hierfstat v0.04-14
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Estimation and tests of hierarchical F-statistics
This R package allows the estimation of hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution, 1998, 52(4):950-956). Functions are also given to test via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G -see Goudet etal (Genetics, 1996, 144(4): 1933-1940)
Functions in hierfstat
| Name | Description | |
| boot.vc | Bootstrap confidence intervals for variance components | |
| getal | Converts diploid genotypic data into allelic data | |
| test.within | Tests the significance of the effect of inner.level on genetic differentiation within blocks defined by outer.level | |
| samp.between.within | Shuffles a sequence | |
| exhier | Example data set with 4 levels, one diploid and one haploid locus | |
| samp.between | Shuffles a sequence among groups defined by the input vector | |
| genot2al | Separates diploid genotypes in its constituant alleles | |
| prepdata | Sort and renumber and recode levels for the hierarchical analysis if necessary | |
| varcomp.glob | Estimate variance components and hierarchical F-statistics over all loci | |
| yangex | Example data set from Yang (1998) appendix | |
| test.between | Tests the significance of the effect of test.lev on genetic differentiation | |
| pop.freq | Allelic frequencies | |
| g.stats.glob | Likelihood ratio G-statistic over loci | |
| getal.b | Converts diploid genotypic data into allelic data | |
| test.between.within | Tests the significance of the effect of test.lev on genetic differentiation | |
| varcomp | Estimates variance components for each allele of a locus | |
| ind.count | individual counts | |
| test.g | Tests the significance of the effect of level on genetic differentiation | |
| read.fstat.data | Reads data from a FSTAT file | |
| hierfstat | General information on the hierfstat package | |
| gtrunchier | Genotypes at 6 microsatellite loci of Galba truncatula from different patches in Western Switzerland | |
| samp.within | Shuffles a sequence within groups defined by the input vector | |
| g.stats | Calculates likelihood-ratio G-statistic on contingency table | |
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Details
| Date | 2014-09-25 |
| License | GPL (>= 2) |
| URL | http://www.r-project.org, http://www.unil.ch/popgen/softwares/hierfstat.htm |
| Packaged | 2014-09-29 14:42:03 UTC; jgoudet |
| NeedsCompilation | no |
| Repository | CRAN |
| Date/Publication | 2014-09-29 18:30:16 |
| depends | ade4 , gtools |
| suggests | adegenet , ape |
| Contributors | Jerome Goudet |
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