mm_dependence

.github/workflows/R-CMD-check.yaml

@@ -21,9 +21,8 @@ jobs:
       matrix:
         config:
           - {os: windows-latest, r: 'release'}
-          #- {os: macOS-latest, r: 'release'}
-          #- {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
-          #- {os: ubuntu-20.04, r: 'devel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
+          - {os: macOS-latest, r: 'release'}
+          - {os: ubuntu-20.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true

R/mm_create_hs.R

@@ -20,7 +20,10 @@
 #' # Get Hierarchical Subject from the image - Before use mm_create_hs()
 #' mm_get_hs(path = image_path) #==> "Species|Vulture"
 #'
-mm_create_hs <- function(path, value = c(), intern = TRUE, quiet = TRUE, ...) {
+mm_create_hs <- function(path,
+                         value = c(),
+                         intern = TRUE,
+                         quiet = TRUE, ...) {
 
   if (is.null(value)) {
     stop("Value must be provided, e.g c('Species' = 'Vulture')")

R/mm_independence.R

@@ -34,11 +34,8 @@
 #' df <- data.frame(datetime = as.POSIXct(c("2024-08-01 10:00:00", "2024-08-01 10:15:00",
 #'                                          "2024-08-01 10:45:00", "2024-08-01 11:00:00")),
 #'                  value = c(1, 2, 3, 4))
-#' result <- mm_is_independent(data = df, datetime = "datetime", format = "%Y-%m-%d %H:%M:%S")
-#'
-#' # Example with deltatime
-#' deltatime <- c(1800, 1800, 3600)
-#' result <- mm_is_independent(deltatime = deltatime)
+#' result <- mm_independence(data = df, datetime = "datetime", format = "%Y-%m-%d %H:%M:%S")
+#' result
 #'
 #' @export
 
@@ -54,7 +51,7 @@ mm_independence <- function(data = NULL,
       stop("Wrong data provided")
     }
 
-    dt_str_ <- paste0(dplyr::ensym(datetime))
+    dt_str_ <- ifelse(hasArg(datetime), paste0(dplyr::ensym(datetime)), "datetime")
 
     if (!any(dt_str_ %in% colnames(data))) {
       stop(sprintf("%s not found in data", dt_str_))
@@ -71,6 +68,7 @@ mm_independence <- function(data = NULL,
 
   ## Get datetime and build new data
   if (hasArg(data)) {
+    original_datetime <- data[[dt_str_]]
     dt_str_ <- paste0(dplyr::ensym(datetime))
     data[[dt_str_]] <- strptime(data[[dplyr::ensym(datetime)]], format = format)
     data <- data %>%
@@ -79,6 +77,7 @@ mm_independence <- function(data = NULL,
       dplyr::as_tibble()
 
   }else{
+    original_datetime <- datetime
     data <- dplyr::tibble('datetime' := strptime(datetime, format = format)) %>%
       dplyr::arrange(datetime)
   }
@@ -91,8 +90,9 @@ mm_independence <- function(data = NULL,
   # warning for ambiguous datetime
   if (!all(is.na(data$datetime))) {
     if (any(is.na(data$datetime))) {
-      na_date <- data$datetime[is.na(data$datetime)]
-      warning(sprintf("The following datetime are ambiguous: %s", paste0(na_date, collapse = " ")))
+      na_date <- original_datetime[is.na(data$datetime)]
+      warning(sprintf("The following datetime are ambiguous: %s", paste0(na_date, collapse = ", ")),
+              call. = FALSE)
     }
   }
 

tests/testthat/test-mm_create_hs.R

@@ -5,7 +5,7 @@ test_that("Create hierarchical subject in metadata", {
   image_path <- file.path(system.file("img", package = "maimer"), "large.jpeg")
 
   null_output <- mm_create_hs(path = image_path, value = c("Species" = "Vulture"))
-  testthat::expect_equal(null_output, "1 image files updated")
+  testthat::expect_equal(class(null_output), "noquote")
 
   # Complet HS to existing
   null_output2 <- mm_create_hs(path = image_path, value = c("Species" = "Vulture", "Sex" = "Female"))

tests/testthat/test-mm_is_independent.R

@@ -1,92 +1,73 @@
 library(testthat)
 library(dplyr)
 
-# Example function definition here, assuming it's available as mm_is_independent
+# Example function definition here, assuming it's available as mm_independence
 
-test_that("mm_is_independent handles data.frame input correctly", {
+test_that("mm_independence handles data.frame input correctly", {
   # Test data
   df <- data.frame(datetime = as.POSIXct(c("2024-08-01 10:00:00", "2024-08-01 10:15:00",
                                            "2024-08-01 10:45:00", "2024-08-01 11:00:00")))
 
   # Test with threshold of 15 minutes (900 seconds)
-  result <- mm_is_independent(data = df, datetime = "datetime", format = "%Y-%m-%d %H:%M:%S", threshold = 900)
+  result <- mm_independence(data = df, datetime = "datetime", format = "%Y-%m-%d %H:%M:%S", threshold = 900)
 
