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Changelog

Source: NEWS.md

msmtools 2.2.1

DOCUMENTATION

  • The package now has a documentation website built with pkgdown and published via GitHub Pages at https://contefranz.github.io/msmtools/.
  • Added a \value{} section to polish() via a new @return roxygen block, addressing CRAN feedback that man/polish.Rd was missing the \value tag.
  • Added the method citation to the DESCRIPTION Description field in the authors (year) <doi:...> form required by CRAN: Grossetti, Ieva and Paganoni (2018) doi:10.1007/s10729-017-9400-z. The same reference was already documented under @references in augment().

msmtools 2.2.0

BREAKING CHANGES

  • survplot() no longer accepts the out argument and now always returns a gg/ggplot object. The fitted survival curve and the Kaplan-Meier curve are exposed as named fields on the returned plot for parity with prevplot():

    p <- survplot(model, km = TRUE)
p           # prints the plot
p$fitted    # data.table — survival probabilities
p$km        # data.table — Kaplan-Meier curve

    Closes #4.

    Code that previously did out <- survplot(..., out = "all") and then unwrapped through out$p, out$fitted, out$km should drop the out argument and access the data tables directly on the plot. The return type collapsing from a wrapper list to a ggplot means that ggplot operations now compose without unwrapping: p + theme_bw(), ggsave("plot.pdf", p), and patchwork-style combinations all work on the returned plot directly.

    Calls passing out = ... raise a clear migration error pointing to the new pattern. The trampoline that catches the legacy argument will itself be removed in v2.3.0.

NEW

  • prevplot() exposes the long-format prevalence data used to build the plot via p$prevalence, so both plotting functions now expose their data through the same $ idiom. The field is populated on both the M = FALSE (ggplot) and M = TRUE (patchwork) return paths.

TESTS

  • Replaced the test suite for survplot() out = ... shapes with attribute-field assertions on the returned plot, plus a regression test for the legacy-argument trampoline.
  • Added a regression test asserting prevplot() populates $prevalence on the M = FALSE, ci = TRUE, and M = TRUE paths.

DOCUMENTATION

  • Rewrote the survplot() roxygen @returns and @details sections around the new contract. The vignette and worked examples in man/survplot.Rd now demonstrate the $fitted / $km access pattern.
  • Documented the $prevalence field on prevplot()’s @returns.

msmtools 2.1.4

BUG FIX

  • augment() now closes the post-discharge observation window of alive subjects at t_cens instead of repeating the last t_end. Previously, the final transition row for any subject who survived to the censoring date carried the same time as the preceding row, silently truncating the at-risk window. Any msm model fitted on the augmented data was therefore biased: transition-rate estimates were systematically pulled downward because every alive subject’s post-discharge follow-up was collapsed to zero duration. Closes #7.

    Models refit on augment() output produced with msmtools 2.1.4 or later will give different (and more correct) parameter estimates than models fitted on output from earlier versions. The behaviour of subjects who died (pattern values 1 or 2) is unchanged.

TESTS

  • The internal regression fixture tests/testthat/fixtures/augment-hosp-date.rds has been regenerated against the corrected augment() output.

  • Added regression coverage for the at-risk window of alive subjects and for the unchanged time semantics of subjects who died.

CODE STYLE

  • Completed the data.table bracket-spacing normalisation started in the 2.1.3 audit. R/augment.R, R/augment-helpers.R, and the testthat files now share the unspaced dt[, col := value] convention already used by the plotting and polish sources.

  • .onAttach() is excluded from coverage reports via # nocov markers; startup messages add nothing to test signal.

msmtools 2.1.3

DEPENDENCIES

  • patchwork moved from Imports to Suggests. It is only required by prevplot(M = TRUE), which now issues an informative error when the package is not installed.

  • scales removed entirely. The single percent formatter used by prevplot() is now an inline labeller, eliminating a hard runtime dependency.

DOCUMENTATION

  • Generalised the package framing to longitudinal observational data of any domain; the bundled hospital dataset remains the worked example but is no longer presented as the only use case.

  • Minor wording tweaks in augment() and prevplot() Rd to drop clinical-specific terminology where it did not add precision.

TESTS

  • Added a conditional regression test for prevplot(M = TRUE) guarded by testthat::skip_if_not_installed("patchwork"), so the suite remains green on CRAN’s --no-suggests runs.

