R/epi_channel.R
In fdzul/boldenr: boldenr: a package designed to generate of Dengue Bulletin of Veracruz state
Defines functions
epi_channel
Documented in
epi_channel
#' epi_channel
#'
#' @param x is the database that contains the 25th, 50th and 75th percentiles of dengue cases by state
#' @param y is the current dataset. Load with \link[boldenr]{read_dataset_bol} function.
#' @param edo is the target state. The epidemiological channel is provided by state.
#' @param jur is the target furidiction.
#' @param mpo is the target municipality.
#' @param loc is the locality target.
#' @param year1 is the year one.
#' @param year2 is the year two.
#' @param x_epi is the x position of the epidemic zone legend.
#' @param y_epi is the y position of the epidemic zone legend.
#' @param x_alerta is the x position of the alert zone legend.
#' @param y_alerta is the y position of the alert zone legend.
#' @param x_seg is the x position of the security zone legend.
#' @param y_seg is the y position of the security zone legend.
#' @param x_exito is the x position of the success zone legend.
#' @param y_exito is the y position of the success zone legend.
#'
#' @author Felipe Antonio Dzul Manzanilla \email{felipe.dzul.m@gmail.com}
#'
#' @return
#' @export
#'
#' @examples
epi_channel <- function(x, y,
edo, jur, mpo, loc,
year1, year2,
x_epi, y_epi,
x_alerta,y_alerta,
x_seg, y_seg,
x_exito, y_exito){
if(is.null(jur)){
x <- x |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% c(edo))
z1 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES == edo) |>
dplyr::filter(ANO == year1) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
z2 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES == edo) |>
dplyr::filter(ANO == year2) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
ggplot2::ggplot(data = x,
ggplot2::aes(x = SEM)) +
ggplot2::geom_area(ggplot2::aes(y = q75),
col = "black",
size = 0.8,
fill = "#F44B1FFF",
alpha = 1) +
ggplot2::theme_classic() +
ggplot2::geom_area(ggplot2::aes(y = q50),
col = "white",
size = 0.8,
fill = "#FF9000FF",
alpha = 1) +
ggplot2::geom_area(ggplot2::aes(y = q25),
col = "white",
size = .8,
fill = "#00F293FF",
alpha = .8) +
ggplot2::ylab("Casos") +
ggplot2::xlab("Semanas epidemiológicas") +
ggplot2::annotate("text",
label = "Epidémico",
x = x_epi,
y = y_epi,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Alerta",
x = x_alerta,
y = y_alerta,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Seguridad",
x = x_seg,
y = y_seg,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Éxito",
x = x_exito,
y = y_exito,
size = 6,
colour = "black") +
ggplot2::scale_x_continuous(breaks = seq(from = 1,
to = 52,
by = 5),
limits = c(1,52)) +
ggplot2::geom_line(data = z1,
ggplot2::aes(x = SEM, y = n),
alpha = 0.5,
linewidth = 1.5,
colour = "grey") +
ggplot2::geom_point(data = z1,
ggplot2::aes(x = SEM, y = n),
colour = "red",
shape = 21,
alpha = 0.5,
fill = "black",
stroke = 2) +
ggplot2::geom_line(data = z2,
ggplot2::aes(x = SEM, y = n),
#alpha = 0.5,s
linewidth = 1.5,
colour = "black") +
ggplot2::geom_point(data = z2,
ggplot2::aes(x = SEM, y = n),
colour = "white",
shape = 21,
alpha = 0.5,
fill = "red",
stroke = 2)
} else{
if(is.null(mpo)){
x <- x |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_JUR_RES = stringr::str_replace_all(string = DES_JUR_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% c(edo) &
DES_JUR_RES %in% c(jur))
z1 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_JUR_RES = stringr::str_replace_all(string = DES_JUR_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_JUR_RES %in% c(jur)) |>
dplyr::filter(ANO == year1) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
z2 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_JUR_RES = stringr::str_replace_all(string = DES_JUR_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_JUR_RES %in% c(jur)) |>
dplyr::filter(ANO == year2) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
} else {
if(is.null(loc)){
x <- x |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_MPO_RES = stringr::str_replace_all(string = DES_MPO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% c(edo) &
DES_MPO_RES %in% c(mpo))
z1 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_MPO_RES = stringr::str_replace_all(string = DES_MPO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_MPO_RES %in% c(mpo)) |>
dplyr::filter(ANO == year1) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
z2 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_MPO_RES = stringr::str_replace_all(string = DES_MPO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_MPO_RES %in% c(mpo)) |>
dplyr::filter(ANO == year2) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
} else {
