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autoreweight()
- Automatically reweight sample units that may be oversampled
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chindex()
- Computes the CH index for selecting clustering thresholds
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chindices()
- Compute CH index over a range of clustering thresholds
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codbinomial()
- Fit a genealogical placement GMRF model using maximum likelihood
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codls()
- Fit a COD GMRF model using weighted least squares
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codml()
- Fit a genealogical placement GMRF model using maximum likelihood
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coef.gpgmrf()
- A Capitalized Title (ideally limited to 65 characters)
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computeclusters()
- Compute phylogenetic clusters by cutting tree at branches with large changes in coalescent odds
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fitgpgmrf()
- A Capitalized Title (ideally limited to 65 characters)
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lbi()
- Compute the local branching index (LBI)
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neffextant()
- Effective number of extant lineages
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optsmooth()
- Optimise smoothing parameter for a given tree and branch statistic
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plot.gpgmrf()
- A Capitalized Title (ideally limited to 65 characters)
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plotclusters()
- Plots a fit from `codls` and cluster assigment from `computeclusters`
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print.gpgmrf()
- A Capitalized Title (ideally limited to 65 characters)
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rmsclo()
- Root mean square coalescent log odds
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tauprofile()
- Evaluate the loss function of the cod model across a range of tau (precision parameter) values