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Changelog

Source: NEWS.md

nlmixr2plot 5.2.0

CRAN release: 2026-09-22

  • Added automatic model diagrams (#10). modelGraph() parses a model’s differential equations (from a model function, rxode2 model/UI or an nlmixr2 fit) into a graph of compartments and flows (mass transfer, eliminations, inputs and non-mass-transfer interactions like effect compartments or PD stimulation/inhibition), detecting dosing compartments from the dosing records. modelDiagram() lays it out with dosing and absorption compartments above the central compartment, peripheral compartments to the left, eliminations/metabolites below and PD models to the right, and draws it with the "DiagrammeR" (Graphviz), "ggplot2" or "dot" (DOT source) engine. Dosing properties (lag(), f(), rate(), dur()) are shown as annotations on their compartment, and delay() terms are understood. The diagrams were checked against all 3043 models of ‘nlmixr2lib’, including large QSP/PBPK models. plot() of an rxode2 user interface (rxUi) object or compiled rxode2 model draws its diagram, and the new “Automatic model diagrams” vignette describes the feature.

  • Fixed vpcPlot() with method = "tidyvpc" when the observed data has observation records with a missing DV. Those records were dropped from the observed data but kept in the simulation, so a stratified (e.g. multiple-endpoint) VPC errored and a single-endpoint VPC paired simulated values with the wrong observations. The matching simulated records are now dropped too (#74).

  • plot() of a multiple-endpoint fit no longer creates empty “Endpoint:” groups for state compartments without observations (like depot or central); only observed endpoints are plotted. plot() of an augPred() object likewise skips endpoints without data (#44).

  • vpcPlot()/vpcPlotTad() of a multiple-endpoint fit whose data codes the endpoints with cmt no longer shows an extra NA panel (or a single NA panel with pred_corr = TRUE); the simulated compartment labels are now matched to the observed ones by name (#44).

  • The censored VPC (vpcCens(), or vpcPlot() with cens = TRUE and the vpc backend) of a multiple-endpoint fit now stratifies by its endpoints only, matching the simulated endpoints to the observed ones; an endpoint whose observations are all missing no longer becomes an NA panel (#44).

  • plot() of a censored multiple-endpoint fit no longer errors in geom_cens() (“argument must be coercible to non-negative integer”) for an endpoint without censored observations (#44).

  • The censored VPC (vpcCens(), vpcCensTad(), or vpcPlot() with cens = TRUE and the vpc backend) now honours the data argument; it previously always used the fitted data, whatever data was supplied (#55). The observed data now comes from the original (or supplied) dataset instead of the fit, so censored records are identified from the CENS column rather than from the fit’s imputed DV (which, for censMethod = "cdf", could land above the limit and be counted as uncensored). Records without an observation are dropped, as in the fit.

  • The VPC observed data now drops records with MDV = 1 even when an EVID column is also present (previously only EVID was checked when both existed).

  • plot() of an augPred() object now accepts a base-R style log argument (log = "y", "x" or "xy") to draw the individual plots on log-scaled axes; non-positive values, which cannot be shown on a log axis, are dropped (#32).

  • vpcPlot(), vpcPlotTad(), vpcCens() and vpcCensTad() now use a supplied nlmixr2est::vpcSim() simulation instead of discarding it and re-simulating with the default n = 300. Supplying n alongside a simulation warns that it is ignored, and pred_corr = TRUE errors unless the simulation was created with pred = TRUE (#57). The observed-data prediction correction for a supplied simulation is computed from that simulation’s own fit rather than from whichever vpcSim(pred = TRUE) ran last.

  • Fixed the VPC simulation ignoring the data argument of vpcPlot(), vpcPlotTad(), vpcCens() and vpcCensTad(); the simulation always used the fit’s dataset, so it did not match the observed data built from data (and tidyvpc warned that xsim did not match the observed x-values). The simulation now uses data when supplied. A supplied nlmixr2est::vpcSim() simulation was made from its own dataset, so passing data alongside one now warns that it only replaces the observed data (#68). Because the simulation now follows data, an endpoint without observations in data is no longer simulated either, so it drops out of a multiple-endpoint VPC instead of being shown as a simulated-only panel. For a model with a non-normal endpoint, data now needs a numeric CMT column (the model’s compartment numbers), since the compartments would otherwise be taken from the fitted data by row number, or read from a factor’s level order, and would not match data.

  • Fixed the prediction-corrected VPC (pred_corr = TRUE) ignoring the data argument; the observed data was rebuilt from the fit’s dataset instead of the supplied data (#62).

  • Fixed stratified censored VPCs (vpcCens()/vpcCensTad(), or vpcPlot() with cens = TRUE) failing with “The following specified stratification columns were NOT found in observation data”; the observed data now comes from the original (or supplied) dataset, which keeps the stratification columns that the fit table drops (#56, #55).

  • Fixed the confidence-band width (and its legend label) for vpcPlot()/ vpcPlotTad() with the tidyvpc backend; ci = c(lower, upper) was passed to tidyvpc::vpcstats() as conf.level = ci[2] instead of the actual interval width ci[2] - ci[1], so the default ci = c(0.05, 0.95) (a 90% CI) was drawn and labeled as a 95% CI.

