictions, Residuals, EBE, Input, Output, IndiPK.
New utility functions for NONMEM data processing and parsing.
Switched from exportPattern to explicit exports in NAMESPACE.
Typos in documentation corrected.
AddCox function for adding a covariate to existing NONMEM dataset.
CombDmExPc function for combining demographics(DM), dosing(EX), and DV(PC) tables.
TrimOut function to beautify the original NONMEM OUTPUT
Errata in manual corrected.
Errata in manual corrected.
TabStep() is added.
Speed is increased.
References are updated.
Vignette is updated.
This package will be used at the workshop on 2017-10-25 at Kyoto Japan 1st APC satellite workshop.
Bug at calculating objective function value for "LAPL" method is fixed.
Bug at scaling other than zero lower bound transformation fixed.
This package will be used at the workshop within US FDA on 2017-03-21.
For the initialization step, Pred function name should be given by the user. It does not read directly from the file any more.
This package was born and used at the Workshop held by Kyun-Seop Bae MD PhD <[email protected]>.
InitStep used Pred function within a file.