From 6306b219ed41d4c305690a708254789cad9cdbfd Mon Sep 17 00:00:00 2001
From: sdgamboa <samuel.gamboa.tuz@gmail.com>
Date: Thu, 11 Jan 2024 11:52:25 -0500
Subject: [PATCH] Add argument for removing asr when importing bp with
 importBugphyzz.

And filtering "all" for validation data.
---
 R/bugphyzz.R          | 12 +++++++++---
 man/importBugphyzz.Rd | 11 +++++++++--
 2 files changed, 18 insertions(+), 5 deletions(-)

diff --git a/R/bugphyzz.R b/R/bugphyzz.R
index 6709ef4e..86a7541b 100644
--- a/R/bugphyzz.R
+++ b/R/bugphyzz.R
@@ -7,7 +7,8 @@
 #' (current file on the GitHub repo waldronlab/bugphyzzExports).
 #' @param force_download Logical value. Force a fresh download of the data or
 #' use the one stored in the cache (if available). Default is FALSE.
-#' @param v Validation value. Deafult 0.5.
+#' @param v Validation value. Default 0.5.
+#' @param remove_asr Logical. Default is TRUE.
 #'
 #' @return A data.frame.
 #' @export
@@ -17,7 +18,7 @@
 #' bp <- importBugphyzz()
 #' names(bp)
 #'
-importBugphyzz <- function(version = 'devel', force_download = FALSE, v = 0.5) {
+importBugphyzz <- function(version = 'devel', force_download = FALSE, v = 0.5, remove_asr = TRUE) {
   types <- c("multistate", "binary", "numeric")
   urls <- paste0(
     "https://github.com/waldronlab/bugphyzzExports/raw/sdgamboa/phylo/bugphyzz_",
@@ -41,7 +42,8 @@ importBugphyzz <- function(version = 'devel', force_download = FALSE, v = 0.5) {
   output <- purrr::list_flatten(output)
   names(output) <- purrr::map_chr(output, ~ unique(.x$Attribute_group))
   val <- .validationData() |>
-    dplyr::select(.data$physiology, .data$attribute, .data$value)
+    dplyr::select(.data$physiology, .data$attribute, .data$value) |>
+    dplyr::filter(.data$rank == "all")
 
   output <- purrr::map(output, ~ {
     attr_type <- unique(.x$Attribute_type)
@@ -57,6 +59,10 @@ importBugphyzz <- function(version = 'devel', force_download = FALSE, v = 0.5) {
        !(.data$value < v & .data$Evidence == "asr")
       )
   })
+
+  if (remove_asr) {
+    output <- purrr::map(output, ~ dplyr::filter(.x, .data$Evidence != "asr"))
+  }
   return(output)
 }
 
diff --git a/man/importBugphyzz.Rd b/man/importBugphyzz.Rd
index 8eba5c31..4f408a10 100644
--- a/man/importBugphyzz.Rd
+++ b/man/importBugphyzz.Rd
@@ -4,7 +4,12 @@
 \alias{importBugphyzz}
 \title{Import bugphyzz}
 \usage{
-importBugphyzz(version = "devel", force_download = FALSE, v = 0.5)
+importBugphyzz(
+  version = "devel",
+  force_download = FALSE,
+  v = 0.5,
+  remove_asr = TRUE
+)
 }
 \arguments{
 \item{version}{Character string. The version to download. Default is 'devel'
@@ -13,7 +18,9 @@ importBugphyzz(version = "devel", force_download = FALSE, v = 0.5)
 \item{force_download}{Logical value. Force a fresh download of the data or
 use the one stored in the cache (if available). Default is FALSE.}
 
-\item{v}{Validation value. Deafult 0.5.}
+\item{v}{Validation value. Default 0.5.}
+
+\item{remove_asr}{Logical. Default is TRUE.}
 }
 \value{
 A data.frame.