<!DOCTYPE html>
bb-page1-catch-bycatch
Exploration of outputs in page 1 of the atlas.
# Sys.setenv("POSTGRES_USER" = "diadesatlas_owner")
# Sys.setenv("POSTGRES_PASS" = "thinkrpassword")
pkgload::load_all(here::here())
#> ℹ Loading diades.atlas
library(dplyr)
session <- shiny::MockShinySession$new() #new.env()
connect(session)
con <- get_con(session)
library(rworldmap)
#> Le chargement a nécessité le package : sp
#> ### Welcome to rworldmap ###
#> For a short introduction type : vignette('rworldmap')
library(rworldxtra)
library(tmap)
library(sf)
#> Linking to GEOS 3.8.0, GDAL 3.0.4, PROJ 6.3.1
library(DBI)
Sys.setenv(
"GOLEM_CONFIG_ACTIVE" = "dev"
)
Liste des espèces
get_active_species(
session = session
)
#> # A tibble: 11 × 5
#> species_id latin_name english_name local_name active
#> <int> <chr> <chr> <chr> <lgl>
#> 1 4 Acipenser sturio European sturgeon ASturio TRUE
#> 2 6 Alosa alosa Allis shad AAlosa TRUE
#> 3 8 Alosa fallax Twaite shad AFallax TRUE
#> 4 13 Anguilla anguilla European eel AAnguilla TRUE
#> 5 18 Lampetra fluviatilis River lamprey LFluviatilis TRUE
#> 6 20 Osmerus eperlanus European smelt OEperlanus TRUE
#> 7 21 Petromyzon marinus Sea lamprey PMarinus TRUE
#> 8 22 Platichthys flesus European flounder PFlesus TRUE
#> 9 25 Salmo salar Atlantic salmon SSalar TRUE
#> 10 26 Salmo trutta Sea trout STrutta TRUE
#> 11 19 Chelon ramada Thinlip grey mullet LRamada TRUE
Conservation status
species <- get_active_species(
session = session
)
for (i in species$species_id) {
cli::cat_rule(i)
print(
get_conservation_status(
6,
con
)
)
cli::cat_line()
}
#> ── 4 ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
#>
#> ── 6 ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
#>
#> ── 8 ───────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
#>
#> ── 13 ──────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
#>
#> ── 18 ──────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
#>
#> ── 20 ──────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
#>
#> ── 21 ──────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
#>
#> ── 22 ──────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
#>
#> ── 25 ──────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
#>
#> ── 26 ──────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
#>
#> ── 19 ──────────────────────────────────────────────────────────────────────────────────────────────────────────
#> species_id latin_name simplified_name english_name iucn_classification_code iucn_level_code
#> 1 6 Alosa alosa A. alosa Allis shad IUCN_Europe LC
#> 2 6 Alosa alosa A. alosa Allis shad IUCN_ES LC
#> 3 6 Alosa alosa A. alosa Allis shad IUCN_FR CR
#> 4 6 Alosa alosa A. alosa Allis shad IUCN_IE DD
#> 5 6 Alosa alosa A. alosa Allis shad IUCN_PT EN
#> iucn_level_name
#> 1 Least Concern
#> 2 Least Concern
#> 3 Critically Endangered
#> 4 Data Deficient
#> 5 Endangered
Tmap code
datasets <- generate_datasets(
get_con(
session
)
)
#> ── generate_datasets ───────────────────────────────────────────────────────────────────────────────────────────
# options("golem.app.prod" = FALSE)
launch_mongo(session = session)
#> MongoDB has not been started or does not exist
#> Using local RAM memory for this session
# NOTE: the species are passed with the latin name in the foreground.
# In the front of the app, the user will have to select an english/french name
tm_draw(
species_latin_name = "Salmo trutta",
spatial_type = "rectangle",
con = con,
dataCatchment = datasets$dataCatchment,
catchment_geom = datasets$catchment_geom,
dataALL = datasets$dataALL,
ices_geom = datasets$ices_geom,
session = session
)
#> Some legend labels were too wide. These labels have been resized to 0.13. Increase legend.width (argument of tm_layout) to make the legend wider and therefore the labels larger.
#> Legend labels were too wide. The labels have been resized to 0.13, 0.15, 0.13, 0.11, 0.18. Increase legend.width (argument of tm_layout) to make the legend wider and therefore the labels larger.
tm_draw(
species_latin_name = "Salmo trutta",
spatial_type = "division",
con = con,
dataCatchment = datasets$dataCatchment,
catchment_geom = datasets$catchment_geom,
dataALL = datasets$dataALL,
ices_geom = datasets$ices_geom,
session = session
)
#> Some legend labels were too wide. These labels have been resized to 0.13. Increase legend.width (argument of tm_layout) to make the legend wider and therefore the labels larger.
#> Legend labels were too wide. The labels have been resized to 0.13, 0.15, 0.13, 0.11, 0.18. Increase legend.width (argument of tm_layout) to make the legend wider and therefore the labels larger.
tm_draw(
species_latin_name = "Chelon ramada",
spatial_type = "rectangle",
con = con,
dataCatchment = datasets$dataCatchment,
catchment_geom = datasets$catchment_geom,
dataALL = datasets$dataALL,
ices_geom = datasets$ices_geom,
session = session
)
#> Some legend labels were too wide. These labels have been resized to 0.13. Increase legend.width (argument of tm_layout) to make the legend wider and therefore the labels larger.
#> Legend labels were too wide. The labels have been resized to 0.13, 0.15, 0.13, 0.11, 0.18. Increase legend.width (argument of tm_layout) to make the legend wider and therefore the labels larger.
tm1 <- tm_draw(
species_latin_name = "Chelon ramada",
spatial_type = "division",
con = con,
dataCatchment = datasets$dataCatchment,
catchment_geom = datasets$catchment_geom,
dataALL = datasets$dataALL,
ices_geom = datasets$ices_geom,
session = session
)
tm1
#> Some legend labels were too wide. These labels have been resized to 0.13. Increase legend.width (argument of tm_layout) to make the legend wider and therefore the labels larger.
#> Legend labels were too wide. The labels have been resized to 0.13, 0.15, 0.13, 0.11, 0.18. Increase legend.width (argument of tm_layout) to make the legend wider and therefore the labels larger.
# tmap_leaflet(tm1)
Disconnect db
DBI::dbDisconnect(con)