Man pages for btmartin721/ClineHelpR
Parses and Plots BGC and INTROGRESS Output
| alphaBetaPlot | Makes Alpha ~ Beta Plots for BGC results |
| clinesXenvironment | Function to correlate INTROGRESS genomic clines with raster... |
| combine_bgc_output | Aggregate BGC Output |
| extractPointValues | Function to extract raster values at each sample point for... |
| genind2bgc | Generate inputs for BGC from genind object. Does not use... |
| genind2introgress | Generate inputs for Introgress from genind object |
| get_bgc_outliers | Parses BGC output and identifies outlier SNPs |
| join_bgc_gff | Reads in BGC Outlier Data and Joins with GFF Data |
| parseGFF | Function to Read and Parse a GFF file |
| partition_raster_bg | Function to make partitions from background and foreground... |
| phiPlot | Makes Phi ~ Hybrid Index Plots for Alpha and Beta |
| plot_outlier_ideogram | Plot an Ideogram for BGC Outlier Genes |
| plot_traces | Plot LnL Traces to Assess Convergence for BGC Log-likelihoods |
| prepare_rasters | Script to extract raster data for all sampling localities and... |
| runENMeval | Function to run ENMeval and MAXENT on the raster layers. |
| runIntrogress | Functions to run INTROGRESS and correlate genomic clines X... |
| subsetIndividuals | Function to subset individuals from the extractRasterPoints... |
| summarize_ENMeval | Function to summarize ENMeval output |
