first commit

DESCRIPTION

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+Package: it_hydrogeo_risk
+Type: Package
+Date: 2022-07-31
+Title: Hazards and Risks from Floods and Landslides In Italy
+Version: 0.1.0
+Authors@R: person("Luca", "Valnegri", email = "l.valnegri@datamaps.co.uk", role = c("aut", "cre"))
+Description: Data and Digital Boundaries for the Analysis of Hazards and Risks from Floods and Landslides In Italy.
+License: file LICENSE
+URL: https://github.com/lvalnegri/it_hydrogeo_risk
+BugReports: https://github.com/lvalnegri/it_hydrogeo_risk/issues
+Encoding: UTF-8
+Depends: R (>= 4.1)
+Imports:
+  data.table,
+  leaflet,
+  rmapshaper,
+  qs,
+  sf
+Suggests:
+  dplyr,
+  fst,
+  shiny,
+  shinyjs
+Remotes:
+LazyData: true
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.2.0

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(dpath)
+export(palette.lst)
+export(risks.lst)

R/data.R

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+#' #' @importFrom data.table data.table
+#' NULL
+#' 
+#' #' @import sf
+#' NULL
+#' 
+#' #' @import leaflet
+#' NULL
+#' 
+#' #' dataset
+#' #'
+#' #' Tabella dati territoriali di rischio idrogeologico
+#' #' 
+#' #' @format Una data.table con i campi seguenti:
+#' #' \describe{
+#' #'   \item{\code{CMN}}{ Codice ISTAT del Comune }
+#' #'   \item{\code{var_id}}{ Identificativo della Variabile (chiave esterna per la tabella metadati `mdts`) }
+#' #'   \item{\code{value}}{ Valore assunto dalla Variabile sul Comune }
+#' #' }
+#' #'
+#' 'dts'
+#' 
+#' #' metadata
+#' #'
+#' #' Tabella di spiegazione delle variabili contenute nella tabella dati `dts` 
+#' #' 
+#' #' @format Una data.table con i campi seguenti:
+#' #' \describe{
+#' #'   \item{\code{var_id}}{ Identificativo della Variabile }
+#' #'   \item{\code{id_orig}}{ Identificativo della Variabile nel file ISPRA }
+#' #'   \item{\code{description}}{ Descrizione della Variabile }
+#' #'   \item{\code{label}}{ Etichetta della Variabile }
+#' #'   \item{\code{source}}{ Sorgente dati }
+#' #'   \item{\code{year}}{ Anno di misurazione }
+#' #'   \item{\code{risk}}{ Tipologia di Rischio }
+#' #'   \item{\code{level}}{ Descrizione del Livello di Rischio }
+#' #'   \item{\code{clevel}}{ Codice del Livello di Rischio }
+#' #'   \item{\code{measure}}{ Dato Territoriale di riferimento }
+#' #'   \item{\code{metric}}{ Specifica se Conteggio o Percentuale }
+#' #' }
+#' #'
+#' 'mdts'
+#' 
+#' #' cmn_lid
+#' #'
+#' #' Tabella di mappatura fra Codici Comuni ed Aree a Rischio
+#' #' 
+#' #' @format Una data.table con i campi seguenti:
+#' #' \describe{
+#' #'   \item{\code{risk}}{ Tipologia di Rischio: `G`eologico (Frana) o `I`drologico (Alluvione) }
+#' #'   \item{\code{lid}}{ Identificativo unico formato come concatenazione fra `livello` e `id` }
+#' #'   \item{\code{level}}{ Valori assunti dal Rischio (si veda la lista `livelli.lst`) }
+#' #'   \item{\code{id}}{ Identificativo di Livello per ogni tipologia di Rischio }
+#' #'   \item{\code{CMN}}{ Codice ISTAT del Comune }
+#' #' }
+#' #'
+#' 'cmn_lid'
+#' 
+#' #' geoCMN
+#' #'
+#' #' Dataset containing the complete list of Municipalities (as of 2022), and corresponding Province 
+#' #' 
+#' #' @format An `data.table` object with the following fields:
+#' #' \describe{
+#' #'   \item{\code{CMN}}{ ISTAT code for the Municipality }
+#' #'   \item{\code{CMNd}}{ Name of the Municipality }
+#' #'   \item{\code{PRV}}{ ISTAT code for the Province }
+#' #'   \item{\code{PRVd}}{ Name of the Province }
+#' #'   \item{\code{PRVs}}{ Road Code of the Province }
+#' #' }
+#' #'
+#' 'geoCMN'
+#' 
+#' #' bndCMN
+#' #'
+#' #' Digital Boundaries for Italian Municipalities 
+#' #' 
+#' #' @format An `sf` object with the following fields:
+#' #' \describe{
+#' #'   \item{\code{CMN}}{ ISTAT code for the Municipality }
+#' #'   \item{\code{CMNd}}{ Name of the Municipality }
+#' #' }
+#' #'
+#' 'bndCMN'
+#' 
+#' #' bndPRV
+#' #'
+#' #' Digital Boundaries for Italian Provinces 
+#' #' 
+#' #' @format An `sf` object with the following fields:
+#' #' \describe{
+#' #'   \item{\code{PRV}}{ ISTAT code for the Province }
+#' #'   \item{\code{PRVd}}{ Name of the Province }
+#' #'   \item{\code{PRVs}}{ Road Code of the Province }
+#' #' }
+#' #'
+#' 'bndPRV'
+#' 
+#' #' mps
+#' #'
+#' #' `Leaflet` object to be used as initial map for shiny apps
+#' #' 
+#' 'mps'

