Files in LEA

LEA: an R package for Landscape and Ecological Association Studies

NEWS

NAMESPACE

DESCRIPTION

build/vignette.rds

src/R_vcf2geno.h

src/R_vcf2geno.c

src/R_createDataSet.c

src/R_pca.c

src/R_geno2lfmm.h

src/Makevars.win

src/R_tracyWidom.h

src/R_LFMM.h

src/R_geno2lfmm.c

src/R_crossEntropy.h

src/R_sNMF.c

src/R_ped2geno.h

src/R_ped2geno.c

src/R_ancestrymap2lfmm.c

src/R_ped2lfmm.h

src/R_sNMF.h

src/R_ped2lfmm.c

src/R_pca.h

src/R_ancestrymap2geno.h

src/Makevars

src/R_crossEntropy.c

src/R_LFMM.c

src/R_ancestrymap2lfmm.h

src/R_ancestrymap2geno.c

src/R_tracyWidom.c

src/R_init_LEA.c

src/R_lfmm2geno.c

src/R_createDataSet.h

src/R_lfmm2geno.h

src/nnlsm/sort.c

src/nnlsm/sort.h

src/nnlsm/nnlsm.h

src/nnlsm/nnlsm.c

src/nnlsm/solvenormaleqcomb.c

src/nnlsm/blockpivot.h

src/nnlsm/solvenormaleqcomb.h

src/nnlsm/blockpivot.c

src/nnlsm/nmf_bpas/nnlsm_activeset.m

src/nnlsm/nmf_bpas/example_1.m

src/nnlsm/nmf_bpas/AtB.txt

src/nnlsm/nmf_bpas/U.txt

src/nnlsm/nmf_bpas/PassiveSet.txt

src/nnlsm/nmf_bpas/README.txt

src/nnlsm/nmf_bpas/nmf.m

src/nnlsm/nmf_bpas/plop.txt

src/nnlsm/nmf_bpas/W.pdf

src/nnlsm/nmf_bpas/R.txt

src/nnlsm/nmf_bpas/example_2.m

src/nnlsm/nmf_bpas/W.txt

src/nnlsm/nmf_bpas/solveNormalEqComb.m

src/nnlsm/nmf_bpas/nnlsm_blockpivot.m

src/crossEntropy/crossEntropy.h

src/crossEntropy/register_ce.c

src/crossEntropy/print_ce.c

src/crossEntropy/print_ce.h

src/crossEntropy/crossEntropy.c

src/crossEntropy/error_ce.h

src/crossEntropy/register_ce.h

src/crossEntropy/error_ce.c

src/bituint/bituint.c

src/bituint/thread_bituint.c

src/bituint/io_geno_bituint.c

src/bituint/thread_bituint.h

src/bituint/calc_bituint.c

src/bituint/calc_bituint.h

src/bituint/slice_bituint.h

src/bituint/bituint.h

src/bituint/io_geno_bituint.h

src/bituint/slice_bituint.c

src/LFMM/thread_lfmm.h

src/LFMM/beta.h

src/LFMM/slice_lfmm.c

src/LFMM/LFMM.c

src/LFMM/data_lfmm.h

src/LFMM/lfmm_k0.h

src/LFMM/LFMM.h

src/LFMM/V.h

src/LFMM/beta_k0.h

src/LFMM/error_lfmm.h

src/LFMM/thread_var.h

src/LFMM/U.c

src/LFMM/thread_var.c

src/LFMM/print_lfmm.c

src/LFMM/thread_lfmm.c

src/LFMM/data_lfmm.c

src/LFMM/beta_k0.c

src/LFMM/register_lfmm.c

src/LFMM/lfmm_algo.c

src/LFMM/V.c

src/LFMM/lfmm_algo.h

src/LFMM/error_lfmm.c

src/LFMM/register_lfmm.h

src/LFMM/U.h

src/LFMM/slice_lfmm.h

src/LFMM/print_lfmm.h

src/LFMM/beta.c

src/LFMM/lfmm_k0.c

src/pca/pca.h

src/pca/calc_cov.c

src/pca/error_pca.c

src/pca/print_pca.c

src/pca/register_pca.c

src/pca/register_pca.h

src/pca/calc_cov.h

src/pca/print_pca.h

src/pca/pca.c

src/pca/error_pca.h

src/stats/ln_beta_function.c

src/stats/beta_distribution.c

src/stats/gamma_function.c

src/stats/beta_function.c

src/stats/factorial.c

src/stats/gamma_distribution.c

src/stats/stats.h

src/stats/entire_incomplete_gamma_function.c

src/stats/gamma_distribution.h

src/stats/ln_gamma_function.c

src/stats/gamma_density.c

src/stats/gamma_dist_tables.c

src/stats/student_t_distribution.h

src/stats/student_t_distribution.c

src/sNMF/print_snmf.h

src/sNMF/print_snmf.c

src/sNMF/als_Q.c

src/sNMF/register_snmf.c

src/sNMF/als_Q.h

src/sNMF/error_snmf.c

src/sNMF/thread_snmf.h

src/sNMF/sNMF.h

src/sNMF/register_snmf.h

src/sNMF/sNMF.c

src/sNMF/error_snmf.h

src/sNMF/als.h

src/sNMF/criteria.c

src/sNMF/thread_Q.c

src/sNMF/thread_F.h

src/sNMF/thread_snmf.c

src/sNMF/als_k1.c

src/sNMF/als.c

src/sNMF/thread_Q.h

src/sNMF/als_F.h

