From 52c6618e4d1233ec3700aba47cdb7fa1c064ca42 Mon Sep 17 00:00:00 2001 From: Thomas Guillerme Date: Mon, 5 Aug 2024 11:48:37 +0100 Subject: [PATCH 1/2] Update 03_specific-tutorials.Rmd --- inst/gitbook/03_specific-tutorials.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/inst/gitbook/03_specific-tutorials.Rmd b/inst/gitbook/03_specific-tutorials.Rmd index 7d7220b7..77c2f957 100755 --- a/inst/gitbook/03_specific-tutorials.Rmd +++ b/inst/gitbook/03_specific-tutorials.Rmd @@ -1497,7 +1497,7 @@ This can be done on `dispRity` objects using the `adonis.dispRity` wrapper funct Basically, this function takes the exact same arguments as `adonis` and a `dispRity` object for data and performs a PERMANOVA based on the distance matrix of the multidimensional space (unless the multidimensional space was already defined as a distance matrix). The `adonis.dispRity` function uses the information from the `dispRity` object to generate default formulas: - * If the object contains customised subsets, it applies the default formula `matrix ~ group` testing the effect of `group` as a predictor on `matrix` (called from the `dispRity` object as `data$matrix` see [`dispRitu` object details](#The-dispRity-object-content)) + * If the object contains customised subsets, it applies the default formula `matrix ~ group` testing the effect of `group` as a predictor on `matrix` (called from the `dispRity` object as `data$matrix` see [`dispRity` object details](#The-dispRity-object-content)) * If the object contains time subsets, it applies the default formula `matrix ~ time` testing the effect of `time` as a predictor (were the different levels of `time` are the different time slices/bins) ```{r} From e5711ad4e44c7eb11eb2123bdff74879b609086b Mon Sep 17 00:00:00 2001 From: Thomas Guillerme Date: Tue, 13 Aug 2024 15:13:56 +0100 Subject: [PATCH 2/2] Update TODO.md --- TODO.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/TODO.md b/TODO.md index e0a8de98..b92d2ae9 100755 --- a/TODO.md +++ b/TODO.md @@ -26,6 +26,15 @@ - [ ] update all the `dispRity` functions that have a `check.dist.matrix` function to use a helper +## Update dtt.dispRity to use the treats pipeline + + - [ ] use `treats::map.traits` instead of `geiger::sim.char` for simulating the character. + - [ ] update the `alternative` argument to use the rank envelope test. + +> for `treats`: check the portability of `geiger::ratematrix`, `geiger::fitContinuous`, `geiger::fitDiscrete` (`?geiger::sim.char`) and try implementing them in `treats`? + + + ## Potential BAT.fun if works with RAM.help * New interface for the `BAT` package with new generic metric function `BAT.metric`. This function allows to use any metric from the `BAT` function as a metric for `dispRity` using the synthax: `dispRity(data, metric = BAT.metric, BAT.fun = "name", ...)`