R/it_hydrogeo_risk.R

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+#' it_hydrogeo_risk
+#' 
+#' Data and Digital Boundaries for the Analysis of Hazards and Risks from Floods and Landslides In Italy.
+#'  
+#' @docType package
+#' @name it_hydrogeo_risk
+NULL

R/zzz.R

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+#' dpath
+#' 
+#' Folder for the `sf` files
+#'
+#' @export
+#' 
+dpath <- file.path(Rfuns::datait_path, 'ispra')
+
+#' #' cmn.lst
+#' #' 
+#' #' Complete List of Italian Municipalities (`CMN`), with Zip Codes and Provinces Roads Codes.
+#' #'
+#' #' @export
+#' #' 
+#' cmn.lst <- create_cmn_lst()
+
+#' palette.lst
+#' 
+#' List of default colours to associate with the various Levels of Hazards and Risks
+#'
+#' @export
+#' 
+palette.lst <- list(
+    'geo'  = list('P4' = '#6E0000', 'P3' = '#DC0000', 'P2' = '#DE6700', 'P1' = '#F1CA2E', 'AA' = '#FEFF68'),
+    'idro' = list('H' = '#0C2775', 'M' = '#2D72FF', 'L' = '#C3E8FF')
+)
+
+#' risks.lst
+#' 
+#' Description of the various Levels of Hazards and Risks
+#'
+#' @export
+#' 
+risks.lst <- list(
+    'geo'  = list('P4' = 'Very High', 'P3' = 'High', 'P2' = 'Medium', 'P1' = 'Moderate', 'AA' = 'Attention'),
+    'idro' = list('H' = 'High', 'M' = 'Medium', 'L' = 'Low')
+)
+
+
+# .onAttach <- function(libname, pkgname) {
+#     packageStartupMessage(
+#     )
+# }
+
+# .onLoad <- function(libname, pkgname) {
+#     oop <- options()
+#     opts <- list(
+#             pkgname.optname = " option value goes here "
+#     )
+#     toset <- !(names(opts) %in% names(oop))
+#     if(any(toset)) options(opts[toset])
+#   
+#     invisible()
+# }
+
+# .onUnload <- function(libname, pkgname) {
+#
+# }
+

R/zzzGV.R

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+utils::globalVariables(c(
+    'id', 'x_lon', 'y_lat' # column names in data.table "table_name" 
+))

README.md

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-# it_hydrogeo_risk
+## Hydrogeologic Risk in Italy
+
+
+
+
+### Resources
+- [Vector Data (shapefiles) for Landslide Risk (v.4.0, 2020-2021)](https://idrogeo.isprambiente.it/opendata/wms/Mosaicatura_ISPRA_2020_2021_aree_pericolosita_frana_PAI.zip)
+- [Vector Data (shapefiles) for Flooding Risk (v.5.0, 2020)](https://idrogeo.isprambiente.it/opendata/wms/Mosaicatura_ISPRA_2020_aree_pericolosita_idraulica.zip)
+- Metrics: 
+    [Country](https://idrogeo.isprambiente.it/api/pir/italia/export?outputFormat=csv), 
+    [Regions](https://idrogeo.isprambiente.it/api/pir/regioni/export?outputFormat=csv), 
+    [Provinces](https://idrogeo.isprambiente.it/api/pir/province/export?outputFormat=csv), 
+    [Municipalities](https://idrogeo.isprambiente.it/api/pir/comuni/export?outputFormat=csv),
+    ([Metadata](https://idrogeo.isprambiente.it/assets/data/Metadati_open_data_PIR.csv))
+- []()
+
+- [Interactive App Web](https://idrogeo.isprambiente.it/app/)

