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

## Documentation for package ‘LEA’ version 1.8.1

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

## Help Pages

LEA-package | LEA: an R package for Landscape and Ecological Associations studies.
$-method | Principal Component Analysis
adjusted.pvalues | adjusted p-values from a lfmm run
adjusted.pvalues-method | Fitting Latent Factor Mixed Models
ancestrymap | 'ancestrymap' format description
ancestrymap2geno | Convert from 'ancestrymap' to 'geno' format
ancestrymap2lfmm | Convert from 'ancestrymap' to 'lfmm' format
combine.lfmmProject | Fitting Latent Factor Mixed Models
combine.lfmmProject-method | Fitting Latent Factor Mixed Models
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 from snmf runs
cross.entropy-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
cross.entropy.estimation | compute the cross-entropy criterion
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
export.lfmmProject-method | Fitting Latent Factor Mixed Models
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 | Ancestral allele frequencies from a snmf run
G-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
geno | Input file for 'snmf'
geno2lfmm | Convert from 'geno' to 'lfmm' format
import.lfmmProject | Fitting Latent Factor Mixed Models
import.lfmmProject-method | Fitting Latent Factor Mixed Models
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.
lfmm | Fitting Latent Factor Mixed Models
lfmm.data | Input file for 'lfmm'
lfmm2geno | Convert from 'lfmm' to 'geno' format
load.lfmmProject | Fitting Latent Factor Mixed Models
load.lfmmProject-method | Fitting Latent Factor Mixed Models
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.
mlog10p.values | -log10(p-values) from a lfmm run
mlog10p.values-method | Fitting Latent Factor Mixed Models
p.values | p-values from a lfmm run
p.values-method | Fitting Latent Factor Mixed Models
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
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 | Admixture coefficients from a snmf run
Q-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
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
remove.lfmmProject-method | Fitting Latent Factor Mixed Models
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.
sdev | Principal Component Analysis
sdev-method | Principal Component Analysis
show-method | Fitting Latent Factor Mixed Models
show-method | Principal Component Analysis
show-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
snmf | Estimates individual ancestry coefficients and ancestral allele frequencies.
summary-method | Fitting Latent Factor Mixed Models
summary-method | Principal Component Analysis
summary-method | Estimates individual ancestry coefficients and ancestral allele frequencies.
tracy.widom | Tracy-Widom test for eigenvalues
tracy.widom-method | Principal Component Analysis
tutorial | Example tutorial data sets
vcf | 'vcf' format description
vcf2geno | Convert from 'vcf' to 'geno' format
vcf2lfmm | Convert from 'vcf' to 'lfmm' format
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.scores | z-scores from a lfmm run
z.scores-method | Fitting Latent Factor Mixed Models
zscore.format | Output file format for 'lfmm'