Correct calculation of numbers of mutations in plotPhyloTrans (counting haplotypes according to correct frequency of occurrence)
phybreak 0.5.1
Minor changes
Added possibility to show the numbers of mutations along the phylogenetic minitrees with plotPhyloTrans
BUG FIXES
shows all transmission links in plotPhyloTrans
phybreak 0.5.0
Major changes
Added plotting function plotPhyloTrans to plot transmission trees with phylogenetic minitrees in each host
phybreak 0.4.2
BUG FIXES
make burnin_phybreak and sample_phybreak work with old phybreak objects (without distance model)
phybreak 0.4.1
BUG FIXES
get_bottlenecks now also works if there are multiple samples per host
phybreak 0.4.0
Major changes
Added distance models, to work with location data and a distance kernel
three distance models, two for euclidean distance (power and exponential), one to work with a genetic distance matrix (poisson)
simulation with the euclidean distance models, analysis with all three (see help(phybreak) for more info)
phybreak 0.3.2
Minor changes
Removed the possibility to simulate obkData-objects
Updata documentation with some functions
phybreak 0.3.1
Minor changes
Removed the possibility of using obkData-objects as input data, because the supporting package OutbreakTools has been removed from CRAN
phybreak 0.3.0
Major changes
Added three within-host models allowing for wide transmission bottlenecks, i.e. bottlenecks with more than 1 lineage:
Change in variable and sample slots of phybreak objects, with separate infector and inftime entries for the transmission tree
More within-host parameters in the parameter slot of phybreak objects
Simulation and analysis with the new models
See help(phybreak) for a description of the new models
Effective sample size calculation with new function ESS
Applied to factor objects, it applies a method similar to the approximate ESS for phylogenetic tree (Lanfaer et al, 2016)
Applied to phybreak objects, it applies ESS.factor for the infectors, and coda::effectiveSize for all other parameters and variables
See help(ESS) for more information
More generic functions working with phybreak objects: c, print, quantile, thin
Dots in function names replaced by underscores
New update protocol for proposing the within-host minitrees. In the "classic" protocol, each proposal of a new infection time and infector for a host included a complete resampling of its minitree. In the new protocol (which is now the default in "burnin_phybreak" and "sample_phybreak") only new coalescent times are proposed, but the topology is not. This is now followed by proposals in which the sampling tips are one by one removed and reattached (by simulation).
Minor changes
Function infectorsets can produce matrix with support for all host-infector pairs
New arguments in "burnin_phybreak" and "sample_phybreak":
classic: to choose the proportion of tree updates with the classic protocol instead of the new default protocol (see above)
parameter_frequency: option to sample the model parameters more frequently than each host in the transmission tree
status_interval: the time interval between the on-screen status updates of the mcmc-chain
function get_bottlenecks to obtain the number of lineages leaving each host to its infector
BUG FIXES
Fixed bug in transtree-method "edmonds" that could occur with much uncertainty in the posterior trees
phybreak 0.2.1
BUG FIXES
Fixed bug in matching samples to hosts in phybreakdata (#4 reported by Gerry Tonkin-Hill)
phybreak 0.2.0
Major changes
Datasets added
Vignette phybreak_intro added
Use more samples per host, with changes in data input, the phybreak object structure, and plotting
Added mcmc-update steps for only the within-host phylogenetic minitree topology (not used by default)
Added transmission tree plotting function plotTrans
Data entry through new S3-class phybreakdata
Simulation with sim.phybreak results in phybreakdata-object, that can directly be plotted
MCMC progress shown on screen (10 sec intervals)
Minor changes
Faster simulation and phybreak construction with long sequences.
Automatic calculation of initial value for mu
Reference date in phybreak object (d-slot) referring to t = 0, used for transtree and plot
Minor changes in get.phybreak functions
BUG FIXES
Fixed bug in transtree with Edmonds method (index case could have been incorrect)
Correct on-screen log-likelihood during MCMC
Bug in sim.phybreak giving error with option output.class = "obkData"
phybreak 0.1.1
BUG FIXES
Solves issue with irreconcilable MCC trees in phylo-class vs table-form (#1) (reported by Mark Schultz)