Last updated: 2019-05-25

Checks: 6 0

Knit directory: 2018-model-comparison/

This reproducible R Markdown analysis was created with workflowr (version 1.3.0). 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(20190523) 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! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.

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:    .Rproj.user/
    Ignored:    .drake/
    Ignored:    code/07-paper/._files
    Ignored:    data/
    Ignored:    log/
    Ignored:    packrat/lib-R/
    Ignored:    packrat/lib-ext/
    Ignored:    packrat/lib/
    Ignored:    rosm.cache/
    Ignored:    tests/testthat/

Untracked files:
    Untracked:  analysis/bibliography.bib
    Untracked:  packrat/src/here/

Unstaged changes:
    Modified:   _drake.R
    Modified:   analysis/about.Rmd
    Modified:   analysis/benchmark-diplodia.Rmd
    Modified:   analysis/benchmark-pathogens.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/pathogen-maps-debugging.Rmd
    Modified:   analysis/prediction-pathogens.Rmd
    Modified:   analysis/vis-opt-paths.Rmd
    Modified:   analysis/vis-tuning-effects.Rmd
    Modified:   code/06-reports.R
    Modified:   code/07-paper/submission/3/latex-source-files/cv_boxplots_final_brier-1.pdf
    Deleted:    docs/figure/vis-partitions.Rmd/spcv_nspcv_folds-1.pdf
    Modified:   inst/
    Modified:   packrat/packrat.lock

Staged changes:
    Modified:   code/99-packages.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.

These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd 6934f35 pat-s 2019-05-25 wflow_publish(knitr_in(“analysis/vis-partitions.Rmd”), view = FALSE)
html 137adf4 pat-s 2019-05-25 Build site.
html be8a48b pat-s 2019-05-25 Build site.
Rmd 0c29475 pat-s 2019-05-25 wflow_publish(knitr_in(“analysis/vis-partitions.Rmd”), view = FALSE)
Rmd 6af4181 pat-s 2019-05-23 update reports
Rmd 769718b pat-s 2019-05-23 Start workflowr project.

Visualization of the first five folds of each resampling setting.

Version Author Date
be8a48b pat-s 2019-05-25

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /opt/spack/opt/spack/linux-centos7-x86_64/gcc-7.3.0/openblas-0.3.5-zncvk4jccaqyfl4z3vszaboeps6hyzta/lib/

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] tidyselect_0.2.5    workflowr_1.3.0     here_0.1           
 [4] kableExtra_1.1.0    ggExtra_0.8         ggrepel_0.8.0      
 [7] reporttools_1.1.2   xtable_1.8-3        cowplot_0.9.3      
[10] hrbrthemes_0.6.0    ggpubr_0.2          future.callr_0.4.0 
[13] furrr_0.1.0.9002    future_1.11.1.1     ggsci_2.9          
[16] clustermq_0.8.6     ggspatial_1.0.3     ggplot2_3.0.0      
[19] rgenoud_5.8-3.0     fs_1.2.6            curl_3.2           
[22] R.utils_2.7.0       R.oo_1.22.0         R.methodsS3_1.7.1  
[25] GSIF_0.5-5          stringr_1.3.1       RSAGA_1.3.0        
[28] plyr_1.8.4          shapefiles_0.7      foreign_0.8-71     
[31] gstat_1.1-6         glue_1.3.0          rasterVis_0.45     
[34] latticeExtra_0.6-28 RColorBrewer_1.1-2  lattice_0.20-35    
[37] raster_2.8-19       viridis_0.5.1       viridisLite_0.3.0  
[40] rgdal_1.4-3         sp_1.3-1            tibble_2.0.1       
[43] forcats_0.3.0       lwgeom_0.1-6        dplyr_0.8.0.1      
[46] sf_0.7-4            parallelMap_1.3     purrr_0.2.5        
[49] mlrMBO_1.1.2        smoof_1.5.1         checkmate_1.8.5    
[52] BBmisc_1.11         magrittr_1.5        mlr_2.13.9000      
[55] ParamHelpers_1.11   drake_7.2.0        

loaded via a namespace (and not attached):
  [1] backports_1.1.2   Hmisc_4.2-0       fastmatch_1.1-0  
  [4] igraph_1.2.2      lazyeval_0.2.1    splines_3.5.1    
  [7] storr_1.2.1       listenv_0.7.0     digest_0.6.15    
 [10] htmltools_0.3.6   base64url_1.4     cluster_2.0.7-1  
 [13] readr_1.3.1       globals_0.12.4    extrafont_0.17   
 [16] xts_0.11-0        extrafontdb_1.0   colorspace_1.3-2 
 [19] rvest_0.3.2       pixmap_0.4-11     xfun_0.7         
 [22] callr_3.1.0       crayon_1.3.4      jsonlite_1.5     
 [25] hexbin_1.27.2     survival_2.42-3   zoo_1.8-3        
 [28] gtable_0.2.0      webshot_0.5.1     Rttf2pt1_1.3.7   
 [31] scales_1.0.0      DBI_1.0.0         miniUI_0.1.1.1   
 [34] Rcpp_1.0.0        plotrix_3.7-4     spData_0.2.9.0   
 [37] htmlTable_1.12    units_0.6-2       Formula_1.2-3    
 [40] intervals_0.15.1  dismo_1.1-4       htmlwidgets_1.3  
 [43] httr_1.3.1        FNN_1.1           aqp_1.17         
 [46] acepack_1.4.1     pkgconfig_2.0.2   reshape_0.8.8    
 [49] XML_3.98-1.16     nnet_7.3-12       RJSONIO_1.3-1.1  
 [52] labeling_0.3      later_0.7.5       rlang_0.3.1      
 [55] munsell_0.5.0     tools_3.5.1       evaluate_0.13    
 [58] yaml_2.2.0        processx_3.2.1    knitr_1.23       
 [61] mime_0.5          whisker_0.3-2     xml2_1.2.0       
 [64] compiler_3.5.1    rstudioapi_0.10   plotly_4.8.0     
 [67] e1071_1.7-0       spacetime_1.2-2   lhs_0.16         
 [70] stringi_1.2.4     ps_1.2.1          gdtools_0.1.7    
 [73] plot3D_1.1.1      Matrix_1.2-14     classInt_0.2-3   
 [76] pillar_1.3.1      plotKML_0.5-9     data.table_1.11.8
 [79] httpuv_1.4.5      colorRamps_2.3    R6_2.2.2         
 [82] promises_1.0.1    gridExtra_2.3     codetools_0.2-15 
 [85] MASS_7.3-50       assertthat_0.2.0  rprojroot_1.3-2  
 [88] withr_2.1.2       hms_0.4.2         parallel_3.5.1   
 [91] grid_3.5.1        rpart_4.1-13      tidyr_0.8.2      
 [94] class_7.3-14      rmarkdown_1.12    misc3d_0.8-4     
 [97] mco_1.0-15.1      git2r_0.23.0      shiny_1.2.0      
[100] base64enc_0.1-3