Leopardus pardalis Data Generation

Author

Florencia Grattarola

Published

October 1, 2024

Data generation for Leopardus pardalis (blobs and rasters).

R Libraries

library(patchwork)
library(knitr)
library(lubridate)
library(terra)
library(sf)
sf::sf_use_s2(FALSE)
library(tidyverse)

Basemaps

equalareaCRS <-  '+proj=laea +lon_0=-73.125 +lat_0=0 +datum=WGS84 +units=m +no_defs'
latam <- st_read('data/latam.gpkg', layer = 'latam', quiet = T)
countries <- st_read('data/latam.gpkg', layer = 'countries', quiet = T)
latam_land <- st_read('data/latam.gpkg', layer = 'latam_land', quiet = T)
latam_raster <- rast('data/latam_raster.tif', lyrs='latam')
latam_countries <- rast('data/latam_raster.tif', lyrs='countries')

lpardalis_IUCN <- sf::st_read('big_data/lpardalis_IUCN.shp', quiet = T) %>% sf::st_transform(crs=equalareaCRS)

Dataset

data_carnivores_PO <- read_csv('data/data_PO.csv')
data_carnivores_PA <- read_csv('data/data_PA.csv')

Check data for each years on example species

Code

# Presence-only
data_carnivores_PO %>% filter(species == 'Leopardus pardalis') %>% filter(year>=2000) %>% 
  mutate(period=ifelse(year<2014, 'first period: 2000-2013', 'second period: 2014-2021')) %>%
  group_by(species, period) %>% count() %>% pivot_wider(names_from = 'period', values_from = n) %>% kable()

PO data
species	first period: 2000-2013	second period: 2014-2021
Leopardus pardalis	378	2212

Code

# Presence-absence
data_carnivores_PA %>% filter(species == 'Leopardus pardalis' & presence ==1) %>% 
  mutate(period=ifelse(year(date_start)<2014, 'first period: 2000-2013', 'second period: 2014-2021')) %>%
  group_by(species, period) %>% count() %>% pivot_wider(names_from = 'period', values_from = n) %>% kable()

PA data
species	first period: 2000-2013	second period: 2014-2021
Leopardus pardalis	1584	1379

Presence-absence data

Create blobs

Blobs contain data on total effort, total temporal span, a list of the records IDs that are included for the blob and an area size of the combined areas.

Code

data_PA_GIS <- data_carnivores_PA %>% 
  filter(species == 'Leopardus pardalis') %>% 
  mutate(year=lubridate::year(date_end)) %>% 
  filter(year>=2000, year<=2021) %>% 
  as.data.frame() %>% 
  sf::st_as_sf(coords=c('decimalLongitude', 'decimalLatitude')) %>% 
  st_set_crs(4326) 

PA <- st_transform(data_PA_GIS, crs=equalareaCRS)

# create a blob for all sites
# blobs are definded as areas where some sampling was done over the entire period
periodStart <- ymd('2000-01-01')
periodEnd <- ymd('2014-01-01')
periodMax <- ymd('2020-12-31')

PA_allsites <- PA %>%
  mutate(start_date=as_date(ifelse(date_end-date_start<0, date_end, date_start)),
         end_date=as_date(ifelse(date_end-date_start<0, date_start, date_end))) %>%
  mutate(span=interval(date_start, date_end),
         target= interval(periodEnd, today()),
         period=ifelse(span %within% target, 'time2', 'time1')) %>% 
  distinct(independentLocation, period, .keep_all = T) 

PA_allsites_buff <- st_buffer(PA_allsites, sqrt(PA_allsites$area_m2/pi))

blobs_time1 <- PA_allsites_buff %>% filter(period=='time1') %>% 
  st_union() %>% st_cast('POLYGON') %>% st_sf('ID'= 1:length(.)) 
blobs_time2 <- PA_allsites_buff %>% filter(period=='time2') %>% 
  st_union() %>% st_cast('POLYGON') %>% st_sf('ID'= 1:length(.)) 

