inst/deploy_scripts/trichinella.R

In SVA-SE/svamap: Package to produce data summaries for the web

library(svamap)
library(sp)

# dt18 <- read.csv("//sva.se/UPP/Enheter/ESS/ESS gemensamt/Projekt/Trichinella/data/Trichinella-2018-falkenrapport.csv", encoding="UTF-8", stringsAsFactors = FALSE)
pt19 <-
  read.csv(
    "//sva.se/UPP/Enheter/ESS/ESS gemensamt/Projekt/Trichinella/data/Trichinella-2019-falkenrapport.csv",
    encoding = "UTF-8",
    stringsAsFactors = FALSE
  )
pt20 <-
  read.csv(
    "//sva.se/UPP/Temp/Falkenrapporter/Trichinella-2020-falkenrapport.csv",
    encoding = "UTF-8",
    stringsAsFactors = FALSE
  )
pt_clean_1920 <-
  read.csv(
    "//sva.se/UPP/Enheter/ESS/ESS gemensamt/Projekt/Trichinella/data/Trichinella_clean-2019-2020.csv",
    encoding = "UTF-8",
    stringsAsFactors = FALSE,
    sep = ';'
  )
names(pt_clean_1920)[1] <- "ID"
pt <- rbind(pt19, pt20)
pt <- pt[pt$Status..numerisk. == 1, ]
pt <-
  pt[pt$Djurslag == "Vildsvin" |
       pt$Djurslag == "Brunbj\u00F6rn" | pt$Djurslag == "Bj\u00F6rn (Sl\u00E4kte)", ]
pt$Date <- as.Date(pt$Ankomstdatum)
pt$Resultat[grep("Trichinella pseudospiralis", pt$Resultat)] <-
  "T. pseudospiralis"
pt$Resultat[grep("Trichinella britovi", pt$Resultat)] <-
  "T. britovi"
pt <-
  pt[, c(
    "Uppdragid",
    "Djurslag",
    "Status..numerisk.",
    "Kundpostnr",
    "Kundort",
    "Resultat",
    "Kommentarer",
    "Date"
  )]
pt <- pt[pt$Date > "2018-12-31", ]
pt <- pt[order(pt$Date), ]
pt$ID <- c(1:length(pt$Uppdragid))
pt <- merge(pt_clean_1920, pt, by = "ID", all.x = TRUE)
pt <- data.frame(
  species = pt$Djurslag.x,
  Kommun = pt$Kommun,
  gender_age_weight = pt[, "K\u00F6n.\u00E5lder.vikt"],
  num_larvae = pt[, "Antal.larver.g.k\u00F6tt"],
  type = pt$Art,
  result = pt$Status..numerisk.,
  Date = pt$Date,
  stringsAsFactors = FALSE
)

## Conver to S4
###############################
kommun <- read.csv2(
  "//sva.se/UPP/Enheter/ESS/ESS gemensamt/Projekt/Trichinella/data/kommun.csv",
  encoding = "UTF-8",
  stringsAsFactors = FALSE
)

pts <- merge(pt, kommun, by = "Kommun", all.x = TRUE)
pts$X <-
  runif(length(pts$X),
        as.numeric(pts$X) - 2500.0,
        as.numeric(pts$X) + 2500.0)
pts$Y <-
  runif(length(pts$Y),
        as.numeric(pts$Y) - 2500.0,
        as.numeric(pts$Y) + 500.0)

pts <- SpatialPointsDataFrame(cbind(pts$X, pts$Y), pts)
proj4string(pts) <- "+init=epsg:3006"
pts <- spTransform(pts, CRS("+init=epsg:4326"))

pts@data <- data.frame(
  species = pts@data$species,
  kommun = pts@data$Kommun,
  result = pts@data$result,
  Date = pts@data$Date,
  gender_age_weight = pts@data$gender_age_weight ,
  num_larvae = pts@data$num_larvae,
  type = pts@data$type,
  stringsAsFactors = FALSE
)



## Read wildboar density
########################
load(
  "//sva.se/UPP/Enheter/ESS/EPIZ/Sjukdomar/CSF ASF/WildboarDensity/2018WildboarDensity.RData"
)

##Write data to geojson
########################
path_to_data <- write_data(list(pts, Wildboar_density_2018))

path <- "deploy_pages/trichinella"
dir.create(path, showWarnings = FALSE, recursive = TRUE)

write_page(
  data = path_to_data,
  path = path,
  template = "trichinella/map.html",
  overwrite = TRUE,
  browse = FALSE
)
file.copy(system.file("assets/images", package = "svamap"),
          file.path(path, "map"),
          recursive = TRUE)