API for poppr
Genetic Analysis of Populations with Mixed Reproduction

Global functions
$,bootgen-method Man page
Aeut Man page
Ia.Rd Source code
MLG Man page
MLG-class Man page
MLG2df Man page
MLG2df,MLG-method Man page
Math,MLG-method Man page
Math2,MLG-method Man page
Ops,MLG,ANY-method Man page
PA.Ia.Rd Source code
PA.pairwise.differences Source code
Pinf Man page
Pram Man page
Summary,MLG-method Man page
[,MLG,ANY,ANY,ANY-method Man page
[,bootgen,ANY,ANY,ANY-method Man page
[,bruvomat,ANY,ANY,ANY-method Man page
[,genclone,ANY,ANY,ANY-method Man page
[,snpclone,ANY,ANY,ANY-method Man page
[<-,MLG,ANY,ANY,ANY-method Man page
\%>\% Man page
a Source code
aboot Man page Source code
add_tied_edges Source code
adjust_position Source code
adjustcurve Source code
all.shuffler Source code
amova Man page
as.genclone Man page Source code
as.genclone,genind-method Man page
as.snpclone Man page Source code
as.snpclone,genlight-method Man page
bitwise.dist Man page Source code
bitwise.ia Man page Source code
boot_per_pop Source code
boot_plot Source code
boot_stats Source code
bootgen-class Man page
bootgen2genind Man page Source code
bootgen2genind,bootgen-method Man page
bootstrap Man page
both.shuff Source code
bruvo.boot Man page Source code
bruvo.dist Man page Source code
bruvo.msn Man page Source code
bruvomat-class Man page
bruvos_distance Source code
check_Hs Source code
clonecorrect Man page Source code
clonecorrector Source code
consistent_replen Source code
correlate_custom_mlgs Source code
cromulent_replen Source code
cutoff Man page
cutoff,MLG-method Man page
cutoff<- Man page
cutoff<-,MLG-method Man page
cutoff_predictor Man page Source code
dcano Source code
dim,bootgen-method Man page
dim,bruvomat-method Man page
diss.dist Man page Source code
distalgo Man page
distalgo,MLG-method Man page
distalgo<- Man page
distalgo<-,MLG-method Man page
distargs Man page
distargs,MLG-method Man page
distargs<- Man page
distargs<-,MLG-method Man page
distname Man page
distname,MLG-method Man page
distname<- Man page
distname<-,MLG-method Man page
diversity_boot Man page Source code
diversity_ci Man page Source code
diversity_stats Man page Source code
duplicated,MLG-method Man page
edwards.dist Man page Source code
evens Source code
extract_samples Source code
fill_zero Source code
fill_zero_locus Source code
filter_at_threshold Source code
filter_stats Man page Source code
final Source code
fix_negative_branch Source code
fix_replen Man page Source code
fix_uneven_diploid Source code
genclone Man page
genclone-class Man page
genclone2genind Man page Source code
genclone2genind,genclone-method Man page
generate_bruvo_mat Source code
genind2genalex Man page Source code
genotype_curve Man page Source code
get_all_ci Source code
get_boot_ci Source code
get_boot_se Source code
get_boot_stats Source code
get_ci Source code
get_gen_dist_labs Source code
get_gen_mat Source code
get_haplotype Source code
get_hexp_from_loci Source code
get_local_ploidy Source code
get_minor_allele_replacement Source code
getfile Man page Source code
greycurve Man page Source code
guesslengths Source code
handle_mlg_index Source code
handle_pops_index Source code
haplotype_detector Source code
hier_incompatible_warning Source code
ia Man page Source code
ia_from_d_and_D Source code
ia_pair_loc Source code
imsn Man page Source code
incomp Man page Source code
infinite_vals_replacement Source code
info_table Man page Source code
informloci Man page Source code
initialize,MLG-method Man page
initialize,bootgen-method Man page
initialize,bruvomat-method Man page
initialize,genclone-method Man page
initialize,snpclone-method Man page
intersp Source code
is.clone Man page Source code
is.genclone Man page Source code
is.snpclone Man page Source code
jack.ia Man page Source code
last.value Source code
length,MLG-method Man page
levels,MLG-method Man page
levels<-,MLG-method Man page
locus.shuffler Source code
locus_table Man page Source code
locus_table_pegas Source code
make_ade_df Source code
make_attributes Source code
make_edge_width Source code
make_poppr_plot_title Source code
make_psex Source code
make_windows Source code
match_replen_to_loci Source code
mean.boot Source code
mismatched_repeat_length_warning Source code
missing_messenger Source code
missingno Man page Source code
mlg Man page Man page Source code
mlg.crosspop Man page Source code
mlg.filter Man page Source code