data-raw/01-create_database.R

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+#########################################################################
+# ISPRA RISCHIO IDROGEO - Creazione databases e tabelle in MySQL server #
+#########################################################################
+
+library(Rfuns)
+
+dbn <- 'ispra'
+dd_create_db(dbn)
+
+## TABLE <dataset> ----------------
+x <- "
+    `CMN` MEDIUMINT UNSIGNED NOT NULL,
+    `var_id` CHAR(14) NOT NULL,
+    `value` DECIMAL(10, 3) NOT NULL,
+    PRIMARY KEY (`CMN`, `var_id`)
+"
+dd_create_dbtable('dataset', dbn, x)
+
+## TABLE <metadata> ----------------
+x <- "
+    `var_id` CHAR(14) NOT NULL,
+    `id_orig` CHAR(12) NOT NULL,
+    `description` VARCHAR(120) NOT NULL,
+    `label` VARCHAR(50) NULL DEFAULT NULL,
+    `source` CHAR(5) NULL DEFAULT NULL,
+    `year` SMALLINT UNSIGNED NULL DEFAULT NULL,
+    `risk` CHAR(10) NULL DEFAULT NULL,
+    `level` CHAR(15) NULL DEFAULT NULL,
+    `clevel` CHAR(5) NULL DEFAULT NULL,
+    `measure` CHAR(15) NULL DEFAULT NULL,
+    `metric` CHAR(11) NULL DEFAULT NULL,
+    PRIMARY KEY (`var_id`),
+    KEY `level` (`level`),
+    KEY `clevel` (`clevel`),
+    KEY `measure` (`measure`),
+    KEY `metric` (`metric`)
+"
+dd_create_dbtable('metadata', dbn, x)
+
+## TABLE <lookups> ----------------
+x <- "
+    `risk` CHAR(1) NOT NULL,
+    `lid` CHAR(6) NOT NULL,
+    `level` CHAR(3) NOT NULL,
+    `id` SMALLINT UNSIGNED NOT NULL,
+    `CMN` MEDIUMINT UNSIGNED NOT NULL,
+    PRIMARY KEY (`risk`, `lid`, `CMN`),
+    KEY `livello` (`level`),
+    KEY `id` (`id`)
+"
+dd_create_dbtable('lookups', dbn, x)
+
+## FINE -------------------------------
+rm(list = ls())
+gc()

data-raw/06-download_files.R

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+#######################################################
+# ISPRA HYDROGEO RISK - download and decompress files #
+#######################################################
+
+Rfuns::load_pkgs()
+
+opath <- file.path(ext_path, 'it', 'ispra')
+tmpf <- tempfile()
+
+# FLOODING (hydro risk)
+download.file('https://idrogeo.isprambiente.it/opendata/wms/Mosaicatura_ISPRA_2020_aree_pericolosita_idraulica.zip', tmpf)
+out_path <- file.path(opath, 'hydro')
+unzip(tmpf, exdir = out_path)
+file.remove(grep('pdf$', list.files(out_path, full.names = TRUE), value = TRUE))
+file.rename(list.files(out_path, full.names = TRUE), file.path(out_path, gsub('(.{1}).*(\\..*$)', '\\1\\2', list.files(out_path))))
+
+# LANDSLIDES (geo risk)
+download.file('https://idrogeo.isprambiente.it/opendata/wms/Mosaicatura_ISPRA_2020_2021_aree_pericolosita_frana_PAI.zip', tmpf)
+out_path <- file.path(opath, 'geo')
+unzip(tmpf, exdir = out_path)
+file.remove(grep('pdf$', list.files(out_path, full.names = TRUE), value = TRUE))
+file.rename(list.files(out_path, full.names = TRUE), file.path(out_path, gsub('(.{1}).*(\\..*$)', 'geo_ori\\2', list.files(out_path))))
+
+unlink(tmpf)
+rm(list = ls())
+gc()

