### Install TransPhylo from GitHub using devtools

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/TransPhylo.html

Install the TransPhylo package from GitHub using the devtools package. Run this command in R if you have not already installed TransPhylo.

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

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

### Example: plot(simulateOutbreak())

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/plot.ctree.html

Example usage of plotting a ctree object generated by simulateOutbreak().

```r
plot(simulateOutbreak())
```

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

### simulateOutbreak examples with output

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/simulateOutbreak.html

Two example calls to simulateOutbreak with their console output. The first uses default parameters; the second specifies off.r, dateStartOutbreak, and dateT, and shows a rejection sampling note.

```R
simulateOutbreak()
#> Colored phylogenetic tree
#> Number of sampled individuals=3
#> Total number of hosts=5
```

```R
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
```

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

### Example: ptreeFromPhylo with ape::rtree(5)

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/ptreeFromPhylo.html

Example usage of ptreeFromPhylo with a random tree of 5 tips and dateLastSample=2020. The output shows the resulting phylogenetic tree with 5 sampled individuals.

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

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

### extractTTree example with simulateOutbreak

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/extractTTree.html

Example call to extractTTree using simulateOutbreak() as input, with the expected output showing a transmission tree with 1 sampled individual and 1 total host.

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

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

### extractPTree example with simulateOutbreak

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/extractPTree.html

Example call to extractPTree with a simulated outbreak. The output shows a phylogenetic tree with one sampled individual.

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

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

### Example: plot a simulated ptree

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/plot.ptree.html

Plots a ptree created from a random phylogenetic tree with 5 tips and a date of 2020.

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

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

### plotCTree example with simulateOutbreak

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/plotCTree.html

Example usage of plotCTree with a simulated outbreak. The output note indicates rejection sampling was used once.

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

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

### Example: plotTTree2 with simulated outbreak

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/plotTTree2.html

Example usage of plotTTree2 with a simulated outbreak. The output note indicates rejection sampling was used once.

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

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

### inferTTree example: infer transmission tree from a random phylogenetic tree

Source: https://github.com/xavierdidelot/transphylo/blob/master/man/inferTTree.Rd

Calls inferTTree with a phylogenetic tree generated from a random tree of 5 tips using ape::rtree, dated to 2020, and runs 100 MCMC iterations. This is the minimal example shown in the documentation.

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

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

### plotTTree example with simulated outbreak

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/plotTTree.html

Example usage of plotTTree with a simulated outbreak, extracting the transmission tree and specifying shape=2 and scale=1.

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

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

### Load TransPhylo library in R

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/TransPhylo.html

Load the TransPhylo package into your R session. This should be done after installation to access its functions.

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

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

### Print a simulated ctree object

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/print.ctree.html

Example of printing a simulated ctree object. The output shows the number of rejection sampling iterations, a colored phylogenetic tree, and counts of sampled individuals and total hosts.

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

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

### Convert a simulated phylogenetic tree to an ape phylo object

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/phyloFromPTree.html

Example usage of phyloFromPTree with the output of extractPTree(simulateOutbreak()). The output shows a phylogenetic tree with 8 tips and 7 internal nodes, with tip labels 1 through 8 and branch lengths included.

```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.
```

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

### Convert an ape phylo object to a phylogenetic tree with ptreeFromPhylo

Source: https://github.com/xavierdidelot/transphylo/blob/master/man/ptreeFromPhylo.Rd

Converts an ape phylo object into a phylogenetic tree. The example creates a random tree with 5 tips using ape::rtree and sets the date of the last sample to 2020.

```r
ptreeFromPhylo(ape::rtree(5),2020)
```

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

### Print a ctree object

Source: https://github.com/xavierdidelot/transphylo/blob/master/man/print.ctree.Rd

Prints details of a ctree object. The example calls print on the result of simulateOutbreak(), which returns a ctree object.

```r
print(simulateOutbreak())
```

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

### Print a ptree object

Source: https://github.com/xavierdidelot/transphylo/blob/master/man/print.ptree.Rd

Prints details of a ptree object created from a simulated outbreak. The example uses extractPTree and simulateOutbreak functions.

```r
print(extractPTree(simulateOutbreak()))
```

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

### Print a ttree object from simulated outbreak

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/print.ttree.html

Example usage of print on a ttree object obtained from extractTTree(simulateOutbreak()). The output shows a note about rejection sampling, the transmission tree header, and counts of sampled individuals and total hosts.

