Merge pull request #23 from b-cubed-eu/update0.2.2

Update0.2.2

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: b3gbi
 Title: General Biodiversity Indicators for Biodiversity Data Cubes
-Version: 0.2.1
+Version: 0.2.2
 Authors@R: c(
     person("Shawn", "Dove", email = "[email protected]",
            role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9465-5638"))

R/plot_methods.R

@@ -721,7 +721,7 @@ plot.occ_turnover <- function(x,
 #'    to exclude far-lying islands (default is TRUE, but does not affect other maps
 #'    or projections). Will not work if crop_to_grid is set to TRUE.
 #' @param crop_to_grid If TRUE, the grid will determine the edges of the map.Overrides
-#'    Europe_crop_EEA.
+#'    Europe_crop_EEA. Default is FALSE.
 #' @param surround If TRUE, includes surrounding land area in gray when plotting
 #'    at the country or continent level. If FALSE, all surrounding area will be colored
 #'    ocean blue (or whatever colour you set manually using panel_bg). Default is TRUE.

R/process_cube_functions.R

@@ -526,21 +526,23 @@ process_cube_old <- function(cube_name,
     # Remove columns that are not needed
     merged_data <-
       merged_data %>%
-      dplyr::select(-min_coord_uncertainty, -taxonomicStatus, -includes, -notes)
+      dplyr::select(-taxonomicStatus, -includes, -notes)
 
   } else {
 
     # Remove columns that are not needed
     merged_data <-
       merged_data %>%
-      dplyr::select(-min_coord_uncertainty, -taxonomicStatus, -includes)
+      dplyr::select(-taxonomicStatus, -includes)
 
   }
 
   # Rename column n to obs
   merged_data <-
     merged_data %>%
-    dplyr::rename(obs = n, cellCode = eea_cell_code)
+    dplyr::rename(obs = n,
+                  cellCode = eea_cell_code,
+                  minCoordUncertaintyInMeters = min_coord_uncertainty)
 
   # Check whether start and end years are within dataset
   first_year <- merged_data %>%

R/utils.R

@@ -379,3 +379,60 @@ rarefy_int <- function (x, sample, se = FALSE, MARGIN = 1)
   S.rare
 }
 
+
+# Copy of function meters_to_decdeg from the occUncertain github repository:
+# https://github.com/mlammens/occUncertain
+# Documentation below also copied from occUncertain repository.
+#
+#' @title Convert from meters to degrees correcting for global position
+#'
+#' @description
+#' \code{meters_to_decdeg} converts from meters to degrees at a specified
+#' position on the globe. The use case this function was developed for was to
+#' calculate occurrence point uncertainty values, which are usually reported in
+#' meters, as degrees.
+#'
+#' The formula for converting from meters to decimal degrees is in part
+#' based on information from the ESRI ArcUser magazine at this site
+#' \url{https://www.esri.com/news/arcuser/0400/wdside.html}
+#'
+#' @param occs_df A \code{data.frame} of occurrence locations that incudes
+#'   \emph{at least these three columns} - latitude, longitude, and a distance
+#'   in meters to be converted to decimal degrees.
+#' @param lat_col Name of column of latitude values. Caps sensitive.
+#' @param lon_col Name of column of longitude values. Caps sensitive.
+#' @param distance Name of column of distance values, in meters. Caps sensitive.
+#' @param na_action Enact distance options for NA values. Caps sensitive
+#' @return dist_dd A \code{data.frame} of latitude and longitude distances in
+#'   units of degree decimal.
+#'
+#' @noRd
+meters_to_decdeg <- function(occs_df, lat_col = "latitude",
+                             lon_col = "longitude", distance, na_action = "NA as 0") {
+  lat <- occs_df[[lat_col]]
+  lon <- occs_df[[lon_col]]
+  dist <- occs_df[[distance]]
+  #enact distance options for NA
+  # treat NA as 0
+  # treat NA as mean dist
+  # treat NA as NA
+  if (na_action == "NA as 0") {
+    dist <- ifelse (is.na(dist), yes = 0, no = dist )
+  } else if (na_action == "NA as mean") {
+    dist <- ifelse (is.na(dist), yes = mean(dist, na.rm = TRUE), no = dist )
+  } else if (na_action == "NA as NA" ) {
+    dist = dist
+  } else {
+    warning("Incorrect na_action chosen")
+    return(0)
+  }
+
+  #each degree the radius line of the Earth corresponds to 111139 meters.
+  lat_uncertainty <- dist/111325
+  #at the equator, longitude approx equals latitude
+  #decrease in a trigonometric cosine-based fashion as one moves toward the earth's poles
+  lon_uncertainty <- dist / (111325  * cos(lat * (pi / 180)))
+  dist_dd <- data.frame(lon_uncertainty = lon_uncertainty,
+                        lat_uncertainty = lat_uncertainty)
+  return(dist_dd)
+}