# to calculate the effort in days for each blob, we need to differenciate the two periods
PA_allsites_effort_and_time  <- PA %>%
  mutate(start_date=as_date(ifelse(date_end-date_start<0, date_end, date_start)),
         end_date=as_date(ifelse(date_end-date_start<0, date_start, date_end))) %>%
  mutate(span=interval(date_start, date_end),
         target= interval(periodEnd, today()),
         period=ifelse(span %within% target, 'time2', 'time1')) %>% 
  group_by(independentLocation, independentYearSpan, area_m2) %>%
  summarise(effort=max(effort),
            period=paste(unique(period)),
            recordIDs=paste(unique(recordID), collapse = ';'),
            maxEndDate=max(end_date),
            minStartDate=min(start_date)) %>% 
  mutate(maxTemporalSpan= maxEndDate-minStartDate)

# to calculate the effort in days for each blob, we need to differenciate the two periods
blobs_efforttime_time1 <- st_join(blobs_time1, 
                            PA_allsites_effort_and_time %>% filter(period=='time1'),
                            left=TRUE)  %>% 
  group_by(ID) %>% 
  summarise(effort=sum(effort),
            temporalSpan=sum(maxTemporalSpan),
            recordIDs=paste(unique(recordIDs), collapse = ';')) %>% 
  mutate(blobArea=st_area(.)) 


blobs_efforttime_time2 <- st_join(blobs_time2, 
                                PA_allsites_effort_and_time %>% filter(period=='time2'),
                                left=TRUE)  %>% 
  group_by(ID) %>% 
  summarise(effort=sum(effort),
            temporalSpan=sum(maxTemporalSpan),
            recordIDs=paste(unique(recordIDs), collapse = ';')) %>% 
  mutate(blobArea=st_area(.))

Calculate PA blobs

Code

# function  to create blobs for time1 and time2 for each species
calculate_PA_sp_blobs <- function(PA, blobs, sp, time){
  periodStart <- ymd('2000-01-01')
  periodEnd <- ymd('2014-01-01')
  df_period <- PA %>% filter(species==sp & presence==1) %>% 
    filter(date_start>=periodStart) %>% 
    mutate(span=interval(date_start, date_end),
           target=interval(periodEnd, today()),
           period=ifelse(span %within% target, 'time2', 'time1')) %>% 
    filter(period==time) %>% select(species, presence)
  
  df_period_blobs <- st_join(blobs, df_period,
                             left=TRUE, join = st_contains) %>%
    group_by(ID) %>% 
    summarise(presence=max(presence),
              temporalSpan=max(temporalSpan),
              effort=max(effort),
              blobArea=max(blobArea)) %>% 
    mutate(presence=ifelse(is.na(presence), 0, presence))
  return(df_period_blobs)
}

# Leopardus pardalis
PA_lpardalis_time1_blobs <- calculate_PA_sp_blobs(PA, blobs_efforttime_time1, 'Leopardus pardalis', 'time1')
PA_lpardalis_time2_blobs <- calculate_PA_sp_blobs(PA, blobs_efforttime_time2, 'Leopardus pardalis', 'time2')

Plots

Code

data_PA_time1_time2 <- rbind(PA_lpardalis_time1_blobs %>% mutate(period='time1'), 
                             PA_lpardalis_time2_blobs %>% mutate(period='time2'))

gg_PA_time1 <- ggplot() + 
    geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
    geom_sf(data=lpardalis_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
    geom_sf(data=data_PA_time1_time2 %>% filter(period=='time1') %>% st_buffer(20000), 
            aes(fill=factor(presence)), col=NA, show.legend = F) +
    coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + # st_bbox(lpardalis_IUCN)
    scale_fill_manual(values = c("#474545","#E31A1C"))+
    scale_color_manual(values = c("#474545","#E31A1C")) +
    labs(title='PA', subtitle='time1: 2000-2013', col='') +
    theme_bw() +    
    theme(text=element_text(size = 14)) 

gg_PA_time2 <- ggplot() + 
    geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
    geom_sf(data=lpardalis_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
    geom_sf(data=data_PA_time1_time2 %>% filter(period=='time2') %>% st_buffer(20000), 
            aes(fill=factor(presence), col=factor(presence)), show.legend = F) +
    coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + # st_bbox(lpardalis_IUCN)
    scale_fill_manual(values = c("#434445","#1F78B4"))+
    scale_color_manual(values = c("#434445","#1F78B4")) +
    labs(title='', subtitle='time2: 2014 to 2021', col='') +
    theme_bw() +    
    theme(text=element_text(size = 14)) 

gg_PA_time1 + gg_PA_time2

Presence-only data

Calculate PO rasters

Code

# rasterisation of the presence-only data
data_PO_GIS <- data_carnivores_PO %>% 
  filter(species == 'Leopardus pardalis') %>% 
  mutate(year=lubridate::year(eventDate)) %>% 
  filter(year>=2000, year<=2021) %>% 
  as.data.frame() %>% 
  sf::st_as_sf(coords=c('decimalLongitude', 'decimalLatitude')) %>% 
  st_set_crs(4326) 

