Mapa de animação de falecimento COVID-19 | R-bloggers

# Animation carto décès COVID 19 France
# avec lissage


# sources -----------------------------------------------------------------

# https://www.data.gouv.fr/fr/datasets/donnees-hospitalieres-relatives-a-lepidemie-de-covid-19/
fichier_covid %
    dplyr::select(geometry) %>%
    st_make_grid(
      cellsize = resolution,
      offset = c(
        plyr::round_any(zone_bbox[1] - bandwidth, resolution, f = floor),
        plyr::round_any(zone_bbox[2] - bandwidth, resolution, f = floor)
      ),
      what = "centers"
    ) %>%
    st_sf() %>%
    st_join(zone, join = st_intersects, left = FALSE) %>%
    st_coordinates() %>%
    as_tibble() %>%
    dplyr::select(x = X, y = Y)
  
  # kernel
  message("computing kernel...")
  kernel %
    cbind(., st_coordinates(.)) %>%
    st_set_geometry(NULL) %>%
    dplyr::select(x = X, y = Y, field) %>%
    btb::kernelSmoothing(
      dfObservations = .,
      sEPSG = out_crs,
      iCellSize = resolution,
      iBandwidth = bandwidth,
      vQuantiles = NULL,
      dfCentroids = zone_xy
    )
  
  # rasterization
  message("nrasterizing...")
  raster::raster(
    xmn = plyr::round_any(zone_bbox[1] - bandwidth, resolution, f = floor),
    ymn = plyr::round_any(zone_bbox[2] - bandwidth, resolution, f = floor),
    xmx = plyr::round_any(zone_bbox[3] + bandwidth, resolution, f = ceiling),
    ymx = plyr::round_any(zone_bbox[4] + bandwidth, resolution, f = ceiling),
    resolution = resolution
  ) %>%
    fasterize::fasterize(kernel, ., field = field)
}


# téléchargement--------------------------------------------------------------

if (!dir_exists("donnees")) dir_create("donnees")
if (!dir_exists("resultats")) dir_create("resultats")
if (!dir_exists("resultats/animation")) dir_create("resultats/animation")

if (!file_exists(fichier_covid) |
    file_info(fichier_covid)$modification_time %
  clean_names() %>%
  st_set_crs(2154)

pop %
  clean_names()


# prétraitement -----------------------------------------------------------

# contour métropole pour grille de référence
fichier_fr %
    st_union() %>%
    st_sf() %>%
    write_rds(fichier_fr)
} else {
  fr %
    left_join(pop, by = c("insee_dep" = "x1")) %>%
    left_join(
      covid %>%
        filter(jour == if_else(is.null(date), max(jour), date),
               sexe == 0) %>%
        group_by(dep) %>%
        summarise(deces = sum(dc, na.rm = TRUE),
                  reanim = sum(rea, na.rm = TRUE),
                  hospit = sum(hosp, na.rm = TRUE)),
      by = c("insee_dep" = "dep")) %>%
    st_point_on_surface()
}

covid_geo_pop %
  lissage("deces", rayon, pixel, fr)


# population métropole et DOM
p %
  lissage("x2020_p", rayon, pixel, fr)

# grilles pour 100000 hab
d100k %
    lissage("deces", rayon, pixel, fr) %>%
    magrittr::divide_by(p) %>%
    magrittr::multiply_by(100000) %>%
    tm_shape() +
    tm_raster(title = glue("décès à l'hôpital
                         pour 100 000 hab."),
              style = "fixed",
              breaks = classes,
              palette = "viridis",
              legend.format = list(text.separator = "à moins de",
                                   digits = 0),
              legend.reverse = TRUE) +
    tm_shape(dep) +
    tm_borders() +
    tm_layout(title = glue("COVID-19 - France - cumul au {date}"),
              legend.position = c("left", "bottom"),
              frame = FALSE) +
    tm_credits(glue("http://r.iresmi.net/
                  lissage noyau bisquare {rayon / 1000} km sur grille {pixel / 1000} km
                  classif. kmeans
                  projections LAEA Europe
                  données départementales Santé publique France,
                  INSEE RP 2020, IGN Adminexpress 2020"),
               size = .5,
               position = c(.5, .025))
  
  tmap_save(m, glue("resultats/animation/covid_fr_{date}.png"),
            width = 800, height = 800, scale = .4,)
}

unique(covid$jour) %>%
  walk(image_animation)

animation %
  map(image_read) %>%
  image_join() %>%
  #image_scale("500x500") %>%
  image_morph(frames = 10) %>%
  image_animate(fps = 10, optimize = TRUE) %>%
  image_write(animation)

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