From 483b59e80fe5fd9b3d4f3fcb74014ce9dc691b60 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Fri, 19 Jul 2024 12:03:12 -0300
Subject: [PATCH 01/42] fst edge delay

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

diff --git a/R/edge_delay.R b/R/edge_delay.R
new file mode 100644
index 00000000..da9654c2
--- /dev/null
+++ b/R/edge_delay.R
@@ -0,0 +1,58 @@
+#' Directional correlation delay edge lists
+#'
+#' Temporal delay in absolute bearing between individuals
+#'
+#' @param DT relocation data
+#' @param edges edges generated with edges_dist
+#' @param window integer window in timegroups generated with group_times
+edge_delay <- function(DT, id = NULL, edges, window = NULL) {
+  stopifnot(!is.null(id))
+  stopifnot(!is.null(window))
+
+  stopifnot(id %in% colnames(DT))
+
+  setnames(DT, id, 'id')
+
+  stopifnot('dyadID' %in% colnames(edges))
+  stopifnot('timegroup' %in% colnames(edges))
+  stopifnot('fusionID' %in% colnames(edges))
+  stopifnot('dyadID' %in% colnames(edges))
+
+  stopifnot('bearing' %in% colnames(DT))
+  stopifnot('timegroup' %in% colnames(DT))
+
+  # TODO: check window isnt in colnames
+
+  setorder(DT, timegroup)
+
+  id_tg <- edges[!is.na(fusionID), .(
+    tg = unique(timegroup),
+    dyadID = unique(dyadID),
+    ID1 = first(ID1),
+    ID2 = first(ID2)
+  ), by = fusionID]
+  id_tg[, min_tg := data.table::fifelse(tg - window < min(tg), min(tg), tg - window),
+        by = fusionID]
+  id_tg[, max_tg := data.table::fifelse(tg + window < min(tg), min(tg), tg + window),
+        by = fusionID]
+
+  id_tg[, delay_tg := {
+    focal_bearing <- DT[timegroup == .BY$tg & id == ID1, bearing]
+    DT[between(timegroup, min_tg, max_tg) & id == ID2,
+       timegroup[which.min(delta_rad(focal_bearing, bearing))]]
+  }, by = .(tg,  dyadID)]
+
+  id_tg[, dir_corr_delay := tg - delay_tg]
+
+  data.table::setnames(id_tg,  c('tg'), c('timegroup'))
+  data.table::set(id_tg, j = c('min_tg', 'max_tg','delay_tg'), value = NULL)
+  data.table::setorder(id_tg, timegroup, ID1, ID2, dir_corr_delay)
+
+  out <- data.table::rbindlist(list(
+    id_tg,
+    id_tg[, .(timegroup,  dyadID, fusionID,
+              ID1 = ID2, ID2 = ID1, dir_corr_delay = - dir_corr_delay)]
+  ), use.names = TRUE)
+
+  return(out)
+}

From 0b89f6d0b286d68c3928852d2583cb67c3ca334f Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Fri, 1 Nov 2024 16:25:21 -0300
Subject: [PATCH 02/42] internal delta_rad function

---
 R/internal.R | 29 +++++++++++++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 R/internal.R

diff --git a/R/internal.R b/R/internal.R
new file mode 100644
index 00000000..2811ff04
--- /dev/null
+++ b/R/internal.R
@@ -0,0 +1,29 @@
+#' Difference of two angles measured in radians
+#'
+#' Internal function
+#'
+#' @param target angle in radians
+#' @param source angle in radians
+#' @param signed boolean if signed difference should be returned, default FALSE
+#'
+#' @return
+#' @references adapted from https://stackoverflow.com/a/7869457
+#'
+#' @examples
+delta_rad <- function(target, source,  signed = FALSE) {
+  if (!inherits(target, 'units') || units(target$numerator != 'rad')) {
+    stop('units(targets) is not radians')
+  }
+  if (!inherits(source, 'units') || units(target$numerator != 'rad')) {
+    stop('units(source) is not radians')
+  }
+
+  d <- source - target
+  d <- (d + pi) %% (2 * pi) - pi
+
+  if (signed) {
+    return(d)
+  } else {
+    return(abs(d))
+  }
+}

From 455568e29e72798de2d783eb815725575f2a91d7 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 16:44:32 -0400
Subject: [PATCH 03/42] title

---
 R/edge_delay.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index da9654c2..65ba66c8 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -1,4 +1,4 @@
-#' Directional correlation delay edge lists
+#' Directional correlation delay based edge lists
 #'
 #' Temporal delay in absolute bearing between individuals
 #'

From a458550ac578104a1dd1c1176424048ab13a7d93 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 16:44:38 -0400
Subject: [PATCH 04/42] description

