Last updated: 2023-10-27

Checks: 6 1

Knit directory: Genomic-Selection-for-Drought-Tolerance-Using-Genome-Wide-SNPs-in-Casava/

This reproducible R Markdown analysis was created with workflowr (version 1.7.1). 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 file has unstaged changes. 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(20221020) 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 38077f1. 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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    data/allchrAR08.txt

Untracked files:
    Untracked:  GETGV.RDS
    Untracked:  analysis/phenotype2.Rmd
    Untracked:  data/Article.docx
    Untracked:  data/Article2.docx
    Untracked:  data/Articles/
    Untracked:  output/BLUPS2.csv
    Untracked:  output/BLUPS3.csv
    Untracked:  output/BLUPS_drgBLUPs__boxplot_med.png
    Untracked:  output/BLUPS_drgBLUPs_density_med.png
    Untracked:  output/BLUPS_drgBLUPs_med.png
    Untracked:  output/BLUPS_par_mmer.Rdata
    Untracked:  output/Figuras_article.rar
    Untracked:  output/GD_matrix.csv
    Untracked:  output/GEBVS_G_BLUP_BGLR.RDS
    Untracked:  output/GEBVS_RR_BLUP.RDS
    Untracked:  output/GEBVxBLUPS.tiff
    Untracked:  output/GEBVxGETV.tiff
    Untracked:  output/GEBVxGETV2.tiff
    Untracked:  output/G_matrix.csv
    Untracked:  output/G_matrix.rds
    Untracked:  output/H2.csv
    Untracked:  output/Tabelas.xlsx
    Untracked:  output/accuracy_all_methods.tiff
    Untracked:  output/correlation_blups.tiff
    Untracked:  output/density_blups.tiff
    Untracked:  output/drgBLUP.csv
    Untracked:  output/indice_selection3.tiff
    Untracked:  output/kappa.tiff
    Untracked:  output/mean_pheno.csv
    Untracked:  output/result_mixed_model.RData
    Untracked:  output/result_mixed_model2.RData
    Untracked:  output/result_mixed_model3.RData
    Untracked:  output/result_sommer.RData
    Untracked:  output/results_cv_BayesA.csv
    Untracked:  output/results_cv_BayesB.csv
    Untracked:  output/results_cv_DOM.csv
    Untracked:  output/results_cv_GETGV.csv
    Untracked:  output/results_cv_G_BLUP.csv
    Untracked:  output/results_cv_G_BLUP2.csv
    Untracked:  output/results_cv_G_BLUP_BGRL.csv
    Untracked:  output/results_cv_G_BLUP_BLUPS2.csv
    Untracked:  output/results_cv_G_BLUP_BLUPS3.csv
    Untracked:  output/results_cv_G_BLUP_sommer.csv
    Untracked:  output/results_cv_RF.csv
    Untracked:  output/results_cv_RKHS.csv
    Untracked:  output/results_cv_RR_BLUP.csv
    Untracked:  output/results_kappa.csv
    Untracked:  output/results_kappa2.csv
    Untracked:  output/varcomp.tiff
    Untracked:  output/varcomp2.csv

Unstaged changes:
    Modified:   analysis/GWS.Rmd
    Deleted:    analysis/gws-multi-enviroment.Rmd
    Modified:   analysis/license.Rmd
    Modified:   analysis/phenotype.Rmd
    Modified:   analysis/phenotype_multi.Rmd
    Deleted:    data/Genomic Selection for Drought Tolerance Using Genome-Wide SNPs in Maize.pdf
    Modified:   data/Phenotyping.xlsx
    Deleted:    data/convet_haplo_diplo.txt
    Deleted:    data/genomic selection.pptx
    Modified:   data/pheno_clean.csv
    Deleted:    output/BLUPS.RDS
    Modified:   output/BLUPS.csv
    Deleted:    output/BLUPS_Multi.csv
    Modified:   output/BLUPS_par.Rdata
    Deleted:    output/BLUPS_par_ind.Rdata
    Deleted:    output/H2_Multi.csv
    Deleted:    output/accuracy.png
    Deleted:    output/accuracy2.png
    Deleted:    output/accuracy_multi.png
    Deleted:    output/blups_med.png
    Deleted:    output/firts_results/accuracy.png
    Deleted:    output/firts_results/accuracy_multi.png
    Deleted:    output/herdabilidade.csv
    Modified:   output/media_pheno.csv
    Deleted:    output/media_pheno_Multi.csv
    Deleted:    output/resultMM.Rdata
    Deleted:    output/result_G_BLUP.csv
    Modified:   output/results_cv.csv
    Deleted:    output/results_cv2.csv
    Modified:   output/varcomp.csv
    Deleted:    output/varcomp_multi.csv