x <- x |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_LOC_RES = stringr::str_replace_all(string = DES_LOC_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% c(edo) &
DES_LOC_RES %in% c(loc))
z1 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_LOC_RES = stringr::str_replace_all(string = DES_LOC_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_LOC_RES %in% c(loc)) |>
dplyr::filter(ANO == year1) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
z2 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_LOC_RES = stringr::str_replace_all(string = DES_LOC_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_LOC_RES %in% c(loc)) |>
dplyr::filter(ANO == year2) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
}
}
}
ggplot2::ggplot(data = x,
ggplot2::aes(x = SEM)) +
ggplot2::geom_area(ggplot2::aes(y = q75),
col = "black",
size = 0.8,
fill = "#F44B1FFF",
alpha = 1) +
ggplot2::theme_classic() +
ggplot2::geom_area(ggplot2::aes(y = q50),
col = "white",
size = 0.8,
fill = "#FF9000FF",
alpha = 1) +
ggplot2::geom_area(ggplot2::aes(y = q25),
col = "white",
size = .8,
fill = "#00F293FF",
alpha = .8) +
ggplot2::ylab("Casos") +
ggplot2::xlab("Semanas epidemiológicas") +
ggplot2::annotate("text",
label = "Epidémico",
x = x_epi,
y = y_epi,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Alerta",
x = x_alerta,
y = y_alerta,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Seguridad",
x = x_seg,
y = y_seg,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Éxito",
x = x_exito,
y = y_exito,
size = 6,
colour = "black") +
ggplot2::scale_x_continuous(breaks = seq(from = 1,
to = 52,
by = 5),
limits = c(1,52)) +
ggplot2::geom_line(data = z1,
ggplot2::aes(x = SEM, y = n),
alpha = 0.5,
linewidth = 1.5,
colour = "grey") +
ggplot2::geom_point(data = z1,
ggplot2::aes(x = SEM, y = n),
colour = "red",
shape = 21,
alpha = 0.5,
fill = "black",
stroke = 2) +
ggplot2::geom_line(data = z2,
ggplot2::aes(x = SEM, y = n),
#alpha = 0.5,s
linewidth = 1.5,
colour = "black") +
ggplot2::geom_point(data = z2,
ggplot2::aes(x = SEM, y = n),
colour = "white",
shape = 21,
alpha = 0.5,
fill = "red",
stroke = 2)
}
fdzul/boldenr documentation built on April 15, 2024, 10:22 p.m.
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Defines functions epi_channel
Documented in epi_channel
#' epi_channel
#'
#' @param x is the database that contains the 25th, 50th and 75th percentiles of dengue cases by state
#' @param y is the current dataset. Load with \link[boldenr]{read_dataset_bol} function.
#' @param edo is the target state. The epidemiological channel is provided by state.
#' @param jur is the target furidiction.
#' @param mpo is the target municipality.
#' @param loc is the locality target.
#' @param year1 is the year one.
#' @param year2 is the year two.
#' @param x_epi is the x position of the epidemic zone legend.
#' @param y_epi is the y position of the epidemic zone legend.
#' @param x_alerta is the x position of the alert zone legend.
#' @param y_alerta is the y position of the alert zone legend.
#' @param x_seg is the x position of the security zone legend.
#' @param y_seg is the y position of the security zone legend.
#' @param x_exito is the x position of the success zone legend.
#' @param y_exito is the y position of the success zone legend.
#'
#' @author Felipe Antonio Dzul Manzanilla \email{felipe.dzul.m@gmail.com}
#'
#' @return
#' @export
#'
#' @examples
epi_channel <- function(x, y,
edo, jur, mpo, loc,
year1, year2,
x_epi, y_epi,
x_alerta,y_alerta,
x_seg, y_seg,
x_exito, y_exito){
if(is.null(jur)){
x <- x |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% c(edo))
z1 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES == edo) |>
dplyr::filter(ANO == year1) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
z2 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES == edo) |>
dplyr::filter(ANO == year2) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
ggplot2::ggplot(data = x,
ggplot2::aes(x = SEM)) +
ggplot2::geom_area(ggplot2::aes(y = q75),
col = "black",
size = 0.8,
fill = "#F44B1FFF",
alpha = 1) +
ggplot2::theme_classic() +
ggplot2::geom_area(ggplot2::aes(y = q50),
col = "white",
size = 0.8,
fill = "#FF9000FF",
alpha = 1) +
ggplot2::geom_area(ggplot2::aes(y = q25),
col = "white",
size = .8,
fill = "#00F293FF",
alpha = .8) +
ggplot2::ylab("Casos") +
ggplot2::xlab("Semanas epidemiológicas") +
ggplot2::annotate("text",
label = "Epidémico",
x = x_epi,
y = y_epi,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Alerta",
x = x_alerta,
y = y_alerta,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Seguridad",
x = x_seg,
y = y_seg,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Éxito",
x = x_exito,
y = y_exito,
size = 6,
