Set up project

## Load project ----
devtools::load_all()

Data acquisition

## Download data ----
dl_wildfinder_data()

Data importation

Mammals species list

## Import species list ----
sp_list  <- read_sp_list(here::here("data", "wildfinder", 
                                    "wildfinder-mammals_list.csv"))

Content of the wildfinder-mammals_list file
species_id	class	order	family	genus	species	common	sci_name
15168	Mammalia	Artiodactyla	Antilocapridae	Antilocapra	americana	Pronghorn	Antilocapra americana
15290	Mammalia	Artiodactyla	Bovidae	Addax	nasomaculatus	Addax	Addax nasomaculatus
15169	Mammalia	Artiodactyla	Bovidae	Aepyceros	melampus	Impala	Aepyceros melampus
15170	Mammalia	Artiodactyla	Bovidae	Alcelaphus	buselaphus	Hartebeest	Alcelaphus buselaphus
15176	Mammalia	Artiodactyla	Bovidae	Alcelaphus	lichtensteinii	Lichtenstein’s Hartebeest	Alcelaphus lichtensteinii
15177	Mammalia	Artiodactyla	Bovidae	Ammodorcas	clarkei	Dibatag	Ammodorcas clarkei

Ecoregions list

## Import ecoregions list ----
eco_list <- read_eco_list(here::here("data", "wildfinder", 
                                     "wildfinder-ecoregions_list.csv"))

Content of the wildfinder-ecoregions_list file
ecoregion_id	ecoregion	realm	biome
AA0106	Halmahera rain forests	Australasia	Tropical and Subtropical Moist Broadleaf Forests
AA0107	Huon Peninsula montane rain forests	Australasia	Tropical and Subtropical Moist Broadleaf Forests
AA0105	Central Range montane rain forests	Australasia	Tropical and Subtropical Moist Broadleaf Forests
AA0102	Banda Sea Islands moist deciduous forests	Australasia	Tropical and Subtropical Moist Broadleaf Forests
AA0103	Biak-Numfoor rain forests	Australasia	Tropical and Subtropical Moist Broadleaf Forests
AA0104	Buru rain forests	Australasia	Tropical and Subtropical Moist Broadleaf Forests

Merging table

## Import merging table ----
sp_eco   <- read_sp_eco(here::here("data", "wildfinder", 
                                   "wildfinder-ecoregions_species.csv"))

Content of the wildfinder-ecoregions_species file
ecoregion_id	species_id
AT0101	17507
AT0101	17688
AT0101	17730
AT0101	17736
AT0101	17741
AT0101	17789

Species selection

## Select species ----
sp_list <- select_species(sp_list, family = params$"mammals_family")

List of World Ursidae species
species_id	sci_name	family
14932	Ailuropoda melanoleuca	Ursidae
14934	Helarctos malayanus	Ursidae
14935	Melursus ursinus	Ursidae
14936	Tremarctos ornatus	Ursidae
14937	Ursus americanus	Ursidae
14938	Ursus arctos	Ursidae
27926	Ursus malayanus	Ursidae
14940	Ursus thibetanus	Ursidae

Add ecoregions

## Add ecoregions to species list ----
sp_eco_list <- add_ecoregions(sp_list, sp_eco, eco_list)

Complete dataset for Ursidae species
sci_name	ecoregion
Ailuropoda melanoleuca	Hengduan Mountains subalpine conifer forests
Ailuropoda melanoleuca	Yunnan Plateau subtropical evergreen forests
Ailuropoda melanoleuca	Daba Mountains evergreen forests
Ailuropoda melanoleuca	Qin Ling Mountains deciduous forests
Ailuropoda melanoleuca	Qionglai-Minshan conifer forests
Ailuropoda melanoleuca	Southeast Tibet shrub and meadows
Helarctos malayanus	Cardamom Mountains rain forests
Helarctos malayanus	Irrawaddy moist deciduous forests
Helarctos malayanus	Kayah-Karen montane rain forests
Helarctos malayanus	Northern Thailand-Laos moist deciduous forests

Count ecoregions

## Count ecoregions by species ----
counts_data <- count_ecoregions(sp_eco_list)

Number of ecoregions per Ursidae species
sci_name	n_ecoregions
Ursus arctos	139
Ursus americanus	82
Ursus thibetanus	78
Helarctos malayanus	37
Tremarctos ornatus	23
Melursus ursinus	21
Ailuropoda melanoleuca	6
Ursus malayanus	1

## Barplot ----
plot_counts(counts_data)

Number of ecoregions per Ursidae species