Staged changes:
    Modified:   analysis/GWS.Rmd
    Deleted:    analysis/figure/GWS.Rmd/unnamed-chunk-11-1.png
    Deleted:    analysis/figure/GWS.Rmd/unnamed-chunk-15-1.png
    Deleted:    analysis/figure/GWS.Rmd/unnamed-chunk-16-1.png
    Deleted:    analysis/figure/GWS.Rmd/unnamed-chunk-19-1.png
    Deleted:    analysis/figure/GWS.Rmd/unnamed-chunk-20-1.png
    Deleted:    analysis/figure/GWS.Rmd/unnamed-chunk-21-1.png
    Deleted:    analysis/figure/phenotype.Rmd/unnamed-chunk-11-1.png
    Deleted:    analysis/figure/phenotype.Rmd/unnamed-chunk-11-2.png
    Deleted:    analysis/figure/phenotype.Rmd/unnamed-chunk-12-1.png
    Deleted:    analysis/figure/phenotype.Rmd/unnamed-chunk-12-2.png
    Deleted:    analysis/figure/phenotype.Rmd/unnamed-chunk-13-1.png
    Deleted:    analysis/figure/phenotype.Rmd/unnamed-chunk-15-1.png
    Deleted:    analysis/figure/phenotype.Rmd/unnamed-chunk-16-1.png
    Deleted:    analysis/figure/phenotype.Rmd/unnamed-chunk-21-1.png
    Deleted:    analysis/figure/phenotype.Rmd/unnamed-chunk-5-1.png
    Deleted:    analysis/figure/phenotype.Rmd/unnamed-chunk-7-1.png
    Modified:   analysis/gws-multi-enviroment.Rmd
    Modified:   data/genomic selection.pptx
    New:        output/accuracy.png
    New:        output/accuracy2.png
    New:        output/firts_results/accuracy.png
    New:        output/firts_results/accuracy_multi.png
    Modified:   output/results_cv.csv
    New:        output/results_cv2.csv

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/license.Rmd) and HTML (docs/license.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
html 90dc112 WevertonGomesCosta 2022-11-17 Update
html d930880 WevertonGomesCosta 2022-11-11 Update
Rmd 5988c27 WevertonGomesCosta 2022-11-11 Update
Rmd bf7b1d3 WevertonGomesCosta 2022-11-11 Update
html bf7b1d3 WevertonGomesCosta 2022-11-11 Update
Rmd b78c842 WevertonGomesCosta 2022-10-20 Start workflowr project.

Este material foi produzido por Costa, W. G. 2023, está licenciado sob a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Isso significa que você é livre para:

Desde que você siga os termos da licença:


sessionInfo()
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=Portuguese_Brazil.utf8  LC_CTYPE=Portuguese_Brazil.utf8   
[3] LC_MONETARY=Portuguese_Brazil.utf8 LC_NUMERIC=C                      
[5] LC_TIME=Portuguese_Brazil.utf8    

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.11       rstudioapi_0.15.0 whisker_0.4.1     knitr_1.44       
 [5] magrittr_2.0.3    workflowr_1.7.1   R6_2.5.1          rlang_1.1.1      
 [9] fastmap_1.1.1     fansi_1.0.4       stringr_1.5.0     tools_4.2.3      
[13] xfun_0.40         utf8_1.2.3        cli_3.6.1         git2r_0.32.0     
[17] jquerylib_0.1.4   htmltools_0.5.6   rprojroot_2.0.3   yaml_2.3.7       
[21] digest_0.6.33     tibble_3.2.1      lifecycle_1.0.3   later_1.3.1      
[25] sass_0.4.7        vctrs_0.6.3       promises_1.2.1    fs_1.6.3         
[29] cachem_1.0.8      glue_1.6.2        evaluate_0.22     rmarkdown_2.25   
[33] stringi_1.7.12    bslib_0.5.1       compiler_4.2.3    pillar_1.9.0     
[37] jsonlite_1.8.7    httpuv_1.6.11     pkgconfig_2.0.3  

  1. Weverton Gomes da Costa, Pós-Doutorando, Embrapa Mandioca e Fruticultura, ↩︎