Man pages for sergeitarasov/PhenoTraits
Trait modeling on phylogenies
| addTipChars | Title Add chars to plot |
| birth_Des | Title Find minimal edge pattern node for birth-death |
| comb2matrices | Combining two matrices |
| data.sim | Tree and two traits for running Sinba |
| edgePatRecode | Title Recode edge props given patternList() |
| ExpMat_C | Matrix Exponential (scalar implementation) |
| getEdgeScenarios | Title Create edge scenarios |
| getPhyloCTMC_distr | Title Calculate analtical distribution of site patterns at... |
| infer2branchTrees | Title Run batch inference on two-branch tree |
| init_char_matrix | Initialize binary matrices |
| iter_new_Qcom | Title Create new Qcom by merging paramter estimates that are... |
| likelihood_Sinba | Title Calculate likilehood for Sinba Model (coorelated... |
| mk_OneRate | Title |
| mk_Pindv | Title |
| mk_Qcom | Title |
| mk_QcomPartitions | Title |
| mk_QcomPartitions8 | Title Get all parametrizations of Q with 8 elements |
| mk_Qindv | Title |
| mk_QindvZero | Title |
| mk_RatePars | Title |
| patternList | Title Get a table of edge scenarios and their ids |
| print.edge_scenarios | Title Print edge scenarios object |
| print.sinba | Title Print sinba object |
| runSinba | Title Infer corrleated evolution of two characters using... |
| simDarwin | Title Simulate Darwin Scenario |
| simulate_ExpLinLn | Title Simulate a two-branch tree with characters |
| simUnrepBurst | Title Simulate Unreolicated Burst |
| vExpMat_C | Matrix Exponential (vector implementation) |
