Last updated: 2023-08-23

Checks: 5 2

Knit directory: multistate2/

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.


The R Markdown is untracked by Git. To know which version of the R Markdown file created these results, you’ll want to first commit it to the Git repo. If you’re still working on the analysis, you can ignore this warning. When you’re finished, you can run wflow_publish to commit the R Markdown file and build the HTML.

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(20230211) 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.

Using absolute paths to the files within your workflowr project makes it difficult for you and others to run your code on a different machine. Change the absolute path(s) below to the suggested relative path(s) to make your code more reproducible.

absolute relative
~/multistate2//code/smoothtest.R code/smoothtest.R
~/multistate2//code/newsmooth.R code/newsmooth.R
~/multistate2/code/fitarray.R code/fitarray.R
~/multistate2//output/dfascvd_newbp.rds output/dfascvd_newbp.rds
~/multistate2/code/frs30_URBUT/fun.frs_30y.R code/frs30_URBUT/fun.frs_30y.R

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 f9e23f9. 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:    .DS_Store
    Ignored:    analysis/.DS_Store
    Ignored:    code/.DS_Store
    Ignored:    data/
    Ignored:    output/
    Ignored:    plots/.DS_Store

Untracked files:
    Untracked:  analysis/predicted_risks.Rmd
    Untracked:  analysis/rmseanalysis.Rmd

Unstaged changes:
    Modified:   code/frs30_URBUT/fun.frs_30y.R

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.


There are no past versions. Publish this analysis with wflow_publish() to start tracking its development.


R Markdown


Attaching package: 'dplyr'
The following objects are masked from 'package:stats':

    filter, lag
The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union
── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ forcats   1.0.0     ✔ readr     2.1.4
✔ ggplot2   3.4.2     ✔ stringr   1.5.0
✔ lubridate 1.9.2     ✔ tibble    3.2.1
✔ purrr     1.0.1     ✔ tidyr     1.3.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
Loading required package: ggpubr


Attaching package: 'survminer'


The following object is masked from 'package:survival':

    myeloma



Attaching package: 'reshape'


The following object is masked from 'package:lubridate':

    stamp


The following objects are masked from 'package:tidyr':

    expand, smiths


The following object is masked from 'package:dplyr':

    rename



Attaching package: 'gridExtra'


The following object is masked from 'package:dplyr':

    combine



Attaching package: 'survMisc'


The following object is masked from 'package:ggplot2':

    autoplot



Attaching package: 'rsq'


The following object is masked from 'package:survMisc':

    rsq


Type 'citation("pROC")' for a citation.


Attaching package: 'pROC'


The following object is masked from 'package:survMisc':

    ci


The following objects are masked from 'package:stats':

    cov, smooth, var



Attaching package: 'data.table'


The following object is masked from 'package:reshape':

    melt


The following objects are masked from 'package:lubridate':

    hour, isoweek, mday, minute, month, quarter, second, wday, week,
    yday, year


The following object is masked from 'package:purrr':

    transpose


The following objects are masked from 'package:dplyr':

    between, first, last



Attaching package: 'plotly'


The following object is masked from 'package:reshape':

    rename


The following object is masked from 'package:ggplot2':

    last_plot


The following object is masked from 'package:stats':

    filter


The following object is masked from 'package:graphics':

    layout

Health

calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
[1] 6.083 6.120
[1] 15.074  7.121
[1] 0.592 2.117
[1] 0.611 2.233
[1] 0.679 0.593
[1] 0.744 0.656
[1] 0.866 0.981

Now do starting at Ht:

calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
[1] 7.051 6.739
[1] 15.456  6.950
[1] 1.474 7.878
[1] 1.482 7.958
[1] 1.468 7.421
[1] 1.363 5.757
[1] 1.367 6.373
   user  system elapsed 
325.656  43.361 369.031 

Now do starting at Dm:

[1] 40
[1] "1"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "2"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "3"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "4"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "5"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "6"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] 45
[1] "1"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "2"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "3"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "4"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "5"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "6"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] 50
[1] "1"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "2"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "3"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "4"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "5"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "6"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] 55
[1] "1"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "2"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "3"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "4"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "5"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "6"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] 60
[1] "1"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "2"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "3"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "4"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "5"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "6"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] 65
[1] "1"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "2"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "3"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "4"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "5"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "6"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] 70
[1] "1"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "2"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "3"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "4"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "5"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1] "6"
calculation original version....
calculation recalibrated version....
[1] 0
[1] 1
[1] 2
[1] 3
[1] 4
[1]  7.246 10.930
[1] 14.956  8.328
[1] 4.018 7.975
[1] 4.101 8.458
[1] 3.954 7.516
[1] 3.927 8.367
[1] 3.924 7.701
   user  system elapsed 
305.224  40.345 345.622 

HyperLip

calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
calculation original version....
calculation recalibrated version....
[1] 7.027 7.028
[1] 16.533 10.010
[1]  3.461 11.394
[1]  3.494 11.536
[1] 3.306 9.158
[1]  3.485 11.209
[1] 3.325 9.950
   user  system elapsed 
306.856  38.841 345.745 

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

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

other attached packages:
 [1] ehaGoF_0.1.1       CVrisk_1.1.0       babynames_1.0.1    gapminder_1.0.0   
 [5] carData_3.0-5      plotly_4.10.2      DT_0.28            gt_0.9.0          
 [9] RColorBrewer_1.1-3 data.table_1.14.8  pROC_1.18.4        rsq_2.5           
[13] survMisc_0.5.6     gridExtra_2.3      ggfortify_0.4.16   reshape_0.8.9     
[17] eulerr_7.0.0       survminer_0.4.9    ggpubr_0.6.0       survival_3.5-5    
[21] lubridate_1.9.2    forcats_1.0.0      stringr_1.5.0      purrr_1.0.1       
[25] readr_2.1.4        tidyr_1.3.0        tibble_3.2.1       ggplot2_3.4.2     
[29] tidyverse_2.0.0    dplyr_1.1.2        ggsci_3.0.0       

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.0  viridisLite_0.4.2 lazyeval_0.2.2    fastmap_1.1.1    
 [5] promises_1.2.0.1  digest_0.6.33     timechange_0.2.0  lifecycle_1.0.3  
 [9] Deriv_4.1.3       magrittr_2.0.3    compiler_4.3.1    rlang_1.1.1      
[13] sass_0.4.7        tools_4.3.1       utf8_1.2.3        yaml_2.3.7       
[17] knitr_1.43        ggsignif_0.6.4    htmlwidgets_1.6.2 xml2_1.3.5       
[21] plyr_1.8.8        abind_1.4-5       workflowr_1.7.0   withr_2.5.0      
[25] grid_4.3.1        fansi_1.0.4       git2r_0.32.0      xtable_1.8-4     
[29] colorspace_2.1-0  scales_1.2.1      MASS_7.3-60       cli_3.6.1        
[33] rmarkdown_2.23    generics_0.1.3    rstudioapi_0.15.0 km.ci_0.5-6      
[37] httr_1.4.6        tzdb_0.4.0        minqa_1.2.5       cachem_1.0.8     
[41] splines_4.3.1     vctrs_0.6.3       boot_1.3-28.1     Matrix_1.6-0     
[45] jsonlite_1.8.7    car_3.1-2         hms_1.1.3         rstatix_0.7.2    
[49] jquerylib_0.1.4   glue_1.6.2        nloptr_2.0.3      stringi_1.7.12   
[53] gtable_0.3.3      later_1.3.1       lme4_1.1-34       munsell_0.5.0    
[57] pillar_1.9.0      htmltools_0.5.5   R6_2.5.1          KMsurv_0.1-5     
[61] rprojroot_2.0.3   evaluate_0.21     lattice_0.21-8    highr_0.10       
[65] backports_1.4.1   broom_1.0.5       httpuv_1.6.11     bslib_0.5.0      
[69] Rcpp_1.0.11       nlme_3.1-162      xfun_0.39         fs_1.6.3         
[73] zoo_1.8-12        pkgconfig_2.0.3