From 416db218ab936111878bf1d6dc56f6603688d5c7 Mon Sep 17 00:00:00 2001 From: William Gearty Date: Mon, 9 Dec 2024 13:29:15 -0500 Subject: [PATCH] Add corHMM and slouch --- Phylogenetics.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/Phylogenetics.md b/Phylogenetics.md index 157a025..f5b5b26 100644 --- a/Phylogenetics.md +++ b/Phylogenetics.md @@ -160,13 +160,14 @@ Packages within the task view fall within one or more of the following task cate - `r pkg("ape")`, `r pkg("picante")`, or `r pkg("caper")` can be used to calculate independent contrasts for continuous characters. `r pkg("caper")` also implements the brunch and crunch algorithms. - `r pkg("geiger")` can be used to perform analyses of discrete trait evolution, including models of unequal rates or rates changing at a given instant of time, as well as Pagel's transformations. +- `r pkg("corHMM")` can be used to fit hidden Markov models of discrete character evolution which allow different transition rate classes on different portions of a phylogeny. - `r pkg("phytools")` can be used to fit multiple models for both discrete and continuous character evolution. For instance, `r pkg("phytools")` fits a Brownian model with and without rate heterogeneity specified as regimes fixed by the user or estimated from the data itself. `r pkg("phytools")` can also be used to fit a range of discrete character evolution models, such as the the extended M*k* model, a heterogenous M*k* model with regime shifts, a polymorphic trait evolution model, a hidden-rates model, the threshold model, and others. - `r pkg("geiger")`, `r pkg("paleotree")`, and `r pkg("motmot")` can be used to fit Brownian motion models. - `r github("cran/RBrownie")` can fit multiple-rate Brownian motion models. - `r pkg("geiger")` and `r pkg("OUwie")` can be used to investigate deviations from Brownian motion. - `r pkg("mvMORPH")` can fit Brownian motion, early burst, ACDC, OU, and shift models to univariate or multivariate data. - `r github("gilles-didier/cauphy")` models trait distribution using the Cauchy Process. -- `r pkg("geiger")`, `r pkg("motmot")`, `r pkg("ouch")`, `r pkg("surface")`, and `r pkg("OUwie")` can be used to fit Ornstein-Uhlenbeck (OU) models. `r pkg("ouch")` can implement models with multiple means, `r pkg("surface")` can implement models with multiple means using stepwise AIC, and `r pkg("OUwie")` can implement models with multiple means, rates, and attraction values. Also see `r github("mongiardino/extendedSurface")` which combines the functionality of `r pkg("surface")` and `r pkg("OUwie")`. +- `r pkg("geiger")`, `r pkg("motmot")`, `r pkg("ouch")`, `r pkg("slouch")`, `r pkg("surface")`, and `r pkg("OUwie")` can be used to fit Ornstein-Uhlenbeck (OU) models. `r pkg("ouch")` and `r pkg("slouch")` can implement models with multiple means, `r pkg("surface")` can implement models with multiple means using stepwise AIC, `r pkg("slouch")` can implement models with continuous covariates, and `r pkg("OUwie")` can implement models with multiple means, rates, and attraction values. Also see `r github("mongiardino/extendedSurface")` which combines the functionality of `r pkg("surface")` and `r pkg("OUwie")`. - `r pkg("motmot")` can be used to fit continuous models that change rate or mode at specific time(s). - `r pkg("Rphylopars")` can be used to fit continuous models such as those described above to datasets with multiple observations per species and/or missing data. - `r pkg("geiger")` implements ANOVA's and MANOVA's in a phylogenetic context.