mlg.filter,genclone-method Man page
mlg.filter,genind-method Man page
mlg.filter,genlight-method Man page
mlg.filter,snpclone-method Man page
mlg.filter.internal Source code
mlg.filter<- Man page
mlg.filter<-,genclone-method Man page
mlg.filter<-,genind-method Man page
mlg.filter<-,genlight-method Man page
mlg.filter<-,snpclone-method Man page
mlg.id Man page Source code
mlg.matrix Source code
mlg.table Man page Source code
mlg.vector Man page Source code
mlg_barplot Source code
mlg_sub_warning Source code
mll Man page Source code
mll,genclone-method Man page
mll,genind-method Man page
mll,genlight-method Man page
mll,snpclone-method Man page
mll.custom Man page Source code
mll.custom,genclone-method Man page
mll.custom,snpclone-method Man page
mll.custom.internal Source code
mll.custom<- Man page
mll.custom<-,genclone-method Man page
mll.custom<-,snpclone-method Man page
mll.gen.internal Source code
mll.internal Source code
mll.levels Man page Source code
mll.levels,genclone-method Man page
mll.levels,snpclone-method Man page
mll.levels.internal Source code
mll.levels<- Man page
mll.levels<-,genclone-method Man page
mll.levels<-,snpclone-method Man page
mll.reset Man page Source code
mll.reset,genclone-method Man page
mll.reset,snpclone-method Man page
mll.reset.internal Source code
mll<- Man page
mll<-,genclone-method Man page
mll<-,snpclone-method Man page
monpop Man page
msn.bruvo Man page
msn.poppr Man page
msn_constructor Source code
multinom_boot Source code
negative_branch_warning Source code
nei.dist Man page Source code
nmll Man page Source code
nmll,genclone-method Man page
nmll,genind-method Man page
nmll,genlight-method Man page
nmll,snpclone-method Man page
non_ssr_data_warning Source code
not_euclid_msg Source code
number_missing_geno Source code
number_missing_locus Source code
old2new_genclone Man page Source code
old_Pinf Man page
old_partial_clone Man page
onAttach Source code
onUnload Source code
pair.ia Man page Source code
pair_diffs Source code
pair_matrix Source code
palette_parser Source code
partial_clone Man page
percent_missing Source code
permut.shuff Source code
pgen Man page Source code
plot.ialist Source code
plot.pairia Source code
plot_filter_stats Man page Source code
plot_poppr_msn Man page Source code
pool_haplotypes Source code
pop.divide Source code
poppr Man page Source code
poppr-package Man page
poppr.all Man page Source code
poppr.amova Man page Source code
poppr.msn Man page Source code
poppr.plot Man page Source code
poppr.plot.phylo Source code
poppr_has_parallel Man page Source code
poppr_message Source code
popsub Man page Source code
pretty_info Source code
prevosti.dist Man page
print,genclone-method Man page
print.amova Source code
print.ialist Source code
print.locustable Source code
print.pairia Source code
print.popprtable Source code
private_alleles Man page Source code
process_file Source code
provesti.dist Man page Source code
psex Man page Source code
rare_allele_correction Man page Source code
rare_sim_boot Source code
read.genalex Man page Source code
recode_polyploids Man page Source code
remove_zeroes Source code
repeat_length_warning Source code
replace_zeroes Source code
rerange Source code
resample.ia Man page Source code
reynolds.dist Man page Source code
rogers.dist Man page Source code
round.poppr Source code
rraf Man page Source code
rrcc Source code
rrccbp Source code
rrmlg Man page Source code
run.jack Source code
samp.ia Man page Source code
sampling Source code
sd.boot Source code
separate_haplotypes Source code
set_pop_from_strata_or_vector Source code
should_poppr_be_quiet Source code
show,MLG-method Man page
show,genclone-method Man page
show,snpclone-method Man page
shufflefunk Source code
shufflepop Man page Source code
snpclone Man page
snpclone-class Man page
sub_index Source code
test_microsat Source code
test_replen Man page Source code
test_table Source code
test_zeroes Source code
treat_G Source code
tree_generator Source code
trimmed_repeats_warning Source code
uninformative_loci_message Source code
unique,MLG-method Man page
unmatched_loci_warning Source code
unmatched_pops_warning Source code
update_colors Source code
update_edge_scales Source code
update_poppr_graph Source code
valid.genclone Source code
visible Man page
visible,MLG-method Man page
visible<- Man page
visible<-,MLG-method Man page
win.ia Man page Source code
poppr documentation built on Sept. 11, 2017, 9:04 a.m.