R Intro

Load R packages.

library(tidyverse)
library(sf)
library(tmap)

Read CSV

Read GBIF CSV.

beaver_df <- read_csv('data/raw/Castor_canadensis-12106.csv')

Preview GBIF data.

glimpse(beaver_df)

Rows: 297
Columns: 16
$ gbifID                        <dbl> 2803114036, 2802971136, 2802941035, 2802…
$ name                          <chr> "Castor canadensis", "Castor canadensis"…
$ basis                         <chr> "HUMAN_OBSERVATION", "HUMAN_OBSERVATION"…
$ catalogNumber                 <chr> "50723465", "50723148", "49373197", "493…
$ collectionCode                <chr> "Observations", "Observations", "Observa…
$ collectionID                  <chr> NA, NA, NA, NA, NA, NA, "http://grbio.or…
$ institutionCode               <chr> "iNaturalist", "iNaturalist", "iNaturali…
$ decimalLatitude               <dbl> 45.38804, 45.15445, 44.69292, 44.75682, …
$ decimalLongitude              <dbl> -117.1105, -117.1680, -118.0682, -118.14…
$ coordinateUncertaintyInMeters <dbl> 27190, 27222, 27285, 27285, 27285, 5, NA…
$ scientificName                <chr> "Castor canadensis Kuhl, 1820", "Castor …
$ year                          <dbl> 2020, 2020, 2020, 2020, 2020, 2020, 2003…
$ month                         <dbl> 6, 6, 6, 6, 6, 6, 6, 5, 6, 6, 5, 5, 5, 5…
$ day                           <dbl> 23, 23, 12, 12, 12, 10, 23, 19, 1, 1, 31…
$ verbatimLocality              <chr> "Oregon, US", "Oregon, US", "Baker Count…
$ eventDate                     <dttm> 2020-06-23 11:45:46, 2020-06-23 11:07:4…

Update GBIF data so that it can plotted on a map. st_as_sf() will create a vector point for each record using decimalLongitude and decimalLatitude, add a geometry column, and set the coordinate reference system.

beaver_sf <- st_as_sf(beaver_df, 
                      coords = c('decimalLongitude', 'decimalLatitude'), 
                      crs=4326, 
                      remove=FALSE)

Read GeoJSON

Read a GeoJSON file that has the boundaries for Oregon state.

oregon_sf <- read_sf('data/cleaned/oregon.geojson')

Check if GBIF data and Oregon boundary have same CRS.

st_crs(oregon_sf) == st_crs(beaver_sf)

[1] FALSE

Update CRS for Oregon boundaries.

oregon_sf <- st_transform(oregon_sf, crs=st_crs(beaver_sf))
st_crs(oregon_sf) == st_crs(beaver_sf)

[1] TRUE

Interactive maps

Create interactive map.

tmap_mode("view")

ℹ tmap mode set to "view".

Create map with GBIF data and Oregon boundary. Color code each GBIF occurrence record using the basis field. Use Open Street Maps as basemap.

tm_shape(oregon_sf) +
  tm_lines() +
  tm_shape(beaver_sf) +
  tm_symbols(fill='basis') +
  tm_basemap("OpenStreetMap")

Static maps

Create static map.

tmap_mode("plot")

ℹ tmap mode set to "plot".

Create map with GBIF data and Oregon boundary. Color code each GBIF occurrence record using the basis field. Use Open Street Maps as basemap.

tm_shape(oregon_sf) +
  tm_lines() +
  tm_shape(beaver_sf) +
  tm_symbols(fill='basis') +
  tm_basemap("OpenStreetMap")

Update map appearance. Add a north arrow, scale bar, and a title.

map <- tm_shape(oregon_sf) +
  tm_lines() +
  tm_shape(beaver_sf) +
  tm_symbols(fill='basis') +
  tm_basemap("OpenStreetMap")  +
  tm_compass(position = c("left", "bottom")) +
  tm_scalebar(position = c("left", "bottom")) +
  tm_title("Beaver occurrence in Oregon")  +
  tm_layout(inner.margins = c(0.1,.1),
            legend.position=c("right", "bottom"),
            legend.bg.color = 'white')

map

Save map as png image.

tmap_save(map, filename = "output/beaver_oregon.png", width = 7, height = 7)

Bar charts

Create bar chart. Use basis values for the x axis.

ggplot(beaver_df) +
  geom_bar(mapping=aes(x=basis))

Update chart appearance. Add color to the bars, a title, and custom theme.

chart <- ggplot(beaver_df) +
  geom_bar(mapping=aes(x=basis), fill='75cd5e')  + 
  labs(title = 'Beaver occurrence in Oregon')  +
  theme_bw() +
  theme(title = element_text(size = 14), 
        panel.grid.major.x = element_blank(),
        panel.grid.minor.x = element_blank())
  
chart

Save chart as png image.

ggsave('output/chart.png', chart, width = 5, height=5)