Function reference • algatr

Genetic data processing

data_processing_packages(): Install data processing packages

gen_to_geno(): Convert dosage matrix or vcf to geno type object (N.B.: this only works for diploids!)

geno_to_dosage(): Convert lfmm/geno matrix to dosage matrix (N.B.: this only works for diploids!)

ld_prune(): ld_prune prunes SNPs based on linkage disequilibrium using SNPRelate and SeqArray packages

simple_impute(): Impute NA values NOTE: use extreme caution when using this form of simplistic imputation. We mainly provide this code for creating test datasets and highly discourage its use in analyses.

str_impute(): Imputation of missing values using population structure inferred with LEA::snmf

vcf_to_dosage(): Convert a vcf to a dosage matrix

Environmental data processing

envirodata_packages(): Install environmental and geographic data processing packages

check_dists(): Check geographic and environmental distances for collinearity

check_env(): Check environmental layers for collinearity

check_vals(): Check extracted values for collinearity

env_dist(): Calculate distance between environmental vars

geo_dist(): Calculate geographic distance between coordinates

get_worldclim(): Download and merge WorldClim data for study area

rm_islands(): Remove islands from mapping

Masking

extrap_mask() range_mask() sd_mask() buffer_mask() chull_mask(): Create raster mask based on coordinates

plot_extrap_mask(): Plot mask on top of map

masking_packages(): Install masking packages

Genetic distances

gen_dist(): Calculate genetic distances

gen_dist_corr(): Plot the relationship between two distance metrics

gen_dist_hm(): Make heatmap of genetic distances

gen_dist_packages(): Install genetic distance packages

TESS

tess_barplot(): Create TESS barplot

tess_col_default(): Create default TESS color palette

tess_do_everything(): TESS function to do everything

tess_ggbarplot(): Create TESS barplot using ggplot2

tess_ggplot(): ggplot of TESS results

tess_krig(): Krige admixture values

tess_ktest(): Test multiple K values

tess_packages(): Install TESS packages

tess_plot_allK(): Plot all kriged Q values for each K

bestK(): Best K Selection based on cross entropy

MMRR

mmrr_df(): Make nice dataframe from MMRR results

mmrr_do_everything(): MMRR function to do everything

mmrr_packages(): Install MMRR packages

mmrr_plot(): Plot MMRR results

mmrr_run(): Run MMRR and return model object

mmrr_table(): Create gt table of MMRR results

mmrr_var_sel(): mmrr_var_sel performs MMRR with backward elimination variable selection

MMRR(): MMRR performs Multiple Matrix Regression with Randomization analysis

unfold(): unfold converts the lower diagonal elements of a matrix into a vector

GDM

gdm_coeffs(): Get coefficients for each predictor

gdm_df(): Create dataframe of GDM results

gdm_do_everything(): GDM function to do everything (fit model, get coefficients, make and save raster)

gdm_format(): Format Data for Generalized Dissimilarity Modeling (GDM)

gdm_map(): Make map from model

gdm_packages(): Install GDM packages

gdm_plot_diss(): Plot compositional dissimilarity spline plots

gdm_plot_isplines(): Plot I-splines for each variable

gdm_plot_vars(): Create a PCA plot for GDM

gdm_run(): Run GDM and return model object

gdm_table(): Create gt table of GDM results

gdm_var_sel(): Get best set of variables from a GDM model

gdm_varimp_table(): Generate a Variable Importance Table for GDM Models

scale01(): Scale genetic distances from 0 to 1

scaleRGB(): Scale three layers of environmental data to R, G, and B for mapping

RDA

rda_cor(): Genotype-environment correlation test

rda_do_everything(): RDA function to do everything

rda_getoutliers(): Get significant outliers from RDA model

rda_packages(): Install RDA packages

rda_plot(): Plot RDA results

rda_run(): Run RDA

rda_table(): Create gt table of RDA results

rda_varpart(): Partial RDA variance partitioning

rda_varpart_table(): Create gt table with RDA variance partitioning results

LFMM

lfmm_df(): Convert LFMM results into a tidy dataframe for downstream processing

lfmm_do_everything(): LFMM function to do everything

lfmm_manhattanplot(): LFMM Manhattan Plot

lfmm_packages(): Install LFMM packages

lfmm_qqplot(): LFMM QQplot

lfmm_run(): Run LFMM

lfmm_table(): Create gt table of LFMM results

select_K() select_K_tw() select_K_elbow() select_K_tess() select_K_fc(): K selection

quick_elbow(): Quickly choose an elbow for a PC

Wingen

wingen_do_everything(): wingen function to do everything (preview and generate moving window maps, krige, and mask)

wingen_packages(): Install wingen packages

Alazygatr

alazygatr_packages(): Install alazygatr packages

do_everything_for_me(): Lazy run of all landscape genomic analyses contained within algatr

Data

load_algatr_example(): Load example data

CA_env: Example environmental data, calculated by performing a raster PCA on 18 bioclimatic variables for state of California

liz_coords: Example coordinates from Bouzid et al. 2022

liz_gendist: Example genetic distance matrix, calculated with Plink using data from Bouzid et al. 2022

liz_vcf: Example VCF from Bouzid et al. 2022

Other

coords_to_sf(): Convert from matrix, data frame, or sf to sf (sf is a pass through)

coords_to_sp(): Convert from matrix, data frame, or sf to formatted sp