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 | Class "RtreemixModel" |
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" |