A Simple Framework to Analyse Population and Landscape Genetic Data

addline | Function to add lines to landscape |

addpoly | Function to add a polygon to a landscape |

allele.dist | Counts and visualises allele frequencies across loci and... |

allel.rich | Calculates the allelic richness for a genind object |

bilby | Bilby data set |

costdistances | Calculates cost distances for a given landscape (resistance... |

emigration | Function to execute emigration on a pops object |

gd.kosman | Individual genetic distance calculation based on Kosman &... |

gd.smouse | Individual genetic distance calculation based on Smouse and... |

genleastcost | Least-cost path analysis based on a friction matrix |

init.popgensim | Initialise a spatial meta-population for a popgen simulation |

landgen | A simulated genind data set with spatial coordinates |

landgenreport | Create a landscape genetic report |

lgrMMRR | Multiple Matrix Regression with Randomization analysis |

mutation | Function to execute mutation on a pop data.frame |

null.all | Checks for the presence of and determine the frequency of... |

opt.landgen | Function for optimising a landscape genetic analysis based on... |

p2p | Function to calculate dispersal distances based on cost... |

pairwise.fstb | Calculates pairwise fsts using a genind object (very fast) |

pairwise.propShared | Calculates proportion of shared alleles per pairs of... |

popgenreport | This is the main function of the package. It analyses an... |

pops2genind | Function converts pops to a genind object |

possums | A genlight object created via the read.genetable functions... |

read.genetable | Function to convert textfiles into a genind object (the... |

reproduction | Function to execute reproduction on a pop data.frame |

run.popgensim | Run a time-forward popgen simulation |

spautocor | Spatial autocorrelation following Smouse and Pekall 1999 |

treeScrub | A raster file [proportion of treeScrub per cell in Hawke Bay,... |

wassermann | Partial Mantel tests on costdistance matrices |

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