library(magrittr)
rm(list=ls())
# Install packages with data and maps
devtools::install_github("helseatlas/kart")
devtools::install_github("helseatlas/data")
# All atlas data and maps
healthatlas_data <- list(
"fodsel" = list("data_no" = data::fodsel, "data_en" = data::fodsel_en, "year" = "2015–2017", "title_no" = "Fødselshjelp", "title_en" = "Obstetrics", "map" = kart::fodsel),
"gyn" = list("data_no" = data::gyn, "data_en" = data::gyn_en, "year" = "2015–2017", "title_no" = "Gynekologi", "title_en" = "Gynaecology", "map" = kart::gyn),
"ortopedi" = list("data_no" = data::ortopedi, "data_en" = data::ortopedi, "year" = "2012–2016", "title_no" = "Ortopedi", "title_en" = "Orthopaedic", "map" = kart::ortopedi),
"dagkir2" = list("data_no" = data::dagkir2, "data_en" = data::dagkir2_en, "year" = "2013–2017", "title_no" = "Dagkirurgi", "title_en" = "Day surgey", "map" = kart::dagkir2),
"kols" = list("data_no" = data::kols, "data_en" = data::kols_en, "year" = "2013–2015", "title_no" = "Kols", "title_en" = "COPD", "map" = kart::kols),
"eldre" = list("data_no" = data::eldre, "data_en" = data::eldre_en, "year" = "2013–2015", "title_no" = "Eldre", "title_en" = "Elderly", "map" = kart::eldre),
"nyfodt" = list("data_no" = data::nyfodt, "data_en" = data::nyfodt_en, "year" = "2009–2014", "title_no" = "Nyfødt", "title_en" = "Neonatal", "map" = kart::nyfodt),
"barn" = list("data_no" = data::barn, "data_en" = data::barn_en, "year" = "2011–2014", "title_no" = "Barn", "title_en" = "Children", "map" = kart::barn),
"dagir" = list("data_no" = data::dagkir, "data_en" = data::dagkir_en, "year" = "2011–2013", "title_no" = "Dagkirurgi", "title_en" = "Day surgey", "map" = kart::dagkir)
)
helseatlas::run_app()
#########################################
# How to run the app through launch_app #
#########################################
helseatlas::launch_app(
dataset = all_data,
publish_app = FALSE
)
####################################################
# How to submit to shinyapps.io through launch_app #
####################################################
# Install the helseatlas package
devtools::install_github("helseatlas/helseatlas")
# Restart R session
.rs.restartR()
# Launch app
helseatlas::launch_app(
dataset = all_data,
publish_app = TRUE,
name = "helseatlas"
)
# How to run the app locally
healthatlas_data <- all_data
healthatlas_data <- helseatlas::kols # or another dataset to use
healthatlas_map <- geojsonio::geojson_read("tests/testthat/data/maps/test.geojson", what = "sp")
language <- "no"
webpage_title <- "Helseatlas kols 2013-2015"
runApp("inst/app")
rm(list = ls())
getwd()
setwd("/Users/arnfinn/repo/helseatlas")
# Example on how to update package data, which will be loadable by helseatlass::testdata
testdata <- readRDS("~/repo/helseatlas/tests/testthat/data/kols.rds")
save(testdata, file = "data/testdata.RData")
testdata <- get(load("data/kols.RData"))
testdata <- readRDS("~/repo/helseatlas/tests/testthat/data/start_plot.rds")
testdata$area_name <- testdata$area
testdata$level1_name <- testdata$level1
testdata$level2_name <- testdata$level2
testdata$level3_name <- testdata$level3
testdata$value <- testdata$rate
testdata <- within(testdata, rm(rate))
testdata$denominator_name <- testdata$name_denominator
testdata <- within(testdata, rm(name_denominator))
testdata$numerator_name <- testdata$name_numerater
testdata <- within(testdata, rm(name_numerater))
testdata$numerator <- testdata$numerater
testdata <- within(testdata, rm(numerater))
start_plot <- testdata
