lab/test-functions.R

In kamapu/vegtableDB: Handling Vegetation Data Sets (Advanced Features)

# TODO:   Add comment
#
# Author: Miguel Alvarez
################################################################################

library(devtools)
install_github("kamapu/vegtableDB")
install_gitlab("kamapu/dbaccess")

library(vegtableDB)
library(RPostgreSQL)
library(biblioDB)
library(dbaccess)

# Selection of sources
Sel <- c(
  "Alvarez2012c", "Alvarez2017", "Alvarez2018a", "Ayichedehou2000",
  "Bronner1990", "deBock2009", "deFoucault1999", "Furness1980",
  "Germain1951", "Guyot1994", "Lebrun1947", "Lejoly2000", "Masens2000",
  "Mullenders1954", "Schmitt1991", "Schmitz1971", "Szafranski1983"
)
Query <- paste0(
  "SELECT *\n",
  "FROM swea_dataveg.header\n",
  "WHERE bibtexkey IN (\'", paste0(Sel, collapse = "','"), "');\n"
)

# Connect to database
conn <- connect_db2(dbname = "veg_databases", user = "miguel")

swea <- import_swea(conn, sql_header = Query)

dbDisconnect(conn)



swea2 <- subset(swea, bibtexkey %in% Sel, slot = "relations", relation = "data_source")
summary(swea2)


### Debu db2vegtable
header <- c("swea_dataveg", "header")
samples <- c("swea_dataveg", "samples")
relations <- list(
  globe_plots = c("swea_dataveg", "globe_plots"),
  swea1_code = c("swea_dataveg", "swea1_code"),
  soil_moisture = c("swea_dataveg", "soil_moisture"),
  soil_texture = c("swea_dataveg", "soil_texture"),
  community_type = c("commons", "community_type"),
  naturalness = c("swea_dataveg", "naturalness"),
  record_type = c("swea_dataveg", "record_type")
)
layers <- list(
  veg_layer = c("swea_dataveg", "veg_layer"),
  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"
get_countries <- TRUE
get_data_sources <- TRUE
bib_args <- list()
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")