merge commit

Merge branch 'master' of github.com:frbcesab/forcis
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

R/database.R

@@ -6,7 +6,7 @@
 #' 
 #' @noRd
 
-forcis_db_version <- function() "v04_26072023"
+forcis_db_version <- function() "v05_14092023"
 
 
 
@@ -18,7 +18,7 @@ forcis_db_version <- function() "v04_26072023"
 #' 
 #' @noRd
 
-forcis_db_url <- function() "https://zenodo.org/record/8186736/files/"
+forcis_db_url <- function() "https://zenodo.org/record/8345072/files/"
 
 
 

R/gets.R

@@ -121,9 +121,23 @@ get_plankton_nets_data <- function(path = ".", version = forcis_db_version(),
 
 
   ## Read data ----
+
+  data <- vroom::vroom(file.path(path, plankton_net_filename()), delim = ";")
+
+
+  ## Check for data_type column ----
+
+  pos <- which("data_type" %in% colnames(data))
+
+  if (length(pos) > 0) {
+
+    data$"data_type" <- "Net"
 
-  data <- vroom::vroom(file.path(path, plankton_net_filename()))
-  data <- data.frame("data_type" = "Net", data)
+  } else {
+
+    data <- data.frame("data_type" = "Net", data)  
+  }
+
 
   taxa_columns <- get_species_names(data)
 
@@ -157,9 +171,23 @@ get_pump_data <- function(path = ".", version = forcis_db_version(),
 
 
   ## Read data ----
+
+  data <- vroom::vroom(file.path(path, pump_filename()), delim = ";")
+
+
+  ## Check for data_type column ----
+
+  pos <- which("data_type" %in% colnames(data))
+
+  if (length(pos) > 0) {
+
+    data$"data_type" <- "Pump"
+
+  } else {
+
+    data <- data.frame("data_type" = "Pump", data)
+  }
 
-  data <- vroom::vroom(file.path(path, pump_filename()))
-  data <- data.frame("data_type" = "Pump", data)
 
   taxa_columns <- get_species_names(data)
 
@@ -194,8 +222,22 @@ get_cpr_north_data <- function(path = ".", version = forcis_db_version(),
 
   ## Read data ----
 
-  data <- vroom::vroom(file.path(path, cpr_north_filename()))
-  data <- data.frame("data_type" = "CPR North", data)
+  data <- vroom::vroom(file.path(path, cpr_north_filename()), delim = ";")
+
+
+  ## Check for data_type column ----
+
+  pos <- which("data_type" %in% colnames(data))
+
+  if (length(pos) > 0) {
+
+    data$"data_type" <- "CPR North"
+
+  } else {
+
+    data <- data.frame("data_type" = "CPR North", data)
+  }
+
 
   data |> 
     dplyr::mutate(dplyr::across(.data$count_bin_min:.data$count_bin_max, 
@@ -229,8 +271,22 @@ get_cpr_south_data <- function(path = ".", version = forcis_db_version(),
 
   ## Read data ----
 
-  data <- vroom::vroom(file.path(path, cpr_south_filename()))
-  data <- data.frame("data_type" = "CPR South", data)
+  data <- vroom::vroom(file.path(path, cpr_south_filename()), delim = ";")
+
+
+  ## Check for data_type column ----
+
+  pos <- which("data_type" %in% colnames(data))
+
+  if (length(pos) > 0) {
+
+    data$"data_type" <- "CPR South"
+
+  } else {
+
+    data <- data.frame("data_type" = "CPR South", data)
+  }
+
 
   taxa_columns <- get_species_names(data)
 
@@ -264,9 +320,23 @@ get_sediment_trap_data <- function(path = ".", version = forcis_db_version(),
 
 
   ## Read data ----
+
+  data <- vroom::vroom(file.path(path, sediment_trap_filename()), delim = ";")
+
+
+  ## Check for data_type column ----
+
+  pos <- which("data_type" %in% colnames(data))
 
-  data <- vroom::vroom(file.path(path, sediment_trap_filename()))
-  data <- data.frame("data_type" = "Sediment trap", data)
+  if (length(pos) > 0) {
+
+    data$"data_type" <- "Sediment trap"
+
+  } else {
+
+    data <- data.frame("data_type" = "Sediment trap", data)
+  }
+
 
   taxa_columns <- get_species_names(data)