  • Fixed vpcPlotTad()/vpcCensTad() (and any idv taken from the fit) with a user-supplied data that is a subset or reordering of the fitted data; tad was merged from the fit by row number, so it silently became NA (or was paired with the wrong row). Each supplied row is now matched by content to the fitted row it came from, and a warning is given for observations that are not in the fitted data (#60).

nlmixr2plot 5.1.0

CRAN release: 2026-08-05

  • Fixed an “object of type ‘closure’ is not subsettable” error in vpcCensTad() (and vpcCens()/vpcPlot()/vpcPlotTad() with cens = TRUE and a non-time idv); the censored VPC now passes the sim/obs column mappings to vpc::vpc_cens() explicitly instead of relying on column guessing (nlmixr2#390).
  • Fixed the censored VPC confidence band, which was computed as if every simulated row were its own replicate. The simulated dv is now mapped to the sim column instead of being copied into a new dv column, so vpc groups the simulated data by replicate as it does for the uncensored VPC.
  • Fixed a quantile() “missing values and NaNs not allowed” error in prediction-corrected vpcPlot()/vpcPlotTad() on censored (LLOQ/ULOQ) fits with the vpc backend; censored records are now dropped before the pred-corrected VPC (which is shown for non-censored data only), matching the vpc package’s stated behavior (nlmixr2#390).
  • Fixed prediction-corrected vpcPlot()/vpcPlotTad() with method = "tidyvpc", cens = TRUE, which previously errored that the observed data had no cens column; the censoring column is now retained when the observed dataset is rebuilt for pred-correction.
  • plot() on a fit with between-subject variability (BSV) now adds a nested "bsv" section (inside each data/compartment group) with QQ plots for each BSV parameter, BSV-BSV correlation plots (when more than one BSV parameter is present) and, via the new covariate argument, BSV-by-covariate plots (box-and-whisker for categorical or low-cardinality covariates, scatter plus a linear trend with confidence interval for continuous ones). Covariate values are taken from each subject’s first record, so they are assumed time-invariant (#51).
  • Plot collections returned by plot() (for fits and augPred objects) are now gglist objects from the ggtibble package instead of the internal nlmixr2PlotList class. They still print/plot all figures at once and support broadcasting ggplot2 additions (e.g. plot(fit) + ggplot2::theme_bw()), and the top-level object remains a named, nested collection (plot(fit)[["Endpoint: ..."]]). The collection can also be converted to a ggtibble for reporting with ggtibble::as_ggtibble().
  • Individual/augPred plots are now paginated with ggforce::facet_wrap_paginate(), removing the hand-written 16-IDs-per-page chunking. Requires ggtibble (>= 1.0.3.9000) and ggforce; the minimum R version is now 4.3.
  • plot() on a fit (and on an augPred object) is now about 3x faster. The paginated individual plots were expanded one-per-page with ggtibble::as_gglist(), which deep-copies the plot through serialize()/unserialize(); because those plots are built inside functions that hold the whole fit, each copy walked the entire fit object. The pages are now produced by re-adding the paginated facet for each page instead.
  • Removed obsolete rxode2::.linCmtSensB() test guards. That internal was removed from rxode2 in 2025, so the try()/skip_if_not() checks always fell through and never skipped. linCmt() gradients are now always available, so the guards are unnecessary and the tests run unconditionally.

nlmixr2plot 5.0.2

CRAN release: 2026-06-11

  • Fixed an error when plotting models without compartments (#33)

nlmixr2plot 5.0.1

CRAN release: 2026-02-28

  • Updated nlmixr2 to optionally use the tidyvpc package

nlmixr2plot 5.0.0

CRAN release: 2025-11-29

  • Updated to use nlmixr2 5.0 file format

nlmixr2plot 3.0.3

CRAN release: 2025-08-23

  • Updated tests and added Ops method (removing + method) to work with ggplot2 version 4 (#39)

nlmixr2plot 3.0.1

CRAN release: 2025-02-14

  • Added the ability to add ggplot items to a nlmixr2 plot list with +

nlmixr2plot 3.0.0

CRAN release: 2024-09-18

  • Update to support new version of rxode2

nlmixr2plot 2.0.9

CRAN release: 2024-05-29

  • Bug fix for vpcPlot() where input data frame for models did not stratify all the time when the columns were upper case.

nlmixr2plot 2.0.8

CRAN release: 2024-01-31

  • plot() now returns a named list of lists so that users can more easily choose which plots to include, if all plots are not desired. Or the user could use those names as the basis of figure captions (fix #8).

  • Models without eta values (between subject variability) now have more consistent plotting to models with eta values (fix #18).

  • The package was updated to align with changes in ggplot2.

  • The package was updated to skip tests with "focei" and linCmt()

nlmixr2plot 2.0.7

CRAN release: 2022-10-20

  • Added fixes for upcoming ‘ggplot2’ 3.4 release

  • Added changes for the generalized log-likelihood supported by ‘nlmixr2est’

  • Added a NEWS.md file to track changes to the package.