---
 R/edge_delay.R | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 65ba66c8..cdcd6317 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -1,11 +1,26 @@
 #' Directional correlation delay based edge lists
 #'
-#' Temporal delay in absolute bearing between individuals
+#' \code{edge_delay} returns edge lists defined by the directional correlation
+#' delay between individuals. The function expects a \code{data.table} with
+#' relocation data, distance based edge lists, individual identifiers and a window argument. The
+#' window argument is used to specify the temporal window within which to consider
+#' the directional correlation delay. Relocation data should be in two columns
+#' representing the X and Y coordinates.
+#'
+#' The \code{DT} and \code{edges} must be \code{data.table}s. If your data is a
+#' \code{data.frame}, you can convert it by reference using
+#' \code{\link[data.table:setDT]{data.table::setDT}}.
+#'
+#' The \code{DT} and \code{edges} are internally matched in this function using
+#' the columns \code{timegroup} (from \code{group_times}) and \code{ID1} and
+#' \code{ID2} (in \code{edges}, from \code{dyad_id}) with \code{id} (in
+#' \code{DT}). This function expects a \code{fusionID} present, generated with
+#' the \code{fusion_id} function. The \code{timegroup} argument expects the
+#' names of a column in \code{edges} which correspond to the timegroup column.
+#' The \code{id}, \code{direction} and \code{timegroup} arguments expect the names
+#' of a column in \code{DT} which correspond to the id, direction and
+#' timegroup columns.
 #'
-#' @param DT relocation data
-#' @param edges edges generated with edges_dist
-#' @param window integer window in timegroups generated with group_times
-edge_delay <- function(DT, id = NULL, edges, window = NULL) {
   stopifnot(!is.null(id))
   stopifnot(!is.null(window))
 

From 79d67929f295bc6ab83d1c8eb8ef1279f23f2a89 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 16:44:41 -0400
Subject: [PATCH 05/42] params

---
 R/edge_delay.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index cdcd6317..b091061d 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -21,6 +21,11 @@
 #' of a column in \code{DT} which correspond to the id, direction and
 #' timegroup columns.
 #'
+#' @inheritParams centroid_fusion
+#' @inheritParams direction_group
+#' @param window temporal window in unit of timegroup column generated with
+#'   \code{group_times}, eg. \code{window = 4} corresponds to the 4 timegroups
+#'   before and after the focal observation
   stopifnot(!is.null(id))
   stopifnot(!is.null(window))
 

From 6f864c60f0fd193f48f601139a6f8f952c3e5a8a Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 16:44:43 -0400
Subject: [PATCH 06/42] return

---
 R/edge_delay.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index b091061d..17795a36 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -26,6 +26,11 @@
 #' @param window temporal window in unit of timegroup column generated with
 #'   \code{group_times}, eg. \code{window = 4} corresponds to the 4 timegroups
 #'   before and after the focal observation
+#'
+#' @return \code{edge_delay} returns the input \code{edges} appended with
+#'   a 'dir_corr_delay' column indicating the temporal delay (in units of
+#'   timegroups) at which ID1's direction of movement is most similar to
+#'   ID2's direction of movement, within the temporal window defined.
   stopifnot(!is.null(id))
   stopifnot(!is.null(window))
 

From 7dfb16a2de1562d7e59eeef80186e21fc291647b Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 16:46:22 -0400
Subject: [PATCH 07/42] example

---
 R/edge_delay.R | 56 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 56 insertions(+)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 17795a36..43d666bf 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -31,6 +31,62 @@
 #'   a 'dir_corr_delay' column indicating the temporal delay (in units of
 #'   timegroups) at which ID1's direction of movement is most similar to
 #'   ID2's direction of movement, within the temporal window defined.
+#'
+#' @export
+#'
+#' @family Edge-list generation
+#'
+#' @examples
+#' # Load data.table
+#' library(data.table)
+#' \dontshow{data.table::setDTthreads(1)}
+#'
+#' # Read example data
+#' DT <- fread(system.file("extdata", "DT.csv", package = "spatsoc"))
+#'
+#' # Select only individuals A, B, C for this example
+#' DT <- DT[ID %in% c('A', 'B', 'C')]
+#'
+#' # Cast the character column to POSIXct
+#' DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
+#'
+#' # Temporal grouping
+#' group_times(DT, datetime = 'datetime', threshold = '20 minutes')
+#'
+#' # Calculate direction
+#' direction_step(
+#'   DT = DT,
+#'   id = 'ID',
+#'   coords = c('X', 'Y'),
+#'   projection = 32736
+#' )
+#'
+#' # Distance based edge list generation
+#' edges <- edge_dist(
+#'   DT,
+#'   threshold = 100,
+#'   id = 'ID',
+#'   coords = c('X', 'Y'),
+#'   timegroup = 'timegroup',
+#'   returnDist = TRUE,
+#'   fillNA = FALSE
+#' )
+#'
+#' # Generate dyad id
+#' dyad_id(edges, id1 = 'ID1', id2 = 'ID2')
+#'
+#' # Generate fusion id
+#' fusion_id(edges, threshold = 100)
+#'
+#' # Directional correlation delay
+#' delay <- edge_delay(
+#'   DT,
+#'   edges,
+#'   window = 3,
+#'   id = 'id'
+#' )
+#'
+#' print(delay)
   stopifnot(!is.null(id))
   stopifnot(!is.null(window))
 

From 331960db91b4a0b8c41f04c31da2e7ec9bb320b3 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 16:46:25 -0400
Subject: [PATCH 08/42] args

---
 R/edge_delay.R | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 43d666bf..650b6da4 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -87,6 +87,14 @@
 #' )
 #'
 #' print(delay)
+edge_delay <- function(
+    DT,
+    edges,
+    window,
+    id = NULL,
+    direction = 'direction',
+    timegroup = 'timegroup') {
+
   stopifnot(!is.null(id))
   stopifnot(!is.null(window))
 

