Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update ggforest.R #604

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Update ggforest.R #604

wants to merge 1 commit into from

Conversation

bnolan7
Copy link

@bnolan7 bnolan7 commented Oct 13, 2022

Proposed fix for ggforest. Error was being presented when attempting to run ggforest with coxph model: Error in match.names(clabs, names(xi)) :
names do not match previous names

Isolated where column names for allTerms were using variable names, which would prevent rbind from working. By relabeling column names before rbind, ggforest functions as expected.

R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] ggstatsplot_0.9.4 survminer_0.4.9 ggpubr_0.4.0 survival_3.4-0 modelsummary_1.0.2 summarytools_1.0.1
[7] SAScii_1.0.1 labelled_2.10.0 forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10 purrr_0.3.5
[13] readr_2.1.3 tidyr_1.2.1 tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.2

Proposed fix for ggforest. Error was being presented when attempting to run ggforest with coxph model:
Error in match.names(clabs, names(xi)) : 
  names do not match previous names

Isolated where column names for allTerms were using variable names, which would prevent rbind from working. By relabeling column names before rbind, ggforest functions as expected. 

R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19044)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                           LC_TIME=English_United States.utf8    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggstatsplot_0.9.4  survminer_0.4.9    ggpubr_0.4.0       survival_3.4-0     modelsummary_1.0.2 summarytools_1.0.1
 [7] SAScii_1.0.1       labelled_2.10.0    forcats_0.5.2      stringr_1.4.1      dplyr_1.0.10       purrr_0.3.5       
[13] readr_2.1.3        tidyr_1.2.1        tibble_3.1.8       ggplot2_3.3.6      tidyverse_1.3.2   

loaded via a namespace (and not attached):
  [1] googledrive_2.0.0      colorspace_2.0-3       ggsignif_0.6.3         pryr_0.1.5             ellipsis_0.3.2        
  [6] markdown_1.1           parameters_0.19.0      base64enc_0.1-3        fs_1.5.2               gridtext_0.1.5        
 [11] ggtext_0.1.2           rstudioapi_0.14        farver_2.1.1           bit64_4.0.5            fansi_1.0.3           
 [16] lubridate_1.8.0        xml2_1.3.3             codetools_0.2-18       splines_4.2.1          cachem_1.0.6          
 [21] knitr_1.40             zeallot_0.1.0          Formula_1.2-4          jsonlite_1.8.2         broom_1.0.1           
 [26] km.ci_0.5-6            dbplyr_2.2.1           compiler_4.2.1         httr_1.4.4             backports_1.4.1       
 [31] assertthat_0.2.1       Matrix_1.5-1           fastmap_1.1.0          gargle_1.2.1           cli_3.4.1             
 [36] htmltools_0.5.3        tools_4.2.1            gtable_0.3.1           glue_1.6.2             reshape2_1.4.4        
 [41] tables_0.9.6           Rcpp_1.0.9             carData_3.0-5          jquerylib_0.1.4        cellranger_1.1.0      
 [46] vctrs_0.4.2            svglite_2.1.0          insight_0.18.5         xfun_0.33              rvest_1.0.3           
 [51] lifecycle_1.0.3        estimatr_1.0.0         rstatix_0.7.0          googlesheets4_1.0.1    MASS_7.3-57           
 [56] zoo_1.8-11             scales_1.2.1           vroom_1.6.0            hms_1.1.2              parallel_4.2.1        
 [61] rematch2_2.1.2         gridExtra_2.3          KMsurv_0.1-5           pander_0.6.5           sass_0.4.2            
 [66] stringi_1.7.8          paletteer_1.4.1        bayestestR_0.13.0      checkmate_2.1.0        systemfonts_1.0.4     
 [71] rlang_1.0.6            pkgconfig_2.0.3        matrixStats_0.62.0     evaluate_0.17          lattice_0.20-45       
 [76] labeling_0.4.2         patchwork_1.1.2        rapportools_1.1        cowplot_1.1.1          bit_4.0.4             
 [81] tidyselect_1.2.0       plyr_1.8.7             magrittr_2.0.3         R6_2.5.1               magick_2.7.3          
 [86] generics_0.1.3         DBI_1.1.3              pillar_1.8.1           haven_2.5.1            withr_2.5.0           
 [91] datawizard_0.6.2       abind_1.4-5            performance_0.10.0     modelr_0.1.9           crayon_1.5.2          
 [96] car_3.1-0              survMisc_0.5.6         utf8_1.2.2             correlation_0.8.3      tzdb_0.3.0            
[101] rmarkdown_2.17         grid_4.2.1             readxl_1.4.1           data.table_1.14.2      webshot_0.5.4         
[106] reprex_2.0.2           digest_0.6.29          xtable_1.8-4           statsExpressions_1.3.4 munsell_0.5.0         
[111] viridisLite_0.4.1      kableExtra_1.3.4       bslib_0.4.0            tcltk_4.2.1
@davedestep
Copy link

@bnolan7 are you able to add @kassambara as a reviewer?

@bnolan7 bnolan7 marked this pull request as draft March 23, 2023 13:00
@bnolan7 bnolan7 marked this pull request as ready for review March 23, 2023 13:00
@bnolan7 bnolan7 marked this pull request as draft March 23, 2023 13:02
@bnolan7 bnolan7 marked this pull request as ready for review March 23, 2023 13:02
@bnolan7
Copy link
Author

bnolan7 commented Mar 23, 2023

@davedestep nope, it doesn't look like I am able to do that. Based on GitHub's docs, it says I must be an owner or collaborator to be able to request @kassambara to specifically review this pull request.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants