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,RtreemixModel-method |
Class "RtreemixModel" |
confIntGPS |
Method for calculating GPS values and their 95% bootstrap
confidence intervals |
confIntGPS,RtreemixData,numeric-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,RtreemixData-method |
Class "RtreemixData" |
Description<- |
Class "RtreemixData" |
Description<-,RtreemixData-method |
Class "RtreemixData" |
distribution |
Method for generating the (scaled) probablility distribution
induced with a given mutagenetic trees mixture model |
distribution,RtreemixModel,character,numeric,numeric-method |
Method for generating the (scaled) probablility distribution
induced with a given mutagenetic trees mixture model |
distribution,RtreemixModel,missing,missing,missing-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 |
generate |
Method for generating a random mutagenetic trees mixture model |
generate,numeric,numeric-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,RtreemixGPS-method |
Class "RtreemixGPS" |
getData,RtreemixModel |
Class "RtreemixModel" |
getData,RtreemixModel-method |
Class "RtreemixModel" |
getData,RtreemixStats |
Class "RtreemixStats" |
getData,RtreemixStats-method |
Class "RtreemixStats" |
getModel |
Class "RtreemixSim" |
getModel,RtreemixSim-method |
Class "RtreemixSim" |
getResp |
Class "RtreemixStats" |
getResp,RtreemixStats-method |
Class "RtreemixStats" |
getTree |
Class "RtreemixModel" |
getTree,RtreemixModel,numeric-method |
Class "RtreemixModel" |
GPS |
Class "RtreemixGPS" |
gps |
Methods for predicting the GPS of given dataset by
using a given mutagenetic trees mixture model |
GPS,RtreemixGPS-method |
Class "RtreemixGPS" |
gps,RtreemixModel,matrix-method |
Methods for predicting the GPS of given dataset by
using a given mutagenetic trees mixture model |
gps,RtreemixModel,missing-method |
Methods for predicting the GPS of given dataset by
using a given mutagenetic trees mixture model |
gps,RtreemixModel,RtreemixData-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,RtreemixGPS-method |
Class "RtreemixGPS" |
Patients |
Class "RtreemixData" |
Patients,RtreemixData-method |
Class "RtreemixData" |
Patients<- |
Class "RtreemixData" |
Patients<-,RtreemixData-method |
Class "RtreemixData" |
plot |
Method for visualizing mutagenetic trees mixture models |
plot,RtreemixModel,missing-method |
Method for visualizing mutagenetic trees mixture models |
plot,RtreemixModel-method, missing-method |
Class "RtreemixModel" |
plot-methods |
Method for visualizing mutagenetic trees mixture models |
print,RtreemixData-method |
Class "RtreemixData" |
print,RtreemixGPS-method |
Class "RtreemixGPS" |
print,RtreemixModel-method |
Class "RtreemixModel" |
print,RtreemixSim-method |
Class "RtreemixSim" |
print,RtreemixStats-method |
Class "RtreemixStats" |
Pval.dist |
p-value of a given similarity value |
Sample |
Class "RtreemixData" |
Sample,RtreemixData-method |
Class "RtreemixData" |
sampleSize |
Class "RtreemixData" |
sampleSize,RtreemixData-method |
Class "RtreemixData" |
SamplingMode |
Class "RtreemixGPS" |
SamplingMode,RtreemixGPS-method |
Class "RtreemixGPS" |
SamplingMode,RtreemixSim |
Class "RtreemixSim" |
SamplingMode,RtreemixSim-method |
Class "RtreemixSim" |
SamplingParam |
Class "RtreemixGPS" |
SamplingParam,RtreemixGPS-method |
Class "RtreemixGPS" |
SamplingParam,RtreemixSim |
Class "RtreemixSim" |
SamplingParam,RtreemixSim-method |
Class "RtreemixSim" |
SamplingTimes |
Class "RtreemixSim" |
SamplingTimes,RtreemixSim-method |
Class "RtreemixSim" |
show,RtreemixData-method |
Class "RtreemixData" |
show,RtreemixGPS-method |
Class "RtreemixGPS" |
show,RtreemixModel-method |
Class "RtreemixModel" |
show,RtreemixSim-method |
Class "RtreemixSim" |
show,RtreemixStats-method |
Class "RtreemixStats" |
sim |
Method for simulating data from a mutagenetic trees mixture model |
sim,RtreemixModel,character,numeric-method |
Method for simulating data from a mutagenetic trees mixture model |
sim,RtreemixModel,missing,missing-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,RtreemixSim-method |
Class "RtreemixSim" |
stability.sim |
Stability analysis of the mutagenetic trees mixture model |
Star |
Class "RtreemixModel" |
Star,RtreemixModel-method |
Class "RtreemixModel" |