From 02886352d99808dc8243a8e7e885db38f33af6e4 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:12:48 -0400
Subject: [PATCH 09/42] rm timegroup arg

---
 R/edge_delay.R | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 650b6da4..36ecf59d 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -15,11 +15,9 @@
 #' the columns \code{timegroup} (from \code{group_times}) and \code{ID1} and
 #' \code{ID2} (in \code{edges}, from \code{dyad_id}) with \code{id} (in
 #' \code{DT}). This function expects a \code{fusionID} present, generated with
-#' the \code{fusion_id} function. The \code{timegroup} argument expects the
-#' names of a column in \code{edges} which correspond to the timegroup column.
-#' The \code{id}, \code{direction} and \code{timegroup} arguments expect the names
-#' of a column in \code{DT} which correspond to the id, direction and
-#' timegroup columns.
+#' the \code{fusion_id} function.
+#' The \code{id}, and \code{direction} arguments expect the names
+#' of a column in \code{DT} which correspond to the id, and direction columns.
 #'
 #' @inheritParams centroid_fusion
 #' @inheritParams direction_group
@@ -92,8 +90,7 @@ edge_delay <- function(
     edges,
     window,
     id = NULL,
-    direction = 'direction',
-    timegroup = 'timegroup') {
+    direction = 'direction') {
 
   stopifnot(!is.null(id))
   stopifnot(!is.null(window))

From 1e431c4aaaaff2f369deb913f63cc279db0e8b8e Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:12:55 -0400
Subject: [PATCH 10/42] fix id colname

---
 R/edge_delay.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 36ecf59d..0535b4a8 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -81,7 +81,7 @@
 #'   DT,
 #'   edges,
 #'   window = 3,
-#'   id = 'id'
+#'   id = 'ID'
 #' )
 #'
 #' print(delay)

From 567aba6cbec32ab64e99a373197f86135f12445c Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:13:00 -0400
Subject: [PATCH 11/42] set window default null

---
 R/edge_delay.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 0535b4a8..1af36441 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -88,7 +88,7 @@
 edge_delay <- function(
     DT,
     edges,
-    window,
+    window = NULL,
     id = NULL,
     direction = 'direction') {
 

From 1b25f48911ceda89a2b8ba533fb7ca393794977e Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:13:06 -0400
Subject: [PATCH 12/42] check dt

---
 R/edge_delay.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 1af36441..d226c9de 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -92,8 +92,9 @@ edge_delay <- function(
     id = NULL,
     direction = 'direction') {
 
-  stopifnot(!is.null(id))
-  stopifnot(!is.null(window))
+  if (is.null(DT)) {
+    stop('input DT required')
+  }
 
   stopifnot(id %in% colnames(DT))
 

From 2918e1c05f1f2564eb80601dd1faf1ce441c836e Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:13:08 -0400
Subject: [PATCH 13/42] check edges

---
 R/edge_delay.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index d226c9de..269ac2d6 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -96,7 +96,9 @@ edge_delay <- function(
     stop('input DT required')
   }
 
-  stopifnot(id %in% colnames(DT))
+  if (is.null(edges)) {
+    stop('input edges required')
+  }
 
   setnames(DT, id, 'id')
 

From 891b1c070de2302b8d298b79ceb7f6b6f0290680 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:13:15 -0400
Subject: [PATCH 14/42] check id colname

---
 R/edge_delay.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 269ac2d6..7ccf91c8 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -100,7 +100,9 @@ edge_delay <- function(
     stop('input edges required')
   }
 
-  setnames(DT, id, 'id')
+  if (is.null(id)) {
+    stop('id column name required')
+  }
 
   stopifnot('dyadID' %in% colnames(edges))
   stopifnot('timegroup' %in% colnames(edges))

From 03908e305d0454cf540472b53e55b891fc1eb8b6 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:13:28 -0400
Subject: [PATCH 15/42] check cols

---
 R/edge_delay.R | 27 +++++++++++++++++++++------
 1 file changed, 21 insertions(+), 6 deletions(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 7ccf91c8..9bf6cd98 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -104,13 +104,28 @@ edge_delay <- function(
     stop('id column name required')
   }
 
-  stopifnot('dyadID' %in% colnames(edges))
-  stopifnot('timegroup' %in% colnames(edges))
-  stopifnot('fusionID' %in% colnames(edges))
-  stopifnot('dyadID' %in% colnames(edges))
+  check_cols_edges <- c('ID1', 'ID2', timegroup)
+  if (any(!(check_cols_edges %in% colnames(edges)))) {
+    stop(paste0(
+      as.character(paste(setdiff(
+        check_cols_edges,
+        colnames(edges)
+      ), collapse = ', ')),
+      ' field(s) provided are not present in input DT'
+    ))
+  }
 
-  stopifnot('bearing' %in% colnames(DT))
-  stopifnot('timegroup' %in% colnames(DT))
+  check_cols_DT <- c(id, timegroup, direction)
+  if (any(!(check_cols_DT %in% colnames(DT)
+  ))) {
+    stop(paste0(
+      as.character(paste(setdiff(
+        check_cols_DT,
+        colnames(DT)
+      ), collapse = ', ')),
+      ' field(s) provided are not present in input DT'
+    ))
+  }
 
   # TODO: check window isnt in colnames
 

From a72103992b497cbc4f2a6e2dee9d60c72d84169c Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:13:31 -0400
Subject: [PATCH 16/42] check window

---
 R/edge_delay.R | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 9bf6cd98..0eac74cf 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -127,6 +127,13 @@ edge_delay <- function(
     ))
   }
 
+  if (is.null(window)) {
+    stop('window is required')
+  }
+
+  if (!is.numeric(window)) {
+    stop('window should be a numeric, in the units of timegroup')
+  }
   # TODO: check window isnt in colnames
 
   setorder(DT, timegroup)

From b74e4b8f1f99f246e4b5a96e7364241c094d418d Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:13:35 -0400
Subject: [PATCH 17/42] check dyad, fusion ids

---
 R/edge_delay.R | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 0eac74cf..a5afc5d9 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -134,6 +134,14 @@ edge_delay <- function(
   if (!is.numeric(window)) {
     stop('window should be a numeric, in the units of timegroup')
   }
+
+  if (!'fusionID' %in% colnames(edges)) {
+    stop('fusionID not present in edges, did you run fusion_id?')
+  }
+
+  if (!'dyadID' %in% colnames(edges)) {
+    stop('dyadID not present in edges, did you run dyad_id?')
+  }
   # TODO: check window isnt in colnames
 
   setorder(DT, timegroup)

From a94bada135fdf5992fa4092143e30ec50c2f1f68 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:32:22 -0400
Subject: [PATCH 18/42] fix check numerator brackets

---
 R/internal.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/internal.R b/R/internal.R
index 2811ff04..3f23d7c0 100644
--- a/R/internal.R
+++ b/R/internal.R
@@ -11,10 +11,10 @@
 #'
 #' @examples
 delta_rad <- function(target, source,  signed = FALSE) {
-  if (!inherits(target, 'units') || units(target$numerator != 'rad')) {
+  if (!inherits(target, 'units') || units(target)$numerator != 'rad') {
     stop('units(targets) is not radians')
   }
-  if (!inherits(source, 'units') || units(target$numerator != 'rad')) {
+  if (!inherits(source, 'units') || units(source)$numerator != 'rad') {
     stop('units(source) is not radians')
   }
 

From 294d5ce7158fdf4d91ce429f849af51612acf2cc Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:32:29 -0400
Subject: [PATCH 19/42] fix units

---
 R/internal.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/internal.R b/R/internal.R
index 3f23d7c0..6811a400 100644
--- a/R/internal.R
+++ b/R/internal.R
@@ -19,7 +19,8 @@ delta_rad <- function(target, source,  signed = FALSE) {
   }
 
   d <- source - target
-  d <- (d + pi) %% (2 * pi) - pi
+  pi_rad <- units::as_units(pi, 'rad')
+  d <- (d + pi_rad) %% (2 * pi_rad) - pi_rad
 
   if (signed) {
     return(d)

From 595ce9da6a3c21c3f87b9e8e3e91b314d32fc21f Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:36:09 -0400
Subject: [PATCH 20/42] check if window in colnames, zz temporarily if so

---
 R/edge_delay.R | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index a5afc5d9..ce6b3d7a 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -142,7 +142,13 @@ edge_delay <- function(
   if (!'dyadID' %in% colnames(edges)) {
     stop('dyadID not present in edges, did you run dyad_id?')
   }
-  # TODO: check window isnt in colnames
+  if ('window' %in% colnames(DT)) {
+    setnames(DT, 'window', 'zz_window')
+  }
+
+  if ('window' %in% colnames(edges)) {
+    setnames(edges, 'window', 'zz_window')
+  }
 
   setorder(DT, timegroup)
 
@@ -175,5 +181,13 @@ edge_delay <- function(
               ID1 = ID2, ID2 = ID1, dir_corr_delay = - dir_corr_delay)]
   ), use.names = TRUE)
 
+  if ('zz_window' %in% colnames(DT)) {
+    setnames(DT, 'zz_window', 'window')
+  }
+
+  if ('zz_window' %in% colnames(edges)) {
+    setnames(edges, 'zz_window', 'window')
+  }
+
   return(out)
 }

From f85b1e894123009ae7ad5e09f805417f9dbfe74f Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:40:41 -0400
Subject: [PATCH 21/42] use three zees

---
 R/edge_delay.R | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index ce6b3d7a..6a82e3b2 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -143,13 +143,14 @@ edge_delay <- function(
     stop('dyadID not present in edges, did you run dyad_id?')
   }
   if ('window' %in% colnames(DT)) {
-    setnames(DT, 'window', 'zz_window')
+    setnames(DT, 'window', 'zzz_window')
   }
 
   if ('window' %in% colnames(edges)) {
-    setnames(edges, 'window', 'zz_window')
+    setnames(edges, 'window', 'zzz_window')
   }
 
+  setnames(DT, id, 'zzz_id')
   setorder(DT, timegroup)
 
   id_tg <- edges[!is.na(fusionID), .(
@@ -165,9 +166,9 @@ edge_delay <- function(
 
   id_tg[, delay_tg := {
     focal_bearing <- DT[timegroup == .BY$tg & id == ID1, bearing]
-    DT[between(timegroup, min_tg, max_tg) & id == ID2,
-       timegroup[which.min(delta_rad(focal_bearing, bearing))]]
-  }, by = .(tg,  dyadID)]
+    DT[between(timegroup, min_tg, max_tg) & zzz_id == ID2,
+       timegroup[which.min(delta_rad(focal_direction, direction))]]
+  by = c('tg',  'dyadID')]
 
   id_tg[, dir_corr_delay := tg - delay_tg]
 
@@ -181,12 +182,12 @@ edge_delay <- function(
               ID1 = ID2, ID2 = ID1, dir_corr_delay = - dir_corr_delay)]
   ), use.names = TRUE)
 
-  if ('zz_window' %in% colnames(DT)) {
-    setnames(DT, 'zz_window', 'window')
+  if ('zzz_window' %in% colnames(DT)) {
+    setnames(DT, 'zzz_window', 'window')
   }
 
-  if ('zz_window' %in% colnames(edges)) {
-    setnames(edges, 'zz_window', 'window')
+  if ('zzz_window' %in% colnames(edges)) {
+    setnames(edges, 'zzz_window', 'window')
   }
 
   return(out)

From 2f434ca734a6424410ac1908dd5bd226c110ae61 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:40:59 -0400
Subject: [PATCH 22/42] tidy

---
 R/edge_delay.R | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 6a82e3b2..cc9233a1 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -142,6 +142,8 @@ edge_delay <- function(
   if (!'dyadID' %in% colnames(edges)) {
     stop('dyadID not present in edges, did you run dyad_id?')
   }
+
+
   if ('window' %in% colnames(DT)) {
     setnames(DT, 'window', 'zzz_window')
   }
@@ -158,11 +160,15 @@ edge_delay <- function(
     dyadID = unique(dyadID),
     ID1 = first(ID1),
     ID2 = first(ID2)
-  ), by = fusionID]
-  id_tg[, min_tg := data.table::fifelse(tg - window < min(tg), min(tg), tg - window),
-        by = fusionID]
-  id_tg[, max_tg := data.table::fifelse(tg + window < min(tg), min(tg), tg + window),
-        by = fusionID]
+  ), by = c('fusionID')]
+
+  id_tg[, min_tg :=
+          data.table::fifelse(tg - window < min(tg), min(tg), tg - window),
+        by = c('fusionID')]
+
+  id_tg[, max_tg :=
+          data.table::fifelse(tg + window < min(tg), min(tg), tg + window),
+        by = c('fusionID')]
 
   id_tg[, delay_tg := {
     focal_bearing <- DT[timegroup == .BY$tg & id == ID1, bearing]

From f55753cc065eed684180107875693fae9527175b Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:41:05 -0400
Subject: [PATCH 23/42] fix direction not bearing

---
 R/edge_delay.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index cc9233a1..517f094b 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -171,9 +171,10 @@ edge_delay <- function(
         by = c('fusionID')]
 
   id_tg[, delay_tg := {
-    focal_bearing <- DT[timegroup == .BY$tg & id == ID1, bearing]
+    focal_direction <- DT[timegroup == .BY$tg & zzz_id == ID1, direction]
     DT[between(timegroup, min_tg, max_tg) & zzz_id == ID2,
        timegroup[which.min(delta_rad(focal_direction, direction))]]
+  },
   by = c('tg',  'dyadID')]
 
   id_tg[, dir_corr_delay := tg - delay_tg]

From 42fbf67fa20dd553ce491fadd5a3bb6f18d99af2 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 17:41:11 -0400
Subject: [PATCH 24/42] tidy

---
 R/edge_delay.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 517f094b..fb47f7d7 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -179,8 +179,9 @@ edge_delay <- function(
 
   id_tg[, dir_corr_delay := tg - delay_tg]
 
-  data.table::setnames(id_tg,  c('tg'), c('timegroup'))
+  data.table::setnames(id_tg,  'tg', 'timegroup')
   data.table::set(id_tg, j = c('min_tg', 'max_tg','delay_tg'), value = NULL)
+
   data.table::setorder(id_tg, timegroup, ID1, ID2, dir_corr_delay)
 
   out <- data.table::rbindlist(list(

From 444652704b0c76db5ec26d678f6383409788bce3 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 18:42:52 -0400
Subject: [PATCH 25/42] fix reset zzz id

---
 R/edge_delay.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index fb47f7d7..6f76c16e 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -190,6 +190,9 @@ edge_delay <- function(
               ID1 = ID2, ID2 = ID1, dir_corr_delay = - dir_corr_delay)]
   ), use.names = TRUE)
 
+
+  setnames(DT, 'zzz_id', id)
+
   if ('zzz_window' %in% colnames(DT)) {
     setnames(DT, 'zzz_window', 'window')
   }

From 981c2acaeb486e8e787d6dbb2924c3fcf4fdfb54 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 18:43:29 -0400
Subject: [PATCH 26/42] todo check max tg

---
 R/edge_delay.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 6f76c16e..cd60e43b 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -168,6 +168,8 @@ edge_delay <- function(
 
   id_tg[, max_tg :=
           data.table::fifelse(tg + window < min(tg), min(tg), tg + window),
+          # TODO: check max_tg
+          # data.table::fifelse(tg + window > max(tg), max(tg), tg + window),
         by = c('fusionID')]
 
   id_tg[, delay_tg := {

From d3b1cbb67413fb91c8ec253f9884ae74b350ebc7 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 19:07:04 -0400
Subject: [PATCH 27/42] fix timegroup char since not arg

---
 R/edge_delay.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index cd60e43b..4e3a7714 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -104,7 +104,7 @@ edge_delay <- function(
     stop('id column name required')
   }
 
