Extract site x locations information from long format data — fb_format_site

Convert a flat data.frame with site coordinates into a proper sf object that can then be used by other functions. This function assumes that the coordinates are given in WGS84 (longitude vs. latitude). The function automatically removes repeated coordinates from the input dataset.

Usage

fb_format_site_locations(
  data,
  site,
  longitude,
  latitude,
  crs = sf::st_crs(4326),
  na_rm = FALSE
)

Arguments

data: a data.frame in a long format (see example).
site: a character of length 1. Name of the column with site labels.
longitude: a character of length 1. Name of the column with longitude. The function assumes coordinates are WGS84 (EPSG:4326).
latitude: a character of length 1. Name of the column with latitude. The function assumes coordinates are WGS84 (EPSG:4326).
crs: a character of length 1 or an object of class crs. Coordinate Reference System (CRS) of the specified coordinates. The CRS should be a valid CRS in R. It can either be a character like "+proj=longlat +datum=WGS84 +no_defs" or as specified using sf::st_crs() like sf::st_crs(4326) the default value.
na_rm: a logical value. If TRUE remove sites with incomplete coordinates. Default is FALSE.

Value

An sf object with a site column specifying site coordinates.

Examples

library("funbiogeo")

filename <- system.file("extdata", "raw_mammals_data.csv", 
                        package = "funbiogeo")
all_data <- read.csv(filename)

head(all_data)
#>   species           order    site longitude latitude count adult_body_mass
#> 1  sp_001 Cetartiodactyla  fb_103  7.271821 59.09736     1        461900.8
#> 2  sp_001 Cetartiodactyla fb_1001 20.771821 52.59736     1        461900.8
#> 3  sp_001 Cetartiodactyla  fb_102  6.771821 59.09736     1        461900.8
#> 4  sp_001 Cetartiodactyla  fb_104  7.771821 59.09736     1        461900.8
#> 5  sp_001 Cetartiodactyla  fb_101  6.271821 59.09736     1        461900.8
#> 6  sp_001 Cetartiodactyla fb_1000 20.271821 52.59736     1        461900.8
#>   gestation_length litter_size max_longevity sexual_maturity_age diet_breadth
#> 1              235        1.25           324               668.2            1
#> 2              235        1.25           324               668.2            1
#> 3              235        1.25           324               668.2            1
#> 4              235        1.25           324               668.2            1
#> 5              235        1.25           324               668.2            1
#> 6              235        1.25           324               668.2            1

site_locations <- fb_format_site_locations(all_data, "site", "longitude", 
                                           "latitude")
head(site_locations)
#> Simple feature collection with 6 features and 1 field
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: 52.59736 ymin: 6.271821 xmax: 59.09736 ymax: 20.77182
#> Geodetic CRS:  WGS 84
#>      site                  geometry
#> 1  fb_103 POINT (59.09736 7.271821)
#> 2 fb_1001 POINT (52.59736 20.77182)
#> 3  fb_102 POINT (59.09736 6.771821)
#> 4  fb_104 POINT (59.09736 7.771821)
#> 5  fb_101 POINT (59.09736 6.271821)
#> 6 fb_1000 POINT (52.59736 20.27182)