BUILD

  • Extended .Rbuildignore to exclude generated tarballs, PDFs, and any local planning scratch directories.

msmtools 2.1.2

CHANGES

  • Added print_plot to survplot() and prevplot(). The default print_plot = TRUE preserves the previous interactive behavior, while print_plot = FALSE returns plot objects without printing them.

  • Added verbosity to survplot() and prevplot() and replaced direct console output with the shared cli verbosity helpers.

  • Added clearer argument validation for plotting flags, grid sizes, bootstrap sizes, time ranges, custom times, and state selectors.

  • Qualified plotting calls to external package functions explicitly instead of relying on roxygen imports.

DOCUMENTATION

  • Documented plotting print controls and verbosity in function help and README.

TESTS

  • Added regression coverage for silent plotting returns, summary verbosity, and invalid plotting arguments.

msmtools 2.1.1

CHANGES

  • Made polish() time-column handling explicit. Omitting time or setting time = NULL now auto-detects augmented_int, then augmented_num; calls error clearly when neither column is available.

  • Replaced remaining polish() console output with the shared cli verbosity helpers used by augment().

  • Qualified polish() calls to external data.table functions explicitly instead of relying on roxygen imports.

  • Added clearer validation for polish() inputs, including missing columns and terminal outcome schemas with anything other than 2 or 3 unique values.

DOCUMENTATION

  • Documented the polish() time-column auto-detection behavior.

TESTS

  • Added regression coverage for polish() time resolution, missing columns, invalid pattern schemas, missing-value checks, and summary verbosity.

msmtools 2.1.0

CHANGES

  • Added a copy argument to augment() and polish(). The default copy = FALSE preserves the historical memory-efficient by-reference behavior, while copy = TRUE protects caller-owned data before preprocessing.

  • Clarified the preprocessing contract around data.table by-reference semantics. augment() may add n_events and change the input key when copy = FALSE; polish() may change the input key while identifying duplicate transitions.

  • Added shared validation for scalar logical flags used by preprocessing functions.

  • Made the augment() state vocabulary stricter and clearer: custom state values must now be supplied as a character vector of three unique labels, not as a list.

  • Made more_status = NULL explicit in augment() so the optional expanded status path is visible in the function signature.

DOCUMENTATION

  • Documented the performance and safety tradeoff behind copy = FALSE and copy = TRUE in the function help, README, and vignette.

  • Clarified that pattern describes the terminal outcome schema, while state describes the generated transition-state labels.

TESTS

  • Added tests covering by-reference preservation with copy = FALSE, input protection with copy = TRUE, and validation of logical flags.

  • Added tests for custom state vectors, invalid state specifications, and explicit more_status = NULL.

msmtools 2.0.10

CHANGES

  • Split augment() into private helpers for validation, event preparation, pattern matching, status construction, time-column creation, and expanded status handling.

  • Replaced the verbose flag in augment() and polish() with a verbosity argument. The accepted levels are "quiet", "summary", and "progress", with a global default available through options(msmtools.verbosity = ...).

  • augment() and polish() now always return data.table objects. The previous convert argument has been removed; use as.data.frame() on the result when a plain data.frame is required.

TESTS

  • Updated preprocessing tests for the data.table-only return contract and added coverage for the new verbosity argument.

msmtools 2.0.9

CHANGES

  • Added dev-only performance baselines for augment() and polish() ahead of the planned internal refactor.

TESTS

  • Added invariant tests for output structure, by-reference behavior, and generated columns that future refactors must preserve.

msmtools 2.0.8

DOCUMENTATION

  • Converted package documentation sources to roxygen2 markdown style.

  • Kept the vignette on the lightweight HTML vignette workflow while cleaning old LaTeX-style bibliography markup.

msmtools 2.0.7

DOCUMENTATION

  • Refreshed the README and vignette around the current 2.x workflow and modern dependency baseline.

  • Replaced heavier multi-state model examples with guarded examples so CRAN checks do not execute model-fitting workflows.

CHANGES

  • Standardized recent NEWS headings around explicit maintenance categories.

msmtools 2.0.6

TESTS

  • Reworked the existing tests so expected warnings are asserted inside test_that() blocks instead of being emitted during test setup.

  • Added regression coverage for augment() across two-state and three-state patterns, date, numeric, and difftime time columns, supplied t_death, expanded statuses, conversion behavior, and generated augmented time columns.

