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psm3mkv

0.3.3Package record

Evaluate Partitioned Survival and State Transition Models

0packages depend
2.9Kdownloads / year
58.5%test coverage
12/13flavors OK

Overview

About
Maintained by Dominic MustonCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funder: Merck & Co., Inc., Rahway, NJ, USA and its affiliates

Fits and evaluates three-state partitioned survival analyses (PartSAs) and Markov models (clock forward or clock reset) to progression and overall survival data typically collected in oncology clinical trials. These model structures are typically considered in cost-effectiveness modeling in advanced/metastatic cancer indications. Muston (2024). "Informing structural assumptions for three state oncology cost-effectiveness models through model efficiency and fit". Applied Health Economics and Health Policy.

Changes in 0.3.3
  • Updated create_dummydata("pharmaonc") for breaking changes from new version of pharmaverseadam
  • Fix bug in constrain_survprob() with thanks to @xm2325
  • Updated author email address

From NEWS.md in the release

Install

Health

CRAN checks
1ERROR12OK
Check messages
ERRORre-building of vignette outputsr-devel-linux-x86_64-debian-gcc
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown

Quitting from example.Rmd:113-124 [find_bestfit]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `purrr::map_chr()`:
ℹ In index: 1.
Caused by error:
! Result must be length 1, not 0.
---
Backtrace:
    ▆
 1. └─psm3mkv::find_bestfit(allfits_spl$ppd, "aic")
 2.   └─purrr::map_chr(fittable$id, ~reglist[[.x]]$result$dlist$name)
 3.     └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
 4.       ├─purrr:::with_indexed_errors(...)
 5.       │ └─base::withCallingHandlers(...)
 6.       └─purrr:::call_with_cleanup(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'example.Rmd' failed with diagnostics:
ℹ In index: 1.
Caused by error:
! Result must be length 1, not 0.
--- failed re-building ‘example.Rmd’

--- re-building ‘mortality-adjustments.Rmd’ using rmarkdown
[WARNING] Deprecated: --mathjax. Use --math-method=mathjax[:URL] instead.
--- finished re-building ‘mortality-adjustments.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
ERRORtestsr-devel-linux-x86_64-debian-gcc
Running ‘testthat.R’ [24s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > # Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(psm3mkv)
  > 
  > test_check("psm3mkv")
  Saving _problems/test-basics-33.R
  Saving _problems/test-fitting-spl-27.R
  Saving _problems/test-lhoods-101.R
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 216 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • On CRAN (1): 'test-discrmd.R:4:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-basics.R:29:1'): (code run outside of `test_that()`) ───────────

...[truncated]...
local) `<fn>`(`<sbscOOBE>`)
   17.   └─cli::cli_abort(...)
   18.     └─rlang::abort(...)
  ── Error ('test-lhoods.R:101:1'): (code run outside of `test_that()`) ──────────
  <purrr_error_indexed/rlang_error/error/condition>
  Error in `purrr::map_chr(fittable$id, ~reglist[[.x]]$result$dlist$name)`: i In index: 1.
  Caused by error:
  ! Result must be length 1, not 0.
  Backtrace:
       ▆
    1. ├─psm3mkv::find_bestfit(af2$ppd, "aic") at test-lhoods.R:101:1
    2. │ └─purrr::map_chr(fittable$id, ~reglist[[.x]]$result$dlist$name)
    3. │   └─purrr:::map_("character", .x, .f, ..., .progress = .progress)
    4. │     ├─purrr:::with_indexed_errors(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─purrr:::call_with_cleanup(...)
    7. └─base::.handleSimpleError(...)
    8.   └─purrr (local) h(simpleError(msg, call))
    9.     └─cli::cli_abort(...)
   10.       └─rlang::abort(...)
  
  [ FAIL 3 | WARN 0 | SKIP 1 | PASS 216 ]
  Error:
  ! Test failures.
  Execution halted

CRAN check page ↗

Slowest check: 7.0 min · r-oldrel-windows-x86_64
Status changes
  • ERROR12 OK, 1 ERROR2026-10-24
  • OK13 OK2026-08-05
  • NOTE12 OK, 1 NOTE2026-08-01
  • OK13 OK2026-06-09
  • ERROR12 OK, 1 ERROR2026-06-08
Show 1 earlier changeHide 1 earlier change
  • OK14 OK2026-03-10
Advisories

none known

Documentation

In release 0.3.3
READMEYes · 717 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.3.3Citation fileYes · cites a publicationWebsiteYes · pkgdown
Help pages
28 (1 internal)includes a package overview page
Examples that run
37%10 run in a plain check · 17 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples
100%
Documented parameters
100%
Return-value docs
100%
Help pages citing references
0%

Downloads

2.9K
CRAN downloads in the past year
Rank #10,801 · ~8/day · ~239/mo
Daily download trend is not available in this view yet.
34530 days
97490 days
2.9K1 year
Compare downloads with other packages →
Also on71 r2u6 autocran

Repository

11Stars
4Forks
1Open issues
0Open PRs
6Releases
312Commits
7Commit identities
License file reads as GPL-3.0 · 312 commits · Last activity 2026-07-10 · 0% stars, 30d
Responsiveness
How these are sampled
PRs merged (all time)
100%
Median days to close, 50 most recently updated closed issues
34
Median days to close, 50 most recently updated closed PRs
0

Stars over time

2025-02-02 · 102026-07-07 · 11
PracticesBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/merck/psm3mkv on 2026-10-21.

Continuous integration (2)
GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (3)
pkgdown

GitHub Pages site last deployed 2026-07-10 · The repository has a site deploy workflow

pkgdown site last built 2026-07-10

Coverage (1)
Coverage reporting (Codecov)
CRAN release process (2)
cran-comments.mdCRAN-SUBMISSION
Show all practicesHide 1 practice
Lint, format, editor (1)
RStudio project
How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies
18 external dependencies (excludes base and recommended)

Installing psm3mkv adds 73 packages (40 with compiled code, 56 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)
R >= 4.1.0
LinkingTo (0)
none
Enhances (0)
none
Reverse dependencies
0direct
0indirect

Nothing depends on this yet.

People & History

People (2)
Author, Maintainer since 0.3.1 (2024)
Releases (3)

Pick two releases to compare their code metrics.

  • 0.3.3Latest
    record
    2026-07-10 · current release · diff ↗
  • R
    R 4.6.0 released · 2026-04-24
  • R
    R 4.5.0 released · 2025-04-11
  • 0.3.2
    record
    2024-06-07 · diff ↗ ·
    added 2 exports
    check_consistent_pfs, compare_psm_likes
  • 0.3.1
    record
    2024-05-07
  • R
    R 4.4.0 released · 2024-04-24

Package metadata

First published
2024-05-07
Total releases
3 / 2 yrs
License
GPL (>= 3) OSI
Minimum R
≥ 4.1.0
Download size
503 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("psm3mkv")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1007/s40258-024-00884-2.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

APA

Balamuta, J. J. (2026). R Observatory: Metrics for psm3mkv version 0.3.3 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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