| ancestrymap | 'ancestrymap' format description |
| ancestrymap2geno | Convert from 'ancestrymap' to 'geno' format |
| ancestrymap2lfmm | Convert from 'ancestrymap' to 'lfmm' format |
| barchart | Bar plot representation of an snmf Q-matrix |
| crossEntropy | Cross-entropy criterion for snmf runs |
| env | Environmental input file format for 'lfmm' |
| G | Ancestral allele frequencies from a snmf run |
| genetic_offset | Population genetic offset under new environments. |
| geno | Input file for 'snmf' |
| geno2lfmm | Convert from 'geno' to 'lfmm' format |
| impute | Impute missing genotypes using an snmf object |
| lfmm | Input file for 'lfmm' |
| lfmm2 | Fitting Latent Factor Mixed Models (Least squares algorithm) |
| lfmm2geno | Convert from 'lfmm' to 'geno' format |
| lfmm2_test | P-values adjusted for latent factors computed by 'lfmm2'. |
| lfmm_pvalues | P-values from lfmm runs |
| main_createDataSet | create a data set with masked data |
| main_crossEntropyEstimation | compute the cross-entropy criterion |
| main_LFMM | Fitting Latent Factor Mixed Models (MCMC algorithm) |
| main_pca | Principal Component Analysis |
| main_sNMF | Estimates individual ancestry coefficients and ancestral... |
| main_tracyWidom | Tracy-Widom test for eigenvalues |
| ped | 'ped' format description |
| ped2geno | Convert from 'ped' to 'geno' format |
| ped2lfmm | Convert from 'ped' to 'lfmm' format |
| Q | Admixture coefficients from a snmf run |
| readEnv | Read environmental file in the 'env'format |
| readGeno | read a file in the 'geno' format |
| readLfmm | Read files in the 'lfmm' format |
| readZscore | Read the output files of 'lfmm' |
| Replop-package | LEA: an R package for Landscape and Ecological Associations... |
| snmf_pvalues | P-values for snmf population differentiation tests |
| struct2geno | Conversion from the STRUCTURE format to the geno format. |
| tutorial | Example tutorial data sets |
| vcf | 'vcf' format description |
| vcf2geno | Convert from 'vcf' to 'geno' format |
| vcf2lfmm | Convert from 'vcf' to 'lfmm' format |
| writeEnv | Write files in the 'env' format |
| writeGeno | Write files in the 'geno' format |
| writeLFMM | Write files in the 'lfmm' format |
| zscore | Output file format for 'lfmm' |
| zscores | z-scores from a lfmm run |
