Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
eval = TRUE,
echo = TRUE,
message = FALSE,
collapse = TRUE,
comment = "#"
)
## ----install, message=FALSE---------------------------------------------------
library(naturaList)
library(raster)
library(rnaturalearth)
library(dplyr)
## ----load_data----------------------------------------------------------------
data("cyathea.br") # occurrence dataset
data("speciaLists") # specialists dataset
## ----classification-----------------------------------------------------------
occ.class <- classify_occ(occ = cyathea.br, spec = speciaLists)
## ----table_res----------------------------------------------------------------
table(occ.class$naturaList_levels)
## ----clim_data----------------------------------------------------------------
# load climate data
data("r.temp.prec")
df.temp.prec <- raster::as.data.frame(r.temp.prec)
# Transform occurrence data in SpatialPointsDataFrame
spdf.occ.cl <- SpatialPoints(occ.class[, c("decimalLongitude", "decimalLatitude")])
## ----env_space----------------------------------------------------------------
### Define the environmental space for analysis
env.space <- define_env_space(df.temp.prec, buffer.size = 0.05, plot = F)
## ----geo_space----------------------------------------------------------------
# delimit the geographic space
# land area
data('BR')
## ----compare------------------------------------------------------------------
# filter by year to be consistent with the environmental data
occ.class.1970 <-
occ.class %>%
dplyr::filter(year >= 1970)
# cleaning evaluation process
cl.eval_all <- clean_eval(occ.cl = occ.class.1970,
env.space = env.space,
geo.space = BR,
r = r.temp.prec)
# the amount of area remained after cleaning process
area_remained <- cl.eval_all$area
## ----clean_evaluation---------------------------------------------------------
rich.before.clean <- rasterFromXYZ(cbind(cl.eval_all$site.coords,
cl.eval_all$rich$rich.BC))
rich.after.clean <- rasterFromXYZ(cbind(cl.eval_all$site.coords,
cl.eval_all$rich$rich.AC))
## ----plotRich-----------------------------------------------------------------
plot(rich.before.clean, main = "Richness before cleaning")
plot(rich.after.clean, main = "Richness after cleaning")
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