Animated map of arbovirus cases by locality and epidemiological week.
mp_animated_loc(
path,
snv_dataset = c("DENV", "ZIKV", "CHIKV"),
year = NULL,
week = NULL,
var = "probable",
multi = c("sum", "facet"),
ncol = NA,
country = TRUE,
cve_edo = NULL,
breaks = NULL,
pal = "-viridis",
text_size = 0.4,
fps = 2,
save = FALSE,
name = NULL,
dir = "./",
width = NULL,
height = NULL,
size_range = c(2.5, 14),
strip_size = 18,
curve = TRUE,
map_legend = TRUE,
legend_title = "Casos por localidad"
)path to the SINAVE txt file (e.g. `"DENGUE2_.txt"`, `"ZIKA2_.txt"` or `"CHIKUNGUNYA2_.txt"`).
arbovirus of the dataset: `"DENV"` (dengue), `"ZIKV"` (Zika) or `"CHIKV"` (chikungunya).
year of the dataset (ANO column). If NULL (default), the most recent year in the dataset is used.
epidemiological weeks to animate (SEM column), e.g. `1:52`. If NULL (default), all weeks are used.
one or more types of cases to map: `"probable"` (probable + confirmed, default), `"confirmado"` (confirmed). Only for `snv_dataset = "DENV"`: `"DNG"` (non-severe dengue), `"DCSA"` (dengue with warning signs), `"DG"` (severe dengue), `"DENV1"`, `"DENV2"`, `"DENV3"` or `"DENV4"` (serotype, RT-PCR triplex). With more than one value, `multi` defines how they are combined.
how to combine several values of `var`: `"sum"` (default) counts together the cases of any of them in one map (e.g. `var = c("DCSA", "DG")`); `"facet"` draws one panel per value in every frame (e.g. `var = c("DENV1", "DENV2", "DENV3", "DENV4")`).
number of columns of panels when `multi = "facet"` (default NA, automatic).
logical. TRUE (default) = whole country with state boundaries; FALSE = the state given in `cve_edo` with municipal boundaries.
INEGI state code ("20" or 20). Required if `country = FALSE`.
numeric, step between the breaks of the legend and of the colour and size scales (e.g. `breaks = 5` gives 1, 6, 11, ...). If NULL (default), 5 integer breaks from 1 to the maximum number of cases are used (e.g. 1, 6, 12, 18, 23). With `"quantile"`, the quartiles of the cases by locality and week are used (minimum, Q1, median, Q3 and maximum); repeated values are dropped, so there may be fewer than 5 breaks when most localities have 1 or 2 cases.
colour palette of the bubbles (default `"-viridis"`; the minus sign reverses it so that more cases are darker).
size of the number of cases inside the bubbles (default 0.4; use 0 to hide it).
frames (weeks) per second (default 2).
logical. If TRUE the gif is saved in `dir`; if FALSE (default) the animation is only shown.
name of the gif file (without extension); `"_loc_animated_map.gif"` is added at the end.
directory where the gif is saved (with "/" at the end).
size of the gif in pixels. `height` defaults to 2000 (1600 without the curve); `width` is computed from the number of panels, `ncol` and the shape of the map, so the curve has the same width as the maps.
minimum and maximum size of the bubbles (default `c(2.5, 14)`).
text size of the panel titles (default 18). Each title shows the category and its cases of the week.
logical. Add below the maps a line chart of the weekly cases of each category, with the current week marked (default TRUE).
logical. Show the legend of the bubbles (size and colour by number of cases) below the maps (default TRUE).
title of the bubble legend (default `"Casos por localidad"`).
a gif file of animation (with `multi = "facet"`, the path of the gif, invisibly).
Reads the SINAVE dataset (same processing as [cases_by_loc()]), counts the cases by locality and epidemiological week and builds an animated map (one frame per week) following the workflow of [mp_animated()]. For the whole country the state boundaries are drawn; for a state, its municipal boundaries.
Only probable and confirmed cases (`ESTATUS_CASO` 1 and 2) are used, counted by locality of report (`CVE_EDO_REP` + `CVE_MPO_REP` + `CVE_LOC_REP`) and joined to the INEGI 2020 localities (`rgeomex::iter_2020_loc`). Colour and size scales are the same in every frame and in every panel, so they can be compared. With `multi = "facet"`, a case can appear in more than one panel (e.g. a confirmed DENV2 case in `"confirmado"` and in `"DENV2"`). Each frame is a ggplot2 figure (one panel per value of `var` with `multi = "facet"`, or a single panel) with the week in the title, and the frames are joined with gifski; the gif is shown in the RStudio Viewer (and saved in `dir` if `save = TRUE`). Saving the gif needs the gifski package.
[mp_animated()], [cases_by_loc()]
if (FALSE) { # \dontrun{
# whole country, with state boundaries
mp_animated_loc(path = "DENGUE2_.txt", snv_dataset = "DENV",
year = 2026, week = 1:52,
save = TRUE, name = "dengue_mexico_2026", dir = "./")
# Oaxaca, confirmed cases, with municipal boundaries
mp_animated_loc(path = "DENGUE2_.txt", snv_dataset = "DENV",
year = 2026, week = 1:52, var = "confirmado",
country = FALSE, cve_edo = "20",
save = TRUE, name = "dengue_oaxaca_2026", dir = "./")
# severe forms together (DCSA + DG) in one map
mp_animated_loc(path = "DENGUE2_.txt", snv_dataset = "DENV",
year = 2026, week = 1:52,
var = c("DCSA", "DG"), multi = "sum",
save = TRUE, name = "dcsa_dg_mexico_2026", dir = "./")
# one panel per serotype
mp_animated_loc(path = "DENGUE2_.txt", snv_dataset = "DENV",
year = 2026, week = 1:52,
var = c("DENV1", "DENV2", "DENV3", "DENV4"),
multi = "facet", ncol = 2,
save = TRUE, name = "serotipos_mexico_2026", dir = "./")
} # }