Merge branch 'main' of github.com:waldronlab/taxPPro

NAMESPACE

@@ -17,5 +17,6 @@ export(inh2)
 export(ltp)
 export(ltp3)
 export(mpa)
+export(roundDec)
 export(scores2Freq)
 export(taxPool)

R/utils.R

@@ -130,7 +130,7 @@ myFun <- function(x, adjF = 0.1) {
 
 #' Clean node
 #'
-#' {cleanNode} deletes the `attribute_tbl` slot in a data.tree node.
+#' \code{cleanNode} deletes the `attribute_tbl` slot in a data.tree node.
 #'
 #' @param node A node in a data.tree object.
 #'
@@ -140,3 +140,20 @@ myFun <- function(x, adjF = 0.1) {
 cleanNode <- function(node) {
     node$attribute_tbl <- NULL
 }
+
+#' Round up to nearest decimal
+#'
+#' \code{roundDec} rounds up to next decimal. Meant to be used for
+#' establishing a threhold for filtering attributes.
+#' @param A character vector (of attributes).
+#' @return A double.
+#' @export
+#'
+roundDec <- function(x) {
+    n <- x |>
+        unique() |>
+        {\(y) y[!is.na(y)]}() |>
+        length()
+    ceiling(((1 / n) + 1e-06) * 10) / 10
+}
+

vignettes/articles/internal_nodes.Rmd

@@ -172,6 +172,61 @@ plot(ace3, args.plotTree = list(direction = "upwards"))
 ```
 
 
+A single value
+
+```{r}
+mat <- matrix(rep(0, (Ntip(t3) * 2)), ncol = 2)
+colnames(mat) <- LETTERS[1:2]
+rownames(mat) <- t3$tip.label
+
+mat[] <- 0.5
+mat[grep('Macaca_gn1', rownames(mat)),] <- c(1, 0)
+
+
+fitX <- fitMk(
+    tree = t3, x = mat, model = myMod, pi = myPi, lik.func = "pruning",
+    logscale = TRUE
+)
+aceX <- ancr(fitX, tips=TRUE)
+plot(aceX, args.plotTree = list(direction = "upwards"))
+```
+
+
+```{r}
+mat2 <- matrix(rep(0, (Ntip(t3) * 2)), ncol = 2)
+colnames(mat2) <- LETTERS[1:2]
+rownames(mat2) <- t3$tip.label
+
+mat2[,1] <- 0
+mat2[,2] <- 1
+mat2[grep('Macaca_gn1', rownames(mat2)),] <- c(1, 0)
+mat2[grep('Cercopithecus_petaurista', rownames(mat2)),] <- c(1, 0)
+
+
+fitY <- fitMk(
+    tree = t3, x = mat2, model = 'ER', pi = myPi, lik.func = "pruning",
+    logscale = TRUE
+)
+aceY <- ancr(fitY, tips=TRUE)
+plot(aceY, args.plotTree = list(direction = "upwards"))
+```
+
+
+```{r}
+mat2 <- matrix(rep(0, (Ntip(t3) * 2)), ncol = 2)
+colnames(mat2) <- LETTERS[1:2]
+rownames(mat2) <- t3$tip.label
+mat2[] <- 0.5
+mat2[grep('Macaca_gn1', rownames(mat2)),] <- c(1, 0)
+mat2[grep('Cercopithecus_petaurista', rownames(mat2)),] <- c(0, 1)
+
+fitY <- fitMk(
+    tree = t3, x = mat2, model = 'ARD', pi = myPi, lik.func = "pruning",
+    logscale = TRUE
+)
+aceY <- ancr(fitY, tips=TRUE)
+plot(aceY, args.plotTree = list(direction = "upwards"))
+```
 
 # Session information