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Last updated: 2021-11-30

Checks: 2 0

Knit directory: Barley1kGBS_Proj/

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: 93537b3

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The results in this page were generated with repository version 93537b3. 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:    analysis/GenomeEnvAssociation_cache/
    Ignored:    analysis/GenomicVarPartitioning_cache/
    Ignored:    analysis/PreprocessEnvData_cache/

Untracked files:
    Untracked:  VennDiagram2021-11-25_14-18-48.log
    Untracked:  VennDiagram2021-11-25_14-20-27.log
    Untracked:  VennDiagram2021-11-25_17-14-55.log
    Untracked:  VennDiagram2021-11-30_11-23-44.log
    Untracked:  VennDiagram2021-11-30_13-32-43.log
    Untracked:  VennDiagram2021-11-30_13-36-01.log
    Untracked:  VennDiagram2021-11-30_13-43-13.log
    Untracked:  VennDiagram2021-11-30_14-13-15.log
    Untracked:  VennDiagram2021-11-30_14-15-28.log
    Untracked:  analysis/GOanalysis.Rmd
    Untracked:  analysis/ResistanceSurface.Rmd
    Untracked:  analysis/not_show/ResistanceSurface.html
    Untracked:  analysis/unPC.rmd
    Untracked:  data/2020-04-10-partial_rda_ALStructure_K4_ancestry_coeff_191B1K+53KS_12envs_27147SNPs_maf0.05.RDS
    Untracked:  data/2020-04-10-simple_rda_191B1K+53KS_12envs_27147SNPs_maf0.05.RDS
    Untracked:  data/2020-04-18-191B1K+53KS_LFMM_K4_27147SNPs_maf0.05_12envs_adj_pvalues.tsv
    Untracked:  data/2020-04-18-191B1K+53KS_LFMM_K4_27147SNPs_maf0.05_12envs_adj_qvalues.tsv
    Untracked:  data/Barley_Morex_V2_gene_annotation_PGSB.all.descriptions.txt
    Untracked:  data/Barley_Morex_V2_gene_annotation_PGSB.all.gff3
    Untracked:  data/Barley_Morex_V2_pseudomolecules_centromere_positions.tsv
    Untracked:  data/BayPass_genotyping_input_191B1K+53KS_in4pops_27147SNPs_maf0.05.alct
    Untracked:  data/TPI_LowRes.tif
    Untracked:  data/baypass_output_191B1K+53KS_in4pops_summary_pi_xtx.out
    Untracked:  data/elevation_LowRes.tif
    Untracked:  data/occurrence_30E_40N_v1_1.tif
    Untracked:  data/slope_LowRes.tif
    Untracked:  data/slope_SLevant.tif
    Untracked:  data/water_LowRes.tif
    Untracked:  data/wildbarley_POD_summary_pi_xtx.out
    Untracked:  output/191B1K+53KS_unPC_visualization_evecArray.r
    Untracked:  output/191B1K+53KS_unPC_visualization_pairwiseDistCalc_unPC.rds
    Untracked:  output/191B1K+53KS_unPC_visualization_pairwiseDistCalc_unPC_popnSamplingTableForPlot.rds
    Untracked:  output/191B1K+53KS_unPC_visualization_unPC_outputPlot__popnLevelMeanAggregated_leastDiffOnTop.pdf
    Untracked:  output/191B1K+53KS_unPC_visualization_unPC_outputPlot__popnLevelMeanAggregated_mostDiffOnTop.pdf
    Untracked:  output/Aspect-LFMM_FDR0.05_SNP2GO_500bp_GOenrichFDR0.05.RDS
    Untracked:  output/BD_sl12-LFMM_FDR0.05_SNP2GO_500bp_GOenrichFDR0.05.RDS
    Untracked:  output/Barley_Morex_V2_gene_annotation_PGSB_append_GO.all.gff
    Untracked:  output/Dps_wild_barley.RDS
    Untracked:  output/Geocoord_pop.csv
    Untracked:  output/OCC_sl4-LFMM_FDR0.05_SNP2GO_500bp_GOenrichFDR0.05.RDS
    Untracked:  output/ResistGA_gdist_wild_barley_geo_bootstrap_AIC.csv
    Untracked:  output/ResistGA_gdist_wild_barley_geo_bootstrap_R2.csv
    Untracked:  output/SLT_sl1234-LFMM_FDR0.05_SNP2GO_500bp_GOenrichFDR0.05.RDS
    Untracked:  output/Slope-LFMM_FDR0.05_SNP2GO_500bp_GOenrichFDR0.05.RDS
    Untracked:  output/TPI_SLevant.tif
    Untracked:  output/XtX0.995_GOenrich_FDR0.05_500bp.RDS
    Untracked:  output/_popnAggregated.txt
    Untracked:  output/partial_RDA_ancescoeff_FDR0.05_4axis_SNP2GO_500bp_FDR0.05.RDS
    Untracked:  output/simple_RDA_FDR0.05_4axis_SNP2GO_500bp_FDR0.05.RDS
    Untracked:  output/unPC_PC_input.evec
    Untracked:  output/unPC_coord_input.txt
    Untracked:  output/unPC_input.evec
    Untracked:  output/water_body_SLevant.tif

Unstaged changes:
    Modified:   README.md
    Modified:   analysis/GenomeEnvAssociation.Rmd
    Deleted:    analysis/not_show/ResistanceSurface.Rmd
    Deleted:    analysis/not_show/unPC.rmd
    Modified:   code/Rfunctions.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 repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (public/index.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	bc726c2	Che-Wei Chang	2021-10-22	Build site.
html	5f82e26	Che-Wei Chang	2021-10-22	Build site.
html	f1ac360	Che-Wei Chang	2021-10-22	Build site.
html	1202876	Che-Wei Chang	2021-10-22	Host with GitLab.
Rmd	7c6b41a	Che-Wei Chang	2021-10-22	wflow_publish(list.files("./analysis", pattern = "*.Rmd", full.names = T))
Rmd	0467ff5	Che-Wei Chang	2021-08-31	Start workflowr project.