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Create adhoc maps for emergences

generate_adhoc_map.Rd

Creates a map of recent emergences. The default will display outbreaks from the past 13 months.

Usage

generate_adhoc_map(
  raw.data,
  country,
  virus_type = "cVDPV 2",
  vdpv = T,
  new_detect = T,
  surv = c("AFP", "ES", "OTHER"),
  labels = "YES",
  owner = "CDC-GID-PEB",
  new_detect_expand = F,
  start_date = NULL,
  end_date = NULL,
  emg_cols = NULL,
  output = NULL,
  image_size = NULL,
  height = 6.2,
  width = 4.5,
  scale = 1.25,
  dpi = 300
)

Arguments

raw.data

list Global polio data. The output of get_all_polio_data(). Make sure the spatial data is attached, otherwise, it will not work.

country

str or list Country name or a list of country names.

virus_type

str or list. Virus type to include. Valid values are:

"cVDPV 1", "cVDPV 2", "cVDPV 3", "WILD 1".

Can pass as a list.

vdpv

logical Whether to include VPDV in maps. Default TRUE.

new_detect

logical Whether to highlight new detections based on WHO HQ report date. Default TRUE.

surv

str or list Surveillance options. Valid values are:

"AFP", "ES", "OTHER"

"OTHER" includes Case Contact, Community, Healthy Children Sampling. Can pass as a list.

labels

str Include labels for regions with virus detections. Options:

  • "ALL": All regions

  • "YES": Recent Detections - <13 months

owner

str Who produced the map. Defaults to "CDC-GID-PEB".

new_detect_expand

logical Whether to expand the reporting window. Defaults to FALSE.

start_date

str Start date. If not specified, defaults to 13 months prior to the download date of raw.data.

end_date

str End date. If not specified, defaults to the download date of raw.data.

emg_cols

list A named list with all of the emergence colors. Defaults to NULL, which will download using set_emergence_colors().

output

str Either a path to a local folder to save the map to, "sharepoint", or NULL. Defaults to NULL.

image_size

str Standard sizes of the map outputs. Options are:

  • "full_slide"

  • "soco_slide"

  • "half_slide"

Defaults to NULL.

height

numeric Height of the map. Defaults to 6.2.

width

numeric Width of the map. Defaults to 4.5.

scale

numeric Scale of the map. Defaults to 1.25.

dpi

numeric DPI of the map. Defaults to 300.

Value

ggplot A map of outbreaks.

Examples

if (FALSE) { # \dontrun{
raw.data <- get_all_polio_data()
p1 <- generate_adhoc_map(raw.data, "algeria")
# Put colors in emergences that don't have a mapped color
emg_cols <- set_emergence_colors(raw.data, c("nigeria", "chad"))
emg_cols["NIE-BOS-1"] <- "yellow"
emg_cols["NIE-YBS-1"] <- "green"
p2 <- generate_adhoc_map(raw.data, c("nigeria", "chad"), emg_cols = emg_cols)
} # }