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B C D E F G H I K L M N P R S T W
| bootstrap | Method for fitting a mutagenetic trees mixture model and analyzing its variance |
| bootstrap-method | Method for fitting a mutagenetic trees mixture model and analyzing its variance |
| bootstrap-methods | Method for fitting a mutagenetic trees mixture model and analyzing its variance |
| comp.models | Functions for comparing the tree topologies of two mutagenetic trees mixture models |
| comp.models.levels | Functions for comparing the tree topologies of two mutagenetic trees mixture models |
| comp.trees | Functions for quantifying the diversity of the nontrivial trees in a mutagenetic trees mixture model |
| comp.trees.levels | Functions for quantifying the diversity of the nontrivial trees in a mutagenetic trees mixture model |
| CompleteMat | Class "RtreemixModel" |
| CompleteMat-method | Class "RtreemixModel" |
| confIntGPS | Method for calculating GPS values and their 95% bootstrap confidence intervals |
| confIntGPS-method | Method for calculating GPS values and their 95% bootstrap confidence intervals |
| confIntGPS-methods | Method for calculating GPS values and their 95% bootstrap confidence intervals |
| cosin.dist | Different distances between two given vectors |
| Description | Class "RtreemixData" |
| Description-method | Class "RtreemixData" |
| Description<- | Class "RtreemixData" |
| Description<--method | Class "RtreemixData" |
| distribution | Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model |
| distribution-method | Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model |
| distribution-methods | Method for generating the (scaled) probablility distribution induced with a given mutagenetic trees mixture model |
| euclidian.dist | Different distances between two given vectors |
| Events | Class "RtreemixData" |
| Events-method | Class "RtreemixData" |
| Events<- | Class "RtreemixData" |
| Events<--method | Class "RtreemixData" |
| eventsNum | Class "RtreemixData" |
| eventsNum-method | Class "RtreemixData" |
| fit | Method for fitting mutagenetic trees mixture model to a given dataset |
| fit-method | Method for fitting mutagenetic trees mixture model to a given dataset |
| fit-methods | Method for fitting mutagenetic trees mixture model to a given dataset |
| generate | Method for generating a random mutagenetic trees mixture model |
| generate-method | Method for generating a random mutagenetic trees mixture model |
| generate-methods | Method for generating a random mutagenetic trees mixture model |
| get.tree.levels | Function for constructing level vectors |
| getData | Class "RtreemixGPS" |
| getData,RtreemixModel | Class "RtreemixModel" |
| getData,RtreemixStats | Class "RtreemixStats" |
| getData-method | Class "RtreemixGPS" |
| getData-method | Class "RtreemixModel" |
| getData-method | Class "RtreemixStats" |
| getModel | Class "RtreemixSim" |
| getModel-method | Class "RtreemixSim" |
| getResp | Class "RtreemixStats" |
| getResp-method | Class "RtreemixStats" |
| getTree | Class "RtreemixModel" |
| getTree-method | Class "RtreemixModel" |
| GPS | Class "RtreemixGPS" |
| gps | Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model |
| GPS-method | Class "RtreemixGPS" |
| gps-method | Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model |
| gps-methods | Methods for predicting the GPS of given dataset by using a given mutagenetic trees mixture model |
| gpsCI | Class "RtreemixGPS" |
| gpsCI-method | Class "RtreemixGPS" |
| hiv.data | Example of an RtreemixData object |
| initialize-method | Class "RtreemixData" |
| initialize-method | Class "RtreemixGPS" |
| initialize-method | Class "RtreemixModel" |
| initialize-method | Class "RtreemixSim" |
| initialize-method | Class "RtreemixStats" |
| kullback.leibler | Kullback-Leibler divergence |
| L1.dist | Different distances between two given vectors |
| L2.norm | L2 norm of a given vector |
| likelihoods | Method for predicting the likelihoods of a set of samples with respect to a mutagenetic trees mixture model |
| likelihoods-method | Method for predicting the likelihoods of a set of samples with respect to a mutagenetic trees mixture model |
| likelihoods-methods | Method for predicting the likelihoods of a set of samples with respect to a mutagenetic trees mixture model |
| LogLikelihoods | Class "RtreemixStats" |
| LogLikelihoods-method | Class "RtreemixStats" |
| Model | Class "RtreemixGPS" |
| Model,RtreemixStats | Class "RtreemixStats" |
| Model-method | Class "RtreemixGPS" |
| Model-method | Class "RtreemixStats" |
| noDraws | Class "RtreemixSim" |
| noDraws,RtreemixSim | Class "RtreemixSim" |
| noDraws-method | Class "RtreemixSim" |
| numTrees | Class "RtreemixModel" |
| numTrees-method | Class "RtreemixModel" |
| Patients | Class "RtreemixData" |
| Patients-method | Class "RtreemixData" |
| Patients<- | Class "RtreemixData" |
| Patients<--method | Class "RtreemixData" |
| plot | Method for visualizing mutagenetic trees mixture models |
| plot-method | Class "RtreemixModel" |
| plot-method | Method for visualizing mutagenetic trees mixture models |
| plot-methods | Method for visualizing mutagenetic trees mixture models |
| print-method | Class "RtreemixData" |
| print-method | Class "RtreemixGPS" |
| print-method | Class "RtreemixModel" |
| print-method | Class "RtreemixSim" |
| print-method | Class "RtreemixStats" |
| Pval.dist | p-value of a given similarity value |
| rank.cor.dist | Different distances between two given vectors |
| Resp | Class "RtreemixModel" |
| Resp-method | Class "RtreemixModel" |
| RtreemixData-class | Class "RtreemixData" |
| RtreemixGPS-class | Class "RtreemixGPS" |
| RtreemixModel-class | Class "RtreemixModel" |
| RtreemixSim-class | Class "RtreemixSim" |
| RtreemixStats-class | Class "RtreemixStats" |
| Sample | Class "RtreemixData" |
| Sample-method | Class "RtreemixData" |
| sampleSize | Class "RtreemixData" |
| sampleSize-method | Class "RtreemixData" |
| SamplingMode | Class "RtreemixGPS" |
| SamplingMode,RtreemixSim | Class "RtreemixSim" |
| SamplingMode-method | Class "RtreemixGPS" |
| SamplingMode-method | Class "RtreemixSim" |
| SamplingParam | Class "RtreemixGPS" |
| SamplingParam,RtreemixSim | Class "RtreemixSim" |
| SamplingParam-method | Class "RtreemixGPS" |
| SamplingParam-method | Class "RtreemixSim" |
| SamplingTimes | Class "RtreemixSim" |
| SamplingTimes-method | Class "RtreemixSim" |
| show-method | Class "RtreemixData" |
| show-method | Class "RtreemixGPS" |
| show-method | Class "RtreemixModel" |
| show-method | Class "RtreemixSim" |
| show-method | Class "RtreemixStats" |
| sim | Method for simulating data from a mutagenetic trees mixture model |
| sim-method | Method for simulating data from a mutagenetic trees mixture model |
| sim-methods | Method for simulating data from a mutagenetic trees mixture model |
| SimPatterns | Class "RtreemixSim" |
| SimPatterns-method | Class "RtreemixSim" |
| stability.sim | Stability analysis of the mutagenetic trees mixture model |
| Star | Class "RtreemixModel" |
| Star-method | Class "RtreemixModel" |
| Trees | Class "RtreemixModel" |
| Trees-method | Class "RtreemixModel" |
| WaitingTimes | Class "RtreemixSim" |
| WaitingTimes-method | Class "RtreemixSim" |
| Weights | Class "RtreemixModel" |
| Weights-method | Class "RtreemixModel" |
| Weights<- | Class "RtreemixModel" |
| Weights<--method | Class "RtreemixModel" |
| WeightsCI | Class "RtreemixModel" |
| WeightsCI-method | Class "RtreemixModel" |
| WLikelihoods | Class "RtreemixStats" |
| WLikelihoods-method | Class "RtreemixStats" |