Update data sets and associated tests

tests/testthat/test_a02_errorchecks.R

@@ -98,15 +98,15 @@ test_that("check_input renames columns (regular)", {
 
   expect_message(r2 <- check_input(r1, input = "animal_id", options = c("animal_id", "bird_id")), "Renaming column 'Animal_ID' to 'animal_id'")
   expect_is(r2, "data.frame")
-  expect_named(r2, c("animal_id", "TIME", "feeder_id", "species", "sex", "lon", "lat"))
+  expect_named(r2, c("animal_id", "date", "TIME", "feeder_id", "species", "age", "sex", "site_name", "lon", "lat"))
 
   expect_message(r3 <- check_input(r2, input = "time", options = "time"), "Renaming column 'TIME' to 'time'")
   expect_is(r3, "data.frame")
-  expect_named(r3, c("animal_id", "time", "feeder_id", "species", "sex", "lon", "lat"))
+  expect_named(r3, c("animal_id", "date", "time", "feeder_id", "species", "age", "sex", "site_name", "lon", "lat"))
 
   expect_message(r4 <- check_input(r3, input = "logger_id", options = c("feeder_id", "logger_id")), "Renaming column 'feeder_id' to 'logger_id'")
   expect_is(r4, "data.frame")
-  expect_named(r4, c("animal_id", "time", "logger_id", "species", "sex", "lon", "lat"))
+  expect_named(r4, c("animal_id", "date", "time", "logger_id", "species", "age", "sex", "site_name", "lon", "lat"))
 
   expect_equal(r4, finches)
 })

tests/testthat/test_a03_load.R

@@ -52,7 +52,7 @@ test_that("load_format fixes names", {
   expect_message(load_format(r1), "Renaming column 'TIME' to 'time'")
 
   expect_named(suppressMessages(load_format(r1)),
-               c("animal_id", "date", "time", "logger_id", "specIes", "SEX", "lon", "lat"))
+               c("animal_id", "date", "time", "logger_id", "specIes", "age", "SEX", "site_name","lon", "lat"))
 })
 
 

tests/testthat/test_b01_visits.R

@@ -11,7 +11,27 @@ test_that("visits() returns appropriate, non-empty dataframe", {
   expect_is(v$logger_id, "factor")
   expect_is(v$start, "POSIXct")
   expect_is(v$end, "POSIXct")
-  expect_true(all(as.numeric(v$end - v$start) >= 0))
+  expect_is(v$date, "Date")
+
+  for(r in list(finches, finches_lg, chickadees)) {
+    v <- visits(r)
+    expect_true(all(!is.na(v$start)))
+    expect_true(all(!is.na(v$end)))
+    expect_true(all(!is.na(v$date)))
+    expect_true(all(as.numeric(v$end - v$start) >= 0))
+    expect_equal(v$date, as.Date(v$start, tz = lubridate::tz(v$start)))
+  }
+
+  for(r in list(finches, finches_lg, chickadees)) {
+    v <- visits(r, bw = 10000000000000000000)
+    expect_true(all(!is.na(v$start)))
+    expect_true(all(!is.na(v$end)))
+    expect_true(all(!is.na(v$date)))
+    expect_equal(v$date, as.Date(v$start, tz = lubridate::tz(v$start)))
+    expect_true(all(as.numeric(v$end - v$start) >= 0))
+  }
+
+
 })
 
 test_that("visits() has correct spacing", {
@@ -92,8 +112,9 @@ test_that("visits() returns correct data", {
   v <- visits(finches)
   expect_equal(v$animal_id[2], factor("041868D396", levels = c("041868D396", "041868D861", "062000043E", "06200004F8", "0620000514")))
   expect_equal(v$logger_id[2], factor("2100", levels = c("2100", "2200", "2400", "2700")))
-  expect_equal(v$start[2], as.POSIXct("2016-01-29 11:21:23", tz = "America/Vancouver"))
-  expect_equal(v$end[2], as.POSIXct("2016-01-29 11:21:26", tz = "America/Vancouver"))
+  expect_equal(v$start[2], as.POSIXct("2016-01-29 11:21:23", tz = "Etc/GMT+8"))
+  expect_equal(v$end[2], as.POSIXct("2016-01-29 11:21:26", tz = "Etc/GMT+8"))
+  expect_equal(v$date[2], as.Date("2016-01-29"))
   expect_equal(v$animal_n[2], 5)
   expect_equal(v$logger_n[2], 4)
   expect_equal(round(v$lon[2], 4), -120.3624)
@@ -118,7 +139,7 @@ test_that("visits() na_rm", {
 
 test_that("visits() pass", {
   expect_length(visits(finches, pass = FALSE), 7)
-  expect_length(visits(finches, pass = TRUE), 11)
+  expect_length(visits(finches, pass = TRUE), 13)
 })
 
 test_that("visits() with group_by", {

tests/testthat/test_b02_presence.R

@@ -8,12 +8,15 @@ test_that("presence() handles single animal", {
 
   ## Format
   expect_is(p, "data.frame")
-  expect_length(p, 12)
+  expect_length(p, 14)
   expect_match(names(p)[1:5], "^logger_id$|^animal_id$|^date$|^start$|^end$|^length$")
   expect_is(p$animal_id, "factor")
   expect_is(p$logger_id, "factor")
+  expect_is(p$date, "Date")
   expect_is(p$start, "POSIXct")
 
+  expect_equal(p$date, as.Date(p$start, tz = lubridate::tz(p$start)))
+
   ## Not impossible nor missing
   expect_equal(sum(is.na(p)), 0)
   expect_true(all(p$end >= p$start))
@@ -28,10 +31,11 @@ test_that("presence() handles multiple animals", {
 
   ## Format
   expect_is(p, "data.frame")
-  expect_length(p, 12)
+  expect_length(p, 14)
   expect_match(names(p)[1:5], "^logger_id$|^animal_id$|^date$|^start$|^end$|^length$")
   expect_is(p$animal_id, "factor")
   expect_is(p$logger_id, "factor")
+  expect_is(p$date, "Date")
   expect_is(p$start, "POSIXct")
 
   ## Not impossible nor missing
@@ -41,6 +45,6 @@ test_that("presence() handles multiple animals", {
 
 test_that("presence() pass", {
   expect_length(presence(visits(finches), pass = FALSE), 6)
-  expect_length(presence(visits(finches), pass = TRUE), 12)
+  expect_length(presence(visits(finches), pass = TRUE), 14)
 })
 

tests/testthat/test_b03_move.R

@@ -9,13 +9,16 @@ test_that("move() returns appropriate, non-empty dataframe", {
 
   ## Format
   expect_is(m, "data.frame")
-  expect_length(m, 15)
+  expect_length(m, 17)
   expect_equal(nrow(m), 30)
   expect_equal(sum(is.na(m)), 0)
   expect_match(names(m)[1:3], "^animal_id$|^date$|^time$|^logger_id$|^direction$|^move_dir$|^move_path$|^strength$")
   expect_is(m$animal_id, "factor")
   expect_is(m$logger_id, "factor")
+  expect_is(m$date, "Date")
   expect_is(m$time, "POSIXct")
+
+
 })
 
 test_that("move() returns non-impossible data", {
@@ -28,7 +31,10 @@ test_that("move() returns expected data", {
   m <- move(visits(finches))
   expect_equal(unique(m$animal_id[1]), factor("041868D396", levels = c("041868D396", "041868D861", "062000043E", "06200004F8", "0620000514")))
   expect_equal(m$logger_id[1:2], factor(c("2400", "2100"), levels = c("2100", "2200", "2400", "2700")))
-  expect_equal(m$time[1:2], as.POSIXct(c("2016-01-29 08:35:26", "2016-01-29 11:21:23"), tz = "America/Vancouver"))
+  expect_equal(m$time[1:2], as.POSIXct(c("2016-01-29 08:35:26", "2016-01-29 11:21:23"),
+                                       tz = "Etc/GMT+8"))
+  expect_equal(m$date[2], as.Date("2016-01-29"))
+  expect_equal(m$date, as.Date(m$time, tz = lubridate::tz(m$time)))
   expect_equal(m$animal_n[1], 5)
   expect_equal(m$logger_n[1], 4)
   expect_equal(round(m$lon[2], 4), -120.3624)
@@ -48,13 +54,13 @@ test_that("move() handles zero movements and single animal", {
   ## No movements (all = TRUE)
   expect_silent(m <- visits(finches) %>% dplyr::filter(animal_id == "062000043E") %>% move(., all = TRUE))
   expect_is(m, "data.frame")
-  expect_length(m, 15)
+  expect_length(m, 17)
   expect_equal(nrow(m), 1)
   expect_equal(m$animal_id[1], factor("062000043E", levels = c("041868D396", "041868D861", "062000043E", "06200004F8", "0620000514")))
 })
 
 test_that("move() pass", {
   expect_length(move(visits(finches), pass = FALSE), 9)
-  expect_length(move(visits(finches), pass = TRUE), 15)
+  expect_length(move(visits(finches), pass = TRUE), 17)
 })
 

tests/testthat/test_b04_disp.R

@@ -14,7 +14,7 @@ test_that("disp() returns appropriate, non-empty dataframe", {
   expect_is(d2 <- d[["summaries"]], "data.frame")
   expect_is(d3 <- d[["interactions"]], "data.frame")
 
