From 93b3b43556a25a3a841d869b2ac9e1aafb4b9a9b Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 27 Mar 2023 10:48:53 +0200
Subject: [PATCH 1/9] Replace data with df

See https://github.com/trias-project/trias/issues/64#issuecomment-1482818789
---
 R/indicator_native_range_year.R    | 12 ++++++------
 man/indicator_native_range_year.Rd |  4 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/indicator_native_range_year.R b/R/indicator_native_range_year.R
index 7f24ae9a..046a7c92 100644
--- a/R/indicator_native_range_year.R
+++ b/R/indicator_native_range_year.R
@@ -4,7 +4,7 @@
 #' Based on
 #' [countYearProvince](https://github.com/inbo/reporting-rshiny-grofwildjacht/blob/exoten/reporting-grofwild/R/countYearProvince.R)
 #' plot from reporting - rshiny - grofwildjacht
-#' @param data input data.frame.
+#' @param df input data.frame.
 #' @param years (numeric) vector years we are interested to. If \code{NULL}
 #'   (default) all years from minimum and maximum of years of first observation
 #'   are taken into account.
@@ -29,7 +29,7 @@
 #' @export
 #' @importFrom dplyr %>% .data
 
-indicator_native_range_year <- function(data, years = NULL,
+indicator_native_range_year <- function(df, years = NULL,
                                         type = c("native_continent", "native_range"),
                                         x_lab = "year",
                                         y_lab = "alien species",
@@ -38,15 +38,15 @@ indicator_native_range_year <- function(data, years = NULL,
   type <- match.arg(type)
 
   # Rename to default column name
-  data <-
-    data %>%
+  df <-
+    df %>%
     dplyr::rename_at(dplyr::vars(first_observed), ~"first_observed")
 
   if (is.null(years)) {
-    years <- sort(unique(data$first_observed))
+    years <- sort(unique(df$first_observed))
   }
 
-  plotData <- data
+  plotData <- df
 
   plotData$location <- switch(type,
     native_range = plotData$native_range,
diff --git a/man/indicator_native_range_year.Rd b/man/indicator_native_range_year.Rd
index d2c78c60..ef1cede1 100644
--- a/man/indicator_native_range_year.Rd
+++ b/man/indicator_native_range_year.Rd
@@ -6,7 +6,7 @@
 and year of introduction}
 \usage{
 indicator_native_range_year(
-  data,
+  df,
   years = NULL,
   type = c("native_continent", "native_range"),
   x_lab = "year",
@@ -16,7 +16,7 @@ indicator_native_range_year(
 )
 }
 \arguments{
-\item{data}{input data.frame.}
+\item{df}{input data.frame.}
 
 \item{years}{(numeric) vector years we are interested to. If \code{NULL}
 (default) all years from minimum and maximum of years of first observation

From 37d33a0bb42060f015226822ed65f46f03b75800 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 27 Mar 2023 10:49:02 +0200
Subject: [PATCH 2/9] Bump version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5cec6fe7..001f9534 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: trias
 Title: Process Data for the Project Tracking Invasive Alien Species
     (TrIAS)
-Version: 2.0.5
+Version: 2.0.6
 Authors@R: c(
     person("Damiano", "Oldoni", email = "damiano.oldoni@inbo.be",
            role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3445-7562")),

From 51d1239dc4d9a70c494b85c263e6f0a8d3bc4e36 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 27 Mar 2023 11:24:29 +0200
Subject: [PATCH 3/9] Add example to function documentation

---
 R/indicator_native_range_year.R | 26 +++++++++++++++++++-------
 1 file changed, 19 insertions(+), 7 deletions(-)

diff --git a/R/indicator_native_range_year.R b/R/indicator_native_range_year.R
index 046a7c92..b3c7a8de 100644
--- a/R/indicator_native_range_year.R
+++ b/R/indicator_native_range_year.R
@@ -28,7 +28,25 @@
 #'   introduced from the native range for a given year. (n/total)*100} } } }
 #' @export
 #' @importFrom dplyr %>% .data
-
+#' @examples
+#' \dontrun{
+#' library(readr)
+#' datafile <- paste0(
+#'   "https://raw.githubusercontent.com/trias-project/indicators/master/data/",
+#'   "interim/data_input_checklist_indicators.tsv"
+#' )
+#' data <- read_tsv(datafile,
+#'   na = "",
+#'   col_types = cols(
+#'     .default = col_character(),
+#'     key = col_double(),
+#'     nubKey = col_double(),
+#'     speciesKey = col_double(),
+#'     first_observed = col_double(),
+#'     last_observed = col_double()
+#'   )
+#' )
+#' indicator_native_range_year(data, years = c(2010,2013))
 indicator_native_range_year <- function(df, years = NULL,
                                         type = c("native_continent", "native_range"),
                                         x_lab = "year",
@@ -56,17 +74,11 @@ indicator_native_range_year <- function(df, years = NULL,
   # Select data
   plotData <- plotData[plotData$first_observed %in% years, c("first_observed", "location")]
   plotData <- plotData[!is.na(plotData$first_observed) & !is.na(plotData$location), ]
-
   # Exclude unused provinces
   plotData$location <- as.factor(plotData$location)
   plotData$location <- droplevels(plotData$location)
 