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

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

### Simulate an outbreak with default parameters

Source: https://github.com/xavierdidelot/transphylo/blob/master/man/simulateOutbreak.Rd

Runs simulateOutbreak with all default parameters, producing a simulated outbreak with default settings.

```R
simulateOutbreak()
```

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

### Print date of last sample

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-Tutorial.pdf

Prints the date of the last sample from the simulation, which is needed for the second part of the tutorial.

```R
print(max(simu$ctree[,1]))
```

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

### makeTTree

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-RefMan.pdf

Creates a transmission tree.

```APIDOC
## makeTTree

### Description
Creates a transmission tree.

### Usage
```r
makeTTree(...)
```

### Arguments
- **...** - Additional arguments.
```

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

### makeTTree: Simulate a transmission tree

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-RefMan.pdf

Simulates a transmission tree using negative binomial offspring distribution and gamma generation/sampling times. Returns a matrix with infection time, sampling time, and infector for each host.

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

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

### Get date of last sample

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/simulate.html

Returns the date of the last sample in the simulated outbreak, which is needed to use the tree later.

```R
dateLastSample(simu)
```

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

### Set simulation parameters (neg, off.r, w.shape, w.scale, pi)

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-Tutorial.pdf

Specifies the effective population size per day (neg=100/365), the basic reproduction number (off.r=5), the shape and scale of the Gamma distribution for generation and sampling times (w.shape=10, w.scale=0.1), and the sampling density (pi=0.25).

```R
neg=100/365
off.r=5

w.shape=10
w.scale=0.1
pi=0.25
```

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

### Plot a simulated ttree

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/plot.ttree.html

Example usage of plot on a ttree object extracted from a simulated outbreak. This produces a plot of the transmission tree.

```r
plot(extractTTree(simulateOutbreak()))
```

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

### plotCTree: Plot combined phylogenetic and transmission trees

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-RefMan.pdf

Plots both phylogenetic and transmission trees using colors on the phylogeny. The example shows usage with simulateOutbreak().

```R
plotCTree(tree, showLabels = TRUE, cols = NA, maxTime = NA)
```

```R
plotCTree(simulateOutbreak())
```

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

### Extract phylogenetic tree with extractPTree

Source: https://github.com/xavierdidelot/transphylo/blob/master/man/extractPTree.Rd

Extracts the phylogenetic tree from a combined tree object. The example uses the output of simulateOutbreak() as the combined tree input.

```r
extractPTree(simulateOutbreak())
```

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

### Simulate an outbreak with custom parameters

Source: https://github.com/xavierdidelot/transphylo/blob/master/man/simulateOutbreak.Rd

Runs simulateOutbreak with off.r set to 2, dateStartOutbreak set to 2010, and dateT set to 2015, simulating an outbreak with a higher offspring rate and a specific time window.

```R
simulateOutbreak(off.r=2,dateStartOutbreak=2010,dateT=2015)
```

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

### makeCTreeFromPTree

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/makeCtreeFromPTree.html

Documentation for the makeCTreeFromPTree function, which creates a transmission tree compatible with a provided phylogenetic tree.

```APIDOC
## makeCTreeFromPTree

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

### Usage
```r
makeCTreeFromPTree(
  ptree,
  off.r = NA,
  off.p = NA,
  neg = NA,
  pi = NA,
  w.shape = NA,
  w.scale = NA,
  ws.shape = NA,
  ws.scale = NA,
  T = NA,
  optiStart = 0
)
```

### Arguments
- **ptree** - Phylogenetic tree
- **off.r** - First parameter of the negative binomial distribution for offspring number
- **off.p** - Second parameter of the negative binomial distribution for offspring number
- **neg** - The within-host effective population size (Ne) times generation duration (g)
- **pi** - Probability of sampling an infected individual
- **w.shape** - Shape parameter of the Gamma probability density function representing the generation time
- **w.scale** - Scale parameter of the Gamma probability density function representing the generation time
- **ws.shape** - Shape parameter of the Gamma probability density function representing the sampling time
- **ws.scale** - Scale parameter of the Gamma probability density function representing the sampling time
- **T** - Date when process stops (this can be Inf for fully simulated outbreaks)
- **optiStart** - Method used to optimised colored tree (0=none, 1=slow, 2=fast)

### Value
A minimal non-zero probability phylogenetic+transmission tree, or an optimised version if parameters are provided.
```

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

### Load TransPhylo package

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-Tutorial.pdf

Loads the TransPhylo package into the R session. The output 'Loading required package: ape' indicates that the ape package is also loaded.

```R
library(TransPhylo)
```

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

### Compute effective sample size with convertToCoda and effectiveSize

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/infer.html

Converts the MCMC result to a CODA object and computes the effective sample size (ESS) for each parameter. The ESS should be at least 100 for each parameter; the example output shows low ESS values, indicating poor mixing.

