# LEA: an R package for Landscape and Ecological Association Studies

## Documentation for package ‘LEA’ version 3.12.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C E G I L M O P Q R S T V W Z misc

LEA-package | LEA: an R package for Landscape and Ecological Associations studies.

## -- A --

adjusted.pvalues-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
ancestrymap | 'ancestrymap' format description
ancestrymap2geno | Convert from 'ancestrymap' to 'geno' format
ancestrymap2lfmm | Convert from 'ancestrymap' to 'lfmm' format

## -- B --

barchart | Bar plot representation of an snmf Q-matrix
barchart-method | Estimates individual ancestry coefficients and ancestral allele frequencies.

## -- C --

combine.lfmmProject | Fitting Latent Factor Mixed Models (MCMC algorithm)
combine.lfmmProject-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
combine.snmfProject | Estimates individual ancestry coefficients and ancestral allele frequencies.
combine.snmfProject-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
create.dataset | create a data set with masked data
cross.entropy | Cross-entropy criterion for snmf runs
cross.entropy-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
cross.entropy.estimation | compute the cross-entropy criterion

## -- E --

eigenvalues | Principal Component Analysis
eigenvalues-method | Principal Component Analysis
eigenvectors | Principal Component Analysis
eigenvectors-method | Principal Component Analysis
env | Environmental input file format for 'lfmm'
example_ancestrymap | 'ancestrymap' format description
example_geno | Input file for 'snmf'
example_lfmm | Input file for 'lfmm'
example_ped | 'ped' format description
example_vcf | 'vcf' format description
export.lfmmProject | Fitting Latent Factor Mixed Models (MCMC algorithm)
export.lfmmProject-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
export.pcaProject | Principal Component Analysis
export.pcaProject-method | Principal Component Analysis
export.snmfProject | Estimates individual ancestry coefficients and ancestral allele frequencies.
export.snmfProject-method | Estimates individual ancestry coefficients and ancestral allele frequencies.

## -- G --

G | Ancestral allele frequencies from a snmf run
G-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
genetic.gap | Genetic gap: genetic offset and genetic distance between environments.
genetic.offset | Genetic offset and genetic distance between environments.
geno | Input file for 'snmf'
geno2lfmm | Convert from 'geno' to 'lfmm' format

## -- I --

import.lfmmProject | Fitting Latent Factor Mixed Models (MCMC algorithm)
import.lfmmProject-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
import.pcaProject | Principal Component Analysis
import.pcaProject-method | Principal Component Analysis
import.snmfProject | Estimates individual ancestry coefficients and ancestral allele frequencies.
import.snmfProject-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
impute | Impute missing genotypes using an snmf object
impute-method | Estimates individual ancestry coefficients and ancestral allele frequencies.

## -- L --

lfmm | Fitting Latent Factor Mixed Models (MCMC algorithm)
lfmm.data | Input file for 'lfmm'
lfmm.pvalues | P-values from lfmm runs
lfmm.pvalues-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
lfmm2 | Fitting Latent Factor Mixed Models (Least squares algorithm)
lfmm2.test | P-values adjusted for latent factors computed by 'lfmm2'.
lfmm2.test-method | Fitting Latent Factor Mixed Models (Least squares algorithm)
lfmm2geno | Convert from 'lfmm' to 'geno' format
lfmmClass-method | z-scores from an lfmm run
load.lfmmProject | Fitting Latent Factor Mixed Models (MCMC algorithm)
load.lfmmProject-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
load.pcaProject | Principal Component Analysis
load.pcaProject-method | Principal Component Analysis
load.snmfProject | Estimates individual ancestry coefficients and ancestral allele frequencies.
load.snmfProject-method | Estimates individual ancestry coefficients and ancestral allele frequencies.

## -- M --

mlog10p.values-method | Fitting Latent Factor Mixed Models (MCMC algorithm)

## -- O --

offset_example | Example data for genetic offset analysis

## -- P --

p.values-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
pca | Principal Component Analysis
ped | 'ped' format description
ped2geno | Convert from 'ped' to 'geno' format
ped2lfmm | Convert from 'ped' to 'lfmm' format
plot-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
plot-method | Principal Component Analysis
plot-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
projections | Principal Component Analysis
projections-method | Principal Component Analysis

## -- Q --

Q | Admixture coefficients from a snmf run
Q-method | Estimates individual ancestry coefficients and ancestral allele frequencies.

## -- R --

read.env | Read environmental file in the 'env'format
read.geno | read a file in the 'geno' format
read.lfmm | Read files in the 'lfmm' format
read.zscore | Read the output files of 'lfmm'
remove.lfmmProject | Fitting Latent Factor Mixed Models (MCMC algorithm)
remove.lfmmProject-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
remove.pcaProject | Principal Component Analysis
remove.pcaProject-method | Principal Component Analysis
remove.snmfProject | Estimates individual ancestry coefficients and ancestral allele frequencies.
remove.snmfProject-method | Estimates individual ancestry coefficients and ancestral allele frequencies.

## -- S --

sdev | Principal Component Analysis
sdev-method | Principal Component Analysis
show-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
show-method | Principal Component Analysis
show-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
snmf | Estimates individual ancestry coefficients and ancestral allele frequencies.
snmf.pvalues | P-values for snmf population differentiation tests
snmf.pvalues-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
struct2geno | Conversion from the STRUCTURE format to the geno format.
summary-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
summary-method | Principal Component Analysis
summary-method | Estimates individual ancestry coefficients and ancestral allele frequencies.

## -- T --

tracy.widom | Tracy-Widom test for eigenvalues
tracy.widom-method | Principal Component Analysis
tutorial | Example tutorial data sets

## -- V --

vcf | 'vcf' format description
vcf2geno | Convert from 'vcf' to 'geno' format
vcf2lfmm | Convert from 'vcf' to 'lfmm' format

## -- W --

write.env | Write files in the 'env' format
write.geno | Write files in the 'geno' format
write.lfmm | Write files in the 'lfmm' format

## -- Z --

z.scores | z-scores from an lfmm run
z.scores-method | Fitting Latent Factor Mixed Models (MCMC algorithm)
zscore.format | Output file format for 'lfmm'

## -- misc --

$-method | Principal Component Analysis