  • Added regression coverage for polish() duplicate-removal and no-duplicate behavior.

msmtools 2.0.5

CI

  • Added GitHub Actions for R CMD check across Windows, macOS, and Ubuntu, plus roxygen consistency and informational coverage workflows.

CHANGES

  • Replaced broad data.table namespace imports with explicit imports for the functions used by msmtools.

DOCUMENTATION

  • Added contributor notes describing the local test, documentation, coverage, and package-check workflow.

msmtools 2.0.4

CHANGES

  • Raised the supported baseline to R 4.1 and current CRAN releases of the main runtime dependencies used by msmtools.

  • Removed the unused development helper usethis from Suggests.

DOCUMENTATION

  • Migrated package documentation metadata to roxygen2 8.0.0 with markdown documentation enabled.

TESTS

msmtools 2.0.3

This is a CRAN resubmission after msmtools was archived because compatibility issues with newer data.table releases were not corrected in time. No user-facing behaviour has changed.

Bug fixes

  • Kept the compatibility fixes for current data.table releases by avoiding deprecated substitute() calls on the left-hand side of := assignments.

  • Retained the focused non-standard evaluation cleanup in augment() and polish() needed for CRAN checks, without introducing the broader refactor attempted on the historical substitute_fix branch.

Documentation

  • Updated release metadata for the CRAN resubmission.

msmtools 2.0.2

This is a maintenance release addressing compatibility issues that caused the package to be removed from CRAN. No user-facing behaviour has changed.

Bug fixes

  • Removed all uses of substitute() on the left-hand side of := in data.table operations inside augment() and polish(). This pattern was deprecated by data.table and produced errors on current CRAN versions. Column assignment now uses the recommended (var) := idiom.

  • Replaced every remaining eval(substitute(data$var)) and eval(substitute(class(data$var))) construct with direct data[[var]] and class(data[[var]]) equivalents across augment() and polish(). The previous forms were fragile and harder to reason about.

  • Replaced class(...) == "type" comparisons with inherits() throughout augment(), as required by current R CMD CHECK.

Documentation

  • Replaced the deprecated @docType "package" / NULL pattern in msmtools.R with the current "_PACKAGE" sentinel required by roxygen2 >= 7.2.

msmtools 2.0.1

This is a maintenance update. There are no major updates worth noting apart from a few tweaks to the vignette, which was not rendered appropriately.

Minor changes

  • Fixed few issues in the vignette where plots were not rendered nicely.

msmtools 2.0.0

msmtools sees several updates which come with potential breaking changes due to the dropping of several arguments in some functions. The most relevant feature being shipped with v2.0.0 is that both survplot() and prevplot() now support ggplot2. All in all, this justifies the jump in versions thus bringing msmtools to version 2.0.0.

Breaking changes

  • survplot() requires much less arguments now but at the same time is a bit less flexible. This is particularly reflected in plot customization which is now “self-imposed”. I summarize what’s different w.r.t. v1.3 below:
    • There are no more arguments related to plot rendering, like colors and linetype. The function always returns the same type of plot as a gg and ggplot object.
    • Also, survplot() returns nothing but the rendered plot by default. The user can tell the function to return additional objects like the fitted data, the Kaplan-Meier data km, or one of them with the argument out.
    • Conversions are gone forever. survplot() always returns a data.table when out requires such object.
    • There are no more controls over the device being used when rendering a plot. The function now just uses the default for simplicity and to avoid confusion due to different OSes. There is no possibility anymore to add lines (i.e. additional plots) to an already rendered plot. Just use survplot() twice with different input parameters and the combine the plots afterwards. The underlying data structures for the plot are always returned and made available through a gg/ggplot object.
    • There are no more controls over what is printed at console. You will get few messages and that’s it.
  • similarly, prevplot() has been greatly improved. There are no more loops in the function and everything is done by reference so it is very efficient. I briefly summarize what’s different w.r.t. v1.3 below:
    • There are no more arguments related to plot rendering. prevplot() always returns a gg/ggplot object.
    • All arguments related to the grid or time steps are gone. Everything is managed consistently by extracting the correct model frame from the prevalence object computed with prevalence.msm().
    • For loops are gone too since plots make use of facet_wrap() to automatically decide how many grobs to render. For now, there is no customization possible since I expect that for most cases the number of states is limited in number anyway. There might be some flexibility added in future releases.
    • When M = TRUE, prevplot() uses patchwork to wrap the two plots in two different rows. The first row has the standard prevalence plot, the second row has the Deviance M.
    • There are no more controls over what is printed at console. You will get few messages and that’s it.

