How to use the tinyForestR package

Getting started

The package is hosted on Github and is a work in progress. It can be installed by running devtools::install_github("julianflowers/tinyForestR").

The package makes use of a number of Application Programming Interfaces (APIs) some of which require API keys which will need to be applied for separately. This is outlined in the relevant sections of this vignette.

It also uses a range of Python packages to access some datasets (in some cases Python packages are better developed than R). For this reason the first step is to run initialise_tf() to intialise the package.

This:

Loads reticulate which R uses to talk to Python
Sets up a Python virtual environment (VE) called tinyforest, and ensures R uses the correct version of Python by specifying the RETICULATE_PYTHON environment variable. It may be necessary to restart R to make sure R correctly uses this.
You will be asked if you want to remove the tinyforest environment. Say “no” unless you have a previous installation and are having trouble. It will create a clean install of the VE.
Installs a number of Python packages to the tinyforest environment. These include
- earthengine-api which enables access to Google Earth Engine (GEE)
- geemap - a set of added value tools to extract and manipulate GEE data
- osdatahub - access to Ordnance Survey National Geographic Database data.
- OSGridConverter - converts lat-longs to UK Grid references
Imports the relevant modules for use in other packages

Install and initialise

if(!require("tinyForestR"))
#devtools::install_github("julianflowers/tinyForestR", force = FALSE)
if(!require("pacman"))install.packages("pacman")
library(pacman)
library(tinyForestR)

p_load(leaflet.extras2, tidyverse, mapview, sf, ggmap, lubridate, geojsonio)

initialise_tf()
#> virtualenv: tinyforest
#> Using virtual environment "tinyforest" ...

Load Tiny Forest data

The next step is to load Tiny Forest (TF) data. Because this only exists in a series of web pages the get_tf_data function identifies the relevant pages and iterates over them to extract name, id, location, area, planters, and types of tree planted (as a list column), for those TFs planted at the time of extraction. It does include TFs planted outside the UK. The function takes about 30 seconds to iterate over all the relevant pages.


tf <- tinyForestR::df

tf_df <- tf |>
  unnest("trees") |>
  mutate(year = year(date), 
         month = month(date))

Once the data is loaded we can save it as a csv file and get some high level information on planting, timings, size and so on.

As of 2023-06-18 there are 178 planted TFs.


needs(patchwork)

## annual planting

tf_year <- tf_df |>
  select(-trees) |>
  distinct() |>
  count(year) |>
  ggplot(aes(year, n)) +
  geom_col() +
  labs(title = "TFs planted per year")

## area distribution

tf_area <- tf_df |>
  select(-trees) |>
  distinct() |>
  ggplot(aes(factor(year), area)) +
  geom_boxplot() +
  labs(title = "TF area year")

tf_trees <- tf_df |>
  group_by(tf_id) |>
  summarise(n_trees = n()) |>
  ggplot() +
  geom_histogram(aes(n_trees)) +
  labs(title = "Distribution of tree species", 
       x = "Number of tree species")

tf_year + tf_area + tf_trees

Locations

It is now straightforward to map locations of TFs using sf and mapview.


library(mapview)

tf_df |>
  select(-trees) |>
  distinct() |>
  mutate(year = factor(year)) |>
  sf::st_as_sf(coords = c("lon", "lat"), crs = 4326) |>
  mapview::mapview(zcol = "year")

Tree species

We can also look at planting frequency for different tree species.


tf_df |>
  ungroup() |>
  unnest("trees") |>
  count(trees, sort = TRUE) |>
  top_n(25) |>
  ggplot() +
  geom_col(aes(n, reorder(trees, n))) +
  labs(y = "", 
       title = "25 most commonly planted tree species") +
  ggthemes::theme_base() +
  theme(plot.title.position = "plot")

Biodiversity data


tf1 <- tf_df |>
 select(lat, lon, tf_id) |>
  distinct()

i <- 1

lat <- tf1$lat[i]
lon <- tf1$lon[i]

