News for Package nmw

Version 0.6.0 (2026-09-20)

• Requires simPDF 0.1.2. Report generation could stop with “attempt to apply non-function” when a block's height equalled the space left on the page to within floating-point error; that was a defect in simPDF 0.1.1, fixed in 0.1.2, and the report writer now relies on the fix instead of working around it.

• The eight diagnostic report functions and nmw_run() gain a format argument: "pdf" (default), "md", or c("pdf", "md"). With "md" the report is written as a Markdown file (the file name with its extension replaced by ‘.md’): headings, text, preformatted dumps and tables become GitHub-flavoured Markdown, and every figure page or inline plot is saved as an SVG file (or PNG with fig_format = "png") in a sibling ‘<name>_files’ directory and linked from the Markdown. The directory is emptied before each run.

• Outline() gains Target = "md": the model development flow diagram is written as a Markdown file (file, default ‘<MDLName>-Model-Flow.md’) with the diagram as an SVG (or PNG, fig_format) figure followed by the table of runs from SumOut(). The figure is sized to the tree (about 1.6 in per leaf column), so folders with dozens of sibling runs stay legible. The default Target = "PDF" still draws on the graphics device opened by the caller, as before; when no device is open (e.g. under Rscript) it now writes a PDF sized to the tree instead of failing. SumOut() no longer aborts on a run folder it cannot summarise (e.g. the empty ‘.ext’ of a simulation run, or a corrupt output file): the run is listed with Reason = "NOESTIMATION" or "UNREADABLE" and a warning names it, and GetEstMethod() returns NA for an empty ‘.ext’.

• The report functions now describe their content with a small internal block layer (‘R/report_writer.R’) that is rendered to simPDF for the PDF and to Markdown for the ‘.md’. The statistics and the PDF layout are unchanged.

• Fixed: headings of blocks that nmw_report_resid() and nmw_report_ebe() build in loops showed the last loop value in the PDF, because simPDF::block_para() evaluates its text lazily. In 0.5.x all three residual-count sections of ‘S4-Residuals.PDF’ were titled "IWRES" and all extreme-value tables "Extreme IWRES values", and in ‘S5-EBE.PDF’ every matrix in "Estimation vs EBE" was titled "Ratios of Cor(EBE)/(Cor from OM)" and every ETA section "ETA <last>". The new block layer evaluates text when the block is built.

• Fixed: nmw_report_indipk() drew its "Individual PK Parameters" heading and the first rows of the table onto the last figure page, where they were invisible, and only the overflow rows reached a fresh page. Flowing text that follows figure pages now always starts on a new page. The report also gained a title page ("Summary C - Individual PK Parameters"), like ‘S3-Predictions.PDF’.

• nmw_report_ebe() drops continuous covariates whose per-subject values are all equal (for example nominal time, day or occasion counters that start at the same value for every subject) from the covariate/EBE correlation matrix, the regressions and the ETA-vs-covariate panels. They produced all-NA rows and columns and flat panels.

• nmw_report_param() recognises runs without a successful $COV step (no <nm:thetase> in the XML): SE, LL, UL, ZERO and ONE are reported as NA with an explanatory note, fixed thetas are identified from the ‘.ext’ fixed-parameter row, and the Omega SE/RSE matrices are replaced by a note. Previously such runs showed SE = 0 for every theta and RSE of about 1e+12 for every omega. With a $COV step, fixed or structurally zero Omega elements are now shown as NA in the SE and RSE matrices instead of 1e+10 and Inf.

• nmw_report_ebe() shows NA instead of +/-Inf in the "Ratios of Cov(EBE)/OM" and "Ratios of Cor(EBE)/(Cor from OM)" matrices where the Omega element is zero, and in the individual RSE column where an ETA is exactly zero (e.g. an inter-occasion ETA of an absent occasion).

• Robustness fixes found by regenerating the reports for several hundred real runs: the ETA distribution panels no longer fail when an ETA has fewer than two non-zero values (e.g. an inter-occasion ETA in a single-occasion sensitivity run) or is constant; the pairs-plot panels restore par("usr") correctly (they emitted "argument 1 does not name a graphical parameter" on every S5 report); TAB characters in preformatted text (e.g. the summary.lm R-squared line) are expanded to spaces instead of triggering "font width unknown" warnings; and large matrices or tables are no longer forced onto one page with their heading, which overflowed the page for models with many ETAs and covariates.

• Data sets of $PRED models that lack MDV and/or AMT (for example the bundled theophylline examples) no longer make S1, S3, S4, S5 and SA fail with "undefined columns selected" or "subscript out of bounds": the missing items are added with NONMEM's implicit values (AMT = 0; MDV = 1 for dosing records, otherwise 0), an sdtab without MDV or CMT takes them from the record-aligned data set, and SA-Input notes which items were assumed and skips the "Individuals with no dosing" check when the data set has no AMT. ETAs that are zero for every subject are omitted from the covariate/EBE correlation matrix with a note instead of producing all-NA rows. The EBE regression no longer fails when there is exactly one covariate (RemoveNA() now keeps a one-column input as a data frame and accepts plain vectors).

• nmw_report_ebe() writes a short report stating that no empirical Bayes estimates are available when all ETAs in the ‘.phi’ file are zero (First Order estimation) and ‘patab’ is missing or also all zero, instead of failing.

• Text that is not valid UTF-8, such as control-stream comments in a legacy code page that NONMEM echoes into ‘PRINT.OUT’, no longer crashes R when drawn on the PDF device: it is converted from the code page in getOption("nmw.codepage") (default "CP949") when that yields valid text, otherwise the offending bytes are shown as <xx>.

• IPRE is optional in ‘sdtab’ (e.g. a PD model without IPRED in $TABLE): S3-Predictions omits the IPRE panels and curves with a note, and S4-Residuals plots CWRES and IWRES against PRED. IPRED, IWRES and CWRESI are accepted for IPRE, IWRE and CWRES. The influence-diagnostic panels of S5-EBE skip non-finite values instead of failing on ylim. A malformed table file (e.g. one containing merge-conflict markers) is reported by name.

• Worked around a simPDF (<= 0.1.1) edge case in which a block whose height equals the remaining page space up to floating-point error made the flow fail with "attempt to apply non-function" after the block had been drawn; the report writer now places blocks one at a time and continues.

• Missing run files now give a clear error naming the file, the run directory and the report that needs it (e.g. ‘patab’ for SC-IndiPK, ‘sdtab’ for S3/S4/S5, ‘FDATA.CSV’ for the data-based reports) instead of "cannot open the connection". ‘FDATA.csv’ is accepted as well as ‘FDATA.CSV’ on case-sensitive file systems.

• nmw_report_pred() and nmw_report_indipk() no longer open a graphics device (‘Rplots.pdf’ under Rscript) when none is open: the caller's par() state is saved and restored only if a device exists.

• Tables of individuals always carry an explicit ID column: the "Individual Statistics", "Individuals with no dosing" and "Individuals with no DV" tables of SA-Input (previously the ID was the row name, which was dropped when the IDs were 1..n), the "Variable Statistics" table gains a Variable column, and SC-IndiPK takes the subject IDs from the record-aligned data set when ‘patab’ was written without ID.

• The invisible return value of every report function now also contains md_file and figures; file and pages are NA when no PDF was requested.

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.