   # Summarize data per native_range and year
-  plotData$first_observed <- with(plotData, factor(first_observed,
-    levels =
-      min(years):max(years)
-  ))
-
   summaryData <- reshape2::melt(table(plotData), id.vars = "first_observed")
   summaryData <- summaryData %>%
     dplyr::group_by(.data$first_observed) %>%

From 03893864404d0d317cb602b4af6ec5e0e057f987 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 27 Mar 2023 11:24:56 +0200
Subject: [PATCH 4/9] Fix #105

---
 R/indicator_native_range_year.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/indicator_native_range_year.R b/R/indicator_native_range_year.R
index b3c7a8de..25bb1df6 100644
--- a/R/indicator_native_range_year.R
+++ b/R/indicator_native_range_year.R
@@ -74,6 +74,10 @@ indicator_native_range_year <- function(df, years = NULL,
   # Select data
   plotData <- plotData[plotData$first_observed %in% years, c("first_observed", "location")]
   plotData <- plotData[!is.na(plotData$first_observed) & !is.na(plotData$location), ]
+  
+  # Exclude unused provinces
+  plotData$first_observed <- as.factor(plotData$first_observed)
+  
   # Exclude unused provinces
   plotData$location <- as.factor(plotData$location)
   plotData$location <- droplevels(plotData$location)

From 703e73503238d04efe3a865680b3be51628a74e2 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Mon, 27 Mar 2023 11:26:26 +0200
Subject: [PATCH 5/9] Import package in testthat for tests

---
 tests/testthat.R                       | 1 +
 tests/testthat/test-gbif_verify_keys.R | 2 --
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/tests/testthat.R b/tests/testthat.R
index 608d88c6..d933c8b9 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,4 +1,5 @@
 library(testthat)
+library(purrr)
 library(trias)
 
 test_check("trias")
diff --git a/tests/testthat/test-gbif_verify_keys.R b/tests/testthat/test-gbif_verify_keys.R
index fab2440b..414abafc 100644
--- a/tests/testthat/test-gbif_verify_keys.R
+++ b/tests/testthat/test-gbif_verify_keys.R
@@ -1,5 +1,3 @@
-#' @importFrom purrr map_chr
-#' 
 context("test_gbif_verify_keys")
 
 test_that("test several input types", {

From 42f6b4d8009255f3d6c4d39683b0371ad0cc79d7 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 29 Mar 2023 16:09:10 +0200
Subject: [PATCH 6/9] Improve documentation and args

---
 R/indicator_native_range_year.R    | 41 ++++++++++++++++++++++--------
 man/indicator_native_range_year.Rd | 31 +++++++++++++++++++---
 2 files changed, 58 insertions(+), 14 deletions(-)

