Files in JeffWeinell/misc.wrappers

Miscellaneous Wrapper Functions for Spatial Population Genomics

R/DAPC_adegenet.R R/check.if.executable.R R/cladesub.R R/config_miscwrappers.R R/coords2sp.poly.R R/create.outer.R R/exepaths_miscwrappers.R R/extract.base.polygons.R R/fracD.R R/genind2diffs.R R/gg2raster.R R/minCladesList.R R/partitions.R R/plot_eems.R R/plot_model.R R/run_SNMF.R R/run_delimitR.R R/run_fastStructure.R R/run_structure.R R/runeems_snps_setup.R R/runtess.R R/simmaphelper.R R/sp2coords.R R/stacks.R README.md inst/extdata/DAPC_simK4_withCoords_v6.pdf inst/extdata/DAPC_simK4_withCoords_v6_BiPlots.pdf inst/extdata/DAPC_simK4_withCoords_v6_desnsityPlots_DF.pdf inst/extdata/DAPC_simK4_withCoords_v6_desnsityPlots_PC.pdf inst/extdata/POPSutilities.r inst/extdata/createouter_exampleOutput_gg_method1_outer.pdf inst/extdata/createouter_exampleOutput_gg_method3_outer.pdf inst/extdata/createouter_exampleOutput_method1_outer.pdf inst/extdata/createouter_exampleOutput_method2_outer.pdf inst/extdata/createouter_exampleOutput_method3_outer.pdf inst/extdata/example_model.pdf inst/extdata/fs_simK4_withCoords.pdf inst/extdata/make_eems_plots_JLW.R inst/extdata/sNMF_simK4_withCoords.pdf inst/extdata/simK2_coords_map.pdf inst/extdata/simK3_coords_map.pdf inst/extdata/simK4_coordsNULL.pdf inst/extdata/simK4_coordsNULL_fs.pdf inst/extdata/simK4_coordsNULL_sNMF.pdf inst/extdata/simK4_coords_map.pdf inst/extdata/tess3r_simK4.pdf man/EvannoPlots.Rd man/Rsh.Rd man/admixtureMap.Rd man/admixturePlots.Rd man/assignmentPlots.Rd man/bbox2points.Rd man/check.if.executable.Rd man/check_mcmcpath_contents.Rd man/check_plot_params.Rd man/cladesub.Rd man/config_miscwrappers.Rd man/coords2sp.poly.Rd man/cpSNPsVCF.Rd man/create.outer.Rd man/create_popfile.Rd man/cstacks_cleanup.Rd man/cstacks_setup.Rd man/dapc.biplot.arrange.Rd man/dapc.plot.arrange.Rd man/dapc.plot.arrange2.Rd man/decompose_distances.Rd man/default_eems_colors.Rd man/dfTransform.Rd man/diffcol.Rd man/dlogunif.Rd man/dunif.quotient.a0.Rd man/dunif.quotient.iid.Rd man/easySFS_fsc2.Rd man/eems_cleanup.Rd man/eems_contours.Rd man/eemsgg2raster.Rd man/equiv.Rd man/equivalencyMats.Rd man/evalfun.Rd man/exepaths_miscwrappers.Rd man/extract.base.polygons.Rd man/fastsimcoalsims_Par.Rd man/filled_contour_graph.Rd man/filled_contour_rates.Rd man/filled_eems_contour.Rd man/filled_prob_contour.Rd man/filter.var.Rd man/filter.vcf.Rd man/find.exe.path.Rd man/fitmodels.Rd man/fracD.Rd man/genind2diffs.Rd man/geo_distm.Rd man/get_dist_metric.Rd man/gg.world110_proj.Rd man/ggscatter.dapc.Rd man/goodcolors.Rd man/goodcolors2.Rd man/gstacks_cleanup.Rd man/gstacks_setup.Rd man/hex2dec.Rd man/is_color.Rd man/load_required_packages.Rd man/minCladesList.Rd man/newpoint.Rd man/pairwise_dist.Rd man/plot.funUnif.Rd man/plot_eems.Rd man/plot_log_posterior.Rd man/plot_model.Rd man/plot_pairwise_dissimilarities_.Rd man/plottable.dapc.Rd man/points.on.land.Rd man/populations_cleanup.Rd man/populations_setup.Rd man/produnif.Rd man/pset.Rd man/rangeBuffer.Rd man/rcoords.Rd man/read_dimns.Rd man/read_matrix.Rd man/read_vector.Rd man/read_voronoi.Rd man/reassign.Rd man/rgb.cb.Rd man/rlogunif.Rd man/rsbatch.Rd man/run_DAPC.Rd man/run_SNMF.Rd man/run_delimitR.Rd man/run_fastStructure.Rd man/run_structure.Rd man/runeems_snps_setup.Rd man/runtess.Rd man/rx2y2.Rd man/sim.vcf.Rd man/sp2coords.Rd man/sq.Rd man/sstacks_cleanup.Rd man/sstacks_setup.Rd man/stacks_cleanup.Rd man/summarize_VCFs.Rd man/summarize_stacks.Rd man/sumnorm.PDF.Rd man/sumunif.Rd man/theme_void.Rd man/tiles2contours.Rd man/transitionModels.Rd man/tsv2bam_cleanup.Rd man/tsv2bam_setup.Rd man/update_miscwrappers.Rd man/ustacks_cleanup.Rd man/ustacks_setup.Rd man/vcf2fastStructure.Rd man/vcf2parts.Rd man/vcf2phy.Rd man/vcf2structure.Rd man/vcfR2geno.Rd man/vcfR2lfmm.Rd man/vcf_getSNP.Rd