| admixtureMap | Generate a pdf with interpolated admixture coefficients for... |
| admixturePlots | Generate a pdf with admixture plots for each K Takes as input... |
| assignmentPlots | Generate a pdf with assignment plots for each K Takes as... |
| bbox2points | corner coordinates of area described by bounding box Returns... |
| check.if.executable | Check Executable Test if a file is executable |
| check_mcmcpath_contents | Check MCMC Path Contents Checks that all of the EEMs output... |
| check_plot_params | Check Plot Parameters Internal function used for making EEMS... |
| cladesub | substitute a clade with another clade replaces a specified... |
| config_miscwrappers | config_miscwrappers function This function is used to tell... |
| coords2sp.poly | coords2sp.poly function Convert a coordinates matrix into a... |
| cpSNPsVCF | copy STACKS SNPs VCF files using informative names Copies... |
| create.outer | create.outer function This function generates an '_.outer'... |
| create_popfile | Generate a popfile from STRUCTURE output Takes as input the... |
| cstacks_cleanup | cleanup cstacks Deletes cstacks bash scripts in a directory.... |
| cstacks_setup | batch setup cstacks For each combination of N and set of... |
| dapc.biplot.arrange | Arrange list of ggplot biplots Function to arrange ggplot... |
| dapc.plot.arrange | Arrange DAPC density plots. Function to arrange plots of... |
| dapc.plot.arrange2 | Arrange DAPC density plots. Function to arrange plots of... |
| decompose_distances | geo distances Used for making EEMS plots This function is... |
| default_eems_colors | default eems colors Use the default DarkOrange to Blue color... |
| dfTransform | Transform CRS coordinates data frame Transform coordinates... |
| diffcol | Cartesian color distance Cartesian distance between two... |
| dlogunif | dlunif function loguniform probability density function |
| dunif.quotient.a0 | Probability density function for the quotient of two uniform... |
| dunif.quotient.iid | Probability density function for the quotient of two... |
| easySFS_fsc2 | Run easySFS even easier to generate input MSFS and population... |
| eems_cleanup | cleanup eems Deletes eems_setup bash and R scripts in a... |
| eems_contours | eems contours Internal function used for making EEMS plots.... |
| eemsgg2raster | eemsgg2raster function Convert one of the four maps produced... |
| equiv | membership to equivalency matrix For a vector with entries... |
| equivalencyMats | ennumerate equivalence relations A list of n x n matrices,... |
| evalfun | Evaluate function name with lists of arguments |
| EvannoPlots | Generate Evanno Method Plots This function uses functions... |
| exepaths_miscwrappers | exepaths_miscwrappers function Function to return the paths... |
| extract.base.polygons | extract.base.polygons function Extract all lowest-level... |
| fastsimcoalsims_Par | fastsimcoalsims_Par Function to run fastsimcoalsims in... |
| filled_contour_graph | filled contour graph Generates a filled countour graph ggplot... |
| filled_contour_rates | filled contour rates Generates a ggplot object with filled... |
| filled_eems_contour | filled eems contour generates ggplot object corresponding to... |
| filled_prob_contour | filled probability contour Generates asthetics for ggplots.... |
| filter.var | Filter (query) genotype by variation Functon to test that a... |
| filter.vcf | Filter a VCF file or vcfR object. Filter or sample... |
| find.exe.path | Find path to program This function searches the system path... |
| fitmodels | Fit data and a list of Mk models with simmap Makes a list of... |
| fracD | fracD function Calculates the fractal dimension of... |
| genind2diffs | genind2diffs function Generates a diffs matrix from a genind... |
| geo_distm | geo distances Used for making EEMS plots This function is... |
| get_dist_metric | get distance metric Get the distance metric from... |
| ggscatter.dapc | Make ggplot with DAPC scatterplot THIS FUNCTION IS LARGELY... |
| gg.world110_proj | ggplot projected Natural Earth This function creates a ggplot... |
| goodcolors | Return a good set of colors to use for clusters in admixture... |
| goodcolors2 | Return my favorite set of colors to use for clusters in... |
| gstacks_cleanup | cleanup gstacks Deletes gstacks bash scripts in a directory.... |
| gstacks_setup | batch setup gstacks For each set samples (processed with... |
| hex2dec | Hex to xyz colors Hex to xyz color coordinates |
| is_color | Is color Check that a string, or a vector of strings,... |
| load_required_packages | load required packages Load packages This function is from... |
