Package: TransPhylo 1.4.10

TransPhylo: Inference of Transmission Tree from a Dated Phylogeny

Inference of transmission tree from a dated phylogeny. Includes methods to simulate and analyse outbreaks. The methodology is described in Didelot et al. (2014) <doi:10.1093/molbev/msu121>, Didelot et al. (2017) <doi:10.1093/molbev/msw275>.

Authors:Xavier Didelot [aut, cre], Yuanwei Xu [ctb]

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TransPhylo.pdf |TransPhylo.html✨
TransPhylo/json (API)

# Install 'TransPhylo' in R:
install.packages('TransPhylo', repos = c('https://xavierdidelot.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/xavierdidelot/transphylo/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

30 exports 60 stars 4.67 score 5 dependencies 25 mentions 67 scripts 214 downloads

Last updated 12 months agofrom:0759ed77a0. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 23 2024
R-4.5-win-x86_64NOTEAug 23 2024
R-4.5-linux-x86_64NOTEAug 23 2024
R-4.4-win-x86_64NOTEAug 23 2024
R-4.4-mac-x86_64NOTEAug 23 2024
R-4.4-mac-aarch64NOTEAug 23 2024
R-4.3-win-x86_64NOTEAug 23 2024
R-4.3-mac-x86_64NOTEAug 23 2024
R-4.3-mac-aarch64NOTEAug 23 2024

Exports:as.mcmc.resTransPhylocomputeMatTDistcomputeMatWIWconsTTreeconvertToCodadateLastSampleextractCTreeextractPTreeextractTTreegetGenerationTimeDistgetIncidentCasesgetInfectionTimeDistgetOffspringDistgetSamplingTimeDistinfer_multittree_share_paraminferTTreemakeCTreeFromPTreemakeTTreemedTTreephyloFromPTreeplotCTreeplotTracesplotTTreeplotTTree2probPTreeGivenTTreeprobPTreeGivenTTreeRprobTTreeptreeFromPhyloselectTTreesimulateOutbreak

Dependencies:apedigestlatticenlmeRcpp

Inference of transmission tree from a dated phylogeny

Xavier Didelot

Rendered frominfer.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2022-02-08
Started: 2020-03-10

Introducing the R package TransPhylo

Xavier Didelot

Rendered fromTransPhylo.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2020-06-03
Started: 2018-06-19

Simulation of outbreak data

Xavier Didelot

Rendered fromsimulate.rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2020-06-03
Started: 2020-05-08

Simultaneous Inference of Multiple Transmission Trees

Yuanwei Xu

Rendered frommultitree.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2020-06-03
Started: 2018-10-29

Readme and manuals

Help Manual

Help pageTopics
Inference of Transmission Tree from a Dated PhylogenyTransPhylo-package TransPhylo
Convert to coda mcmc formatas.mcmc.resTransPhylo
Build a matrix indicating for each pairs of individuals how many intermediates there are in the transmission chaincomputeMatTDist
Build a matrix of probability of who infected whom from a MCMC outputcomputeMatWIW
Build a consensus transmission tree from a MCMC outputconsTTree
Convert to coda mcmc formatconvertToCoda
Return the date of last sample from a ttree or ctree or ptreedateLastSample
Return the combined tree corresponding to a given iteration of the TransPhylo resultsextractCTree
Extracts phylogenetic tree from a combined phylogenetic/transmission treeextractPTree
Extracts transmission tree from a combined phylogenetic/transmission treeextractTTree
Extract and return realised generation time distributiongetGenerationTimeDist
Returns and/or plot numbers of sampled and unsampled cases over timegetIncidentCases
Extract and return distribution of infection time of given sampled case(s)getInfectionTimeDist
Extract and return offspring distribution of given sampled case(s)getOffspringDist
Extract and return realised sampling time distributiongetSamplingTimeDist
Simultaneously infer transmission trees given phylogenetic trees User can specify any subset of parameters that will be shared by providing a character vector of parameter names to the argument "share".infer_multittree_share_param
Infer transmission tree given a phylogenetic treeinferTTree
Create a transmission tree compatible with the provided phylogenetic treemakeCTreeFromPTree
Simulate a transmission treemakeTTree
Return the medoid from a MCMC outputmedTTree
Converts a phylogenetic tree into an ape phylo objectphyloFromPTree
Plotting for ctreeplot.ctree
Plotting for ptreeplot.ptree
Plotting for resTransPhyloplot.resTransPhylo
Plotting for ttreeplot.ttree
Plot both phylogenetic and transmission trees using colors on the phylogenyplotCTree
Plot MCMC tracesplotTraces
Plot a transmission tree in a detailed formatplotTTree
Plot a transmission tree in an economic formatplotTTree2
Print function for ctree objectsprint.ctree
Print function for ptree objectsprint.ptree
Print function for resTransPhylo objectsprint.resTransPhylo
Print function for ttree objectsprint.ttree
Calculate the probability of a phylogenetic tree given a transmission treeprobPTreeGivenTTree
Calculate the probability of a phylogenetic tree given a transmission treeprobPTreeGivenTTreeR
Calculates the log-probability of a transmission treeprobTTree
Calculates the log-probability of a transmission treeprobTTreeR
Converts an ape phylo object into a phylogenetic treeptreeFromPhylo
Select the most representative transmission tree from a MCMC outputselectTTree
Simulate an outbreaksimulateOutbreak
Summary function for resTransPhylo objectssummary.resTransPhylo