From 31d38dfa49b8beeebc9d897cfaa74208b4e4d2b3 Mon Sep 17 00:00:00 2001
From: sdgamboa <samuel.gamboa.tuz@gmail.com>
Date: Thu, 28 Sep 2023 15:18:16 -0400
Subject: [PATCH] add function for converting confidence_in_curation to factor

---
 NAMESPACE       |  1 +
 R/utils.R       | 16 ++++++++++++++++
 man/conf2Fct.Rd | 18 ++++++++++++++++++
 3 files changed, 35 insertions(+)
 create mode 100644 man/conf2Fct.Rd

diff --git a/NAMESPACE b/NAMESPACE
index 1743ac8..486e108 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,6 +14,7 @@ export(calcParentScores)
 export(chooseColVal)
 export(classif2Table)
 export(cleanNode)
+export(conf2Fct)
 export(fillNAs)
 export(freq2Scores)
 export(getAgreements)
diff --git a/R/utils.R b/R/utils.R
index 4a97d22..1a8b569 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -41,6 +41,22 @@ scores2Freq <- function(x) {
     )
 }
 
+
+#' Confidence in curation to factor
+#'
+#' \code{conf2Fct} converts a vector from the Confidence_in_curation
+#' column in a bugphyzz dataset to a factor.
+#'
+#' @param x A character vector.
+#'
+#' @return A factor.
+#'
+#' @export
+#'
+conf2Fct <- function(x) {
+    factor(x, levels = c('low', 'medium', 'high'), ordered = TRUE)
+}
+
 ## Function with valid ranks for taxa
 .validRanks <- function() {
     c('strain', 'species', 'genus', 'family', 'order', 'class', 'phylum',
diff --git a/man/conf2Fct.Rd b/man/conf2Fct.Rd
new file mode 100644
index 0000000..c4ba097
--- /dev/null
+++ b/man/conf2Fct.Rd
@@ -0,0 +1,18 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{conf2Fct}
+\alias{conf2Fct}
+\title{Confidence in curation to factor}
+\usage{
+conf2Fct(x)
+}
+\arguments{
+\item{x}{A character vector.}
+}
+\value{
+A factor.
+}
+\description{
+\code{conf2Fct} converts a vector from the Confidence_in_curation
+column in a bugphyzz dataset to a factor.
+}