colour = "black") +
ggplot2::scale_x_continuous(breaks = seq(from = 1,
to = 52,
by = 5),
limits = c(1,52)) +
ggplot2::geom_line(data = z1,
ggplot2::aes(x = SEM, y = n),
alpha = 0.5,
linewidth = 1.5,
colour = "grey") +
ggplot2::geom_point(data = z1,
ggplot2::aes(x = SEM, y = n),
colour = "red",
shape = 21,
alpha = 0.5,
fill = "black",
stroke = 2) +
ggplot2::geom_line(data = z2,
ggplot2::aes(x = SEM, y = n),
#alpha = 0.5,s
linewidth = 1.5,
colour = "black") +
ggplot2::geom_point(data = z2,
ggplot2::aes(x = SEM, y = n),
colour = "white",
shape = 21,
alpha = 0.5,
fill = "red",
stroke = 2)
} else{
if(is.null(mpo)){
x <- x |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_JUR_RES = stringr::str_replace_all(string = DES_JUR_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% c(edo) &
DES_JUR_RES %in% c(jur))
z1 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_JUR_RES = stringr::str_replace_all(string = DES_JUR_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_JUR_RES %in% c(jur)) |>
dplyr::filter(ANO == year1) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
z2 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_JUR_RES = stringr::str_replace_all(string = DES_JUR_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_JUR_RES %in% c(jur)) |>
dplyr::filter(ANO == year2) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
} else {
if(is.null(loc)){
x <- x |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_MPO_RES = stringr::str_replace_all(string = DES_MPO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% c(edo) &
DES_MPO_RES %in% c(mpo))
z1 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_MPO_RES = stringr::str_replace_all(string = DES_MPO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_MPO_RES %in% c(mpo)) |>
dplyr::filter(ANO == year1) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
z2 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_MPO_RES = stringr::str_replace_all(string = DES_MPO_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_MPO_RES %in% c(mpo)) |>
dplyr::filter(ANO == year2) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
} else {
x <- x |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_LOC_RES = stringr::str_replace_all(string = DES_LOC_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% c(edo) &
DES_LOC_RES %in% c(loc))
z1 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_LOC_RES = stringr::str_replace_all(string = DES_LOC_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_LOC_RES %in% c(loc)) |>
dplyr::filter(ANO == year1) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
z2 <- y |>
dplyr::filter(!DES_EDO_RES %in% c("OTROS PAISES",
"OTROS PAISES DE LATINOAMERICA",
"ESTADOS UNIDOS DE NORTEAMERICA")) |>
dplyr::filter(DES_DIAG_FINAL %in% c("DENGUE CON SIGNOS DE ALARMA",
"DENGUE GRAVE",
"DENGUE NO GRAVE",
"FIEBRE HEMORRAGICA POR DENGUE",
"FIEBRE POR DENGUE")) |>
dplyr::mutate(DES_EDO_RES = stringr::str_replace_all(string = DES_EDO_RES,
pattern = " ",
repl = " "),
DES_LOC_RES = stringr::str_replace_all(string = DES_LOC_RES,
pattern = " ",
repl = " ")) |>
dplyr::filter(DES_EDO_RES %in% edo &
DES_LOC_RES %in% c(loc)) |>
dplyr::filter(ANO == year2) |>
dplyr::group_by(SEM) |>
dplyr::summarise(n = dplyr::n(), .groups = "drop")
}
}
}
ggplot2::ggplot(data = x,
ggplot2::aes(x = SEM)) +
ggplot2::geom_area(ggplot2::aes(y = q75),
col = "black",
size = 0.8,
fill = "#F44B1FFF",
alpha = 1) +
ggplot2::theme_classic() +
ggplot2::geom_area(ggplot2::aes(y = q50),
col = "white",
size = 0.8,
fill = "#FF9000FF",
alpha = 1) +
ggplot2::geom_area(ggplot2::aes(y = q25),
col = "white",
size = .8,
fill = "#00F293FF",
alpha = .8) +
ggplot2::ylab("Casos") +
ggplot2::xlab("Semanas epidemiológicas") +
ggplot2::annotate("text",
label = "Epidémico",
x = x_epi,
y = y_epi,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Alerta",
x = x_alerta,
y = y_alerta,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Seguridad",
x = x_seg,
y = y_seg,
size = 6,
colour = "black") +
ggplot2::annotate("text",
label = "Éxito",
x = x_exito,
y = y_exito,
size = 6,
colour = "black") +
ggplot2::scale_x_continuous(breaks = seq(from = 1,
to = 52,
by = 5),
limits = c(1,52)) +
ggplot2::geom_line(data = z1,
ggplot2::aes(x = SEM, y = n),
alpha = 0.5,
linewidth = 1.5,
colour = "grey") +
ggplot2::geom_point(data = z1,
ggplot2::aes(x = SEM, y = n),
colour = "red",
shape = 21,
alpha = 0.5,
fill = "black",
stroke = 2) +
ggplot2::geom_line(data = z2,
ggplot2::aes(x = SEM, y = n),
#alpha = 0.5,s
linewidth = 1.5,
colour = "black") +
ggplot2::geom_point(data = z2,
ggplot2::aes(x = SEM, y = n),
colour = "white",
shape = 21,
alpha = 0.5,
fill = "red",
stroke = 2)
}
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