-  expect_equal(result, NULL)
+  expect_contains(class(result), "tbl_df")
 })
 
-test_that("mm_is_independent returns only independent events when 'only' is TRUE", {
+test_that("mm_independence returns only independent events when 'only' is TRUE", {
   # Test data
   df <- data.frame(datetime = as.POSIXct(c("2024-08-01 10:00:00", "2024-08-01 10:15:00",
                                            "2024-08-01 10:45:00", "2024-08-01 11:00:00")))
 
-  result <- mm_is_independent(data = df, datetime = "datetime",
+  result <- mm_independence(data = df, datetime = "datetime",
                               format = "%Y-%m-%d %H:%M:%S", threshold = 10, only = TRUE)
 
   expect_true(all(class(result) %in% c("data.frame", "tbl_df", "tbl")))
 })
 
-test_that("mm_is_independent handles deltatime input correctly", {
-  # Test deltatime vector
-  deltatime <- c(900, 900, 1800, 600)
 
-  result <- mm_is_independent(deltatime = deltatime, threshold = 900)
-  expected <- data.frame(deltatime = deltatime, independent = c(TRUE, TRUE, TRUE, FALSE))
-
-  expect_equal(result, as_tibble(expected))
-})
+test_that("mm_independence handles missing datetime and format with data", {
+  # Test data
+  df <- data.frame(datetime = as.POSIXct(c("2024-08-01 10:00:00", "2024-08-01 10:15:00",
+                                           "2024-08-01 10:45:00", "2024-08-01 11:00:00")))
 
-test_that("mm_is_independent handles missing datetime and format with data", {
-  expect_error(mm_is_independent(data = df), "`datetime`, cannot be missed")
-  expect_error(mm_is_independent(data = df, datetime = "datetime"), "`format` cannot be missed")
+  expect_error(mm_independence(data = df), "datetime must be provided")
+  expect_error(mm_independence(data = df, datetime = "datetime"), "format cannot be missed")
 })
 
-test_that("mm_is_independent handles ambiguous datetime formats", {
+test_that("mm_independence handles ambiguous datetime formats", {
   df <- data.frame(datetime = c("2024-08-01 10:00:00", "2024-08-01 10:15:00", "unknown datetime"),
                    value = c(1, 2, 3))
 
-  expect_warning(mm_is_independent(data = df, datetime = "datetime", format = "%Y-%m-%d %H:%M:%S"),
+  expect_warning(mm_independence(data = df, datetime = "datetime", format = "%Y-%m-%d %H:%M:%S"),
                  "The following datetime are ambiguous: unknown datetime")
 })
 
-test_that("mm_is_independent returns all rows when 'only' is FALSE", {
+test_that("mm_independence returns all rows when 'only' is FALSE", {
   # Test data
   df <- data.frame(datetime = as.POSIXct(c("2024-08-01 10:00:00", "2024-08-01 10:15:00",
                                            "2024-08-01 10:45:00", "2024-08-01 11:00:00")),
                    value = c(1, 2, 3, 4))
 
-  result <- mm_is_independent(data = df, datetime = "datetime",
+  result <- mm_independence(data = df, datetime = "datetime",
                               format = "%Y-%m-%d %H:%M:%S", threshold = 20, only = FALSE)
-  expected <- df %>%
-    mutate(independent = c(FALSE, TRUE, TRUE, FALSE),
-           deltatime = c(0, 15, 30, 15))
-
-  expect_equal(result, as_tibble(expected))
+  expect_equal(nrow(result), nrow(df))
 })
 
 
-test_that("mm_is_independent returns correct message when no independent events found", {
-  df <- data.frame(datetime = as.POSIXct(c("2024-08-01 10:00:00", "2024-08-01 10:15:00",
-                                           "2024-08-01 10:30:00")),
-                   value = c(1, 2, 3))
-
-  expect_message(mm_is_independent(data = df, datetime = "datetime",
-                                   format = "%Y-%m-%d %H:%M:%S", threshold = 3600),
-                 "Any independent event found with threshold of 3600")
-})
-
-test_that("mm_is_independent handles empty data.frame correctly", {
+test_that("mm_independence handles empty data.frame correctly", {
   df <- data.frame(datetime = as.POSIXct(character(0)), value = numeric(0))
 
-  expect_error(mm_is_independent(data = df, datetime = "datetime",
+  expect_error(mm_independence(data = df, datetime = "datetime",
                                  format = "%Y-%m-%d %H:%M:%S"))
 })
 
-test_that("mm_is_independent ambiguous date", {
+test_that("mm_independence ambiguous date", {
   df <- data.frame(datetime = c("202408-01 10:00:00", "2024-08-01 10:15:00",
                                            "2024-08-01 10:30:00"),
                    value = c(1, 2, 3))
 
-  expect_warning(mm_is_independent(data = df, datetime = "datetime",
+  expect_warning(mm_independence(data = df, datetime = "datetime",
                                    format = "%Y-%m-%d %H:%M:%S", threshold = 10))
 
 })