-  expect_length(d1, 12)
+  expect_length(d1, 14)
   expect_length(d2, 4)
   expect_length(d3, 3)
 
@@ -49,7 +49,11 @@ test_that("disp() returns correct data", {
   ## Data
   expect_equal(unique(d1$animal_id[1]), factor("0620000514", levels = c("041868D396", "041868D861", "062000043E", "06200004F8", "0620000514")))
   expect_equal(d1$logger_id[1], factor(c("2200"), levels = c("2100", "2200", "2400", "2700")))
-  expect_equal(d1$left[1], as.POSIXct(c("2016-01-28 12:34:28"), tz = "America/Vancouver"))
+  expect_equal(d1$left[1], as.POSIXct(c("2016-01-28 12:34:28"), tz = "Etc/GMT+8"))
+  expect_equal(d1$date[1], as.Date("2016-01-28"))
+
+  expect_equal(d1$date, as.Date(d1$left, tz = lubridate::tz(d1$left)))
+
   expect_equal(d1$animal_n[1], 5)
   expect_equal(d1$logger_n[1], 4)
   expect_equal(round(d1$lon[2], 4), -120.3612)
@@ -63,5 +67,5 @@ test_that("disp() returns correct data", {
 
 test_that("disp() pass", {
   expect_length(visits(finches) %>% disp(., bw = 30, pass = FALSE) %>% .$displacements, 6)
-  expect_length(visits(finches) %>% disp(., bw = 30, pass = TRUE) %>% .$displacements, 12)
+  expect_length(visits(finches) %>% disp(., bw = 30, pass = TRUE) %>% .$displacements, 14)
 })

tests/testthat/test_b06_activity.R

@@ -15,12 +15,16 @@ test_that("activity() in general", {
   expect_match(names(a)[1:6], "^animal_id$|^time$|^date$|^activity$|^activity_c$|^logger_id$")
   expect_is(a$animal_id, "factor")
   expect_is(a$logger_id, "factor")
+  expect_is(a$date, "Date")
   expect_is(a$time, "POSIXct")
 
   expect_equal(a$animal_id[1], factor("06200004F8", levels = c("041868D396", "041868D861", "062000043E", "06200004F8", "0620000514")))
   expect_equal(a$logger_id[1], factor(NA, levels = c("2100", "2200", "2400", "2700")))
-  expect_equal(a$time[1], as.POSIXct("2016-01-28", tz = "America/Vancouver"))
+  expect_equal(a$date[1], as.Date("2016-01-28"))
+  expect_equal(a$time[1], as.POSIXct("2016-01-28", tz = "Etc/GMT+8"))
   expect_equal(nrow(a), 386)
+
+  expect_equal(a$date, as.Date(a$time, tz = lubridate::tz(a$time)))
 })
 
 # activity()
@@ -76,14 +80,14 @@ test_that("daily() by_logger == FALSE", {
 
   expect_equal(d$animal_id[1], factor("06200004F8", levels = c("041868D396", "041868D861", "062000043E", "06200004F8", "0620000514")))
   expect_equal(d$logger_id[1], factor(NA, levels = c("2100", "2200", "2400", "2700")))
-  expect_equal(d$time[1], as.POSIXct("1970-01-01", tz = "America/Vancouver"))
+  expect_equal(d$time[1], as.POSIXct("1970-01-01", tz = "Etc/GMT+8"))
   expect_equal(nrow(d), 192)
 
   a <- activity(p, by_logger = TRUE)
   d <- daily(a)
 
   expect_equal(d$animal_id[1], factor("06200004F8", levels = c("041868D396", "041868D861", "062000043E", "06200004F8", "0620000514")))
   expect_equal(d$logger_id[1], factor(2100, levels = c("2100", "2200", "2400", "2700")))
-  expect_equal(d$time[1], as.POSIXct("1970-01-01", tz = "America/Vancouver"))
+  expect_equal(d$time[1], as.POSIXct("1970-01-01", tz = "Etc/GMT+8"))
   expect_equal(nrow(d), 768)
 })

tests/testthat/test_b07_convert.R

@@ -252,7 +252,7 @@ test_that("convert_activity converts as expected", {
   expect_is(i, "list")
   expect_named(i, as.character(sort(unique(r$animal_id))))
   expect_is(i[[1]], "numeric")
-  expect_equal(i[["062000043E"]], c(3.067125, 3.067271), tolerance = 0.0000001)
+  expect_equal(i[["062000043E"]], c(2.805326, 2.805471), tolerance = 0.0000001)
 })
 
 test_that("convert_activity runs activity functions as expected", {