The get_nbn_buffer downloads occurrence data from the NBN Atlas in a set buffer around a given longitude and latitude. For example we can download 10000 records around lat=51.777889, lon=-1.469139 (Witney TF).¹


safe_buff <- safely(tinyForestR::get_nbn_buffer)

nbn_data <- safe_buff(lon, lat, n = 10000)
#> 2.67 sec elapsed

nbn_data$result |>
  head()
#>    kingdom       phylum        classs         order    family     genus
#> 1  Plantae Tracheophyta Magnoliopsida       Rosales  Rosaceae Crataegus
#> 2 Animalia     Chordata          Aves Passeriformes   Paridae     Parus
#> 3  Plantae Tracheophyta Magnoliopsida   Gentianales Rubiaceae    Galium
#> 4  Plantae Tracheophyta Magnoliopsida       Fabales  Fabaceae      <NA>
#> 5 Animalia     Chordata          Aves Passeriformes  Turdidae    Turdus
#> 6 Animalia     Chordata          Aves Passeriformes  Turdidae    Turdus
#>   decimalLatitude decimalLongitude year month
#> 1        51.78306        -1.474075 2017    04
#> 2        51.78298        -1.472293 2010    10
#> 3        51.78256        -1.476333 2017    04
#> 4        51.77845        -1.465098 1968  <NA>
#> 5        51.78298        -1.472293 2010    12
#> 6        51.78298        -1.472293 2019    03
#>                         dataProviderName           speciesGroups
#> 1 Botanical Society of Britain & Ireland Plants, FloweringPlants
#> 2          British Trust for Ornithology          Animals, Birds
#> 3 Botanical Society of Britain & Ireland Plants, FloweringPlants
#> 4 Botanical Society of Britain & Ireland Plants, FloweringPlants
#> 5          British Trust for Ornithology          Animals, Birds
#> 6          British Trust for Ornithology          Animals, Birds
#>     vernacularName             species
#> 1 Midland Hawthorn Crataegus laevigata
#> 2        Great Tit         Parus major
#> 3         Cleavers      Galium aparine
#> 4             Bean                <NA>
#> 5        Blackbird       Turdus merula
#> 6        Blackbird       Turdus merula

Plant diversity using BSBI data

I have also included functions to extract data for the 2020 Botanic Society of Britain and Ireland survey. This is publicly available from for UK National Grid 1k hectads. This requires conversion of lat-longs to UK grids.


grid_ref <- tinyForestR::os_lat_lon_to_grid(lat = lat, lon = lon)
#> Using virtual environment "tinyforest" ...

grid_ref$grid
#> [1] "SP3672"


bsbi_data <- tinyForestR::get_bsbi_data(grid_ref = grid_ref$grid)

bsbi_data |>
  enframe() |>
  unnest("value") |>
  unnest("value") |>
  # slice(-c(168:173)) |>
  mutate(year = str_extract(value, "20\\d{2}"),
         value = str_remove(value, year),
         count = parse_number(value),
         value = str_remove(value, as.character(count)), 
         value = str_remove(value, "\\d{1,}"), 
         grid = grid_ref$grid, 
         tf_id = tf_df$tf_id[i]) |>
  arrange(value)  |>
  drop_na()
#> # A tibble: 7 × 6
#>   name    value                       year  count grid   tf_id
#>   <chr>   <chr>                       <chr> <dbl> <chr>  <dbl>
#> 1 records "Clinopodium ascendens()  " 2018      1 SP3672    85
#> 2 records "Cochlearia danica()  "     2016      1 SP3672    85
#> 3 records "Crataegus monogyna()  "    2015      1 SP3672    85
#> 4 records "Cupressus × leylandii()  " 2016      1 SP3672    85
#> 5 records "Galeopsis bifida()  "      2015      1 SP3672    85
#> 6 records "Hesperis matronalis()  "   2017      1 SP3672    85
#> 7 records "Oenothera stricta()  "     2017      1 SP3672    85

