From 7ce011a7adac8f823a3ca5d4b345868d0925f521 Mon Sep 17 00:00:00 2001
From: mjanuario <januario@umich.edu>
Date: Thu, 6 Jul 2023 16:55:52 -0400
Subject: [PATCH] adding binarize

---
 R/binarize.R | 58 ++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)
 create mode 100644 R/binarize.R

diff --git a/R/binarize.R b/R/binarize.R
new file mode 100644
index 0000000..529a881
--- /dev/null
+++ b/R/binarize.R
@@ -0,0 +1,58 @@
+#' Bin true occurrences into geologic intervals
+#'
+#' Given the output of \code{sample.clade(..., returnTrue = FALSE)}, returns 
+#' the occurrence counts in each bin (i.e., the same as 
+#' \code{sample.clade(..., returnTrue = TRUE)}). This helps to trace 
+#' perfect parallels between both output formats of \code{sample.clade()}.
+#'
+#' @param fossil A \code{data.frame} exactly as returned 
+#' by sample.clade(..., returnTrue = FALSE). See \code{help(sample.clade)} 
+#' for details.
+#'
+#' @param bins A vector of time intervals corresponding to geological time 
+#' ranges.
+#'
+#' @return A \code{data.frame} exactly as returned 
+#' by sample.clade(..., returnTrue = TRUE). See \code{help(sample.clade)} 
+#' for details.
+#'
+#' @author Matheus Januario and Bruno do Rosario Petrucci
+#'
+#' @details This function helps a user to bins "true occurrences" directly into
+#'  binned occurrences, allowing for comparisons among "perfectly known" fossils
+#'  records and records that have a certain resolution (given by the \code{bins}
+#'    inputted).
+#'
+#' @examples
+#'
+#' # run a birth-death simulation:
+#' sim= bd.sim(n0 = 1, lambda = .1, mu = .05, tMax = 50)
+#' 
+#' # choose bins
+#' bins = seq(0,50,by=1)
+#' 
+#' # generate "true" fossil occurrences
+#' fsls1 = sample.clade(sim, rho = 1, tMax=50, returnTrue = T)
+#' 
+#' # bin the true occurrences:
+#' fsls2 = binarize(fsls1, bins)
+#' 
+#' @name binarize
+#' @rdname binarize
+#' @export
+
+binarize=function(fossil, bins){
+
+  bins = sort(bins, decreasing = T)
+
+  res=fossil[-ncol(fossil)]
+  res$MaxT=NA
+  res$MinT=NA
+  for(i in 1:nrow(fossil)){
+    id = hist(fossil$SampT[i], breaks=bins, plot=FALSE)$counts
+    res$MaxT[i]= bins[which(id==1)+1]
+    res$MinT[i]= bins[which(id==1)]
+  }
+  return(res) 
+}
+