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. |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.