-  check_cols_edges <- c('ID1', 'ID2', timegroup)
+  check_cols_edges <- c('ID1', 'ID2', 'timegroup')
   if (any(!(check_cols_edges %in% colnames(edges)))) {
     stop(paste0(
       as.character(paste(setdiff(
@@ -115,7 +115,7 @@ edge_delay <- function(
     ))
   }
 
-  check_cols_DT <- c(id, timegroup, direction)
+  check_cols_DT <- c(id, 'timegroup', direction)
   if (any(!(check_cols_DT %in% colnames(DT)
   ))) {
     stop(paste0(
@@ -153,7 +153,7 @@ edge_delay <- function(
   }
 
   setnames(DT, id, 'zzz_id')
-  setorder(DT, timegroup)
+  data.table::setorderv(DT, 'timegroup')
 
   id_tg <- edges[!is.na(fusionID), .(
     tg = unique(timegroup),

From d54bf05eae7481438ed5bde152db69f7caa8e76b Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 19:36:23 -0400
Subject: [PATCH 28/42] rm setnames, use env

---
 R/edge_delay.R | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 4e3a7714..6f6cba9f 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -152,7 +152,6 @@ edge_delay <- function(
     setnames(edges, 'window', 'zzz_window')
   }
 
-  setnames(DT, id, 'zzz_id')
   data.table::setorderv(DT, 'timegroup')
 
   id_tg <- edges[!is.na(fusionID), .(
@@ -173,9 +172,11 @@ edge_delay <- function(
         by = c('fusionID')]
 
   id_tg[, delay_tg := {
-    focal_direction <- DT[timegroup == .BY$tg & zzz_id == ID1, direction]
-    DT[between(timegroup, min_tg, max_tg) & zzz_id == ID2,
-       timegroup[which.min(delta_rad(focal_direction, direction))]]
+    focal_direction <- DT[timegroup == .BY$tg &
+                            id == ID1, direction]
+    DT[between(timegroup, min_tg, max_tg) & id == ID2,
+       timegroup[which.min(delta_rad(focal_direction, direction))],
+       env = list(id = 'id')]
   },
   by = c('tg',  'dyadID')]
 
@@ -192,9 +193,6 @@ edge_delay <- function(
               ID1 = ID2, ID2 = ID1, dir_corr_delay = - dir_corr_delay)]
   ), use.names = TRUE)
 
-
-  setnames(DT, 'zzz_id', id)
-
   if ('zzz_window' %in% colnames(DT)) {
     setnames(DT, 'zzz_window', 'window')
   }
@@ -205,3 +203,4 @@ edge_delay <- function(
 
   return(out)
 }
+

From ada1d55cf4ad1539da90a745bf203df792f9936c Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 19:39:26 -0400
Subject: [PATCH 29/42] fst test edge_delay

---
 tests/testthat/test-edge-delay.R | 2 ++
 1 file changed, 2 insertions(+)
 create mode 100644 tests/testthat/test-edge-delay.R

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
new file mode 100644
index 00000000..8a98ed50
--- /dev/null
+++ b/tests/testthat/test-edge-delay.R
@@ -0,0 +1,2 @@
+# Test edge_delay
+context('test edge_delay')

From 5538f3080f816467c815fbafc2462c91efdb3a3f Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 19:39:51 -0400
Subject: [PATCH 30/42] test setup

---
 tests/testthat/test-edge-delay.R | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index 8a98ed50..5f89f8f8 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -1,2 +1,29 @@
 # Test edge_delay
 context('test edge_delay')
+
+library(spatsoc)
+
+DT <- fread('../testdata/DT.csv')
+id <- 'ID'
+datetime <- 'datetime'
+timethreshold <- '20 minutes'
+threshold <- 50
+coords <- c('X', 'Y')
+timegroup <- 'timegroup'
+group <- 'group'
+projection <- 32736
+window <- 3
+
+
+DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
+group_times(DT, datetime = datetime, threshold = timethreshold)
+direction_step(DT, id, coords, projection)
+edges <- edge_dist(DT, threshold = threshold, id = id,
+                   timegroup = timegroup, returnDist = TRUE, fillNA = FALSE)
+dyad_id(edges, id1 = 'ID1', id2 = 'ID2')
+fusion_id(edges, threshold = threshold)
+
+clean_DT <- copy(DT)
+clean_edges <- copy(edges)
+
+# edge_delay(DT = DT, edges = edges, id = id, window = window)

From ac2091a5ae0e3594bac11402903fa23604ba6e0a Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 19:41:48 -0400
Subject: [PATCH 31/42] reorg args

---
 R/edge_delay.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index 6f6cba9f..bb05a702 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -7,11 +7,11 @@
 #' the directional correlation delay. Relocation data should be in two columns
 #' representing the X and Y coordinates.
 #'
-#' The \code{DT} and \code{edges} must be \code{data.table}s. If your data is a
+#' The \code{edges} and \code{DT} must be \code{data.table}s. If your data is a
 #' \code{data.frame}, you can convert it by reference using
 #' \code{\link[data.table:setDT]{data.table::setDT}}.
 #'
-#' The \code{DT} and \code{edges} are internally matched in this function using
+#' The \code{edges} and \code{DT} are internally matched in this function using
 #' the columns \code{timegroup} (from \code{group_times}) and \code{ID1} and
 #' \code{ID2} (in \code{edges}, from \code{dyad_id}) with \code{id} (in
 #' \code{DT}). This function expects a \code{fusionID} present, generated with
@@ -78,16 +78,16 @@
 #'
 #' # Directional correlation delay
 #' delay <- edge_delay(
-#'   DT,
-#'   edges,
+#'   edges = edges,
+#'   DT = DT,
 #'   window = 3,
 #'   id = 'ID'
 #' )
 #'
 #' print(delay)
 edge_delay <- function(
-    DT,
     edges,
+    DT,
     window = NULL,
     id = NULL,
     direction = 'direction') {

