Nothing
## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
warning = FALSE,
message = FALSE,
eval = FALSE,
fig.width = 8,
fig.height = 6
)
## ----Get data, results='hide', message=FALSE, warning=FALSE, echo=FALSE-------
# my_dir <- file.path(file.path(tempdir(), "florabr"))
# dir.create(my_dir)
# get_florabr(output_dir = my_dir, #directory to save the data
# data_version = "latest", #get the most recent version available
# overwrite = T) #Overwrite data, if it exists
## ----message=FALSE, warning=F-------------------------------------------------
# library(florabr)
# library(terra)
# #Folder where you stored the data with the function get_florabr()
# #Load data
# bf <- load_florabr(data_dir = my_dir,
# data_version = "Latest_available",
# type = "short") #short version
# #> Loading version 393.401
## -----------------------------------------------------------------------------
# #Load Flora e Funga do Brasil data
# data("bf_data")
# #Select endemic and native species of trees with occurrence only in Amazon
# am_trees <- select_species(data = bf_data,
# include_subspecies = FALSE,
# include_variety = FALSE,
# kingdom = "Plantae",
# group = "All", subgroup = "All",
# family = "All", genus = "All",
# lifeForm = "Tree", filter_lifeForm = "only",
# habitat = "All", filter_habitat = "in",
# biome = "Amazon",
# filter_biome = "only",
# state = "All", filter_state = "and",
# vegetation = "All",
# filter_vegetation = "in",
# endemism = "Endemic", origin = "Native",
# taxonomicStatus = "Accepted",
# nomenclaturalStatus = "All")
# #Get presence-absence matrix
# pam_am <- get_pam(data = am_trees, by_biome = TRUE, by_state = TRUE,
# by_vegetation = FALSE, remove_empty_sites = TRUE,
# return_richness_summary = TRUE,
# return_spatial_richness = TRUE,
# return_plot = TRUE)
# #Visualize (as tibble) the PAM for the first 5 species and 7 sites
# tibble::tibble(pam_am$PAM[1:7, 1:5])
# # # A tibble: 7 × 5
# # Biome States `Euxylophora paraensis` `Galipea congestiflora` `Hortia longifolia`
# # <fct> <fct> <dbl> <dbl> <dbl>
# # 1 Amazon AM 1 0 1
# # 2 Amazon MA 1 1 0
# # 3 Amazon PA 1 1 1
# # 4 Amazon TO 1 1 0
# # 5 Amazon MT 0 0 1
# # 6 Amazon RR 0 0 1
# # 7 Amazon AC 0 0 0
## -----------------------------------------------------------------------------
# #Visualize (as tibble) the richness summary table
# tibble::tibble(pam_am$Richness_summary[1:7,])
# # # A tibble: 7 × 3
# # Biome States Richness
# # <fct> <fct> <dbl>
# # 1 Amazon AM 606
# # 2 Amazon MA 34
# # 3 Amazon PA 296
# # 4 Amazon TO 7
# # 5 Amazon MT 63
# # 6 Amazon RR 45
# # 7 Amazon AC 107
## ----IMG09, eval=TRUE, echo = FALSE-------------------------------------------
knitr::include_graphics("vignettes_img/Image_09.png")
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