MeanSiteFChange_cherry
                        Compute the Mean Site Frequency of Methylation
                        Changes per Cherry
categorize_islandGlbSt
                        Categorize Global States of CpG Islands
categorize_siteMethSt   Categorize Methylation Frequencies Based on
                        Thresholds
cftpStepGenerator       cftpStepGenerator
combiStructureGenerator
                        combiStructureGenerator
compare_CherryFreqs     Compare Methylation Frequencies Between Two
                        Tips
computeFitch_islandGlbSt
                        Compute Fitch Parsimony for Global Methylation
                        States at CpG Islands
compute_fitch           Compute Fitch Parsimony for Methylation
                        Categories
compute_meanCor_i       Compute the Mean Correlation of Methylation
                        State in Islands
compute_meanCor_ni      Compute the Mean Correlation of Methylation
                        State in Non-islands
countSites_cherryMethDiff
                        Count Methylation Differences Between Cherry
                        Pairs
count_upm               Count Methylation States
freqSites_cherryMethDiff
                        Compute Methylation Frequency Differences
                        Between Cherry Pairs
get_cherryDist          Get Cherry Pair Distances from a Phylogenetic
                        Tree
get_islandMeanFreqM     Calculate the Mean Frequency of Methylated
                        Sites in Islands
get_islandMeanFreqP     Calculate the Mean Frequency of Partially
                        Methylated Sites in Islands
get_islandSDFreqM       Calculate the Mean Standard Deviation of
                        Methylated Sites in Islands
get_islandSDFreqP       Calculate the Mean Standard Deviation of
                        Partially Methylated Sites in Islands
get_meanMeth_islands    Compute the Mean Methylation of CpG Islands
get_nonislandMeanFreqM
                        Calculate the Mean Frequency of Methylated
                        Sites in Non-Islands
get_nonislandMeanFreqP
                        Calculate the Mean Frequency of Partially
                        Methylated Sites in Non-Islands
get_nonislandSDFreqM    Calculate the Mean Standard Deviation of
                        Methylated Sites in Non-Islands
get_nonislandSDFreqP    Calculate the Mean Standard Deviation of
                        Partially Methylated Sites in Non-Islands
get_parameterValues     Get Default Parameter Values
get_siteFChange_cherry
                        Compute Site Frequency of Methylation Changes
                        per Cherry
mean_CherryFreqsChange_i
                        Mean Number of Significant Methylation
                        Frequency Changes per Island in Cherries
mean_TreeFreqsChange_i
                        Mean Number of Significant Frequency Changes
                        per Island Across all Tree Tips
pValue_CherryFreqsChange_i
                        Compute p-Values for Methylation Frequency
                        Changes in Cherries
simulate_evolData       Simulate Data Evolution along a Tree
simulate_initialData    Simulate Initial Data
singleStructureGenerator
                        singleStructureGenerator
treeMultiRegionSimulator
                        treeMultiRegionSimulator
validate_dataAcrossTips
                        Validate Data Structure Across Tips
validate_data_cherryDist
                        Validate Structure of Input Data for Cherry
                        Distance Computation
validate_structureIndices
                        Validate Structure Indices for Island and
                        Non-Island Data
validate_tree           Validate and Parse a Phylogenetic Tree
