Inference of Spatial Population Genetic Structure

as.qmatrix | Converts into Q matrix |

barplot.tess3Q | Barplot representation of a Q-matrix |

CalculateEmpiricalGenSemivariogram | Calculate empirical semi variance from genotype matrix. |

CalculateEmpiricalSemivariogram | Calculate empirical semi-variance. |

CheckCoord | Raise error if coord is not well formated. |

CheckW | Raise error if W is not well formated. |

CheckWCoord | Raise error if W and coord are not consistent. |

CheckX | Raise error if X is not well formated. |

CheckXBin | Raise error if XBin is not well formated. |

CheckXBinCoord | Raise error if XBin and coord are not consistent. |

CheckXBinW | Raise error if XBin and W are not consistent. |

CheckXCoord | Raise error if X and coord are not consistent. |

CheckXW | Raise error if X and W are not consistent. |

ComputeAveragedCrossEntropy | Compute average cross entropy |

ComputeChi2AndPvalue | Convert Fst into chi2 and compute p value |

ComputeEigenValuesWithIgraphArpack | Compute eigen values with IgraphArpack. |

ComputeEigenValuesWithRSpectra | Compute eigen values with RSpectra. |

ComputeExponetialWeight | Compute graph matrix with an exponiential function. |

ComputeFst | Compute Fst statistic |

ComputeGraphLaplacian | Compute laplacian of a graph. |

ComputeHeatKernelWeight | Compute graph matrix with the heat kernel function. |

ComputeHeatKernelWeightSparse | Compute graph sparse matrix with the heat kernel function. |

ComputeMeanDist | Compute the average distance between points. |

ComputeRmse | Compute root squared mean error |

ComputeRmseWithBestPermutation | Compute the root mean square error between matrix by... |

ComputeRmseWithBestPermutationGreedy | Compute the root mean square error between matrix by... |

ComputeSpatialPenalty | Compute the value spatial penalty used in TESS3 objectif... |

ComputeTscoreAndPvalue | Convert Fst into t-score and compute p value |

ComputeWindow | Compute the graph window. |

CreatePalette | Create a list of palettes |

data.at | TODOC |

data.for.test | TODOC |

DebugMessage | Print a message if getOption("tess3r.debug") is not null |

durand09 | TODOC |

FieldsKrigModel | Return an interpolation function. Return a wrapper function... |

FieldsTpsModel | Return an interpolation function. Return a wrapper function... |

Gettess3res | Get tess3 run result |

ggtess3Q | Display geographic maps of ancestry coefficients using the... |

GtoFreq | Compute allele frequency matrix from genotype frequency... |

ImputeRandom | Impute missing values |

is.tess3 | Test if x is a tess3project object |

is.tess3Main | Title |

PlotInterpotationAll | Plot all the interpolation surfaces on several graphs. |

PlotInterpotationMax | Plot map with the maximum values of the interpolation... |

PlotPiechartAncestryCoef | Plot pie chart of ancestry coefficient. |

plot.tess3 | Plot cross-validation errors for all values of number of... |

plot.tess3Main | Title |

plot.tess3pvalue | Manhattan plot for tess3 significance values. |

plot.tess3Q | Display geographic maps of ancestry coefficients |

pvalue | Get p-values from a genome scan for selection |

qmatrix | Get Q matrix estimate |

rmse.tess3Main | Title |

run.ms | Helper function which call ms. |

SampleDistFromCenterDirichletQ | For population the center mu_k is computed. Then D_i_k =... |

SampleDistFromCenterQ | For population the center mu_k is computed. Then D_i_k =... |

SampleFuncQ | Sample ancestral coefficient matrix such as Q = f(coord). |

SampleGenoFromGenerativeModelTESS3 | Sample genotype from the TESS3 generative model. |

SampleGenoOFWithMs | Sample ancestral population with ms 2 island model. Then... |

SampleNormalClusterCoord | sample coord such as a mixture of K cluster distributed with... |

SampleTESS2.3Q | sample Q as describe in "Spatial Inference of Admixture... |

SampleUnifDirichletG | sample G such as G_dl+._k ~ Dirichlet(1/(ploidy + 1)) |

SampleUnifQ | Sample ancestral coefficient matrix such as alpha ~ unif(0,1)... |

summary.tess3 | Title |

summary.tess3Main | Summary of tess3 object. |

tess2tess3 | Import input files from the STRUCTURE and TESS formats |

tess3 | Estimate ancestry coefficients and run genome scans for... |

tess3Main | Estimate ancestry coefficients and run genome scans for... |

tess3r | tess3r : estimation of spatial population structure |

TestRequiredPkg | Test if a package is installed. |

X2XBin | Binary coding of the genotype data matrix. |

XBin2X | Convert the binary genotype matrix into genotype matrix. |

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