working on benchmark rmd, trying to setup gh pages

.Rbuildignore

@@ -21,3 +21,7 @@ ubuntu_16_installation.sh
 ubuntu_17_installation.sh
 ^cran-comments\.md$
 ^codecov\.yml$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/workflows/pkgdown.yaml

@@ -0,0 +1,45 @@
+on:
+  push:
+    branches: master
+
+name: pkgdown
+
+jobs:
+  pkgdown:
+    runs-on: macOS-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        uses: actions/cache@v1
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
+
+      - name: Install dependencies
+        run: |
+          install.packages("remotes")
+          remotes::install_deps(dependencies = TRUE)
+          remotes::install_dev("pkgdown")
+        shell: Rscript {0}
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Deploy package
+        run: pkgdown::deploy_to_branch(new_process = FALSE)
+        shell: Rscript {0}

.gitignore

@@ -36,3 +36,4 @@ vignettes/*.md
 .Rprofile
 # Local files
 /local/
+docs

sandbox/benchmark.Rmd

@@ -0,0 +1,135 @@
+---
+title: "**tmap** benchmark"
+author: "Martijn Tennekes"
+date: "2020-06-20"
+output: html_document
+---
+
+```{r setup, include=FALSE}
+knitr::opts_chunk$set(echo = TRUE)
+library(tmap)
+library(readxl)
+library(grid)
+library(dplyr)
+library(sf)
+library(ggplot2)
+library(microbenchmark)
+
+```
+
+## Large choroplth
+
+```{r preprocess-poly,cache=TRUE,include = FALSE}
+
+
+# function to obtain Food Environment Atlas data (2014)
+get_food_envir_data <- function() {
+	dir <- tempdir()
+	if (!file.exists(file.path(dir, "DataDownload.xls"))) {
+		download.file("https://www.ers.usda.gov/webdocs/DataFiles/48731/February2014.xls?v=41688", destfile = file.path(dir, "DataDownload.xls"), mode = "wb")
+	}
+	res <- tryCatch({
+		read_excel(file.path(dir, "DataDownload.xls"), sheet = "HEALTH")	
+	}, error = function(e) {
+		stop("The excel file cannot be read. Please open it, and remove all sheets except HEALTH. The location of the file is: ", normalizePath(file.path(dir, "DataDownload.xls")))
+	})
+}
+
+# function to obtain US county shape
+get_US_county_2010_shape <- function() {
+	dir <- tempdir()
+	download.file("http://www2.census.gov/geo/tiger/GENZ2010/gz_2010_us_050_00_20m.zip", destfile = file.path(dir, "gz_2010_us_050_00_20m.zip"))
+	unzip(file.path(dir, "gz_2010_us_050_00_20m.zip"), exdir = dir)
+	US <- sf::read_sf(file.path(dir, "gz_2010_us_050_00_20m.shp"))
+	levels(US$NAME) <- iconv(levels(US$NAME), from = "latin1", to = "utf8")
+	US
+}
+
+# obtain Food Environment Atlas data
+FEA <- get_food_envir_data()
+
+# obtain US county shape
+US <- get_US_county_2010_shape()
+
+
+US$FIPS <- paste0(US$STATE, US$COUNTY)
+
+# append data to shape
+#US <- append_data(US, FEA, key.shp = "FIPS", key.data = "FIPS", ignore.duplicates = TRUE)
+US <- left_join(US, FEA, by = c("FIPS", "FIPS"))
+
+US_cont <- US %>% 
+	subset(!STATE %in% c("02", "15", "72"))
+```
+
+
+
+```{r}
+poly_tmap = function() {
+	print(tm_shape(US_cont) + tm_polygons("PCT_OBESE_ADULTS10"))	
+}
+poly_sf = function() {
+	plot(US_cont[, "PCT_OBESE_ADULTS10"])
+}
+poly_ggplot2 = function() {
+	print(ggplot(data = US_cont, aes(fill = PCT_OBESE_ADULTS10)) + geom_sf())
+}
+```
+
+
+```{r fig.cap="tmap choropleth"}
+poly_tmap()
+```
+
+**sf** 
+
+```{r fig.cap="sf choropleth"}
+poly_sf()
+```
+
+**ggplot2** 
+
+```{r fig.cap="ggplot2 choropleth"}
+poly_ggplot2()
+```
+
+
+```{r fig.cap="Benchmark results",echo=FALSE}
+write2png = function(e) {
+	tmp = tempfile(fileext = ".png")
+	png(tmp, width = 2000, height = 2000)
+	e
+	dev.off()
+}
+
+autoplot(microbenchmark(list = alist(
+tmap = write2png(poly_tmap()),
+sf = write2png(poly_sf()),
+ggplot2 = write2png(poly_ggplot2())), 
+times = 3))
+```
+
+# Large dot map
+
+```{r preprocess-poly,cache=TRUE,include = FALSE}
+denuncia_v = read.csv("https://github.com/hbermeo/datos_espaciales/raw/master/denuncia_vial.csv", encoding = "UTF-8")
+
+denuncias = st_as_sf(denuncia_v, coords = c("long", "lat"), crs = 4326)
+
+```
+
+
+
+```{r}
+dot_tmap = function() {
+	print(tm_shape(denuncias) + tm_dots("genero", size = .1))
+}
+
+dot_ggplot2 = function() {
+	ggplot(data= denuncias, aes(color = genero)) + geom_sf()	
+}
+
+dot_sf = function() {
+	plot(denuncias[, "genero"])
+}
+```