| minCladesList | minimum length set of clades with tip labels Returns a... |
| newpoint | Coordinates of point on ray Used in the function... |
| pairwise_dist | pairwise distances between demes Internal function used for... |
| plot_eems | plot_eems function Invokes the reemsplots2 function... |
| plot.funUnif | plot PDF for sum or product of two uniform distributions... |
| plot_log_posterior | plot eems log posterior Used for making EEMS plot 8 This... |
| plot_model | Plot Demographic Model This function creates a graphical... |
| plot_pairwise_dissimilarities_ | plot pairwise dissimilarities between demes Internal function... |
| plottable.dapc | Components plottable Creates a list with two logical data... |
| points.on.land | Return coordinates over land Returns the set of input... |
| populations_cleanup | cleanup populations Deletes populations bash scripts in a... |
| populations_setup | batch setup populations For each set samples (processed with... |
| produnif | PDF or CDF for the product of n independent uniformly... |
| pset | Powerset Function to return the powerset for a numeric or... |
| rangeBuffer | Buffered range Calculate the limits of a buffered range for a... |
| rcoords | Sample points in a random-centered area or tethered group of... |
| read_dimns | Read dimns Internal function used for making EEMS plots. This... |
| read_matrix | read matrix Internal function used for making EEMS plots.... |
| read_vector | read vector Internal function used for making EEMS plots.... |
| read_voronoi | read voronoi Reads EEMs output and constructs parameters for... |
| reassign | reassign Transforms a vector or matrix (mode character or... |
| rgb.cb | Transform sRGB colorspace into colorblind colorspaces Uses... |
| rlogunif | Sample from loguniform distribution |
| rsbatch | sbatch setup and submit Creates slurm sbatch submission... |
| Rsh | write bash and Rscript files for R code Creates .sh (bash)... |
| run_DAPC | Run DAPC and Plot Run adagenet DAPC analyses and generate... |
| run_delimitR | Run delimitR Function to use delimitR to setup standard... |
| runeems_snps_setup | runeems_snps_setup function Wrapper function for preparing to... |
| run_fastStructure | Run run_fastStructure from SNP data in a VCF file and and... |
| run_SNMF | Wrapper for LEA snmf Runs LEA function snmf function and... |
| run_structure | Run run_structure from SNP data in a VCF file and and plot... |
| runtess | Run tess3r and plot results Pipeline with wrappers for... |
| rx2y2 | Random point conditioned on distance Return x and y... |
| sim.vcf | Simulate SNPs as VCF |
| sp2coords | sp2coords function Function to extract the coordinates matrix... |
| sq | sh single quote Calls the base function shQuote with default... |
| sstacks_cleanup | cleanup sstacks Deletes sstacks bash scripts in a directory.... |
| sstacks_setup | batch setup sstacks For each set samples (processed with... |
| stacks_cleanup | cleanup stacks Deletes cstacks, sstacks, tsv2bam, gstacks,... |
| summarize_stacks | summarize_stacks For each set of samples processed with... |
| summarize_VCFs | summarize_VCFs Same as 'summarize_stacks', except the full... |
| sumnorm.PDF | PDF sum of normal distributions Probability distribution for... |
| sumunif | PDF or CDF for the sum of n independent uniformly continuous... |
| theme_void | theme void mostly blank ggplot theme This function is from... |
| tiles2contours | tiles2contours Converts tiles two contours This function is... |
| transitionModels | Generate transition models Makes a list of all possible model... |
| tsv2bam_cleanup | cleanup tsv2bam Deletes tsv2bam bash scripts in a directory.... |
| tsv2bam_setup | batch setup tsv2bam For each set samples (processed with... |
| update_miscwrappers | update miscwrappers Updates misc.wrappers by calling... |
| ustacks_cleanup | cleanup ustacks Deletes ustacks bash scripts in a directory.... |
| ustacks_setup | batch setup ustacks This function creates a bash job file for... |
| vcf2fastStructure | Convert VCF file/object to fastStructure input file (for SNP... |
| vcf2parts | vcf2parts Generate a phylip format partition file from VCF... |
| vcf2phy | VCF format to Phylip format Converts VCF to phylip and saves... |
| vcf2structure | Convert VCF file/object to STRUCTURE file (for SNP data)... |
| vcf_getSNP | Get Best SNP for each locus from VCF From a VCF with multiple... |
| vcfR2geno | Convert VCF object/file to genotypic matrix The object... |
| vcfR2lfmm | Reads a VCF object (including those not usually compatible... |
