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Resubmission

This is a resubmission. In this version I have:

  • Updated version nr to 1.4.0.
  • Added a new function nri_cox.R for reclassification analyses of Cox models.
  • Added the possibility to pool stratified Cox models in the function psfmi_coxr.

── R CMD check results ─────────────────────────────────────────── psfmi 1.4.0 ──── Duration: 3m 18.1s

Test environments

  • R studio 2023.06.0, R version 4.3.0
  • win-builder Development: * DONE Status: OK
  • win-builder Release: * DONE Status: OK

Resubmission

This is a resubmission. In this version I have:

  • Updated version nr to 1.1.0.
  • Added df_com to the D1 and D2 method for small sample correction.
  • Defined strata=strata in functions cv_MI and cv_MI_RR.

devtools::test()

ℹ Testing psfmi ✔ | F W S OK | Context ⠏ | 0 | testthat.R
══ Results ═══════════════════════════════════════════════════════════════════════════════════════════════════ Duration: 0.2 s

[ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]

Nice code.

R CMD check results

── R CMD check results ──────────────────────────────────────────────────────────────────────── psfmi 1.1.0 ──── Duration: 5m 22.6s

0 errors ✔ | 0 warnings ✔ | 0 notes ✔

Test environments

  • R studio 2022.07.1, R version 4.2.1
  • win-builder Development: * DONE Status: OK
  • win-builder Release: * DONE Status: OK

Resubmission

This is a resubmission. In this version I have:

  • Updated version nr to 1.0.0.
  • Added the functions psfmi_lm, psfmi_lm_fw, psfmi_lr_bw for pooling and backward and forward selection of linear regression models.
  • Added the functions glm_bw, glm_fw, coxph_bw and coxph_fw for backward and forward selection of linear, logistic and Cox models in a single dataset based on the likelihood ratio statistic.
  • Function psfmi_perform is now deprecated, use psfmi_validate instead.
  • Function bw_single is now deprecated, use glm_bw instead.
  • Added the function hoslem_test and implemented this in the function pool_performance.
  • Added pooled concordance and R-squared measures for Cox regression to function pool_performance.
  • Added the function pool_D2, to pool chi-square statistics.
  • Added the function pool_D4, to pool likelihood ratio tests.
  • Added the internal function pool_performance_internal, used internally by psfmi_perform.
  • Option plot.indiv in function pool_performance and mivalext_lr is deprecated, use plot.method instead.
  • Created a new vignette for the psfmi_lm function and updated the other ones.
  • corrected other bug fixes.
  • Updated package website with pkgdown (included citation).

R CMD check results

Duration: 6m 8.1s

0 errors √ | 0 warnings √ | 0 notes √

devtools::test()

i Loading psfmi i Testing psfmi √ | OK F W S | Context / | 0 | testthat.R
== Results ================================================================================================= [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]

Nice code.

Test environments

  • R studio 1.4.1717, R version 4.1.1
  • win-builder Development: * DONE Status: OK
  • win-builder Release: * DONE Status: OK
  • on Travis CI: R session information Running under: Ubuntu 16.04.6 LTS Done. Your build exited with 0.

Resubmission

This is a resubmission. In this version I have: Updated version nr to 0.7.1. Added new functions to compare models, the functions pool_compare_models and pool_reclassification. Applied some bug fixes in the function bw_single. Added internal function RR_diff_prop to pool difference in proportions. Updated vignettes and package website with pkgdown and added datasets to be used in tutorials.

R CMD check results

Duration: 5m 19.8s

0 errors √ | 0 warnings √ | 0 notes √

devtools::test()

Loading psfmi Testing psfmi √ | OK F W S | Context / | 0 | testthat.R
== Results ============================================================================================================= [ FAIL 0 | WARN 0 | SKIP 0 | PASS 0 ]

Test environments

  • R studio 1.4.970, R version 4.0.3
  • win-builder Development: * DONE Status: OK
  • win-builder Release: * DONE Status: OK
  • on Travis CI: R session information $ Rscript -e 'sessionInfo()' R version 4.0.2 (2020-06-22) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS Done. Your build exited with 0.