From 21808d2ac4a44e10df361afeeff2ee2cf92baf0c Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 19:46:47 -0400
Subject: [PATCH 32/42] test required arg

---
 tests/testthat/test-edge-delay.R | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index 5f89f8f8..b2136760 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -27,3 +27,16 @@ clean_DT <- copy(DT)
 clean_edges <- copy(edges)
 
 # edge_delay(DT = DT, edges = edges, id = id, window = window)
+
+test_that('edges, DT are required', {
+  expect_error(edge_delay(edges, DT = NULL))
+  expect_error(edge_delay(edges = NULL, DT))
+})
+
+test_that('arguments required, otherwise error detected', {
+  expect_error(edge_delay(edges, DT, id = NULL),
+               'id column name required')
+  expect_error(edge_delay(edges, DT, id = id, window = NULL),
+               'window is required')
+})
+

From 6a12bb57ec687d5b7df84cdd67e85911054c9f97 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 19:46:52 -0400
Subject: [PATCH 33/42] test window numeric

---
 tests/testthat/test-edge-delay.R | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index b2136760..459644d9 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -40,3 +40,8 @@ test_that('arguments required, otherwise error detected', {
                'window is required')
 })
 
+test_that('window is numeric', {
+  expect_error(edge_delay(edges, DT, id = id, window = 'potato'),
+               'numeric')
+})
+

From 8ad56a552faa4a3d1f201dee17ebe708546ab8a1 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 19:47:02 -0400
Subject: [PATCH 34/42] test colnames exist

---
 tests/testthat/test-edge-delay.R | 28 ++++++++++++++++++++++++++++
 1 file changed, 28 insertions(+)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index 459644d9..49c501ac 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -45,3 +45,31 @@ test_that('window is numeric', {
                'numeric')
 })
 
+test_that('column names must exist in DT', {
+  expect_error(edge_delay(edges, DT, id = 'potato'),
+               'potato field')
+
+  copy_edges <- copy(clean_edges)
+  copy_edges[, timegroup := NULL]
+  expect_error(edge_delay(edges, DT, id = id),
+               'timegroup field')
+
+  copy_edges <- copy(clean_edges)
+  copy_edges[, fusionID := NULL]
+  expect_error(edge_delay(edges, DT, id = id),
+               'fusionID field')
+
+  copy_edges <- copy(clean_edges)
+  copy_edges[, dyadID := NULL]
+  expect_error(edge_delay(edges, DT, id = id),
+               'dyadID field')
+
+  expect_error(edge_delay(edges, DT, id = id, direction = 'potato'),
+               'direction field')
+
+  copy_DT <- copy(clean_DT)
+  copy_DT[, timegroup := NULL]
+  expect_error(edge_delay(edges, DT, id = id),
+               'timegroup field')
+})
+

From ccadff47ec5dafdbba9285111b8eca0f2b62fdf1 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 19:47:11 -0400
Subject: [PATCH 35/42] test returned object

---
 tests/testthat/test-edge-delay.R | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index 49c501ac..003ce81f 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -73,3 +73,23 @@ test_that('column names must exist in DT', {
                'timegroup field')
 })
 
+test_that('no rows are added to the result edges', {
+  expect_equal(nrow(edges),
+               nrow(edge_delay(edges, DT, id = id, window = window)))
+})
+
+test_that('two columns added to the result DT', {
+  copyEdges <- copy(edges)
+
+  expect_equal(ncol(copyEdges) + 1,
+               ncol(edge_delay(edges, DT, id = id, window = window)))
+})
+
+test_that('column added to the result DT is double', {
+  expect_type(edge_delay(edges, DT, id = id, window = window)$dir_corr_delay, 'double')
+})
+
+test_that('returns a data.table', {
+  expect_s3_class(edge_delay(edges, DT, id = id, window = window), 'data.table')
+})
+

From 7752d041174c6929f36a103e394f7dcdd5351087 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 19:52:05 -0400
Subject: [PATCH 36/42] fix missing coords arg

---
 tests/testthat/test-edge-delay.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index 003ce81f..ce37680f 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -19,7 +19,8 @@ DT[, datetime := as.POSIXct(datetime, tz = 'UTC')]
 group_times(DT, datetime = datetime, threshold = timethreshold)
 direction_step(DT, id, coords, projection)
 edges <- edge_dist(DT, threshold = threshold, id = id,
-                   timegroup = timegroup, returnDist = TRUE, fillNA = FALSE)
+                   coords = coords, timegroup = timegroup,
+                   returnDist = TRUE, fillNA = FALSE)
 dyad_id(edges, id1 = 'ID1', id2 = 'ID2')
 fusion_id(edges, threshold = threshold)
 