PO <- st_transform(data_PO_GIS, crs=equalareaCRS)

# functions to create presence-only rasters for time1 and time2 for each species
calculate_PO_sp_period_raster <- function(PO, sp, raster, time){
  periodStart <- 2000
  periodEnd <- 2014
  df_period <- PO %>% filter(species==sp & !is.na(year)) %>% 
    filter(year>=periodStart) %>% 
    mutate(period=ifelse(year>=periodEnd , 'time2', 'time1'),
           occurrence=1) %>% filter(period==time)
  
  df_period$countryCode <- as.factor(df_period$countryCode)
  
  df_period_raster <- terra::rasterize(x = vect(df_period),
                                       y = raster,
                                       field = 'occurrence',
                                       fun = 'count', na.rm=T,
                                       sum = T, background=0) %>% mask(., raster)
  
  
  df_country_raster <- terra::rasterize(x = vect(df_period),
                                        y = raster,
                                        field = 'countryCode',
                                        fun = first) %>% mask(., raster)
  
  df_country_raster <- as.factor(df_country_raster)
  
  levels(df_country_raster) <- data.frame(
    ID = 0:(length(levels(df_period$countryCode))-1),
    countryCode = levels(df_period$countryCode)
  )
  
  names(df_period_raster) <- 'count'
  names(df_country_raster) <- 'country'
  df_raster <- c(df_period_raster, df_country_raster)
  return(df_raster)
}

# Leopardus pardalis
PO_lpardalis_time1_raster <- calculate_PO_sp_period_raster(PO, 'Leopardus pardalis', latam_raster, 'time1')
PO_lpardalis_time2_raster <- calculate_PO_sp_period_raster(PO, 'Leopardus pardalis', latam_raster, 'time2')

Plots

Code

data_PO_time1_time2 <- data_PO_GIS %>% 
  mutate(period=ifelse(year>=2014 , 'time2', 'time1'), occurrence=1) 

gg_PO_time1 <- ggplot() + 
    geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
    geom_sf(data=lpardalis_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
    geom_sf(data=data_PO_time1_time2 %>% filter(period=='time1'), col="#E31A1C", size=0.5, show.legend = F) +
    coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + # st_bbox(lpardalis_IUCN)
    labs(title='PO time1: 2000-2013', col='') +
    theme_bw() +
    theme(text=element_text(size = 14))

gg_PO_time2 <- ggplot() + 
    geom_sf(data=countries, fill='#fafaf8', col='#bfc5c7', size=0.2) +
    geom_sf(data=lpardalis_IUCN, fill='grey60', alpha=0.5, col='grey90', size=0.1) +
    geom_sf(data=data_PO_time1_time2 %>% filter(period=='time2'), col="#1F78B4", size=0.5, show.legend = F) +
    coord_sf(xlim = c(-3500000, 4100000), ylim = c(-4400000, 3000000)) + # st_bbox(lpardalis_IUCN)
    labs(title='PO time2: 2014 to 2021', col='') +
    theme_bw() +
    theme(text=element_text(size = 14))
    
gg_PO_time1 + gg_PO_time2

Save data

# blobs
saveRDS(PA_lpardalis_time1_blobs, 'data/species_POPA_data/PA_lpardalis_time1_blobs.rds')
saveRDS(PA_lpardalis_time2_blobs, 'data/species_POPA_data/PA_lpardalis_time2_blobs.rds')

# presence-only rasters
terra::writeRaster(PO_lpardalis_time1_raster, 'data/species_POPA_data/PO_lpardalis_time1_raster.tif', overwrite=TRUE)
terra::writeRaster(PO_lpardalis_time2_raster, 'data/species_POPA_data/PO_lpardalis_time2_raster.tif', overwrite=TRUE)

saveRDS(data_PA_time1_time2, 'data/species_POPA_data/data_lpardalis_PA.rds')
saveRDS(data_PO_time1_time2, 'data/species_POPA_data/data_lpardalis_PO.rds')