Last updated: 2022-11-30

Checks: 7 0

Knit directory: ampel-leipzig-meld/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.


Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.

The command set.seed(20210604) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Great job! Recording the operating system, R version, and package versions is critical for reproducibility.

Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.

Great job! Using relative paths to the files within your workflowr project makes it easier to run your code on other machines.

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version e1aebf7. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:


Ignored files:
    Ignored:    _targets/
    Ignored:    analysis/article.md
    Ignored:    container/
    Ignored:    logs/
    Ignored:    scripts/R.sh

Untracked files:
    Untracked:  analysis/bibliography/bibliography.bib.sav.tmp
    Untracked:  submission/

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the repository in which changes were made to the R Markdown (analysis/roc.Rmd) and HTML (docs/roc.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
Rmd fba81f5 Sebastian Gibb 2022-11-27 feat: add MELD 3.0 score
html 65d58c4 Sebastian Gibb 2022-07-18 chore: rebuild site
html fb43d01 Sebastian Gibb 2022-06-19 chore: rebuild site
html ebe29cf Sebastian Gibb 2022-06-16 chore: rebuild site
html 8035219 Sebastian Gibb 2022-06-15 chore: rebuild site
Rmd 7ffaeb9 Sebastian Gibb 2022-06-15 feat: add analysis of complete cases
html d3e9462 Sebastian Gibb 2022-06-06 chore: rebuild site
html b20484a Sebastian Gibb 2022-06-06 chore: rebuild site
html 983ec69 Sebastian Gibb 2022-03-17 chore: rebuild site
Rmd 057f935 Sebastian Gibb 2022-03-17 feat: add elastic net bootstrap and timeROC evaluations

library("targets")
library("ameld")
tar_load(timeROC_MELD)
tar_load(timeROC_MELDNa)
tar_load(timeROC_MELD3)
tar_load(timeROC_MELDPlus7)
tar_load(timeROC_RCV)
tar_load(timeROC_RCVcc)
tar_load(timeROC_MELDNacc)
tar_load(timeROC_ARCV)

1 ROC day 90

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
                    MELD                  MELD-Na MELD-Na (complete cases) 
               0.9338468                0.9357808                0.9122839 
                MELD 3.0               MELD-Plus7                      RCV 
               0.9362360                0.9217082                0.9609230 
    RCV (complete cases)                     ARCV 
               0.9356413                0.9656049 
attr(,"CI")
                    MELD                  MELD-Na MELD-Na (complete cases) 
 "(95% CI, 0.908-0.960)"  "(95% CI, 0.910-0.962)"  "(95% CI, 0.873-0.952)" 
                MELD 3.0               MELD-Plus7                      RCV 
 "(95% CI, 0.910-0.963)"  "(95% CI, 0.893-0.951)"  "(95% CI, 0.942-0.980)" 
    RCV (complete cases)                     ARCV 
 "(95% CI, 0.903-0.969)"  "(95% CI, 0.949-0.982)" 

2 ROC trend

plot_surv_roc_trend(m)

Version Author Date
ebe29cf Sebastian Gibb 2022-06-16
8035219 Sebastian Gibb 2022-06-15
b20484a Sebastian Gibb 2022-06-06
983ec69 Sebastian Gibb 2022-03-17

sessionInfo()
R version 4.2.0 (2022-04-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

Matrix products: default
BLAS/LAPACK: /gnu/store/ras6dprsw3wm3swk23jjp8ww5dwxj333-openblas-0.3.18/lib/libopenblasp-r0.3.18.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] ameld_0.0.30   survival_3.3-1 glmnet_4.1-4   Matrix_1.4-1   targets_0.12.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3        mvtnorm_1.1-3       lattice_0.20-45    
 [4] listenv_0.8.0       ps_1.7.0            rprojroot_2.0.3    
 [7] digest_0.6.29       foreach_1.5.2       utf8_1.2.2         
[10] parallelly_1.31.1   R6_2.5.1            backports_1.4.1    
[13] evaluate_0.15       highr_0.9           pillar_1.7.0       
[16] rlang_1.0.2         data.table_1.14.2   whisker_0.4        
[19] callr_3.7.0         jquerylib_0.1.4     rmarkdown_2.14     
[22] splines_4.2.0       stringr_1.4.0       igraph_1.3.1       
[25] numDeriv_2016.8-1.1 compiler_4.2.0      httpuv_1.6.5       
[28] xfun_0.31           pkgconfig_2.0.3     timeROC_0.4        
[31] shape_1.4.6         globals_0.15.0      htmltools_0.5.2    
[34] tidyselect_1.1.2    tibble_3.1.7        prodlim_2019.11.13 
[37] bookdown_0.26       workflowr_1.7.0     codetools_0.2-18   
[40] fansi_1.0.3         future_1.26.1       crayon_1.5.1       
[43] withr_2.5.0         later_1.3.0         timereg_2.0.2      
[46] grid_4.2.0          jsonlite_1.8.0      lifecycle_1.0.1    
[49] git2r_0.30.1        magrittr_2.0.3      future.apply_1.9.0 
[52] cli_3.3.0           stringi_1.7.6       fs_1.5.2           
[55] promises_1.2.0.1    bslib_0.3.1         ellipsis_0.3.2     
[58] vctrs_0.4.1         lava_1.6.10         iterators_1.0.14   
[61] tools_4.2.0         glue_1.6.2          purrr_0.3.4        
[64] pec_2022.05.04      processx_3.5.3      parallel_4.2.0     
[67] fastmap_1.1.0       yaml_2.3.5          base64url_1.4      
[70] knitr_1.39          sass_0.4.1