pminternal

Internal Validation of Clinical Prediction Models

v0.1.0 · Mar 18, 2025 · GPL-3

Description

Conduct internal validation of a clinical prediction model for a binary outcome. Produce bias corrected performance metrics (c-statistic, Brier score, calibration intercept/slope) via bootstrap (simple bootstrap, bootstrap optimism, .632 optimism) and cross-validation (CV optimism, CV average). Also includes functions to assess model stability via bootstrap resampling. See Steyerberg et al. (2001) <doi:10.1016/s0895-4356(01)00341-9>; Harrell (2015) <doi:10.1007/978-3-319-19425-7>; Riley and Collins (2023) <doi:10.1002/bimj.202200302>.

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CRAN Check Status

13 OK

Show all 13 flavors

Flavor	Status	Time
r-devel-linux-x86_64-debian-clang	OK	250.7s
r-devel-linux-x86_64-debian-gcc	OK	184.4s
r-devel-linux-x86_64-fedora-clang	OK	446.7s
r-devel-linux-x86_64-fedora-gcc	OK	466.3s
r-devel-windows-x86_64	OK	331s
r-oldrel-macos-arm64	OK
r-oldrel-macos-x86_64	OK	203s
r-oldrel-windows-x86_64	OK	426s
r-patched-linux-x86_64	OK	242.5s
r-release-linux-x86_64	OK
r-release-macos-arm64	OK	101s
r-release-macos-x86_64	OK	299s
r-release-windows-x86_64	OK	319s

Check History

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026

ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026

ERROR r-devel-linux-x86_64-debian-gcc

package dependencies

Package required but not available: ‘pmcalibration’

Packages suggested but not available for checking: 'Hmisc', 'rms', 'mice'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 15, 2026

ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE May 12, 2026

ERROR r-release-windows-x86_64

re-building of vignette outputs

Error(s) in re-building vignettes:
--- re-building 'missing-data.Rmd' using rmarkdown
--- finished re-building 'missing-data.Rmd'

--- re-building 'pminternal.Rmd' using rmarkdown

Quitting from pminternal.Rmd:31-49 [setup]
~~~~~~~~~~~~~~~~~~~~~~~~~~
...[truncated]...
ilding 'pminternal.Rmd'

--- re-building 'validate-examples.Rmd' using rmarkdown
--- finished re-building 'validate-examples.Rmd'

SUMMARY: processing the following file failed:
  'pminternal.Rmd'

Error: Vignette re-building failed.
Execution halted

WARNING 12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE May 11, 2026

WARNING r-devel-linux-x86_64-debian-gcc

PDF version of manual

LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:

OK 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE May 2, 2026

ERROR 11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 25, 2026

ERROR r-release-macos-x86_64

examples

Running examples in ‘pminternal-Ex.R’ failed
The error most likely occurred in:

> ### Name: cal_plot
> ### Title: Plot apparent and bias-corrected calibration curves
> ### Aliases: cal_plot
> 
> ### ** Examples
> 
> library(pminternal)
> set.seed(45
...[truncated]...
bs/data_table.so
  Expected in:     <0A9590E7-21FF-3C2D-B0BD-160A5BF4B716> /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/lib/libR.dylib
Calls: validate ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted

OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026