diff --git a/R/indicator_native_range_year.R b/R/indicator_native_range_year.R
index 25bb1df6..5d612f76 100644
--- a/R/indicator_native_range_year.R
+++ b/R/indicator_native_range_year.R
@@ -9,12 +9,16 @@
 #'   (default) all years from minimum and maximum of years of first observation
 #'   are taken into account.
 #' @param type character, native_range level of interest should be one of
-#'   \code{c("native_continent", "native_range")}.
+#'   `c("native_range", "native_continent")`. Default: `"native_range"`. A
+#'   column called as the selected `type` must be present in `df`.
 #' @param x_lab character string, label of the x-axis. Default: "year".
 #' @param y_lab character string, label of the y-axis. Default: "number of alien
 #'   species".
-#' @param relative (logical) if TRUE, each bar is standardised before stacking
-#' @param first_observed (character) Name of the column in \code{data} containing temporal information about introduction of the alien species. Expressed as years.
+#' @param relative (logical) if TRUE (default), each bar is standardised before
+#'   stacking.
+#' @param first_observed (character) Name of the column in `data`
+#'   containing temporal information about introduction of the alien species.
+#'   Expressed as years.
 #' @return list with: \itemize{ \item{'static_plot': }{ggplot object, for a
 #'   given species the observed number per year and per native range is plotted
 #'   in a stacked bar chart} \item{'interactive_plot': }{plotly object, for a
@@ -46,15 +50,30 @@
 #'     last_observed = col_double()
 #'   )
 #' )
-#' indicator_native_range_year(data, years = c(2010,2013))
-indicator_native_range_year <- function(df, years = NULL,
-                                        type = c("native_continent", "native_range"),
-                                        x_lab = "year",
-                                        y_lab = "alien species",
-                                        relative = FALSE,
-                                        first_observed = "first_observed") {
+#' indicator_native_range_year(data, "native_continent", years = c(2010,2013))
+#' }
+indicator_native_range_year <- function(
+    df,
+    years = NULL,
+    type = c("native_range", "native_continent"),
+    x_lab = "year",
+    y_lab = "alien species",
+    relative = FALSE,
+    first_observed = "first_observed") {
+  # initial input checks
+  assertthat::assert_that(is.data.frame(df))
+  if (!is.null(years)) {
+    assertthat::assert_that(all(is.numeric(years)),
+                            msg = "Argument years has to be a number."
+    )
+    assertthat::assert_that(
+      all(years < as.integer(format(Sys.Date(), "%Y"))),
+      msg = sprintf(
+        "All values in years has to be less than %s.", format(Sys.Date(), "%Y")
+      )
+    )
+  }
   type <- match.arg(type)
-
   # Rename to default column name
   df <-
     df %>%
diff --git a/man/indicator_native_range_year.Rd b/man/indicator_native_range_year.Rd
index ef1cede1..24b6c349 100644
--- a/man/indicator_native_range_year.Rd
+++ b/man/indicator_native_range_year.Rd
@@ -23,16 +23,20 @@ indicator_native_range_year(
 are taken into account.}
 
 \item{type}{character, native_range level of interest should be one of
-\code{c("native_continent", "native_range")}.}
+\code{c("native_continent", "native_range")}. Default: \code{"native_continent"}. A
+column called as the selected \code{type} must be present in \code{df}.}
 
 \item{x_lab}{character string, label of the x-axis. Default: "year".}
 
 \item{y_lab}{character string, label of the y-axis. Default: "number of alien
 species".}
 
-\item{relative}{(logical) if TRUE, each bar is standardised before stacking}
+\item{relative}{(logical) if TRUE (default), each bar is standardised before
+stacking.}
 
-\item{first_observed}{(character) Name of the column in \code{data} containing temporal information about introduction of the alien species. Expressed as years.}
+\item{first_observed}{(character) Name of the column in \code{data}
+containing temporal information about introduction of the alien species.
+Expressed as years.}
 }
 \value{
 list with: \itemize{ \item{'static_plot': }{ggplot object, for a
@@ -52,3 +56,24 @@ Based on
 \href{https://github.com/inbo/reporting-rshiny-grofwildjacht/blob/exoten/reporting-grofwild/R/countYearProvince.R}{countYearProvince}
 plot from reporting - rshiny - grofwildjacht
 }
+\examples{
+\dontrun{
+library(readr)
+datafile <- paste0(
+  "https://raw.githubusercontent.com/trias-project/indicators/master/data/",
+  "interim/data_input_checklist_indicators.tsv"
+)
+data <- read_tsv(datafile,
+  na = "",
+  col_types = cols(
+    .default = col_character(),
+    key = col_double(),
+    nubKey = col_double(),
+    speciesKey = col_double(),
+    first_observed = col_double(),
+    last_observed = col_double()
+  )
+)
+indicator_native_range_year(data, "native_continent", years = c(2010,2013))
+}
+}

From 5c14711dfebb138dedd4053243e97e0606121da9 Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 29 Mar 2023 16:09:25 +0200
Subject: [PATCH 7/9] Improve assertions

---
 R/indicator_native_range_year.R | 27 ++++++++++++++++++++++++---
 1 file changed, 24 insertions(+), 3 deletions(-)