src/sNMF/als_k1.h

src/sNMF/als_F.c

src/sNMF/criteria.h

src/sNMF/thread_F.c

src/matrix/slice_matrix.h

src/matrix/thread_matrix.h

src/matrix/cholesky.c

src/matrix/sylvester.c

src/matrix/diagonalize.h

src/matrix/error_matrix.h

src/matrix/sylvester.h

src/matrix/cholesky.h

src/matrix/inverse.c

src/matrix/data.h

src/matrix/matrix.h

src/matrix/diagonalize.c

src/matrix/rand.c

src/matrix/inverse.h

src/matrix/normalize.h

src/matrix/random_projection.c

src/matrix/rand.h

src/matrix/matrix.c

src/matrix/random_projection.h

src/matrix/data.c

src/matrix/error_matrix.c

src/matrix/slice_matrix.c

src/matrix/normalize.c

src/matrix/thread_matrix.c

src/createDataSet/error_cds.c

src/createDataSet/print_cds.h

src/createDataSet/print_cds.c

src/createDataSet/register_cds.h

src/createDataSet/register_cds.c

src/createDataSet/error_cds.h

src/createDataSet/createDataSet.c

src/createDataSet/createDataSet.h

src/io/io_tools.h

src/io/print_bar.c

src/io/read.h

src/io/io_error.c

src/io/io_data_float.c

src/io/io_data_double.c

src/io/io_data_int.h

src/io/io.h

src/io/io_tools.c

src/io/io_data_int.c

src/io/io_data_double.h

src/io/print_bar.h

src/io/io_error.h

src/io/io_data_float.h

src/convert/ancestrymap.c

src/convert/vcf2geno.h

src/convert/geno.h

src/convert/convert.h

src/convert/geno2lfmm.h

src/convert/geno.c

src/convert/lfmm2geno.h

src/convert/register_convert.h

src/convert/ped.h

src/convert/register_convert.c

src/convert/lfmm2geno.c

src/convert/ancestrymap.h

src/convert/vcf2geno.c

src/convert/ped.c

src/convert/geno2lfmm.c

src/tracyWidom/print_tracyWidom.h

src/tracyWidom/error_tracyWidom.c

src/tracyWidom/print_tracyWidom.c

src/tracyWidom/register_tracyWidom.h

src/tracyWidom/tracyWidom.c

src/tracyWidom/twtable.h

src/tracyWidom/error_tracyWidom.h

src/tracyWidom/tracyWidom.h

src/tracyWidom/register_tracyWidom.c

data/example_ped.txt.gz

data/example_vcf.txt.gz

data/tutorial.RData

data/datalist

data/example_lfmm.txt.gz

data/example_ancestrymap.txt.gz

data/example_geno.tab.gz

R/lfmm2.R R/lfmm2geno.R R/tools.R R/test_double.R R/vcf2lfmm.R R/snmfClass.R R/ancestrymap2geno.R R/pca.R R/writeLfmm.R R/writeEnv.R R/geno2lfmm.R R/readLfmm.R R/pcaProject.R R/createDataSet.R R/ped2lfmm.R R/ancestrymap2lfmm.R R/struct2geno.R R/sNMF.R R/test_extension.R R/readEnv.R R/lfmmProject.R R/readZscore.R R/writeGeno.R R/test_integer.R R/vcf2geno.R R/lfmmClass.R R/snmfProject.R R/test_input_file.R R/ped2geno.R R/crossEntropyEstimation.R R/test_character.R R/test_logical.R R/LFMM.R R/readGeno.R

vignettes/biblio.bib

vignettes/LEA.Rnw

vignettes/cse.bst

man/lfmm2.Rd man/main_createDataSet.Rd man/ancestrymap.Rd man/main_LFMM.Rd man/writeLFMM.Rd man/tutorial.Rd man/snmf_pvalues.Rd man/G.Rd man/main_pca.Rd man/Replop-package.Rd man/readZscore.Rd man/vcf.Rd man/vcf2geno.Rd man/barchart.Rd man/readGeno.Rd man/ped.Rd man/writeGeno.Rd man/lfmm_pvalues.Rd man/ancestrymap2geno.Rd man/crossEntropy.Rd man/main_crossEntropyEstimation.Rd man/Q.Rd man/readLfmm.Rd man/main_sNMF.Rd man/vcf2lfmm.Rd man/main_tracyWidom.Rd man/lfmm2geno.Rd man/readEnv.Rd man/genetic_offset.Rd man/geno2lfmm.Rd man/lfmm.Rd man/zscores.Rd man/zscore.Rd man/env.Rd man/lfmm2_test.Rd man/impute.Rd man/ancestrymap2lfmm.Rd man/writeEnv.Rd man/geno.Rd man/ped2lfmm.Rd man/struct2geno.Rd man/ped2geno.Rd

inst/CITATION

inst/doc/LEA.R

inst/doc/LEA.Rnw

inst/doc/LEA.pdf

LEA documentation built on Nov. 8, 2020, 8:19 p.m.