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

```r
##       pi      neg    off.r    off.p 
## 6.648218 3.688619 6.650971 0.000000
```

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

### simulateOutbreak()

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/index.html

Simulates an outbreak.

```APIDOC
## simulateOutbreak()

### Description
Simulate an outbreak

```

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

### Load required packages

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/multitree.html

Loads the required R packages for the TransPhylo workflow.

```r
library(ape)
library(TransPhylo)
```

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

### Date of last sample output

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/simulate.html

The date of the last sample as printed by the previous command.

```text
## [1] 2007.964
```

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

### Define simulation parameters

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/simulate.html

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

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

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

### simulateOutbreak function signature

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/simulateOutbreak.html

Function signature for simulateOutbreak with all parameters and defaults.

```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
)
```

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

### Create data frame of parameter estimates from multiple runs

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/multitree.html

Builds a data frame of posterior parameter estimates from three runs (tp1, tp2, tp_multitree) for comparison. The helper get_param_estimates extracts a named parameter from each element of a record list. Because parameters are shared, either element of record_tpj can be used.

```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")))
```

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

### print.ttree()

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/index.html

Prints a ttree object.

```APIDOC
## print.ttree()

### Description
Print function for ttree objects

```

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

### print.ptree()

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/index.html

Prints a ptree object.

```APIDOC
## print.ptree()

### Description
Print function for ptree objects

```

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

### makeTTree

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/makeTTree.html

Function to simulate a transmission tree with parameters for offspring distribution, sampling probability, and generation/sampling time distributions.

```APIDOC
## makeTTree

### Description
Simulate a transmission tree.

### Usage
```r
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.
```

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

### makeCtreeFromPTree

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-RefMan.pdf

Constructs a combined tree from a phylogenetic tree.

```APIDOC
## makeCtreeFromPTree

### Description
Constructs a combined tree from a phylogenetic tree.

### Usage
```r
makeCtreeFromPTree(ptree)
```

### Arguments
- **ptree** - Phylogenetic tree.
```

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

### Build and plot consensus transmission tree

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-Tutorial.pdf

Constructs a consensus transmission tree from the MCMC record and plots it, using the generation time parameters for visualization.

```R
cons=consTTree(record)
plotTTree(cons,w.shape,w.scale)
```

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

### print.ctree()

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/index.html

Prints a ctree object.

```APIDOC
## print.ctree()

### Description
Print function for ctree objects

```

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

### Convert phylogenetic tree to phylo object

Source: https://github.com/xavierdidelot/transphylo/blob/master/man/phyloFromPTree.Rd

Demonstrates the conversion of a simulated outbreak tree into an ape phylo object.

```R
phyloFromPTree(extractPTree(simulateOutbreak()))
```

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

### print(x, ...)

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/print.ptree.html

S3 method for printing ptree objects, which are phylogenetic trees used in TransPhylo.

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

### Description
Print function for ptree objects.

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

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

### Value
Print out details of the ptree.

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

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

### makeCtreeFromPTree: Create transmission tree from phylogenetic tree

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-RefMan.pdf

Creates a transmission tree compatible with a given phylogenetic tree. Optional parameters for offspring distribution, sampling, and generation times can be provided to optimize the tree.

```R
makeCtreeFromPTree(ptree, off.r = NA, off.p = NA, neg = NA, pi = NA,
w.shape = NA, w.scale = NA, ws.shape = NA, ws.scale = NA, T = NA, allowTransPostSamp = NA)
```

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

### Simulate two outbreaks with simulateOutbreak

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/multitree.html

Defines simulation parameters and generates two outbreaks with the same parameters using TransPhylo's simulateOutbreak. The seed is set for reproducibility.