diff --git a/R/indicator_native_range_year.R b/R/indicator_native_range_year.R
index 5d612f76..dfc76699 100644
--- a/R/indicator_native_range_year.R
+++ b/R/indicator_native_range_year.R
@@ -74,6 +74,29 @@ indicator_native_range_year <- function(
     )
   }
   type <- match.arg(type)
+  assertthat::assert_that(type %in% names(df),
+                          msg = sprintf("Column %s not present in df.", type)
+  )
+  if (!is.null(x_lab)) {
+    assertthat::assert_that(is.character(x_lab),
+                            msg = "Argument x_lab has to be a character or NULL."
+    )
+  }
+  if (!is.null(y_lab)) {
+    assertthat::assert_that(is.character(y_lab),
+                            msg = "Argument y_lab has to be a character or NULL."
+    )
+    
+  }
+  assertthat::assert_that(is.logical(relative),
+                          msg = "Argument relative has to be a logical."
+  )
+  assertthat::assert_that(is.character(first_observed),
+                          msg = "Argument first_observed has to be a character."
+  )
+  assertable::assert_colnames(df, first_observed, only_colnames = FALSE)
+  
+  
   # Rename to default column name
   df <-
     df %>%
@@ -94,10 +117,8 @@ indicator_native_range_year <- function(
   plotData <- plotData[plotData$first_observed %in% years, c("first_observed", "location")]
   plotData <- plotData[!is.na(plotData$first_observed) & !is.na(plotData$location), ]
   
-  # Exclude unused provinces
+  # Set location and first_observed to factors
   plotData$first_observed <- as.factor(plotData$first_observed)
-  
-  # Exclude unused provinces
   plotData$location <- as.factor(plotData$location)
   plotData$location <- droplevels(plotData$location)
 

From 67fc4cbd1df09dae6a1f5a1136da04f0c6d4473b Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 29 Mar 2023 16:09:32 +0200
Subject: [PATCH 8/9] Add unit-tests

---
 .../test-indicator_native_range_year.R        | 146 ++++++++++++++++++
 1 file changed, 146 insertions(+)
 create mode 100644 tests/testthat/test-indicator_native_range_year.R

diff --git a/tests/testthat/test-indicator_native_range_year.R b/tests/testthat/test-indicator_native_range_year.R
new file mode 100644
index 00000000..f3109566
--- /dev/null
+++ b/tests/testthat/test-indicator_native_range_year.R
@@ -0,0 +1,146 @@
+context("test_indicator_native_range_year")
+
+# test df
+input_test_df <- read.delim(
+  test_path("data_test_input_graphs_indicators/test_visualization_df.tsv"),
+  sep = "\t"
+)
+
+nrow_no_first_obs <-
+  nrow(input_test_df[is.na(input_test_df$first_observed), ])
+
+cleaned_input_test_df <- input_test_df[!is.na(input_test_df$first_observed), ]
+
+test_that("Arg: df", {
+  expect_error(
+    indicator_native_range_year(3),
+    "df is not a data frame"
+  )
+})
+
+
+test_that("Arg: type", {
+  expect_error(
+    indicator_native_range_year(cleaned_input_test_df, 
+                                type = 2, 
+                                years = 2001),
+    "'arg' must be NULL or a character vector"
+  )
+  expect_error(
+    indicator_native_range_year(cleaned_input_test_df, 
+                                type = "aaa", 
+                                years = 2001),
+    "'arg' should be one of “native_range”, “native_continent”"
+  )
+  a <- cleaned_input_test_df
+  colnames(a)[colnames(a) == "native_range"] <- "l"
+  expect_error(
+    indicator_native_range_year(a, 
+                                type = "native_range", 
+                                years = 2001),
+    "Column native_range not present in df."
+  )
+})
+
+
+test_that("Arg: years", {
+  expect_error(
+    indicator_native_range_year(cleaned_input_test_df,
+      years = "2000"
+    ),
+    "Argument years has to be a number."
+  )
+  expect_error(
+    indicator_native_range_year(cleaned_input_test_df,
+                                years = c(2000,3000)
+    ),
+    sprintf("All values in years has to be less than %s.", format(Sys.Date(), "%Y"))
+  )
+})
+
+test_that("Arg: first_observed", {
+  expect_error(
+    indicator_native_range_year(input_test_df, 
+                                years = 2010, 
+                                first_observed = 3),
+    "Argument first_observed has to be a character."
+  )
+  expect_error(
+    indicator_native_range_year(input_test_df,
+                                year = 2010,
+                                first_observed = "bad_colname"
+    )
+  )
+})
+
+test_that("Param: labels", {
+  expect_error(
+    indicator_native_range_year(input_test_df, x_lab = input_test_df),
+    "Argument x_lab has to be a character or NULL."
+  )
+  expect_error(
+    indicator_native_range_year(input_test_df, y_lab = 4),
+    "Argument y_lab has to be a character or NULL."
+  )
+})
+
+test_that("Test output type, class, slots and columns", {
+  plot_output <-
+    indicator_native_range_year(cleaned_input_test_df,
+                                years = c(2000,2005)
+  )
+  plot_output_rel <-
+    indicator_native_range_year(cleaned_input_test_df,
+                                years = c(2000,2005),
+                                relative = TRUE
+  )
+  # output is a list
+  expect_type(plot_output, type = "list")
+  expect_type(plot_output_rel, type = "list")
+  
+  # output has the right three slots
+  slots <- c("static_plot", "interactive_plot", "data")
+  expect_equal(names(plot_output), slots)
+  expect_equal(names(plot_output_rel), slots)
+  
+  # static plot slot is a list with gg as class
+  expect_type(plot_output$static_plot, type = "list")
+  expect_type(plot_output_rel$static_plot, type = "list")
+  expect_s3_class(plot_output$static_plot, class = c("gg", "ggplot"))
+  expect_s3_class(plot_output_rel$static_plot, class = c("gg", "ggplot"))
+  
+  # interactive plot slot is a list with plotly and htmlwidget as class
+  expect_type(plot_output$interactive_plot, type = "list")
+  expect_type(plot_output_rel$interactive_plot, type = "list")
+  expect_s3_class(plot_output$interactive_plot, class = c("plotly", "htmlwidget"))
+  expect_s3_class(plot_output_rel$interactive_plot, class = c("plotly", "htmlwidget"))
+  
+  # data is a data.frame (tibble)
+  expect_type(plot_output$data, type = "list")
+  expect_s3_class(plot_output$data, class = c("data.frame", "tbl_df"))
+  expect_type(plot_output_rel$data, type = "list")
+  expect_s3_class(plot_output_rel$data, class = c("data.frame", "tbl_df"))
+  
+  # data contains only columns year, native_range, n, total and perc in this
+  # order
+  expect_equal(
+    names(plot_output$data),
+    c("year", "native_range", "n", "total", "perc")
+  )
+  expect_equal(
+    names(plot_output_rel$data),
+    c("year", "native_range", "n", "total", "perc")
+  )
+  
+  # columns year and native_range of data slot are factors
+  expect_true(is.factor(plot_output$data$year))
+  expect_true(is.factor(plot_output$data$native_range))
+  # columns n and total of data slot are integers
+  expect_true(is.integer(plot_output$data$n))
+  expect_true(is.integer(plot_output$data$total))
+  # column perc of data slot is double
+  expect_true(is.double(plot_output$data$perc))
+  
+  # data slot is not affected by value of related arg
+  expect_identical(plot_output$data, plot_output_rel$data)
+})

