Skip to content
Snippets Groups Projects

Repository graph

You can move around the graph by using the arrow keys.
Select Git revision
  • master default protected
1 result
Created with Raphaël 2.2.09May7Feb20Dec26Aug1612111012Nov1020Sep10corrected hypergeom of coealesecnce parameter + grouping evals and performings + creating temp node instead of poping nodes directlymastermasteradded deme compartment + root.edge + warning if verbose of how many leaves are compared to as expected if differentnew compartment attribute -> isDeme (required when summing size of deme compartments after rooting) + warning with name of compartment now addedupdate citationfixed warnings when installing TiPS at CRAN du to new clang-16 compiler + updated doicitation addedupdate readmecorrected output traj typo + now can read traj outfile if simulating trajectorycorrect method typo optioonfinalizerR/generator.Rcorrect math mode in README of GitLabtest for latex styletest for latex styletest for latex stylenew option : add seed to simulate phylogenies + update vignette + option to write traj and tree output filesbetter function desc for man descunit tests for traj and tree simulationfile with deterministic trajectory for unit test of traj exactitutde by comparing stoch. vs determ.new options : seed (if 0 then generate if randomly) + output file name + format (newick or nexus) ; Need to handle the trajectory file situationnow possibility to write directly trajectory in tab delimited file (file name given by user with argument outFile) -> less stored in memory ; the R object results is still same but instead of traj in list we now have outFile informing where it got saved ; hence if tree simulation needed, the function tree_sim can read.table the outFilenew method to check that each compartment's size is not negative in case of tau-leap algo ; if it's the case, warning for a smaller tau value and simulation is ended ; NOTE : need to implement a modified poisson tau-leaping version (Cao et al 2005)require testthat package + new version comingcorrect sample case when defining the number of resampling (- become +)Message number of unrooted nodes if case and verbose =Thandle birth reactionsexposants problem : now can handle if decimal value after ^added new options : msaIt => the number of maximum iterations (by default 10) to compute deltaT by GDA & msaTau => user-defined threshold of the deltaT from wich MSA switches from GDA to GTA ; now can handle exposants by converting the X^n to pow(X,n) in Rcpp codecorrect url for R packageadd citation for article + URLs for repos and issus bugreportsadd option to specify seed for reproducible simulationscorect path to imagescorect path to imagesNew readme from vignetteAdd readme : vignette to github mdlast updates for package structurehandling warning messagesadding doc for each functionremove useless filesInitial commit