Major changes

  • survplot() lets you specify the type of confidence intervals for the Kaplan-Meier in addition to the already available types for the fitted curve. The argument is ci_km.
  • Specify what is the desired output through the argument out which takes a vector of characters.
  • By default, survplot() always renders the plot and returns it.
  • prevplot() drops plot layering in favor of direct ggplot2 support.
  • prevplot() has become faster due to smarter data extraction and binding.

Minor changes

  • Updated vignette.

msmtools 1.3

Major changes

  • The new function polish() is introduced. This adds support in the preprocessing part of the analysis. polish() addresses the specific problem of different transitions occurring at the same exact time within a given subject. This is a case for which a multi-state model fails to estimate the probability associated with the two transitions. At the moment, the whole subject specified by data_key is deleted.

Minor changes

  • Global variables are now correctly declared on top of functions using utils::globalVariables(). This prevents the assignment to NULL in the preamble of functions which decreases the elegance of the code.

  • The printing of information is now way more simpler and is not based on sink() anymore. This has been done to be less intrusive into the OS when redirecting on console messages. Also, no more OS type check is done so that the control with argument verbose is the most general possible. Warnings are still controlled as usual, so that they get printed, if any, just after the function call.

Other changes

  • The vignette has been updated to include new features and it is now in HTML format which provides a faster and lighter access.

  • Improved the documentation’s readability in the ‘Value’ section for augment() and survplot().

  • In the documentation of augment() now there is an explicit example which returns a data.frame.

  • Windows builds of msmtools are now constantly checked through Appveyor.

  • The author/maintainer e-mail has changed to match his new affiliation and now is .

Bug fixes

  • After augment() has been run, results are now visible at the very first call. This means that you can finally print on console the augmented dataset right away.

  • pandoc versions prior to 1.17 do not fully support spaces in file names and caused a warning when compiling msmtools under Fedora using both clang and gcc. Now all file names are without spaces. msmtools 1.3 has been built using pandoc 1.19.2 and pandoc-citeproc 0.10.4.1

msmtools 1.2

Major changes

  • msmtools can now run with R 3.0.0 and above for retro compatibility reasons.

  • augment() gains the new argument check_NA which allows the user to decide if the function should run some checks to find missing data in the following arguments: data_key, n_events, pattern, t_start and t_end. Default is FALSE. Missing data checks are always carried out on more_status.

  • augment() gains the new argument convert which if set to TRUE efficiently converts the output to the old school data.frame class.

  • survplot() gains the new argument return.all which saves you some typing time when requesting both the data of the Kaplan-Meier and the fitted survival. Arguments return.km and return.p now are set to NULL by default instead of FALSE.

  • survplot() gains the new argument convert which if set to TRUE efficiently converts any object returned to the old school data.frame class.

Changes in functions

  • augment() now also accepts an object of class data.frame as input. If so, the function internally converts it to a data.table.

  • augment() now accepts t_augmented without quotes too. Default name is still “augmented”.

  • augment() gets a whole new implementation which comes into play when pattern has only 2 values (‘alive’ and ‘dead’). Now the procedure runs with computational time only slightly longer than the standard 3 values in pattern. This is due thanks to the fast joins method adopted.

  • augment() now is much faster when defining the target size for the reshaping. This was a bottleneck which caused memory issues and wasted time.

  • General memory optimization in the function augment(). Now the function uses ~ 30% less memory.

Other changes

  • All the functions now have more detailed and better written helps.

  • Some minor changes in the vignette to encapsulate new functionalities.

Bug fixes

  • In augment(), the sequential status is now correctly computed. There was a wrong call which blocked the object defined by n_events.

  • In augment(), when pattern was detected with two unique values, inconsistent results were produced during the status flag assignment. This was due to a wrong rounding of the amount of augmenting factor for each unit.

msmtools 1.1

Changes in functions

  • augment() now is way faster then in v1.0 thanks to a new implementation when defining patterns.

  • augment() now uses the faster uniqueN() to extract the number of unique values in a vector.

Bug fixes

  • augment() now correctly positions new created variables.

Other changes

  • augment() in-line help now provides correct information on what it returns.