From 7221ea2235f8295174700deb339a93f35de3089e Mon Sep 17 00:00:00 2001
From: Damiano Oldoni <damiano.oldoni@inbo.be>
Date: Wed, 29 Mar 2023 16:36:03 +0200
Subject: [PATCH 9/9] Remove test around match.arg
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Problematic in R CMD check as “ “ are converted to \" \"
---
 man/indicator_native_range_year.Rd                | 4 ++--
 tests/testthat/test-indicator_native_range_year.R | 6 ------
 2 files changed, 2 insertions(+), 8 deletions(-)

diff --git a/man/indicator_native_range_year.Rd b/man/indicator_native_range_year.Rd
index 24b6c349..d82fbd0a 100644
--- a/man/indicator_native_range_year.Rd
+++ b/man/indicator_native_range_year.Rd
@@ -8,7 +8,7 @@ and year of introduction}
 indicator_native_range_year(
   df,
   years = NULL,
-  type = c("native_continent", "native_range"),
+  type = c("native_range", "native_continent"),
   x_lab = "year",
   y_lab = "alien species",
   relative = FALSE,
@@ -23,7 +23,7 @@ indicator_native_range_year(
 are taken into account.}
 
 \item{type}{character, native_range level of interest should be one of
-\code{c("native_continent", "native_range")}. Default: \code{"native_continent"}. A
+\code{c("native_range", "native_continent")}. Default: \code{"native_range"}. A
 column called as the selected \code{type} must be present in \code{df}.}
 
 \item{x_lab}{character string, label of the x-axis. Default: "year".}
diff --git a/tests/testthat/test-indicator_native_range_year.R b/tests/testthat/test-indicator_native_range_year.R
index f3109566..5374163c 100644
--- a/tests/testthat/test-indicator_native_range_year.R
+++ b/tests/testthat/test-indicator_native_range_year.R
@@ -26,12 +26,6 @@ test_that("Arg: type", {
                                 years = 2001),
     "'arg' must be NULL or a character vector"
   )
-  expect_error(
-    indicator_native_range_year(cleaned_input_test_df, 
-                                type = "aaa", 
-                                years = 2001),
-    "'arg' should be one of “native_range”, “native_continent”"
-  )
   a <- cleaned_input_test_df
   colnames(a)[colnames(a) == "native_range"] <- "l"
   expect_error(