News for Package nmw

Version 0.5.1 (2026-08-21)

• nmw_report_resid() now omits unavailable residual diagnostics cleanly when sdtab lacks WRES, CWRES, or IWRE, or when such a column contains no finite values. Binomial tests, extreme-value tables, distribution plots, and subject plots are generated only for usable residuals; missing panels contain an explanatory placeholder rather than failing on non-finite plot limits.

• Diagnostic report functions now document their invisible summary return values. The model argument documentation for nmw_report_output() and nmw_report_indipk() now states that it is accepted only for a uniform report API because those reports read the fixed files ‘PRINT.OUT’ and ‘patab’.

• The minimum simPDF version is now 0.1.1, the first CRAN release, and the minimum R version is aligned with simPDF at 3.6.0.

• Regression tests now exercise PDF generation and the missing IWRE case using the bundled NONMEM example.

Version 0.5.0 (2026-07-11)

• The eight diagnostic report functions (nmw_report_ofv, nmw_report_param, nmw_report_pred, nmw_report_resid, nmw_report_ebe, nmw_report_input, nmw_report_output, nmw_report_indipk) are re-implemented on the simPDF report engine (now in Imports). The statistics/parsing is unchanged; the former dead-reckoned pdf() + PrinTxt/split.screen layout is replaced by a measured flowing layout, which eliminates the text/matrix overlap that appeared in S2-Parameters.PDF for models with many random effects (validated overlap-free across hundreds of real runs, up to 14 ETAs). Each report gained file and model arguments (backward compatible).

• nmw_report_pred no longer errors on subjects/compartments with no observation records (the "zero-length labels" crash); nmw_report_resid tolerates an sdtab that is missing a residual column (e.g. IWRE).

• The low-level layout helpers PrepPDF, PrinTxt, AddPage, PrinMTxt and ClosePDF are removed (superseded by simPDF); DxPlotPost is retained.

Version 0.4.0 (2026-07-08)

• New function ctl2nmw(): reads a closed-form $PRED NONMEM control stream and auto-generates the PRED function (with its deriv() companions) and the initial estimates (THETAinit, OMinit, SGinit, LB, UB, METHOD) needed by InitStep(). This removes the main inconvenience of the package: hand-writing the PRED function. The generated PRED reproduces the hand-written example PRED numerically (verified to floating-point tolerance for FO, FOCE-INTER and Laplace on the bundled THEO control streams).

• The generator classifies free symbols over both the structural model F and the error model Y, so a THETA or data item that appears only in the residual error (e.g. a combined additive-plus-proportional W term) is wired into H correctly. Random-effect subscripts are ordered numerically (so ETA10 follows ETA9), and $PRED ETA/EPS indices are cross-checked against $OMEGA/$SIGMA.

• Out-of-scope control streams fail with an informative message rather than generating incorrect code: ODE models ($PK/$DES/$SUBROUTINE/ADVAN), IF/THEN branching, MU-referencing, mixtures, unsupported estimation methods, and FIXed parameters. Assigning the same symbol more than once in $PRED (sequential reassignment) or referencing a symbol before it is defined is likewise rejected, as is a $THETA initial estimate on or outside its bounds (InitStep() scaling needs LB < init < UB). A diagonal $OMEGA is promoted to a full block, a non-diagonal $SIGMA is reduced to its diagonal, and an unbounded $THETA with a non-positive initial estimate gets LB = -1e6 instead of the usual default 0, each with a note.

• The environment e is exported again. It had been exported up to 0.1.6 via exportPattern() and was inadvertently dropped in 0.2.0's switch to explicit exports. Without it, a user-written PRED function referencing e$METHOD – the documented workflow, and also the code that ctl2nmw() generates – stopped with “object 'e' not found” when EstStep() ran it, and reading results with get("EBE", envir=e) failed likewise.

• Internal refactoring (prepared as an unreleased 0.3.2) is included in this release. It changes no other public API and no numerical result of the estimation steps (FO, FOCE-INTER, Laplace) or of any diagnostic report; verified by comparing the estimation output and all eight report PDFs against the pre-refactor sources on the bundled example run.

• De-duplication: the covariate-classification block repeated three times inside report_ebe is now the internal helper ClassifyCovariates(); the shared record-count extraction is GetNRecFromXML(); NMVarStat() reuses the AllNA()/AllSame() helpers.

• Bug fix: the “Sigmas” section of nmw_report_param (S2-Parameters) no longer errors for models with two or more SIGMA elements (e.g. a combined additive-plus-proportional error model); a test that mixed && and & produced a condition of length greater than one.

• Bug fix: PanelCor() no longer errors when an explicit cex.cor value is supplied (an undefined cex was referenced).

• InitStep(): the documented LB/UB defaults (0 and 1e6) are now applied before they are used, so omitting these arguments works as documented instead of raising an error. Passing LB/UB explicitly behaves exactly as before.

• Loop bounds in the data-handling utilities (AddDoNoTaLD, ExpandDoseHist, RemoveNA, RmvFixed, RmvZero, RenCol) and in the shared report helpers now use seq_len()/seq_along() so they no longer misbehave on zero-row input.

• Housekeeping: removed leftover working files and dead commented code from R/, replaced T/F literals with TRUE/FALSE, corrected user-visible typos in report titles and labels (“Individiual”, “Estitmate”, “Recods”), and corrected the TrimOut() return-value documentation.

Version 0.3.1 (2026-06-09)

• 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.

Version 0.3.0 (2026-05-08)

• 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.

Version 0.2.0 (2026-03-08)

• 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.

Version 0.1.6 (2026-03-08)

• Typos in documentation corrected.

Version 0.1.5 (2023-05-09)

• 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.

Version 0.1.4 (2018-04-10)

• Errata in manual corrected.

Version 0.1.3 (2017-10-23)

• TabStep() is added.

• Speed is increased.

• References are updated.

• Vignette is updated.

Version 0.1.2 (2017-10-20)

• 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.

Version 0.1.1 (2017-03-14)

• 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.

Version 0.1.0 (2017-02-21)

• This package was born and used at the Workshop held by Kyun-Seop Bae MD PhD <k@acr.kr>.

• InitStep used Pred function within a file.