### Install TransPhylo from GitHub

Source: https://xavierdidelot.github.io/TransPhylo/articles/TransPhylo.html

Use this command to install the TransPhylo package from the specified GitHub repository.

```R
devtools::install_github('xavierdidelot/TransPhylo')
```

--------------------------------

### simulateOutbreak usage examples

Source: https://xavierdidelot.github.io/TransPhylo/reference/simulateOutbreak.html

Examples of calling simulateOutbreak with default settings and with custom parameters for offspring distribution and outbreak dates.

```R
simulateOutbreak()
#> Colored phylogenetic tree
#> Number of sampled individuals=3
#> Total number of hosts=5
simulateOutbreak(off.r=2,dateStartOutbreak=2010,dateT=2015)
#> Note that rejection sampling was used 1 times
#> Colored phylogenetic tree
#> Number of sampled individuals=12
#> Total number of hosts=16
```

--------------------------------

### Plotting a ctree example

Source: https://xavierdidelot.github.io/TransPhylo/reference/plot.ctree.html

A basic example showing how to plot a ctree object generated by simulateOutbreak.

```R
plot(simulateOutbreak())
```

--------------------------------

### Plotting a ptree example

Source: https://xavierdidelot.github.io/TransPhylo/reference/plot.ptree.html

Example of plotting a ptree object created from a random phylogenetic tree.

```R
plot(ptreeFromPhylo(ape::rtree(5),2020))
```

--------------------------------

### plotTTree example usage

Source: https://xavierdidelot.github.io/TransPhylo/reference/plotTTree.html

An example of plotting a transmission tree by extracting it from a simulated outbreak.

```R
plotTTree(extractTTree(simulateOutbreak()),2,1)
```

--------------------------------

### ptreeFromPhylo example with ape::rtree

Source: https://xavierdidelot.github.io/TransPhylo/reference/ptreeFromPhylo.html

Example call converting a random ape phylo tree with 5 tips to a phylogenetic tree, with the last sample date set to 2020. The output shows the resulting tree has 5 sampled individuals.

```R
ptreeFromPhylo(ape::rtree(5),2020)
#> Phylogenetic tree
#> Number of sampled individuals=5
```

--------------------------------

### inferTTree example usage

Source: https://xavierdidelot.github.io/TransPhylo/reference/inferTTree.html

A basic example of running the inferTTree function with a generated phylogenetic tree and 100 MCMC iterations.

```R
inferTTree(ptreeFromPhylo(ape::rtree(5),2020),mcmcIterations=100)
#> 
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```

--------------------------------

### plotCTree example usage

Source: https://xavierdidelot.github.io/TransPhylo/reference/plotCTree.html

A basic example of using plotCTree with a simulated outbreak dataset.

```R
plotCTree(simulateOutbreak())
#> Note that rejection sampling was used 1 times
```

--------------------------------

### Print ctree object example

Source: https://xavierdidelot.github.io/TransPhylo/reference/print.ctree.html

Example of printing a ctree object generated by simulateOutbreak, including the expected console output.

```R
print(simulateOutbreak())
#> Note that rejection sampling was used 1 times
#> Colored phylogenetic tree
#> Number of sampled individuals=1
#> Total number of hosts=1
```

--------------------------------

### plotTTree2 example usage

Source: https://xavierdidelot.github.io/TransPhylo/reference/plotTTree2.html

An example of plotting a transmission tree by extracting it from a simulated outbreak.

```R
plotTTree2(extractTTree(simulateOutbreak()))
#> Note that rejection sampling was used 1 times
```

--------------------------------

### Print a transmission tree example

Source: https://xavierdidelot.github.io/TransPhylo/reference/print.ttree.html

Example of printing a transmission tree object generated by simulateOutbreak and extracted via extractTTree.

```R
print(extractTTree(simulateOutbreak()))
#> Note that rejection sampling was used 1 times
#> Transmission tree
#> Number of sampled individuals=5
#> Total number of hosts=9
```

--------------------------------

### Example: extractTTree on simulated outbreak

Source: https://xavierdidelot.github.io/TransPhylo/reference/extractTTree.html

Example call to extractTTree with simulateOutbreak() and its expected output showing the transmission tree summary.

```r
extractTTree(simulateOutbreak())
#> Transmission tree
#> Number of sampled individuals=1
#> Total number of hosts=1
```

--------------------------------

### Load TransPhylo and ape libraries

Source: https://xavierdidelot.github.io/TransPhylo/articles/multitree.html

Initial setup to load the required R packages for phylogenetic and transmission tree analysis.

```R
library(ape)
library(TransPhylo)
```

--------------------------------

### Load the TransPhylo library

Source: https://xavierdidelot.github.io/TransPhylo/articles/TransPhylo.html

Load the installed TransPhylo package into your R session.

```R
library('TransPhylo')
```

--------------------------------

### Example of phyloFromPTree with simulation

Source: https://xavierdidelot.github.io/TransPhylo/reference/phyloFromPTree.html

Converts a simulated outbreak tree into a phylo object and displays the resulting tree structure.

```R
phyloFromPTree(extractPTree(simulateOutbreak()))
#> 
#> Phylogenetic tree with 8 tips and 7 internal nodes.
#> 
#> Tip labels:
#>   1, 2, 3, 4, 5, 6, ...
#> 
#> Rooted; includes branch lengths.
```

--------------------------------

### Print a ptree object

Source: https://xavierdidelot.github.io/TransPhylo/reference/print.ptree.html

Example of printing a ptree object generated from a simulated outbreak.

```R
print(extractPTree(simulateOutbreak()))
#> Phylogenetic tree
#> Number of sampled individuals=1
```

--------------------------------

### Get date of last sample

Source: https://xavierdidelot.github.io/TransPhylo/articles/simulate.html

Retrieves the date of the last sample from the simulation object.

```R
dateLastSample(simu)

## [1] 2007.964
```

--------------------------------

### Simulate outbreak

Source: https://xavierdidelot.github.io/TransPhylo/articles/simulate.html

Generates an outbreak simulation starting in 2005 and observed until 2008.

```R
simu <- simulateOutbreak(neg=neg,pi=pi,off.r=off.r,w.shape=w.shape,
                         w.scale=w.scale,dateStartOutbreak=2005,dateT=2008)
```

--------------------------------

### Plotting a simulated outbreak ttree

Source: https://xavierdidelot.github.io/TransPhylo/reference/plot.ttree.html

Example of plotting a transmission tree generated from a simulated outbreak.

```R
plot(extractTTree(simulateOutbreak()))
```

--------------------------------

### makeTTree(off.r, off.p, pi, w.shape, w.scale, ws.shape, ws.scale, maxTime, nSampled)

Source: https://xavierdidelot.github.io/TransPhylo/reference/makeTTree.html

Simulates a transmission tree based on the provided parameters for offspring distribution, sampling probability, and generation/sampling time distributions. Returns a matrix with infection times, sampling times, and infector information.

```APIDOC
## makeTTree(off.r, off.p, pi, w.shape, w.scale, ws.shape, ws.scale, maxTime, nSampled)

### Description
Simulates a transmission tree.

### Usage
makeTTree(off.r, off.p, pi, w.shape, w.scale, ws.shape = w.shape, ws.scale = w.scale, maxTime = Inf, nSampled = NA)

### Arguments
- **off.r** (numeric) - Required - First parameter of the negative binomial distribution for offspring number.
- **off.p** (numeric) - Required - Second parameter of the negative binomial distribution for offspring number.
- **pi** (numeric) - Required - Probability of sampling an infected individual.
- **w.shape** (numeric) - Required - Shape parameter of the Gamma probability density function representing the generation time.
- **w.scale** (numeric) - Required - Scale parameter of the Gamma probability density function representing the generation time.
- **ws.shape** (numeric) - Optional - Shape parameter of the Gamma probability density function representing the sampling time. Defaults to w.shape.
- **ws.scale** (numeric) - Optional - Scale parameter of the Gamma probability density function representing the sampling time. Defaults to w.scale.
- **maxTime** (numeric) - Optional - Duration of simulation (can be Inf). Defaults to Inf.
- **nSampled** (numeric) - Optional - Number of sampled individuals (can be NA for any). Defaults to NA.

### Value
A N*3 matrix in the following format with one row per infected host, first column is time of infection, second column is time of sampling, third column is infector.
```

--------------------------------

### simulateOutbreak()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Simulates an outbreak, generating a transmission tree and phylogenetic tree.

```APIDOC
## simulateOutbreak()

### Description
Simulate an outbreak.

### Usage
simulateOutbreak(...)

### Arguments
- **...** - Parameters for the simulation.

### Value
A list containing simulated trees.
```

--------------------------------

### Plot the first simulated outbreak

Source: https://xavierdidelot.github.io/TransPhylo/articles/multitree.html

Visualize the phylogenetic and transmission trees for the first simulated outbreak.

```R
plot(simu1)
```

--------------------------------

### makeCTreeFromPTree()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Creates a transmission tree compatible with the provided phylogenetic tree.

```APIDOC
## makeCTreeFromPTree()

### Description
Create a transmission tree compatible with the provided phylogenetic tree.

### Usage
makeCTreeFromPTree(ptree, ...)

### Arguments
- **ptree** - A phylogenetic tree (ptree) object.
- **...** - Additional parameters.

### Value
A combined tree (ctree) object.
```

--------------------------------

### getOffspringDist(record, burnin = 0.5, k, show.plot = F)

Source: https://xavierdidelot.github.io/TransPhylo/reference/getOffspringDist.html

Extracts and returns the offspring distribution of given sampled case(s) from MCMC output produced by inferTTree. The function returns a vector or matrix of posterior offspring distributions depending on the number of cases specified.

```APIDOC
## getOffspringDist(record, burnin = 0.5, k, show.plot = F)

### Description
Extract and return offspring distribution of given sampled case(s).

### Usage
```r
getOffspringDist(record, burnin = 0.5, k, show.plot = F)
```

### Arguments
- **record** - MCMC output produced by inferTTree
- **burnin** - Proportion of the MCMC output to be discarded as burnin (default: 0.5)
- **k** - Case(s) whose offspring distribution are to be extracted. Either a string matching one of the case names in the data, or a vector of such strings
- **show.plot** - Show a barplot of the distribution (default: FALSE)

### Value
Posterior offspring distribution for the case(s) in k. If length(k)==1 then a vector is returned, otherwise a matrix.
```

--------------------------------

### Assess MCMC convergence with CODA

Source: https://xavierdidelot.github.io/TransPhylo/articles/infer.html

Uses the CODA package to calculate the effective sample size (ESS) of parameters.

```R
library(coda)
mcmc=convertToCoda(res)
effectiveSize(mcmc)
```

--------------------------------

### Visualize simulation

Source: https://xavierdidelot.github.io/TransPhylo/articles/simulate.html

Plots the colored phylogenetic tree representing the transmission and within-host trees.

```R
plot(simu)
```

--------------------------------

### Define simulation parameters

Source: https://xavierdidelot.github.io/TransPhylo/articles/simulate.html

Specifies the effective within-host population size, reproduction number, generation time distribution, and sampling density.

```R
neg=100/365
off.r=5
w.shape=10
w.scale=0.1
pi=0.25
```

--------------------------------

### print(x, ...)

Source: https://xavierdidelot.github.io/TransPhylo/reference/print.ctree.html

S3 method for ctree objects that prints details of the colored phylogenetic tree.

```APIDOC
## print(x, ...)

### Description
Print function for ctree objects, i.e. colored phylogenetic trees.

### Usage
print(x, ...)

### Arguments
- **x** (ctree) - Required - Object of class ctree, i.e. a colored phylogenetic tree.
- **...** - Optional - Additional parameters are passed on.

### Value
Print out details of the ctree.

### Examples
```r
print(simulateOutbreak())
#> Note that rejection sampling was used 1 times
#> Colored phylogenetic tree
#> Number of sampled individuals=1
#> Total number of hosts=1
```
```

--------------------------------

### simulateOutbreak function signature

Source: https://xavierdidelot.github.io/TransPhylo/reference/simulateOutbreak.html

The function signature for simulateOutbreak with default parameter values.

```R
simulateOutbreak(
  off.r = 1,
  off.p = 0.5,
  neg = 0.25,
  nSampled = NA,
  pi = 0.5,
  w.shape = 2,
  w.scale = 1,
  ws.shape = NA,
  ws.scale = NA,
  w.mean = NA,
  w.std = NA,
  ws.mean = NA,
  ws.std = NA,
  dateStartOutbreak = 2000,
  dateT = Inf
)
```

--------------------------------

### Plot MCMC traces

Source: https://xavierdidelot.github.io/TransPhylo/articles/infer.html

Visualizes the MCMC iteration traces to check for stability.

```R
plot(res)
```

--------------------------------

### Run single and multiple tree inference with inferTTree and infer_multittree_share_param

Source: https://xavierdidelot.github.io/TransPhylo/articles/multitree.html

Extracts phylogenetic trees from simulated data and runs single tree inference for each tree separately, then runs joint inference using infer_multittree_share_param while sharing parameters neg, off.r, off.p, and pi. The off.p parameter is included but not updated by default. The beta prior parameters are set to 1 for a uniform prior on the sampling rate.

```R
ptree1 <- extractPTree(simu1)
ptree2 <- extractPTree(simu2)

iters <- 2e3; thin <- 10
record_tp1 <- inferTTree(ptree1, w.shape, w.scale, ws.shape, ws.scale,
                         mcmcIterations = iters, thinning = thin, dateT = 2005)
record_tp2 <- inferTTree(ptree2, w.shape, w.scale, ws.shape, ws.scale,
                         mcmcIterations = iters, thinning = thin, dateT = 2005)
record_tpj <- infer_multittree_share_param(list(ptree1,ptree2), w.shape, w.scale, ws.shape, ws.scale, 
                                    mcmcIterations = iters, thinning = thin, dateT = 2005,
                                    share = c("neg", "off.r", "off.p", "pi"))
```

--------------------------------

### probTTree()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Calculates the log-probability of a transmission tree.

```APIDOC
## probTTree()

### Description
Calculates the log-probability of a transmission tree.

### Usage
probTTree(ttree, ...)

### Arguments
- **ttree** - A transmission tree (ttree) object.
- **...** - Additional parameters.

### Value
The log-probability value.
```

--------------------------------

### consTTree(record, burnin = 0.5, minimum = 0.2, debug = F)

Source: https://xavierdidelot.github.io/TransPhylo/reference/consTTree.html

Builds a consensus transmission tree from an MCMC output. The function discards a proportion of the MCMC output as burnin and includes partitions with a minimum probability in the consensus.

```APIDOC
## consTTree(record, burnin = 0.5, minimum = 0.2, debug = F)

### Description
Builds a consensus transmission tree from an MCMC output.

### Usage
consTTree(record, burnin = 0.5, minimum = 0.2, debug = F)

### Arguments
- **record** - Output from inferTTree function.
- **burnin** - Proportion of the MCMC output to be discarded as burnin.
- **minimum** - Minimum probability for inclusion of a partition in the consensus.
- **debug** - Used for debugging.

### Value
The consensus transmission tree.
```

--------------------------------

### Plot the second simulated outbreak

Source: https://xavierdidelot.github.io/TransPhylo/articles/multitree.html

Visualize the phylogenetic and transmission trees for the second simulated outbreak.

```R
plot(simu2)
```

--------------------------------

### getOffspringDist()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Extracts and returns offspring distribution of given sampled case(s).

```APIDOC
## getOffspringDist()

### Description
Extract and return offspring distribution of given sampled case(s).

### Usage
getOffspringDist(res, k, ...)

### Arguments
- **res** - An object of class resTransPhylo.
- **k** - Index of sampled case(s).
- **...** - Additional parameters.

### Value
A vector of offspring counts.
```

--------------------------------

### ptreeFromPhylo()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Converts an ape phylo object into a phylogenetic tree.

```APIDOC
## ptreeFromPhylo()

### Description
Converts an ape phylo object into a phylogenetic tree.

### Usage
ptreeFromPhylo(phylo)

### Arguments
- **phylo** - An ape phylo object.

### Value
A phylogenetic tree (ptree) object.
```

--------------------------------

### phyloFromPTree()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Converts a phylogenetic tree into an ape phylo object.

```APIDOC
## phyloFromPTree()

### Description
Converts a phylogenetic tree into an ape phylo object.

### Usage
phyloFromPTree(ptree)

### Arguments
- **ptree** - A phylogenetic tree (ptree) object.

### Value
An ape phylo object.
```

--------------------------------

### plotTTree()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Plots a transmission tree in a detailed format.

```APIDOC
## plotTTree()

### Description
Plot a transmission tree in a detailed format.

### Usage
plotTTree(ttree, ...)

### Arguments
- **ttree** - A transmission tree (ttree) object.
- **...** - Additional plotting parameters.

### Value
No return value, used for plotting.
```

--------------------------------

### computeMatWIW(record, burnin = 0.5)

Source: https://xavierdidelot.github.io/TransPhylo/reference/computeMatWIW.html

Builds a matrix of probability of who infected whom from a MCMC output. The function takes the output from inferTTree and an optional burnin proportion, and returns a matrix of infection probabilities.

```APIDOC
## computeMatWIW(record, burnin = 0.5)

### Description
Builds a matrix of probability of who infected whom from a MCMC output.

### Usage
computeMatWIW(record, burnin = 0.5)

### Arguments
- **record** - Output from inferTTree function
- **burnin** - Proportion of the MCMC output to be discarded as burnin

### Value
Matrix of probability of who infected whom
```

--------------------------------

### plotTraces()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Plots MCMC traces.

```APIDOC
## plotTraces()

### Description
Plot MCMC traces.

### Usage
plotTraces(res, ...)

### Arguments
- **res** - An object of class resTransPhylo.
- **...** - Additional plotting parameters.

### Value
No return value, used for plotting.
```

--------------------------------

### plotTTree2()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Plots a transmission tree in an economic format.

```APIDOC
## plotTTree2()

### Description
Plot a transmission tree in an economic format.

### Usage
plotTTree2(ttree, ...)

### Arguments
- **ttree** - A transmission tree (ttree) object.
- **...** - Additional plotting parameters.

### Value
No return value, used for plotting.
```

--------------------------------

### print(<ptree>)

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Print function for ptree objects.

```APIDOC
## print(<ptree>)

### Description
Print function for ptree objects.

### Usage
print(x, ...)

### Arguments
- **x** - A ptree object.
- **...** - Additional printing parameters.

### Value
No return value, used for printing.
```

--------------------------------

### probTTreeR()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Calculates the log-probability of a transmission tree (R implementation).

```APIDOC
## probTTreeR()

### Description
Calculates the log-probability of a transmission tree.

### Usage
probTTreeR(ttree, ...)

### Arguments
- **ttree** - A transmission tree (ttree) object.
- **...** - Additional parameters.

### Value
The log-probability value.
```

--------------------------------

### plot(<ptree>)

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Plotting for ptree objects.

```APIDOC
## plot(<ptree>)

### Description
Plotting for ptree.

### Usage
plot(x, ...)

### Arguments
- **x** - A ptree object.
- **...** - Additional plotting parameters.

### Value
No return value, used for plotting.
```

--------------------------------

### Set generation time parameters

Source: https://xavierdidelot.github.io/TransPhylo/articles/infer.html

Defines the shape and scale parameters for the Gamma distribution of generation times.

```R
w.shape=10
w.scale=0.1
```

--------------------------------

### getGenerationTimeDist(record, burnin, maxi, numBins, show.plot)

Source: https://xavierdidelot.github.io/TransPhylo/reference/getGenerationTimeDist.html

Extracts and returns the realised generation time distribution from MCMC output. It allows specifying burnin proportion, maximum generation time, number of bins, and whether to show a plot.

```APIDOC
## getGenerationTimeDist(record, burnin, maxi, numBins, show.plot)

### Description
Extract and return realised generation time distribution.

### Usage
```
getGenerationTimeDist(
  record,
  burnin = 0.5,
  maxi = 2,
  numBins = 20,
  show.plot = F
)
```

### Arguments
- **record** - MCMC output produced by inferTTree
- **burnin** - Proportion of the MCMC output to be discarded as burnin
- **maxi** - Maximum generation time to consider
- **numBins** - Number of time bins to compute and display distribution
- **show.plot** - Show a barplot of the distribution

### Value
Vector of times between becoming infected and infecting others (generation times) in the posterior
```

--------------------------------

### print(<ctree>)

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Print function for ctree objects.

```APIDOC
## print(<ctree>)

### Description
Print function for ctree objects.

### Usage
print(x, ...)

### Arguments
- **x** - A ctree object.
- **...** - Additional printing parameters.

### Value
No return value, used for printing.
```

--------------------------------

### plot(<ctree>)

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Plotting for ctree objects.

```APIDOC
## plot(<ctree>)

### Description
Plotting for ctree.

### Usage
plot(x, ...)

### Arguments
- **x** - A ctree object.
- **...** - Additional plotting parameters.

### Value
No return value, used for plotting.
```

--------------------------------

### Run MCMC inference

Source: https://xavierdidelot.github.io/TransPhylo/articles/infer.html

Executes the MCMC procedure to infer the transmission tree.

```R
res<-inferTTree(ptree,mcmcIterations=1000,w.shape=w.shape,w.scale=w.scale,dateT=dateT)
```

--------------------------------

### Plot offspring distribution for specific individuals

Source: https://xavierdidelot.github.io/TransPhylo/articles/infer.html

Plots the offspring distribution for individuals '1' and '2'.

```R
a=getOffspringDist(res,k=c('1','2'),show.plot = T)
```

--------------------------------

### computeMatTDist(record, burnin = 0.5)

Source: https://xavierdidelot.github.io/TransPhylo/reference/computeMatTDist.html

Builds a matrix indicating for each pair of individuals how many intermediates there are in the transmission chain. It takes the output from the inferTTree function and an optional burnin proportion, and returns a matrix of intermediates.

```APIDOC
## computeMatTDist(record, burnin = 0.5)

### Description
Builds a matrix indicating for each pair of individuals how many intermediates there are in the transmission chain.

### Usage
computeMatTDist(record, burnin = 0.5)

### Arguments
- **record** - Output from inferTTree function
- **burnin** - Proportion of the MCMC output to be discarded as burnin

### Value
Matrix of intermediates in transmission chains between pairs of hosts
```

--------------------------------

### print(<ttree>)

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Print function for ttree objects.

```APIDOC
## print(<ttree>)

### Description
Print function for ttree objects.

### Usage
print(x, ...)

### Arguments
- **x** - A ttree object.
- **...** - Additional printing parameters.

### Value
No return value, used for printing.
```

--------------------------------

### getOffspringDist function signature

Source: https://xavierdidelot.github.io/TransPhylo/reference/getOffspringDist.html

The function signature for extracting the offspring distribution from MCMC output.

```R
getOffspringDist(record, burnin = 0.5, k, show.plot = F)
```

--------------------------------

### getSamplingTimeDist(record, burnin, maxi, numBins, show.plot)

Source: https://xavierdidelot.github.io/TransPhylo/reference/getSamplingTimeDist.html

Extracts and returns the realised sampling time distribution from MCMC output. The function returns a vector of times between becoming infected and becoming sampled in the posterior.

```APIDOC
## getSamplingTimeDist(record, burnin, maxi, numBins, show.plot)

### Description
Extracts and returns the realised sampling time distribution from MCMC output. The function returns a vector of times between becoming infected and becoming sampled in the posterior.

### Usage
```
getSamplingTimeDist(
  record,
  burnin = 0.5,
  maxi = 2,
  numBins = 20,
  show.plot = F
)
```

### Arguments
- **record** - MCMC output produced by inferTTree.
- **burnin** - Proportion of the MCMC output to be discarded as burnin. Default is 0.5.
- **maxi** - Maximum generation time to consider. Default is 2.
- **numBins** - Number of time bins to compute and display distribution. Default is 20.
- **show.plot** - Show a barplot of the distribution. Default is FALSE.

### Value
Vector of times between becoming infected and becoming sampled in the posterior.
```

--------------------------------

### plotCTree()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Plots both phylogenetic and transmission trees using colors on the phylogeny.

```APIDOC
## plotCTree()

### Description
Plot both phylogenetic and transmission trees using colors on the phylogeny.

### Usage
plotCTree(ctree, ...)

### Arguments
- **ctree** - A combined tree (ctree) object.
- **...** - Additional plotting parameters.

### Value
No return value, used for plotting.
```

--------------------------------

### plot(<ttree>)

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Plotting for ttree objects.

```APIDOC
## plot(<ttree>)

### Description
Plotting for ttree.

### Usage
plot(x, ...)

### Arguments
- **x** - A ttree object.
- **...** - Additional plotting parameters.

### Value
No return value, used for plotting.
```

--------------------------------

### summary(object, ...)

Source: https://xavierdidelot.github.io/TransPhylo/reference/summary.resTransPhylo.html

S3 method for resTransPhylo objects that prints details of TransPhylo results. The object is the output from inferTTree, and additional arguments are passed to print.phylo.

```APIDOC
## summary(object, ...)

### Description
S3 method for resTransPhylo objects that prints details of TransPhylo results.

### Usage
summary(object, ...)

### Arguments
- **object** - Output from inferTTree.
- **...** - Passed on to print.phylo.

### Value
Print out details of TransPhylo results.
```

--------------------------------

### print(x, ...)

Source: https://xavierdidelot.github.io/TransPhylo/reference/print.resTransPhylo.html

S3 method for resTransPhylo objects that prints out details of TransPhylo results.

```APIDOC
## print(x, ...)

### Description
S3 method for resTransPhylo objects that prints out details of TransPhylo results.

### Method
print

### Signature
print(x, ...)

### Parameters
- **x** - output from inferTTree
- **...** - Additional parameters are passed on

### Value
Print out details of TransPhylo results
```

--------------------------------

### Extract and plot phylogenetic tree

Source: https://xavierdidelot.github.io/TransPhylo/articles/simulate.html

Extracts the phylogenetic tree from the simulation and displays it.

```R
ptree<-extractPTree(simu)
plot(ptree)
```

--------------------------------

### selectTTree function signature

Source: https://xavierdidelot.github.io/TransPhylo/reference/selectTTree.html

The basic syntax for calling the selectTTree function.

```R
selectTTree(record, burnin = 0.5)
```

--------------------------------

### Find and plot medoid tree

Source: https://xavierdidelot.github.io/TransPhylo/articles/infer.html

Identifies the most representative (medoid) tree from the MCMC sample and plots it.

```R
med=medTTree(res)
plot(med)
```

--------------------------------

### computeMatTDist()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Builds a matrix indicating for each pair of individuals how many intermediates there are in the transmission chain.

```APIDOC
## computeMatTDist()

### Description
Build a matrix indicating for each pairs of individuals how many intermediates there are in the transmission chain.

### Usage
computeMatTDist(res, ...)

### Arguments
- **res** - An object of class resTransPhylo.
- **...** - Additional parameters.

### Value
A matrix of distances.
```

--------------------------------

### S3 method for ptree print signature

Source: https://xavierdidelot.github.io/TransPhylo/reference/print.ptree.html

The signature for the print method for ptree objects.

```R
# S3 method for ptree
print(x, ...)
```

--------------------------------

### Display Newick string

Source: https://xavierdidelot.github.io/TransPhylo/articles/simulate.html

Prints the Newick representation of the tree to the console.

```R
write.tree(p,'')

## [1] "((4:1.257652937,(1:1.231048819,5:1.519248672):0.303038892):0.784065883,(3:1.643413444,(6:0.656820028,2:0.007344035611):0.7562780805):1.293120815);"
```

--------------------------------

### infer_multittree_share_param function signature

Source: https://xavierdidelot.github.io/TransPhylo/reference/infer_multittree_share_param.html

The function signature for infer_multittree_share_param, showing all available parameters including the 'share' argument for parameter sharing.

```R
infer_multittree_share_param(
  ptree_lst,
  w.shape = 2,
  w.scale = 1,
  ws.shape = w.shape,
  ws.scale = w.scale,
  mcmcIterations = 1000,
  thinning = 1,
  startNeg = 100/365,
  startOff.r = 1,
  startOff.p = 0.5,
  startPi = 0.5,
  prior_pi_a = 1,
  prior_pi_b = 1,
  updateNeg = TRUE,
  updateOff.r = TRUE,
  updateOff.p = FALSE,
  updatePi = TRUE,
  share = NULL,
  startCTree_lst = rep(NA, length(ptree_lst)),
  updateTTree = TRUE,
  optiStart = 2,
  dateT = Inf,
  delta_t = 0.01,
  verbose = F
)
```

--------------------------------

### Extract and plot transmission tree

Source: https://xavierdidelot.github.io/TransPhylo/articles/simulate.html

Extracts the transmission tree from the simulation and displays it.

```R
ttree<-extractTTree(simu)
plot(ttree)
```

--------------------------------

### medTTree()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Returns the medoid from a MCMC output.

```APIDOC
## medTTree()

### Description
Return the medoid from a MCMC output.

### Usage
medTTree(res, ...)

### Arguments
- **res** - An object of class resTransPhylo.
- **...** - Additional parameters.

### Value
The medoid transmission tree.
```

--------------------------------

### plot(x, ...)

Source: https://xavierdidelot.github.io/TransPhylo/reference/plot.ptree.html

S3 method for ptree objects that plots the phylogenetic tree. Additional parameters are passed to ape::plot.phylo.

```APIDOC
## plot(x, ...)

### Description
S3 method for ptree objects that plots the phylogenetic tree. Additional parameters are passed to ape::plot.phylo.

### Usage
plot(x, ...)

### Arguments
- **x** (ptree) - Required - Object of class ptree, i.e., a phylogenetic tree.
- **...** - Optional - Additional parameters passed to ape::plot.phylo.

### Value
Plot of ptree.

### Examples
```r
plot(ptreeFromPhylo(ape::rtree(5), 2020))
```
```

--------------------------------

### S3 method print.ctree signature

Source: https://xavierdidelot.github.io/TransPhylo/reference/print.ctree.html

The signature for the S3 print method for ctree objects.

```R
# S3 method for ctree
print(x, ...)
```

--------------------------------

### Extract and combine parameter estimates from three runs

Source: https://xavierdidelot.github.io/TransPhylo/articles/multitree.html

Defines a helper function get_param_estimates to extract a named parameter from each element of a record list. Builds a data frame with columns run, pi, off.r, and neg, combining estimates from record_tp1, record_tp2, and record_tpj[[1]]. The run column labels each group as tp1, tp2, or tp_multitree.

```R
get_param_estimates <- function(record, p){
  sapply(record, function(x) x[[p]])
}

df <- data.frame(run = rep(c("tp1","tp2","tp_multitree"), each = length(record_tp1)),
           pi = c(get_param_estimates(record_tp1, "pi"),
                  get_param_estimates(record_tp2, "pi"),
                  get_param_estimates(record_tpj[[1]], "pi")),
           off.r = c(get_param_estimates(record_tp1, "off.r"),
                     get_param_estimates(record_tp2, "off.r"),
                     get_param_estimates(record_tpj[[1]], "off.r")),
           neg = c(get_param_estimates(record_tp1, "neg"),
                   get_param_estimates(record_tp2, "neg"),
                   get_param_estimates(record_tpj[[1]], "neg")))
```

--------------------------------

### Convert TransPhylo output to coda mcmc format

Source: https://xavierdidelot.github.io/TransPhylo/reference/as.mcmc.resTransPhylo.html

Converts the result of inferTTree into an mcmc object, with an optional burnin parameter to discard a portion of the MCMC output.

```R
as.mcmc.resTransPhylo(x, burnin = 0.5)
```

--------------------------------

### probPTreeGivenTTreeR()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Calculates the probability of a phylogenetic tree given a transmission tree (R implementation).

```APIDOC
## probPTreeGivenTTreeR()

### Description
Calculate the probability of a phylogenetic tree given a transmission tree.

### Usage
probPTreeGivenTTreeR(ctree, ...)

### Arguments
- **ctree** - A combined tree (ctree) object.
- **...** - Additional parameters.

### Value
The probability value.
```

--------------------------------

### print(x, ...)

Source: https://xavierdidelot.github.io/TransPhylo/reference/print.ttree.html

S3 method for ttree objects that prints details of the transmission tree. It accepts the ttree object and optional additional arguments.

```APIDOC
## print(x, ...)

### Description
S3 method for ttree objects that prints out details of the transmission tree.

### Usage
print(x, ...)

### Arguments
- **x** (ttree) - Required - Object of class ttree, i.e., a transmission tree.
- **...** - Optional - Additional parameters are passed on.

### Value
Print out details of the ttree.

### Examples
```r
print(extractTTree(simulateOutbreak()))
#> Note that rejection sampling was used 1 times
#> Transmission tree
#> Number of sampled individuals=5
#> Total number of hosts=9
```
```

--------------------------------

### as.mcmc.resTransPhylo()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Converts TransPhylo results to coda mcmc format.

```APIDOC
## as.mcmc.resTransPhylo()

### Description
Convert to coda mcmc format.

### Usage
as.mcmc.resTransPhylo(res)

### Arguments
- **res** - An object of class resTransPhylo.

### Value
An mcmc object.
```

--------------------------------

### plotTraces function usage

Source: https://xavierdidelot.github.io/TransPhylo/reference/plotTraces.html

Basic syntax for calling the plotTraces function to visualize MCMC traces.

```R
plotTraces(record, burnin = 0, extend = F)
```

--------------------------------

### Load and plot dated phylogeny

Source: https://xavierdidelot.github.io/TransPhylo/articles/infer.html

Loads a dated phylogeny tree and visualizes it.

```R
library(ape)
phy<-read.tree(text='((4:1.257652937,(1:1.231048819,5:1.519248672):0.303038892):0.784065883,(3:1.643413444,(6:0.656820028,2:0.007344035611):0.7562780805):1.293120815);')
plot(phy)
axisPhylo(backward = F)
```

--------------------------------

### summary(<resTransPhylo>)

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Summary function for resTransPhylo objects.

```APIDOC
## summary(<resTransPhylo>)

### Description
Summary function for resTransPhylo objects.

### Usage
summary(object, ...)

### Arguments
- **object** - A resTransPhylo object.
- **...** - Additional summary parameters.

### Value
A summary object.
```

--------------------------------

### print(x, ...)

Source: https://xavierdidelot.github.io/TransPhylo/reference/print.ptree.html

S3 method for ptree objects that prints details of the phylogenetic tree. It accepts an object of class ptree and optional additional parameters.

```APIDOC
## print(x, ...)

### Description
Print function for ptree objects. Prints out details of the ptree.

### Method
S3 method for ptree

### Signature
print(x, ...)

### Parameters
- **x** (ptree) - Required - Object of class ptree, i.e., a phylogenetic tree.
- **...** - Optional - Additional parameters are passed on.

### Value
Print out details of the ptree.

### Example
```r
print(extractPTree(simulateOutbreak()))
#> Phylogenetic tree
#> Number of sampled individuals=1
```
```

--------------------------------

### plotTraces(record, burnin = 0, extend = F)

Source: https://xavierdidelot.github.io/TransPhylo/reference/plotTraces.html

Plots MCMC traces from the output of the inferTTree function. The burnin argument specifies the proportion of the MCMC output to discard, and extend controls whether to also show traces of off.r and off.p.

```APIDOC
## plotTraces(record, burnin = 0, extend = F)

### Description
Plots MCMC traces from the output of the inferTTree function.

### Usage
plotTraces(record, burnin = 0, extend = F)

### Arguments
- **record** - Output from inferTTree function.
- **burnin** - Proportion of the MCMC output to be discarded as burnin.
- **extend** - Whether to also show traces of off.r and off.p.

### Value
Returns invisibly the first parameter.
```

--------------------------------

### dateLastSample(x)

Source: https://xavierdidelot.github.io/TransPhylo/reference/dateLastSample.html

Returns the date of the last sample from a transmission tree, colored tree, or phylogenetic tree.

```APIDOC
## dateLastSample(x)

### Description
Returns the date of the last sample from a transmission tree, colored tree, or phylogenetic tree.

### Usage
```r
dateLastSample(x)
```

### Arguments
- **x** - A transmission tree or colored tree or phylogenetic tree.

### Value
The date of the last sample.
```

--------------------------------

### Save tree to Newick file

Source: https://xavierdidelot.github.io/TransPhylo/articles/simulate.html

Exports the phylogenetic tree to a Newick file for use in inference tutorials.

```R
write.tree(p,'tree.nwk')
```

--------------------------------

### Usage of phyloFromPTree

Source: https://xavierdidelot.github.io/TransPhylo/reference/phyloFromPTree.html

Basic syntax for converting a phylogenetic tree object.

```R
phyloFromPTree(ptree)
```

--------------------------------

### Plot infection time distribution for specific individuals

Source: https://xavierdidelot.github.io/TransPhylo/articles/infer.html

Plots the distribution of infection times for individuals '1' and '2'.