saveRDS(start_plot, file = "~/repo/helseatlas/tests/testthat/data/start_plot.rds")
save(kols, file = "data/kols.RData")
save(testdata, file = "data/testdata.RData")
# Make the testmap data
testmap <- kart::barn
usethis::use_data(testmap, overwrite = TRUE)
plot(helseatlas::testmap)
# Make the testdata
testdata <- data::barn
testdata$area_name <- as.factor(gsub("å", "aa", testdata$area_name))
testdata$area_name <- as.factor(gsub("ø", "o", testdata$area_name))
testdata$area_name <- as.factor(gsub("æ", "ae", testdata$area_name))
testdata$area_name <- as.factor(gsub("Å", "AA", testdata$area_name))
testdata$area_name <- as.factor(gsub("Ø", "O", testdata$area_name))
testdata$area_name <- as.factor(gsub("Æ", "AE", testdata$area_name))
testdata$level1_name <- as.factor(gsub("å", "aa", testdata$level1_name))
testdata$level1_name <- as.factor(gsub("ø", "o", testdata$level1_name))
testdata$level1_name <- as.factor(gsub("æ", "ae", testdata$level1_name))
testdata$level1_name <- as.factor(gsub("Å", "AA", testdata$level1_name))
testdata$level1_name <- as.factor(gsub("Ø", "O", testdata$level1_name))
testdata$level1_name <- as.factor(gsub("Æ", "AE", testdata$level1_name))
testdata$level2_name <- as.factor(gsub("å", "aa", testdata$level2_name))
testdata$level2_name <- as.factor(gsub("ø", "o", testdata$level2_name))
testdata$level2_name <- as.factor(gsub("æ", "ae", testdata$level2_name))
testdata$level2_name <- as.factor(gsub("Å", "AA", testdata$level2_name))
testdata$level2_name <- as.factor(gsub("Ø", "O", testdata$level2_name))
testdata$level2_name <- as.factor(gsub("Æ", "AE", testdata$level2_name))
testdata$level3_name <- as.factor(gsub("å", "aa", testdata$level3_name))
testdata$level3_name <- as.factor(gsub("ø", "o", testdata$level3_name))
testdata$level3_name <- as.factor(gsub("æ", "ae", testdata$level3_name))
testdata$level3_name <- as.factor(gsub("Å", "AA", testdata$level3_name))
testdata$level3_name <- as.factor(gsub("Ø", "O", testdata$level3_name))
testdata$level3_name <- as.factor(gsub("Æ", "AE", testdata$level3_name))
usethis::use_data(testdata, overwrite = TRUE)
helseatlas::testdata
# How two extra test maps were made
testmap <- geojsonio::geojson_read("tests/testthat/data/maps/test.geojson", what = "sp")
geojsonio::geojson_write(testmap, file = "tests/testthat/data/maps/utm33.geojson")
new <- utm33_to_leaflet(testmap)
geojsonio::geojson_write(new, file = "tests/testthat/data/maps/epsg4326.geojson")
##############
# Plot a map #
##############
# Eldre
map <- geojsonio::geojson_read("tests/testthat/data/maps/eldre.geojson", what = "sp")
eldre <- utm33_to_leaflet(map)
leaflet::leaflet(eldre) %>%
leaflet::addTiles() %>%
leaflet::addPolygons(stroke = FALSE,
smoothFactor = 0.3,
fillOpacity = 0.2,
fillColor = c("green", "blue", "red",
"yellow", "orange", "purple"))
# Map from https://kartkatalog.geonorge.no/metadata/geonorge/norske-fylker-og-kommuner-illustrasjonsdata-2018-klippet-etter-kyst/cbbdf78c-fa3a-48bf-8f3f-9eec74e428fd
# Reduced in size with reduce_map_size function
map <- geojsonio::geojson_read("tests/testthat/data/maps/kommuner.geojson", what = "sp")
new <- utm33_to_leaflet(map)
leaflet::leaflet(new) %>%
leaflet::addTiles() %>%
leaflet::addPolygons(stroke = FALSE, smoothFactor = 0.3, fillOpacity = 0.2, fillColor = c("green", "blue", "red", "yellow", "orange", "purple"))
# Save map to disk
map$Kommunenav <- NULL # rm kommunenavn (trouble with norwegian letters)
geojsonio::geojson_write(map, file = "tests/testthat/data/maps/kommuner.geojson")
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