Last updated: 2021-07-14

Checks: 2 0

Knit directory: implementGMSinCassava/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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.

Repository version: 2953ee6

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 2953ee6. 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:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    analysis/accuracies.png
    Ignored:    analysis/fig2.png
    Ignored:    analysis/fig3.png
    Ignored:    analysis/fig4.png
    Ignored:    code/.DS_Store
    Ignored:    data/.DS_Store

Untracked files:
    Untracked:  accuracies.png
    Untracked:  analysis/docs/
    Untracked:  analysis/speedUpPredCrossVar.Rmd
    Untracked:  code/AlphaAssign-Python/
    Untracked:  code/calcGameticLD.cpp
    Untracked:  code/col_sums.cpp
    Untracked:  code/convertDart2vcf.R
    Untracked:  code/helloworld.cpp
    Untracked:  code/imputationFunctions.R
    Untracked:  code/matmult.cpp
    Untracked:  code/misc.cpp
    Untracked:  code/test.cpp
    Untracked:  data/CassavaGeneticMap/
    Untracked:  data/DatabaseDownload_2021May04/
    Untracked:  data/GBSdataMasterList_31818.csv
    Untracked:  data/IITA_GBStoPhenoMaster_33018.csv
    Untracked:  data/NRCRI_GBStoPhenoMaster_40318.csv
    Untracked:  data/PedigreeGeneticGainCycleTime_aafolabi_01122020.xls
    Untracked:  data/blups_forCrossVal.rds
    Untracked:  data/chr1_RefPanelAndGSprogeny_ReadyForGP_72719.fam
    Untracked:  data/dosages_IITA_filtered_2021May13.rds
    Untracked:  data/genmap_2021May13.rds
    Untracked:  data/haps_IITA_filtered_2021May13.rds
    Untracked:  data/recombFreqMat_1minus2c_2021May13.rds
    Untracked:  fig2.png
    Untracked:  fig3.png
    Untracked:  figure/
    Untracked:  output/IITA_CleanedTrialData_2021May10.rds
    Untracked:  output/IITA_ExptDesignsDetected_2021May10.rds
    Untracked:  output/IITA_blupsForModelTraining_twostage_asreml_2021May10.rds
    Untracked:  output/IITA_trials_NOT_identifiable.csv
    Untracked:  output/crossValPredsA.rds
    Untracked:  output/crossValPredsAD.rds
    Untracked:  output/cvAD_5rep5fold_markerEffects.rds
    Untracked:  output/cvAD_5rep5fold_meanPredAccuracy.rds
    Untracked:  output/cvAD_5rep5fold_parentfolds.rds
    Untracked:  output/cvAD_5rep5fold_predMeans.rds
    Untracked:  output/cvAD_5rep5fold_predVars.rds
    Untracked:  output/cvAD_5rep5fold_varPredAccuracy.rds
    Untracked:  output/cvDirDom_5rep5fold_markerEffects.rds
    Untracked:  output/cvDirDom_5rep5fold_meanPredAccuracy.rds
    Untracked:  output/cvDirDom_5rep5fold_parentfolds.rds
    Untracked:  output/cvDirDom_5rep5fold_predMeans.rds
    Untracked:  output/cvDirDom_5rep5fold_predVars.rds
    Untracked:  output/cvDirDom_5rep5fold_varPredAccuracy.rds
    Untracked:  output/cvMeanPredAccuracyA.rds
    Untracked:  output/cvMeanPredAccuracyAD.rds
    Untracked:  output/cvPredMeansA.rds
    Untracked:  output/cvPredMeansAD.rds
    Untracked:  output/cvVarPredAccuracyA.rds
    Untracked:  output/cvVarPredAccuracyAD.rds
    Untracked:  output/genomicPredictions_ModelAD.rds
    Untracked:  output/genomicPredictions_ModelDirDom.rds
    Untracked:  output/kinship_A_IITA_2021May13.rds
    Untracked:  output/kinship_D_IITA_2021May13.rds
    Untracked:  output/markEffsTest.rds
    Untracked:  output/markerEffects.rds
    Untracked:  output/markerEffectsA.rds
    Untracked:  output/markerEffectsAD.rds
    Untracked:  output/maxNOHAV_byStudy.csv
    Untracked:  output/obsCrossMeansAndVars.rds
    Untracked:  output/parentfolds.rds
    Untracked:  output/ped2check_genome.rds
    Untracked:  output/ped2genos.txt
    Untracked:  output/pednames2keep.txt
    Untracked:  output/pednames_Prune100_25_pt25.log
    Untracked:  output/pednames_Prune100_25_pt25.nosex
    Untracked:  output/pednames_Prune100_25_pt25.prune.in
    Untracked:  output/pednames_Prune100_25_pt25.prune.out
    Untracked:  output/potential_dams.txt
    Untracked:  output/potential_sires.txt
    Untracked:  output/predVarTest.rds
    Untracked:  output/samples2keep_IITA_2021May13.txt
    Untracked:  output/samples2keep_IITA_MAFpt01_prune50_25_pt98.log
    Untracked:  output/samples2keep_IITA_MAFpt01_prune50_25_pt98.nosex
    Untracked:  output/samples2keep_IITA_MAFpt01_prune50_25_pt98.prune.in
    Untracked:  output/samples2keep_IITA_MAFpt01_prune50_25_pt98.prune.out
    Untracked:  output/verified_ped.txt

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/about.Rmd) and HTML (docs/about.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 e66bdad wolfemd 2021-06-10 Build site.
Rmd 8a0c50e wolfemd 2021-05-04 Start workflowr project.

Describe your project.