From 90bc8ed88563b547f2b44b10e0f74d08957c64a2 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 20:04:30 -0400
Subject: [PATCH 37/42] fix use copy edges/dt

---
 tests/testthat/test-edge-delay.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index ce37680f..267928ac 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -52,17 +52,17 @@ test_that('column names must exist in DT', {
 
   copy_edges <- copy(clean_edges)
   copy_edges[, timegroup := NULL]
-  expect_error(edge_delay(edges, DT, id = id),
+  expect_error(edge_delay(copy_edges, DT, id = id, window = window),
                'timegroup field')
 
   copy_edges <- copy(clean_edges)
   copy_edges[, fusionID := NULL]
-  expect_error(edge_delay(edges, DT, id = id),
+  expect_error(edge_delay(copy_edges, DT, id = id, window = window),
                'fusionID field')
 
   copy_edges <- copy(clean_edges)
   copy_edges[, dyadID := NULL]
-  expect_error(edge_delay(edges, DT, id = id),
+  expect_error(edge_delay(copy_edges, DT, id = id, window = window),
                'dyadID field')
 
   expect_error(edge_delay(edges, DT, id = id, direction = 'potato'),
@@ -70,7 +70,7 @@ test_that('column names must exist in DT', {
 
   copy_DT <- copy(clean_DT)
   copy_DT[, timegroup := NULL]
-  expect_error(edge_delay(edges, DT, id = id),
+  expect_error(edge_delay(edges, copy_DT, id = id, window = window),
                'timegroup field')
 })
 

From 116dab6cf33ad1e20922017e0ac9724de47ca352 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 20:04:40 -0400
Subject: [PATCH 38/42] fix len to match expected output cols

---
 tests/testthat/test-edge-delay.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index 267928ac..7b7004a4 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -82,7 +82,8 @@ test_that('no rows are added to the result edges', {
 test_that('two columns added to the result DT', {
   copyEdges <- copy(edges)
 
-  expect_equal(ncol(copyEdges) + 1,
+  expect_equal(length(c('ID1', 'ID2', 'timegroup',
+                        'dyadID', 'fusionID', 'dir_corr_delay')),
                ncol(edge_delay(edges, DT, id = id, window = window)))
 })
 

From 86c2b969f1dfe0bda6b24435aafc8364dde30c8d Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 20:04:50 -0400
Subject: [PATCH 39/42] fix integer returned

---
 tests/testthat/test-edge-delay.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index 7b7004a4..b32bae99 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -87,8 +87,8 @@ test_that('two columns added to the result DT', {
                ncol(edge_delay(edges, DT, id = id, window = window)))
 })
 
-test_that('column added to the result DT is double', {
-  expect_type(edge_delay(edges, DT, id = id, window = window)$dir_corr_delay, 'double')
+test_that('column added to the result DT is integer', {
+  expect_type(edge_delay(edges, DT, id = id, window = window)$dir_corr_delay, 'integer')
 })
 
 test_that('returns a data.table', {

From 2f67e07623acadb70de21dace4ae36becd6557dd Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 20:04:58 -0400
Subject: [PATCH 40/42] fix potato field

---
 tests/testthat/test-edge-delay.R | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index b32bae99..064e42de 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -65,8 +65,9 @@ test_that('column names must exist in DT', {
   expect_error(edge_delay(copy_edges, DT, id = id, window = window),
                'dyadID field')
 
-  expect_error(edge_delay(edges, DT, id = id, direction = 'potato'),
-               'direction field')
+  expect_error(edge_delay(edges, DT, id = id, window = window,
+                          direction = 'potato'),
+               'potato field')
 
   copy_DT <- copy(clean_DT)
   copy_DT[, timegroup := NULL]

From 39fc13643086ba4b9eb4e00aa9096776ec1db2bd Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 20:05:18 -0400
Subject: [PATCH 41/42] fix make consistent error msg

---
 R/edge_delay.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/edge_delay.R b/R/edge_delay.R
index bb05a702..b3a3c629 100644
--- a/R/edge_delay.R
+++ b/R/edge_delay.R
@@ -136,11 +136,11 @@ edge_delay <- function(
   }
 
   if (!'fusionID' %in% colnames(edges)) {
-    stop('fusionID not present in edges, did you run fusion_id?')
+    stop('fusionID field not present in edges, did you run fusion_id?')
   }
 
   if (!'dyadID' %in% colnames(edges)) {
-    stop('dyadID not present in edges, did you run dyad_id?')
+    stop('dyadID field not present in edges, did you run dyad_id?')
   }
 
 

From 68d9221e25ca2eb27cd525f27ee941cdae125b50 Mon Sep 17 00:00:00 2001
From: "Alec L. Robitaille" <robit.alec@gmail.com>
Date: Tue, 19 Nov 2024 20:16:00 -0400
Subject: [PATCH 42/42] todo expected tests

---
 tests/testthat/test-edge-delay.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/testthat/test-edge-delay.R b/tests/testthat/test-edge-delay.R
index 064e42de..b98b3a72 100644
--- a/tests/testthat/test-edge-delay.R
+++ b/tests/testthat/test-edge-delay.R
@@ -96,3 +96,4 @@ test_that('returns a data.table', {
   expect_s3_class(edge_delay(edges, DT, id = id, window = window), 'data.table')
 })
 
+# TODO: expected results tests