```R
a=getInfectionTimeDist(res,k=c('1','2'),show.plot = T)
```

--------------------------------

### getIncidentCases function signature

Source: https://xavierdidelot.github.io/TransPhylo/reference/getIncidentCases.html

The function signature for getIncidentCases, showing parameters for MCMC burnin, binning, date constraints, and plotting.

```R
getIncidentCases(
  record,
  burnin = 0.5,
  numBins = 10,
  dateT = NA,
  show.plot = FALSE
)
```

--------------------------------

### print(<resTransPhylo>)

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Print function for resTransPhylo objects.

```APIDOC
## print(<resTransPhylo>)

### Description
Print function for resTransPhylo objects.

### Usage
print(x, ...)

### Arguments
- **x** - A resTransPhylo object.
- **...** - Additional printing parameters.

### Value
No return value, used for printing.
```

--------------------------------

### getSamplingTimeDist()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Extracts and returns realised sampling time distribution.

```APIDOC
## getSamplingTimeDist()

### Description
Extract and return realised sampling time distribution.

### Usage
getSamplingTimeDist(res, ...)

### Arguments
- **res** - An object of class resTransPhylo.
- **...** - Additional parameters.

### Value
A vector of sampling times.
```

--------------------------------

### probPTreeGivenTTree()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Calculates the probability of a phylogenetic tree given a transmission tree.

```APIDOC
## probPTreeGivenTTree()

### Description
Calculate the probability of a phylogenetic tree given a transmission tree.

### Usage
probPTreeGivenTTree(ctree, ...)

### Arguments
- **ctree** - A combined tree (ctree) object.
- **...** - Additional parameters.

### Value
The probability value.
```

--------------------------------

### Convert and plot phylo object

Source: https://xavierdidelot.github.io/TransPhylo/articles/simulate.html

Converts the extracted phylogenetic tree to an ape phylo object and plots it with a time axis.

```R
library(ape)
p<-phyloFromPTree(ptree)
plot(p)
axisPhylo(backward = F)
```

--------------------------------

### selectTTree()

Source: https://xavierdidelot.github.io/TransPhylo/reference/index.html

Selects the most representative transmission tree from a MCMC output.

```APIDOC
## selectTTree()

### Description
Select the most representative transmission tree from a MCMC output.

### Usage
selectTTree(res, ...)

### Arguments
- **res** - An object of class resTransPhylo.
- **...** - Additional parameters.

### Value
The selected transmission tree.
```

--------------------------------

### plot(x, ...)

Source: https://xavierdidelot.github.io/TransPhylo/reference/plot.ctree.html

S3 method for ctree objects that plots a colored phylogenetic tree. Additional parameters are passed on to the underlying plotting function.

```APIDOC
## plot(x, ...)

### Description
S3 method for ctree objects that plots a colored phylogenetic tree.

### Usage
plot(x, ...)

### Arguments
- **x** (ctree) - Required - Object of class ctree, i.e., a colored phylogenetic tree.
- **...** - Optional - Additional parameters are passed on.

### Value
Plot of ctree

### Examples
```r
plot(simulateOutbreak())
```
```

--------------------------------

### Take the last 50% of MCMC samples

Source: https://xavierdidelot.github.io/TransPhylo/articles/multitree.html

Computes the indices for the last 50% of the MCMC iterations and subsets the recorded results for both single and multiple tree inference. The multiple tree inference returns a list of length two, each element corresponding to one input phylogenetic tree.

```R
begin <- (iters * 0.5) / thin + 1
end <- iters / thin
record_tp1 <- record_tp1[begin:end]
record_tp2 <- record_tp2[begin:end]
record_tpj[[1]] <- record_tpj[[1]][begin:end]
record_tpj[[2]] <- record_tpj[[2]][begin:end]
```

--------------------------------

### S3 method for ptree plot signature

Source: https://xavierdidelot.github.io/TransPhylo/reference/plot.ptree.html

The signature for the plot method for ptree objects.

```R
# S3 method for ptree
plot(x, ...)
```

--------------------------------

### S3 method for ttree print function signature

Source: https://xavierdidelot.github.io/TransPhylo/reference/print.ttree.html

The signature for the print method for ttree objects.

```R
# S3 method for ttree
print(x, ...)
```

--------------------------------

### ptreeFromPhylo function signature

Source: https://xavierdidelot.github.io/TransPhylo/reference/ptreeFromPhylo.html

Shows the usage of ptreeFromPhylo with arguments tr and dateLastSample.

```R
ptreeFromPhylo(tr, dateLastSample)
```

--------------------------------

### Extract and plot transmission tree

Source: https://xavierdidelot.github.io/TransPhylo/articles/infer.html

Extracts the transmission tree from the medoid tree and plots it in detail.

```R
ttree=extractTTree(med)
plot(ttree,type='detailed',w.shape,w.scale)
```

--------------------------------

### plot(x, ...)

Source: https://xavierdidelot.github.io/TransPhylo/reference/plot.resTransPhylo.html

S3 method for resTransPhylo that plots TransPhylo results. The primary argument is the output from inferTTree, and additional parameters are passed on to the plotting function.

```APIDOC
## plot(x, ...)

### Description
S3 method for resTransPhylo that plots TransPhylo results.

### Method
S3 method for class resTransPhylo

### Signature
plot(x, ...)

### Parameters
- **x** - Output from inferTTree
- **...** - Additional parameters are passed on

### Value
Plot of TransPhylo results

```