doc: use new sample dataset in example

R/filter_by_bbox.R

@@ -22,22 +22,22 @@
 #' library("forcis")
 #' 
 #' # Import example dataset ----
-#' file_name <- system.file(file.path("extdata", "FORCIS_pump_sample.csv"), 
+#' file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
 #'                          package = "forcis")
 #' 
-#' pump_data <- vroom::vroom(file_name, delim = ";", show_col_types = FALSE)
+#' net_data <- read.table(file_name, dec = ".", sep = ";")
 #' 
 #' # Add 'data_type' column ----
-#' pump_data$"data_type" <- "Pump"
+#' net_data$"data_type" <- "Net"
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 #' 
 #' # Filter by oceans ----
-#' pump_data_sub <- filter_by_bbox(pump_data, bbox = c(35, 0, 45, 30))
+#' net_data_sub <- filter_by_bbox(net_data, bbox = c(45, -61, 82, -24))
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data_sub)
+#' dim(net_data_sub)
 
 filter_by_bbox <- function(data, bbox) {
 

R/filter_by_month.R

@@ -16,22 +16,22 @@
 #' library("forcis")
 #' 
 #' # Import example dataset ----
-#' file_name <- system.file(file.path("extdata", "FORCIS_pump_sample.csv"), 
+#' file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
 #'                          package = "forcis")
 #' 
-#' pump_data <- vroom::vroom(file_name, delim = ";", show_col_types = FALSE)
+#' net_data <- read.table(file_name, dec = ".", sep = ";")
 #' 
 #' # Add 'data_type' column ----
-#' pump_data$"data_type" <- "Pump"
+#' net_data$"data_type" <- "Net"
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 #' 
 #' # Filter by months ----
-#' pump_data_sub <- filter_by_month(pump_data, months = 1:2)
+#' net_data_sub <- filter_by_month(net_data, months = 1:2)
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data_sub)
+#' dim(net_data_sub)
 
 filter_by_month <- function(data, months) {
 

R/filter_by_ocean.R

@@ -17,25 +17,25 @@
 #' library("forcis")
 #' 
 #' # Import example dataset ----
-#' file_name <- system.file(file.path("extdata", "FORCIS_pump_sample.csv"), 
+#' file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
 #'                          package = "forcis")
 #' 
-#' pump_data <- vroom::vroom(file_name, delim = ";", show_col_types = FALSE)
+#' net_data <- read.table(file_name, dec = ".", sep = ";")
 #' 
 #' # Add 'data_type' column ----
-#' pump_data$"data_type" <- "Pump"
+#' net_data$"data_type" <- "Net"
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 #' 
 #' # Get ocean names ----
 #' get_ocean_names()
 #' 
 #' # Filter by oceans ----
-#' pump_data_sub <- filter_by_ocean(pump_data, ocean = "Indian Ocean")
+#' net_data_sub <- filter_by_ocean(net_data, ocean = "Indian Ocean")
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data_sub)
+#' dim(net_data_sub)
 
 filter_by_ocean <- function(data, ocean) {
 

R/filter_by_polygon.R

@@ -17,16 +17,16 @@
 #' library("forcis")
 #' 
 #' # Import example dataset ----
-#' file_name <- system.file(file.path("extdata", "FORCIS_pump_sample.csv"), 
+#' file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
 #'                          package = "forcis")
 #' 
-#' pump_data <- vroom::vroom(file_name, delim = ";", show_col_types = FALSE)
+#' net_data <- read.table(file_name, dec = ".", sep = ";")
 #' 
 #' # Add 'data_type' column ----
-#' pump_data$"data_type" <- "Pump"
+#' net_data$"data_type" <- "Net"
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 #' 
 #' # Import Indian Ocean spatial polygons ----
 #' file_name <- system.file(file.path("extdata", "IHO_Indian_ocean_polygon.gpkg"), 
@@ -35,10 +35,10 @@
 #' indian_ocean <- sf::st_read(file_name)
 #' 
 #' # Filter by polygon ----
-#' pump_data_sub <- filter_by_polygon(pump_data, polygon = indian_ocean)
+#' net_data_sub <- filter_by_polygon(net_data, polygon = indian_ocean)
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data_sub)
+#' dim(net_data_sub)
 
