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  "Title": "A Simple Framework to Analyse Population and Landscape Genetic\nData",
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      "date": "2012-11-28"
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      "date": "2013-05-22"
    },
    {
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      "date": "2013-09-03"
    },
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      "date": "2013-12-12"
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    },
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    },
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    "allele.dist",
    "costdistances",
    "emigration",
    "gd.kosman",
    "gd.smouse",
    "genleastcost",
    "init.popgensim",
    "landgenreport",
    "lgrMMRR",
    "mutation",
    "null.all",
    "opt.landgen",
    "p2p",
    "pairwise.fstb",
    "pairwise.propShared",
    "popgenreport",
    "pops2genind",
    "read.genetable",
    "reproduction",
    "run.popgensim",
    "spautocor",
    "wassermann"
  ],
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    {
      "name": "bilby",
      "title": "Bilby data set",
      "object": "bilby",
      "class": [
        "genind"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "landgen",
      "title": "A simulated genind data set with spatial coordinates",
      "object": "landgen",
      "class": [
        "genind"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "possums",
      "title": "A genlight object created via the read.genetable functions [possum data set from Sarre et al. 2015]",
      "object": "possums",
      "class": [
        "genind"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "addline",
      "title": "Function to add lines to landscape",
      "topics": [
        "addline"
      ]
    },
    {
      "page": "addpoly",
      "title": "Function to add a polygon to a landscape",
      "topics": [
        "addpoly"
      ]
    },
    {
      "page": "allel.rich",
      "title": "Calculates the allelic richness for a genind object",
      "topics": [
        "allel.rich"
      ]
    },
    {
      "page": "allele.dist",
      "title": "Counts and visualises allele frequencies across loci and subpopulations",
      "topics": [
        "allele.dist"
      ]
    },
    {
      "page": "bilby",
      "title": "Bilby data set",
      "topics": [
        "bilby"
      ]
    },
    {
      "page": "costdistances",
      "title": "Calculates cost distances for a given landscape (resistance matrix)",
      "topics": [
        "costdistances"
      ]
    },
    {
      "page": "emigration",
      "title": "Function to execute emigration on a pops object",
      "topics": [
        "emigration"
      ]
    },
    {
      "page": "gd.kosman",
      "title": "Individual genetic distance calculation based on Kosman & Leonhard 2005",
      "topics": [
        "gd.kosman"
      ]
    },
    {
      "page": "gd.smouse",
      "title": "Individual genetic distance calculation based on Smouse and Peakall 1999",
      "topics": [
        "gd.smouse"
      ]
    },
    {
      "page": "genleastcost",
      "title": "Least-cost path analysis based on a friction matrix",
      "topics": [
        "genleastcost"
      ]
    },
    {
      "page": "init.popgensim",
      "title": "Initialise a spatial meta-population for a popgen simulation",
      "topics": [
        "init.popgensim"
      ]
    },
    {
      "page": "landgen",
      "title": "A simulated genind data set with spatial coordinates",
      "topics": [
        "landgen"
      ]
    },
    {
      "page": "landgenreport",
      "title": "Create a landscape genetic report",
      "topics": [
        "landgenreport"
      ]
    },
    {
      "page": "lgrMMRR",
      "title": "Multiple Matrix Regression with Randomization analysis",
      "topics": [
        "lgrMMRR"
      ]
    },
    {
      "page": "mutation",
      "title": "Function to execute mutation on a pop data.frame",
      "topics": [
        "mutation"
      ]
    },
    {
      "page": "null.all",
      "title": "Checks for the presence of and determine the frequency of null alleles",
      "topics": [
        "null.all"
      ]
    },
    {
      "page": "opt.landgen",
      "title": "Function for optimising a landscape genetic analysis based on resistance layers",
      "topics": [
        "opt.landgen"
      ]
    },
    {
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      "title": "Function to calculate dispersal distances based on cost distances",
      "topics": [
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      ]
    },
    {
      "page": "pairwise.fstb",
      "title": "Calculates pairwise fsts using a genind object (very fast)",
      "topics": [
        "pairwise.fstb"
      ]
    },
    {
      "page": "pairwise.propShared",
      "title": "Calculates proportion of shared alleles per pairs of populations",
      "topics": [
        "pairwise.propShared"
      ]
    },
    {
      "page": "popgenreport",
      "title": "This is the main function of the package. It analyses an object of class 'genind' and then creates a report containing the results of the analysis. There are several routines that can be optionally included in the analysis and there are multiple output options including a PDF with the report, R-code and an object ('fname.results') containing all of the results, which can be used for further analyses.",
      "topics": [
        "popgenreport"
      ]
    },
    {
      "page": "pops2genind",
      "title": "Function converts pops to a genind object",
      "topics": [
        "pops2genind"
      ]
    },
    {
      "page": "possums",
      "title": "A genlight object created via the read.genetable functions [possum data set from Sarre et al. 2015]",
      "topics": [
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      ]
    },
    {
      "page": "read.genetable",
      "title": "Function to convert textfiles into a genind object (the format required for popgenreport)",
      "topics": [
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      ]
    },
    {
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      "title": "Function to execute reproduction on a pop data.frame",
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      ]
    },
    {
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      "title": "Run a time-forward popgen simulation",
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      "title": "Spatial autocorrelation following Smouse and Pekall 1999",
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      ]
    },
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      "title": "Partial Mantel tests on costdistance matrices",
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