```r
neg <- 100/365
off.r <- 1.5
w.shape <- 10
w.scale <- 0.1
ws.shape <- w.shape
ws.scale <- w.scale
pi <- 0.8

set.seed(1234)
simu1 <- simulateOutbreak(neg=neg, off.r=off.r, pi=pi, w.shape=w.shape,
                         w.scale=w.scale, dateStartOutbreak=2000,dateT=2005)
simu2 <- simulateOutbreak(neg=neg, off.r=off.r, pi=pi, w.shape=w.shape,
                         w.scale=w.scale, dateStartOutbreak=2000,dateT=2005)
```

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

### Run inferTTree with MCMC iterations

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/inferTTree.html

Runs the inferTTree function on a phylogenetic tree generated with ape::rtree(5) and a date of 2020, using 100 MCMC iterations. The output shows a progress bar with percentages from 0% to 29% as the MCMC runs.

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

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

### print(x, ...)

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/print.ctree.html

S3 method for ctree objects that prints details of the colored phylogenetic tree, such as the number of sampled individuals and total number of hosts.

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

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

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

### Arguments
- **x** - Object of class ctree, i.e., a colored phylogenetic tree.
- **...** - 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
```
```

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

### Plot generation time distribution with getGenerationTimeDist

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/infer.html

Plots the distribution of realised generation times from the MCMC result.

```r
a=getGenerationTimeDist(res,show.plot = T)
```

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

### Find and plot medoid tree with medTTree

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/infer.html

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

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

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

### getOffspringDist()

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/index.html

Extracts and returns the offspring distribution for specified sampled cases.

```APIDOC
## getOffspringDist()

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

```

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

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

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/getOffspringDist.html

Extracts and returns the offspring distribution of given sampled case(s) from MCMC output produced by inferTTree. The function takes the MCMC record, a burnin proportion, the case(s) of interest, and an optional plotting flag.

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

### Description
Extract and return offspring distribution of given sampled case(s) from MCMC output produced by inferTTree.

### Function Signature
```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 is 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 is FALSE.

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

```

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

### S3 method signature for print.ptree

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/print.ptree.html

Usage signature for the S3 method print for ptree objects. The method takes an object of class ptree and optional additional arguments.

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

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

### Run MCMC inference with inferTTree

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/infer.html

Runs the MCMC procedure to infer the transmission tree from the phylogenetic tree, using 1000 iterations and the specified generation time and observation stop date.

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

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

### S3 method signature for print.ctree

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/print.ctree.html

S3 method signature for printing ctree objects. The x argument is the ctree object, and ... passes additional parameters.

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

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

### Set generation time Gamma parameters

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/infer.html

Sets the shape and scale parameters of the Gamma distribution representing the generation time. These values match the simulation tutorial; for your own data, set them appropriately for your pathogen.

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

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

### simulateOutbreak usage

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-RefMan.pdf

Usage signature for the simulateOutbreak function, which simulates an outbreak with configurable parameters for offspring distribution, sampling, generation time, and outbreak timing.

```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 = w.shape,
ws.scale = w.scale, dateStartOutbreak = 2000, dateT = Inf)
```

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

### Plot colored phylogenetic tree with plotCTree()

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-Tutorial.pdf

Visualizes the simulated colored phylogenetic tree, where each host is represented by a unique color.

```R
plotCTree(simu)
```

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

### summary.resTransPhylo(object, ...)

Source: https://github.com/xavierdidelot/transphylo/blob/master/man/summary.resTransPhylo.Rd

Prints a summary of a resTransPhylo object, which is the output from inferTTree. Additional arguments are passed to print.phylo.

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

### Description
Summary function for resTransPhylo objects, printing details of TransPhylo results.

### Usage
\method{summary}{resTransPhylo}(object, ...)

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

### Value
Print out details of TransPhylo results.

```

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

### Simulate an outbreak with simulateOutbreak

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/articles/simulate.html

Runs the outbreak simulation from 2005 to 2008 using the previously defined parameters.

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

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

### probTTree usage

Source: https://github.com/xavierdidelot/transphylo/wiki/TransPhylo-RefMan.pdf

Usage signature for the probTTree function, which computes the probability of a transmission tree given parameters for the negative binomial offspring distribution, sampling probability, generation time, and sampling time distributions.

```R
probTTree(ttree, off.r, off.p, pi, w.shape, w.scale, ws.shape, ws.scale, dateT,
allowTransPostSamp)
```

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

### S3 method signature for print.ttree

Source: https://github.com/xavierdidelot/transphylo/blob/master/docs/reference/print.ttree.html

Signature for the S3 print method for objects of class ttree, which represents a transmission tree. Additional parameters are passed on.

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