In dd-harp/globalrc: Computes Control Reproductive Number, Rc, from PfPR and Treatment Levels

library(raster)
library(rprojroot)
library(rampdata)
library(sp)
library(sf)
library(tmap)
library(GISTools)

outline_rp <- ramp_path("/inputs/country_outlines/201122")
admin0 <- sf::st_read(as.path(add_path(outline_rp, file = "ne_10m_admin_0_countries")))
admin0lakes <- sf::st_read(as.path(add_path(outline_rp, file = "ne_10m_admin_0_countries_lakes")))
admin0pop <- sf::st_read(as.path(add_path(outline_rp, file = "ne_10m_populated_places")))
admin0pop_df <- st_set_geometry(admin0pop, NULL)
admin0popsimple <- sf::st_read(as.path(add_path(outline_rp, file = "ne_10m_populated_places_simple")))
admin0popsimple_df <- st_set_geometry(admin0popsimple, NULL)

admin_max <- admin0pop[admin0pop$SCALERANK < 3,]
tm_shape(admin0lakes) + tm_borders() + tm_shape(admin_max) + tm_bubbles(size = 0.01)

raster_rp <- ramp_path("/globalrc/outputs/basicr/201121_split100")
rc_median <- raster(as.path(add_path(raster_rp, file = "rc_median_2018.tif")))
vc_median <- raster(as.path(add_path(raster_rp, file = "vc_median_2018.tif")))
aeir_median <- raster(as.path(add_path(raster_rp, file = "aeir_median_2018.tif")))

aplot <- tm_shape(rc_median) +
  tm_raster(
    breaks = c(0.0, 0.5, 1, 2, 5, 10, 100, Inf),
    title = "Rc Median 2018"
    ) +
  tm_layout(
    legend.position = c("left", "bottom") 
  ) +
  tm_shape(admin0lakes) +
  tm_borders() +
  tm_shape(admin_max) +
  tm_bubbles(size = 0.01) +
  tm_text("NAME", size = 0.5)
tmap_save(aplot, "rc_median_2018.png", asp = 0, height = 1500)
aplot

aplot <- tm_shape(aeir_median) +
  tm_raster(
    breaks = c(0.0, 0.5, 1, 2, 5, 10, 100, Inf),
    title = "Annual EIR Median 2018"
    ) +
  tm_layout(
    legend.position = c("left", "bottom") 
  ) +
  tm_shape(admin0lakes) +
  tm_borders() +
  tm_shape(admin_max) +
  tm_bubbles(size = 0.01) +
  tm_text("NAME", size = 0.5)
tmap_save(aplot, "aeir_median_2018.png", asp = 0, height = 1500)
aplot

aplot <- tmap::tm_shape(vc_median) +
  tm_raster(
    breaks = c(0.0, 0.1, 0.5, 1, 5, 10, 100, Inf),
    title = "Vectorial Capacity Median 2018"
    ) +
  tm_layout(
    legend.position = c("left", "bottom") 
  ) +
  tm_shape(admin0lakes) +
  tm_borders() +
  tm_shape(admin_max) +
  tm_bubbles(size = 0.01) +
  tm_text("NAME", size = 0.5)
tmap_save(aplot, "vc_median_2018.png", asp = 0, height = 1500)
aplot

dd-harp/globalrc documentation built on Sept. 20, 2021, 12:31 a.m.