From 3d6bd053a899884660d4bdb34ef8044e64694fe9 Mon Sep 17 00:00:00 2001
From: leifeld <philip.leifeld@essex.ac.uk>
Date: Sat, 10 Feb 2024 10:05:35 +0000
Subject: [PATCH] Fixed as.POSIXct origin bug in phase transitions functions

---
 rDNA/rDNA/DESCRIPTION |  2 +-
 rDNA/rDNA/R/rDNA.R    | 10 +++++-----
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/rDNA/rDNA/DESCRIPTION b/rDNA/rDNA/DESCRIPTION
index 504ace0b..22068348 100755
--- a/rDNA/rDNA/DESCRIPTION
+++ b/rDNA/rDNA/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rDNA
 Version: 3.0.11
-Date: 2024-02-04
+Date: 2024-02-10
 Title: Discourse Network Analysis in R
 Authors@R: 
   c(person(given = "Philip",
diff --git a/rDNA/rDNA/R/rDNA.R b/rDNA/rDNA/R/rDNA.R
index 8703bb2e..bf5d6848 100644
--- a/rDNA/rDNA/R/rDNA.R
+++ b/rDNA/rDNA/R/rDNA.R
@@ -4882,7 +4882,7 @@ dna_phaseTransitions <- function(distanceMethod = "absdiff",
 
   # temporal embedding via MDS
   if (!requireNamespace("MASS", quietly = TRUE)) {
-    mem <- data.frame("date" = as.POSIXct(dates, format = "%d-%m-%Y", tz = "UTC"),
+    mem <- data.frame("date" = as.POSIXct(dates, tz = "UTC", origin = "1970-01-01"),
                       "state" = l[[best]]$memberships)
     results$states <- mem
     warning("Skipping temporal embedding because the 'MASS' package is not installed. Consider installing it.")
@@ -4892,7 +4892,7 @@ dna_phaseTransitions <- function(distanceMethod = "absdiff",
     distmat <- distance_mat + 1e-12
     mds <- MASS::isoMDS(distmat) # MDS of distance matrix
     points <- mds$points
-    mem <- data.frame("date" = as.POSIXct(dates, format = "%d-%m-%Y", tz = "UTC"),
+    mem <- data.frame("date" = as.POSIXct(dates, tz = "UTC", origin = "1970-01-01"),
                       "state" = l[[best]]$memberships,
                       "X1" = points[, 1],
                       "X2" = points[, 2])
@@ -5084,7 +5084,7 @@ dna_phaseTransitions2 <- function(distanceMethod = "absdiff",
 
   # retrieve mid-point dates (gamma)
   m <- .jcall(exporter, "[Lexport/Matrix;", "getMatrixResultsArray") # get list of Matrix objects from Exporter object
-  dates <- sapply(m, function(x) as.POSIXct(.jcall(x, "J", "getDateTimeLong"), origin = "1970-01-01"))
+  dates <- sapply(m, function(x) .jcall(x, "J", "getDateTimeLong")) # long integers, still needs conversion to date
 
   # define clustering function
   hclustMethods <- c("single", "average", "complete", "ward")
@@ -5216,7 +5216,7 @@ dna_phaseTransitions2 <- function(distanceMethod = "absdiff",
 
   # temporal embedding via MDS
   if (!requireNamespace("MASS", quietly = TRUE)) {
-    mem <- data.frame("date" = as.POSIXct(dates, format = "%d-%m-%Y", tz = "UTC"),
+    mem <- data.frame("date" = as.POSIXct(dates, tz = "UTC", origin = "1970-01-01"),
                       "state" = l[[best]]$memberships)
     results$states <- mem
     warning("Skipping temporal embedding because the 'MASS' package is not installed. Consider installing it.")
@@ -5226,7 +5226,7 @@ dna_phaseTransitions2 <- function(distanceMethod = "absdiff",
     distmat <- distance_mat + 1e-12
     mds <- MASS::isoMDS(distmat) # MDS of distance matrix
     points <- mds$points
-    mem <- data.frame("date" = as.POSIXct(dates, format = "%d-%m-%Y", tz = "UTC"),
+    mem <- data.frame("date" = as.POSIXct(dates, tz = "UTC", origin = "1970-01-01"),
                       "state" = l[[best]]$memberships,
                       "X1" = points[, 1],
                       "X2" = points[, 2])