cran-comments.md
In mwheymans/psfmi: Prediction Model Pooling, Selection and Performance Evaluation Across Multiply Imputed Datasets
title: "cran_comments"
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)
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!
mwheymans/psfmi documentation built on June 30, 2023, 5:25 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
title: "cran_comments"
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)
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!
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