lab/test-db2taxlist.R

# TODO:   Neede to re-write function
#
# Author: Miguel Alvarez
################################################################################

library(divDB)
library(RPostgreSQL)

# Arguments to parameters
conn = connect_db(dbname = "vegetation_v3", user = "miguel")
## conceps
taxonomy = "sam_splist"
schema = "plant_taxonomy"
subset_levels = TRUE
keep_parents = FALSE
keep_children = FALSE
as_list = FALSE








Test <- import_swea(conn)

header <- c("swea_dataveg", "header")
samples <- c("swea_dataveg", "samples")
relations <- list(community_type = c("commons", "community_type"))
layers <- list(spec_miguel = c("specimens", "specimens_miguel"))
coverconvert <- list(
  br_bl = c("commons", "br_bl"),
  b_bbds = c("commons", "b_bbds"),
  ordinal = c("commons", "ordinal")
)
geometry <- "plot_centroid"
as_list <- FALSE




taxon_names <- c("tax_commons", "taxonNames")
taxon_relations <- c("swea_dataveg", "taxonRelations")
taxon_traits <- c("swea_dataveg", "taxonTraits")
taxon_views <- "bib_references"
taxon_levels <- c("tax_commons", "taxonLevels")
names2concepts <- c("swea_dataveg", "names2concepts")
subset_levels <- TRUE
# subset_views = TRUE
as_list <- FALSE
# verbose = TRUE



Test <- postgres2taxlist(conn,
  taxon_names = c("tax_commons", "taxonNames"),
  taxon_relations = c("swea_dataveg", "taxonRelations"),
  taxon_traits = c("swea_dataveg", "taxonTraits"),
  taxon_views = "bib_references",
  taxon_levels = c("tax_commons", "taxonLevels"),
  names2concepts = c("swea_dataveg", "names2concepts")
)

summary(Test)
kamapu/vegtableDB documentation built on June 18, 2024, 1:13 a.m.