Resubmission

This is a resubmission. In this version I have: Updated version nr to 0.5.0. Added new methods to combine cross-validation with multiple imputation in function psfmi_perform and added the possibility for forward and backward selection in the functions psfmi_lr and psfmi_coxr. Updated the vignettes.

R CMD check results

Duration: 4m 55s

0 errors √ | 0 warnings √ | 1 note x

checking installed package size ... NOTE installed size is 7.0Mb sub-directories of 1Mb or more: doc 6.5Mb

Known note.

devtools::test()

Loading psfmi Testing psfmi √ | OK F W S | Context √ | 0 | testthat.R

== Results ===================================================================== OK: 0 Failed: 0 Warnings: 0 Skipped: 0

Nice code.

Test environments

  • R studio 1.3.1073, R version 4.0.2
  • win-builder Development: Status: OK, R version 4.0.2
  • win-builder Release: Status: OK, R version 4.0.2
  • on Travis CI: Operating System Details Distributor ID: Ubuntu Description: Ubuntu 16.04.6 LTS Release: 16.04 Codename: xenial (on Travis CI) (Done. Your build exited with 0)

Resubmission

This is a resubmission. In this version I have: Updated version nr to 0.2.0. Added the new functions pool_intadj.R, pool_performance.R, psfmi_mm.R, psfmi_mm_multiparm, psfmi_perform, psfmi_stab. Excluded function miperform_lr. Updated the vignettes.

R CMD check results

Duration: 2m 45.6s

0 errors √ | 0 warnings √ | 0 notes √

devtools::test()

Loading psfmi Testing psfmi √ | OK F W S | Context √ | 0 | testthat.R

== Results ===================================================================== OK: 0 Failed: 0 Warnings: 0 Skipped: 0

Resubmission

This is a resubmission. In this version I have: Added small executable examples in all the exported functions' Rd files to illustrate the use of the exported function. Deleted comments in examples.

Resubmission

This is a resubmission. In this version I have: Provided small executable examples. Omitted cat()/print() in functions and used message() on a minority basis. Changed the functions so that the user can extract separate objects.

Test environments

  • MacOS Mojave versie 10.14.4, R studio 1.1.383, R version 3.5.3
  • win-builder (devel and release), R version 3.6.0
  • Ubuntu 14.04.5 LTS (on Travis CI) (Done. Your build exited with 0)

R CMD check results

Duration: 1m 29.8s

0 errors √ | 0 warnings √ | 0 notes √

devtools::test()

Loading psfmi Testing psfmi √ | OK F W S | Context √ | 0 | testthat.R == Results ===================================================================== OK: 0 Failed: 0 Warnings: 0 Skipped: 0

Resubmission

This is a resubmission. In this version I have: Excluded annotated lines at location of example.

Resubmission

This is a resubmission. In this version I have: Started the Description with just "Provides..." and did not capitalize non-names (e.g. Likelihood - likelihood).

I have added references as (year) doi:...

I have changed my examples into small executable examples in all of my Rd-files.

Resubmission

This is a resubmission. In this version I have: Omitted the mis-spelled words, the date field and adjusted the examples so that they run <5s.

Test environments

  • MacOS Mojave versie 10.14.4, R studio 1.1.383, R version 3.5.3
  • win-builder (devel and release)
  • Ubuntu 14.04.5 LTS (on Travis CI) (Done. Your build exited with 0)

R CMD check results

errors √ | 0 warnings √ | 0 notes √

devtools::test()

Loading psfmi Testing psfmi √ | OK F W S | Context √ | 0 | testthat.R == Results ===================================================================== OK: 0 Failed: 0 Warnings: 0 Skipped: 0

You are a coding rockstar!