data-raw/11-hydro_risk.R

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+###########################################
+# ISPRA HYDROGEO RISK - Polygons Flooding #
+###########################################
+
+Rfuns::load_pkgs('data.table', 'dplyr', 'qs', 'sf')
+
+in_path <- file.path(ext_path, 'it', 'ispra', 'hydro')
+out_path <- file.path(datait_path, 'ispra', 'hydro')
+
+# LETTURA e PULIZIA SHAPEFILES CON AGGIUNTA id
+yb <- rbind(
+        st_read(file.path(in_path, 'L.shp'), quiet = TRUE) |> select(-1) |> mutate(level = 'L', id = 1:n()),
+        st_read(file.path(in_path, 'M.shp'), quiet = TRUE) |> select(-1) |> mutate(level = 'M', id = 1:n()),
+        st_read(file.path(in_path, 'H.shp'), quiet = TRUE) |> select(-1) |> mutate(level = 'H', id = 1:n())
+) |> dplyr::mutate(lid = paste0(id, level))
+st_write(yb, file.path(in_path, 'idro.shp'))
+qsave(yb, file.path(out_path, 'idro.qs'), nthreads = 10)
+
+# CREA TABELLA LEGAMI id-CMN (intersezione con comuni)
+ybc <- RbndIT::CMN |> st_transform(3035)
+ye <- st_intersects(yb, ybc)
+yt <- yb |> st_drop_geometry()
+yc <- ybc |> st_drop_geometry()
+ye <- rbindlist(lapply( 1:nrow(ye), \(x) data.table( yt[x,], yc[ye[[x]],] ) )) |> setnames('V2', 'CMN')
+ye[, lid := paste0(id, livello)]
+fwrite(ye, './data-raw/csv/idro_comuni.csv')
+fst::write_fst(ye, file.path(out_path, 'idro.fst'))
+
+# ESTRAI PROVINCIE
+ybp <- RbndIT::PRV |> st_transform(3035)
+yc <- RgeoIT::comuni[, .(CMN = as.integer(CMN), PRV)][order(PRV, CMN)]
+y <- list()
+for(p in ybp$PRV){
+    message('Provincia ', p)
+    ycp <- yc[PRV == p, CMN]
+    y[[p]] <- st_intersection( yb |> subset(lid %in% ye[CMN %in% ycp, lid]), ybp |> subset(PRV == p) ) |> select(-PRV)
+    qsave(y[[p]], file.path(out_path, p), nthreads = 10)
+}
+qsave(y, file.path(out_path, 'idro.prv'), nthreads = 10)
+
+# ESTRAI COMUNI e CALCOLO DIFFERENZE
+st_stuff <- \(x){
+    if(is.na(sum(st_bbox(x)))) return(NULL)
+    # if(!(st_is(x, 'MULTIPOLYGON') | st_is(x, 'POLYGON'))) x <- x |> st_collection_extract('POLYGON') 
+    x |> st_collection_extract('POLYGON') |> st_union() |> st_transform(4326)
+}
+yy <- list()
+for(p in ybp$PRV){
+    message('Provincia ', p)
+    for(pc in yc[PRV == p, CMN]){
+        yt <- st_intersection(ybc |> subset(CMN == pc), y[[p]] ) |> select(livello)
+        if(nrow(yt) > 0){
+            yy[[as.character(pc)]] <- list(
+                        'bbx' = st_bbox(yt |> st_transform(4326)),
+                        'H' = yt |> subset(livello == 'H') |> st_stuff(),
+                        'M' = st_difference(yt |> subset(livello == 'M') |> st_union(), yt |> subset(livello == 'H') |> st_union()) |> st_stuff(),
+                        'L' = st_difference(yt |> subset(livello == 'L') |> st_union(), yt |> subset(livello %in% c('H', 'M')) |> st_union()) |> st_stuff(),
+                        'CMN' = masteRconfini::CMN |> subset(CMN == pc)
+            )
+        } else { 
+            yy[[as.character(pc)]] <- list( 'bbx' = NULL, 'CMN' = masteRconfini::CMN |> subset(CMN == pc) )
+        }
+        qsave(yy[[as.character(p)]], file.path(out_path, pc), nthreads = 10)
+    }
+}
+qsave(yy, file.path(out_path, 'idro.cmn'), nthreads = 10)
+
+# library(leaflet)
+# leaflet() |>
+#     aggiungi_tessera(tiles.lst[[19]]) |>
+#     addPolygons(data = yt |> subset(livello == 'H'), group = 'H', fillColor = colori.lst$idro$H, opacity = 0, fillOpacity = 1) |> 
+#     addPolygons(data = yt |> subset(livello == 'M'), group = 'M', fillColor = colori.lst$idro$M, opacity = 0, fillOpacity = 1) |> 
+#     addPolygons(data = yt |> subset(livello == 'L'), group = 'L', fillColor = colori.lst$idro$L, opacity = 0, fillOpacity = 1) |> 
+#     addLayersControl(overlayGroups = c('H', 'M', 'L'))
+
+# ESCI
+rm(list = ls())
+gc()