 filter_by_polygon <- function(data, polygon) {
 

R/filter_by_species.R

@@ -17,42 +17,43 @@
 #'
 #' @examples
 #' # Import example dataset ----
-#' file_name <- system.file(file.path("extdata", "FORCIS_pump_sample.csv"), 
+#' file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
 #'                          package = "forcis")
 #' 
-#' pump_data <- vroom::vroom(file_name, delim = ";", show_col_types = FALSE)
+#' net_data <- read.table(file_name, dec = ".", sep = ";")
 #' 
 #' # Add 'data_type' column ----
-#' pump_data$"data_type" <- "Pump"
+#' net_data$"data_type" <- "Net"
 #' 
 #' # Select a taxonomy ----
-#' pump_data <- select_taxonomy(pump_data, taxonomy = "OT")
+#' net_data <- select_taxonomy(net_data, taxonomy = "VT")
 #' 
 #' # Select only required columns (and taxa) ----
-#' pump_data <- select_columns(pump_data)
+#' net_data <- select_columns(net_data)
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 #' 
 #' # Convert data into long format ----
-#' pump_data <- reshape_data(pump_data)
+#' net_data <- reshape_data(net_data)
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 #' 
 #' # Total number of species ----
-#' length(unique(pump_data$"taxa"))
+#' length(unique(net_data$"taxa"))
 #' 
 #' # Select records for three species ----
-#' pump_data_sub <- filter_by_species(data    = pump_data, 
-#'                                    species = c("g_inflata", "g_ruber", 
-#'                                                "g_glutinata"))
+#' net_data_sub <- filter_by_species(data    = net_data, 
+#'                                   species = c("g_inflata_VT", 
+#'                                               "g_elongatus_VT", 
+#'                                               "g_glutinata_VT"))
 #'
 #' # Dimensions of the data.frame ----
-#' dim(pump_data_sub)
+#' dim(net_data_sub)
 #' 
 #' # Total number of species ----
-#' length(unique(pump_data_sub$"taxa"))
+#' length(unique(net_data_sub$"taxa"))
 
 filter_by_species <- function(data, species, rm_na = FALSE) {
 

R/filter_by_year.R

@@ -16,22 +16,22 @@
 #' library("forcis")
 #' 
 #' # Import example dataset ----
-#' file_name <- system.file(file.path("extdata", "FORCIS_pump_sample.csv"), 
+#' file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
 #'                          package = "forcis")
 #' 
-#' pump_data <- vroom::vroom(file_name, delim = ";", show_col_types = FALSE)
+#' net_data <- read.table(file_name, dec = ".", sep = ";")
 #' 
 #' # Add 'data_type' column ----
-#' pump_data$"data_type" <- "Pump"
+#' net_data$"data_type" <- "Net"
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 #' 
 #' # Filter by years ----
-#' pump_data_sub <- filter_by_year(pump_data, years = 1985)
+#' net_data_sub <- filter_by_year(net_data, years = 1992)
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data_sub)
+#' dim(net_data_sub)
 
 filter_by_year <- function(data, years) {
 

R/ggmap_data.R

@@ -18,19 +18,19 @@
 #' library("forcis")
 #' 
 #' # Import example dataset ----
-#' file_name <- system.file(file.path("extdata", "FORCIS_pump_sample.csv"), 
+#' file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
 #'                          package = "forcis")
 #' 
-#' pump_data <- vroom::vroom(file_name, delim = ";", show_col_types = FALSE)
+#' net_data <- read.table(file_name, dec = ".", sep = ";")
 #' 
 #' # Add 'data_type' column ----
-#' pump_data$"data_type" <- "Pump"
+#' net_data$"data_type" <- "Net"
 #' 
 #' # Map data (default) ----
-#' ggmap_data(pump_data)
+#' ggmap_data(net_data)
 #' 
 #' # Map data ----
-#' ggmap_data(pump_data, col = "black", fill = "red", shape = 21, size = 2)
+#' ggmap_data(net_data, col = "black", fill = "red", shape = 21, size = 2)
 
 ggmap_data <- function(data, col = "red", ...) {
 

R/select_columns.R

@@ -20,28 +20,28 @@
 #' library("forcis")
 #' 
 #' # Import example dataset ----
-#' file_name <- system.file(file.path("extdata", "FORCIS_pump_sample.csv"), 
+#' file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
 #'                          package = "forcis")
 #' 
-#' pump_data <- vroom::vroom(file_name, delim = ";", show_col_types = FALSE)
+#' net_data <- read.table(file_name, dec = ".", sep = ";")
 #' 
 #' # Add 'data_type' column ----
-#' pump_data$"data_type" <- "Pump"
+#' net_data$"data_type" <- "Net"
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 #' 
 #' # Select a taxonomy ----
-#' pump_data <- select_taxonomy(pump_data, taxonomy = "OT")
+#' net_data <- select_taxonomy(net_data, taxonomy = "VT")
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 #' 
 #' # Select only required columns (and taxa) ----
-#' pump_data <- select_columns(pump_data)
+#' net_data <- select_columns(net_data)
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 
 select_columns <- function(data, cols = NULL) {
 

R/select_taxonomy.R

@@ -19,22 +19,22 @@
 #' library("forcis")
 #' 
 #' # Import example dataset ----
-#' file_name <- system.file(file.path("extdata", "FORCIS_pump_sample.csv"), 
+#' file_name <- system.file(file.path("extdata", "FORCIS_net_sample.csv"), 
 #'                          package = "forcis")
 #' 
-#' pump_data <- vroom::vroom(file_name, delim = ";", show_col_types = FALSE)
+#' net_data <- read.table(file_name, dec = ".", sep = ";")
 #' 
 #' # Add 'data_type' column ----
-#' pump_data$"data_type" <- "Pump"
+#' net_data$"data_type" <- "Net"
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 #' 
 #' # Select a taxonomy ----
-#' pump_data <- select_taxonomy(pump_data, taxonomy = "OT")
+#' net_data <- select_taxonomy(net_data, taxonomy = "VT")
 #' 
 #' # Dimensions of the data.frame ----
-#' dim(pump_data)
+#' dim(net_data)
 
 select_taxonomy <- function(data, taxonomy) {
 
@@ -69,4 +69,4 @@ select_taxonomy <- function(data, taxonomy) {
   }
 
   data
-}
+}