From 85c412f347d2fc28a874f7099d0da1a8def6b3fb Mon Sep 17 00:00:00 2001
From: Waldir Leoncio <w.l.netto@medisin.uio.no>
Date: Wed, 16 Nov 2022 10:23:57 +0100
Subject: [PATCH] Translated `testaaKoordinaatit()` (#3)

---
 NAMESPACE                 |  1 +
 R/testaaKoordinaatit.R    | 77 +++++++++++++++++++++++++++++++++++++++
 man/testaaKoordinaatit.Rd | 19 ++++++++++
 3 files changed, 97 insertions(+)
 create mode 100644 R/testaaKoordinaatit.R
 create mode 100644 man/testaaKoordinaatit.Rd

diff --git a/NAMESPACE b/NAMESPACE
index aff9bfb..3b8b822 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -35,6 +35,7 @@ export(simulateIndividuals)
 export(simuloiAlleeli)
 export(suoritaMuutos)
 export(takeLine)
+export(testaaKoordinaatit)
 export(testaaOnkoKunnollinenBapsData)
 export(testaaPop)
 export(writeMixtureInfo)
diff --git a/R/testaaKoordinaatit.R b/R/testaaKoordinaatit.R
new file mode 100644
index 0000000..d56cd6e
--- /dev/null
+++ b/R/testaaKoordinaatit.R
@@ -0,0 +1,77 @@
+#' @title Test the coordinates
+#' @param ninds ninds
+#' @param coordinates coordinates
+#' @param interactive prompt user for relevant questions during execution
+#' @return a list of defectives ("viallinen") and coordinates
+#' @export
+testaaKoordinaatit <- function(ninds, coordinates, interactive = TRUE) {
+ # Testaa onko koordinaatit kunnollisia.
+ # modified by Lu Cheng, 05.12.2012
+  viallinen <- 1
+  if (any(sapply(coordinates, class) != "numeric")) {
+    warning('Coordinates are not numerical!')
+    return()
+  }
+  oikeanKokoinen <- size(coordinates, 1) == ninds & (size(coordinates, 2) == 2)
+  if (!oikeanKokoinen) {
+    warning('Wrong coordinates dimension!')
+    return()
+  }
+  posstr <- sapply(coordinates, function(x) sprintf('%.10f', x))
+  posstr <- gsub('\\.0.+', '.', posstr)
+  posstr <- matrix(posstr, nrow = nrow(coordinates))
+  uni1 <- unique(posstr[, 1])
+  uni2 <- unique(posstr[, 2])
+  posstr_new <- posstr
+  if (length(uni1) == ninds && length(uni2) == ninds) {
+    viallinen <- 0
+    return(list(viallinen = viallinen, coordinates = coordinates))
+  } else {
+    ans <- "Yes"
+    if (interactive) {
+      ans <- questdlg(
+        'Input coordinates are not unique. Do you want to make them unique?',
+        'coordinates NOT unique', c('Yes', 'No'), 'Yes'
+      )
+    }
+    if (strcmp(tolower(ans), 'no')) {
+      warning('Coordinates are not unique!')
+      return(list(viallinen = viallinen, coordinates = coordinates))
+    }
+  }
+
+  for (i in 1:length(uni1)) {
+    tmpinds <- find(posstr[, 1] %in% uni1[i])
+    tmpNinds <- length(tmpinds)
+    if (tmpNinds == 1) {
+      next
+    }
+    if (tmpNinds >= 100) stop("Assertion failed. tmpNinds not < 100")
+    tmparr <- round(seq(0, 99, length.out = tmpNinds))
+    tmparr <- tmparr[sample(tmpNinds)]
+    for (j in 1:tmpNinds) {
+      posstr_new[tmpinds[j], 1] <- sprintf('%s%02d', posstr[tmpinds[j], 1], tmparr[j])
+    }
+  }
+
+  for (i in 1:length(uni2)) {
+    tmpinds <- find(posstr[, 2] %in% uni2[i])
+    tmpNinds <- length(tmpinds)
+    if (tmpNinds == 1) next
+    if (tmpNinds >= 100) stop("Assertion failed. tmpNinds not < 100")
+    tmparr <- round(seq(0, 99, length.out = tmpNinds))
+    tmparr <- tmparr[sample(tmpNinds)]
+      for (j in 1:tmpNinds) {
+          posstr_new[tmpinds[j], 2] <- sprintf('%s%02d', posstr[tmpinds[j], 2], tmparr[j])
+      }
+  }
+  coordinates <- matrix(sapply(posstr_new, as.double), ncol = 2)
+  uni1 <- unique(coordinates[, 1])
+  uni2 <- unique(coordinates[, 2])
+  if (length(uni1 )== ninds && length(uni2) == ninds) {
+      viallinen <- 0
+  } else {
+      warning('Can not make coordinates unique!')
+  }
+  return(list(viallinen = viallinen, coordinates = coordinates))
+}
diff --git a/man/testaaKoordinaatit.Rd b/man/testaaKoordinaatit.Rd
new file mode 100644
index 0000000..719f5c2
--- /dev/null
+++ b/man/testaaKoordinaatit.Rd
@@ -0,0 +1,19 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/testaaKoordinaatit.R
+\name{testaaKoordinaatit}
+\alias{testaaKoordinaatit}
+\title{Test the coordinates}
+\usage{
+testaaKoordinaatit(ninds, coordinates)
+}
+\arguments{
+\item{ninds}{ninds}
+
+\item{coordinates}{coordinates}
+}
+\value{
+a list of defectives ("viallinen") and coordinates
+}
+\description{
+Test the coordinates
+}