Rapid calculation of biodiversity metrics

The calc_bd_metrics function takes an output from get_nbn_buffer or get_bsbi_data, converts the data from long to wide format, creates a species matrix for a specified class (for get_nbn_buffer data), and outputs a list containing:

diversity metrics (Simpson)
species richness by month (plotted)
Bray-Curtis matrix
Raup matrix


metrics <- calc_bd_metrics(df = nbn_data$result, class = "Aves")


metrics$metrics
#>    month richness   N     ratio diversity
#> 1     01       17  60 0.2833333 0.9294444
#> 2     02       17  58 0.2931034 0.9256837
#> 3     03       24  74 0.3243243 0.9382761
#> 4     04       16  56 0.2857143 0.9266582
#> 5     05       43 104 0.4134615 0.9613536
#> 6     06       16  57 0.2807018 0.9258233
#> 7     07       19  53 0.3584906 0.9284443
#> 8     08       14  41 0.3414634 0.9125521
#> 9     09       24  59 0.4067797 0.9399598
#> 10    10       16  48 0.3333333 0.9253472
#> 11    11       15  60 0.2500000 0.9205556
#> 12    12       17  58 0.2931034 0.9304400

metrics$plot +
  labs(title = "Monthly species richness for ",
         subtitle = paste("Aves", tf1$tf_id[1]), 
       y = "Richness", 
       x = "Month") +
  ggthemes::theme_base() +
  theme(plot.title.position = "plot")

Vegatation indices

The package includes a calc_ndvi_buff function to enable the calculation of normalized vegetation index (NDVI) for the buffer area around a given point. It uses Sentinel2 surface reflectance satellite images which are available at 10m resolution and are regularly updated. The function extracts images via the Google Earth Engine API and requires registration and authentication prior to use (see…).

The function returns a list including, image dates, NDVI statistics for the image, an interactive map and a raster. Note it may take few minutes to run.

The code chunk below calculates the NDVI for each image containing the buffer around the Witney TF for 2019 and 2022 and maps them side-by-side. (Note, the function selects only those S2 images with cloud cover < 10%).


test <- calc_ndvi_buff(lon = -1.469, lat = 51.7779, dist1 = 1000, dist2 = 80, start_date = "2019-01-01", end_date = "2022-12-31", cloud_cover = 10, tf_id = 85)
#> ── rgee 1.1.5 ─────────────────────────────────────── earthengine-api 0.1.357 ── 
#>  ✔ user: not_defined
#>  ✔ Google Drive credentials:
 ✔ Google Drive credentials:  FOUND
#>  ✔ Initializing Google Earth Engine:
 ✔ Initializing Google Earth Engine:  DONE!
#> 
 ✔ Earth Engine account: users/julianflowers12 
#> ──────────────────────────────────────────────────────────────────────────────── 
#> Number of features: Calculating ...
Number of features: 1                     
#> Number of features: Calculating ...
Number of features: 1


test1 <- calc_ndvi_buff(lon = -1.469, lat = 51.7779, dist1 = 1000, dist2 = 80, start_date = "2017-01-01", end_date = "2018-12-31", cloud_cover = 10, tf_id = 85)
#> ── rgee 1.1.5 ─────────────────────────────────────── earthengine-api 0.1.357 ── 
#>  ✔ user: not_defined
#>  ✔ Google Drive credentials:
 ✔ Google Drive credentials:  FOUND
#>  ✔ Initializing Google Earth Engine:
 ✔ Initializing Google Earth Engine:  DONE!
#> 
 ✔ Earth Engine account: users/julianflowers12 
#> ──────────────────────────────────────────────────────────────────────────────── 
#> Number of features: Calculating ...
Number of features: 1                     
#> Number of features: Calculating ...
Number of features: 1


test$map + test1$map

Note this may sometimes time out depending on traffic on the NBN Atlas webservice↩︎

How to use the `tinyForestR` package

What is the `tinyForestR` package?

Getting started

Install and initialise

Load Tiny Forest data

Locations

Tree species

Biodiversity data

Plant diversity using BSBI data

Rapid calculation of biodiversity metrics

Vegatation indices

Environmental and ecological variables

How to use the tinyForestR package

What is the tinyForestR package?

Getting started

Install and initialise

Load Tiny Forest data

Locations

Tree species

Biodiversity data

Plant diversity using BSBI data

Rapid calculation of biodiversity metrics

Vegatation indices

Environmental and ecological variables

How to use the `tinyForestR` package

What is the `tinyForestR` package?