#' Clean data
#'
#' This is a simple function that clean the data
#'
#' @param data A data frame with raw data
#'
#' @return This function returns a dataframe with the information from the file after being cleaned.
#'
#' @importFrom tidyr unite
#' @importFrom dplyr %>% tbl_df select mutate
#' @importFrom lubridate ymd_h
#'
#' @examples
#' \dontrun{
#' data <- readr::read_delim("signif.tsv.gz", delim = "\t")
#' eq_clean_data(data)
#' }
#'
#' @export
eq_clean_data<-function(data){
data %>%
dplyr::select(COUNTRY,LOCATION_NAME, LATITUDE, LONGITUDE,YEAR, MONTH, DAY, HOUR, EQ_MAG_ML,DEATHS) %>%
dplyr::mutate(LATITUDE= as.numeric(LATITUDE)) %>%
dplyr::mutate(LONGITUDE= as.numeric(LONGITUDE))%>%
tidyr::unite(Date, YEAR, MONTH, DAY, HOUR) %>%
dplyr::mutate(Date = lubridate::ymd_h(Date))%>%
dplyr::mutate(DEATHS=as.numeric(DEATHS)) %>%
eq_location_clean()
}
#' Clean location
#'
#' This is a simple function that clean the column location in a dataframe
#'
#' @param data A data frame with raw data
#'
#' @return This function returns a dataframe with a cleaned LOCATION_NAME column
#'
#' @importFrom dplyr %>% mutate funs
#' @importFrom stringi stri_trans_totitle
#' @importFrom stringr str_trim
#'
#' @examples
#' \dontrun{
#' eq_location_clean(data)
#' }
#'
#' @export
eq_location_clean<-function(data){
data%>%
dplyr::mutate_each(dplyr::funs(gsub(".*: ", "", LOCATION_NAME)),LOCATION_NAME)%>%
dplyr::mutate(LOCATION_NAME=stringi::stri_trans_totitle(LOCATION_NAME)) %>%
dplyr::mutate(LOCATION_NAME=stringr::str_trim(LOCATION_NAME))
}
#' Time line of earthquakes
#'
#' @description This geom for ggplot2 called geom_timeline() for plotting a time line
#' of earthquakes ranging from xmin to xmaxdates with a point for each earthquake.
#' Optional aesthetics include color, size, and alpha (for transparency)
#'
#' @importFrom ggplot2 layer
#'
#' @examples
#' \dontrun{
#' data %>% eq_clean_data() %>%
#' dplyr::filter(Date >= "1980-01-01" & Date <="2014-01-01" & COUNTRY == c("ITALY","USA", "JORDAN")) %>%
#' ggplot(aes(x = Date,
#' y = COUNTRY,
#' color = DEATHS,
#' size = EQ_MAG_ML
#' )) +
#' geom_timeline() +
#' theme_timeline()
#'
#' }
#'
#' @export
geom_timeline <- function(mapping = NULL, data = NULL, stat = "identity",
position = "identity", na.rm = FALSE,
show.legend = NA, inherit.aes = TRUE, ...) {
ggplot2::layer(
geom = GeomTimeline, mapping = mapping,
data = data, stat = stat, position = position,
show.legend = show.legend, inherit.aes = inherit.aes,
params = list(na.rm = na.rm, ...)
)
}
#' @importFrom ggplot2 ggproto Geom aes draw_key_point
#' @importFrom grid pointsGrob gList gpar
#' @importFrom scales alpha
GeomTimeline <-
ggplot2::ggproto(
"GeomTimeline", ggplot2::Geom,
required_aes = c("x"),
default_aes = ggplot2::aes(colour = "grey", size = 1.5, alpha = 0.5,
shape = 21, fill = "grey", stroke = 0.5),
draw_key = ggplot2::draw_key_point,
draw_panel = function(data, panel_scales, coord) {
if (!("y" %in% colnames(data))) {
data$y <- 0.15
}
coords <- coord$transform(data, panel_scales)
points <- grid::pointsGrob(
coords$x, coords$y,
pch = coords$shape, size = unit(coords$size / 4, "char"),
gp = grid::gpar(
col = scales::alpha(coords$colour, coords$alpha),
fill = scales::alpha(coords$colour, coords$alpha)
)
)
y_lines <- unique(coords$y)
lines <- grid::polylineGrob(
x = unit(rep(c(0, 1), each = length(y_lines)), "npc"),
y = unit(c(y_lines, y_lines), "npc"),
id = rep(seq_along(y_lines), 2),
gp = grid::gpar(col = "grey",
lwd = .pt)
)
grid::gList(points, lines)
}
)
#' Time line labels of earthquakes
#'
#' @description This geom for adding annotations to the earthquake data. This geom adds a vertical line
#' to each data point with a text annotation (e.g. the location of the earthquake) attached to each line
#'
#' @param n_max An integer. number of earthquakes, where we take the n_max largest (by magnitude) earthquakes
#'
#' @importFrom ggplot2 layer
#'
#' @examples
#' \dontrun{
#' data %>% eq_clean_data() %>%
#' dplyr::filter(Date >= "1980-01-01" & Date <="2014-01-01" & COUNTRY == c("ITALY","USA", "JORDAN")) %>%
#' ggplot(aes(x = Date,
#' y = COUNTRY,
#' color = DEATHS,
#' size = EQ_MAG_ML
#' )) +
#' geom_timeline() +
#' geom_timeline_label(aes(label = LOCATION_NAME), n_max = 5) +
#' theme_timeline()
#'
#' }
#'
#' @export
geom_timeline_label <- function(mapping = NULL, data = NULL, stat = "identity",
position = "identity", ..., na.rm = FALSE,
n_max = NULL, show.legend = NA,
inherit.aes = TRUE) {
ggplot2::layer(
geom = GeomTimelineLabel, mapping = mapping,
data = data, stat = stat, position = position,
show.legend = show.legend, inherit.aes = inherit.aes,
params = list(na.rm = na.rm, n_max = n_max, ...)
)
}
#' @importFrom ggplot2 ggproto Geom aes draw_key_point
#' @importFrom grid polylineGrob gList gpar textGrob
#' @importFrom dplyr %>% group_by_ top_n ungroup
GeomTimelineLabel <-
ggplot2::ggproto(
"GeomTimelineLabel", ggplot2::Geom,
required_aes = c("x", "label"),
draw_key = ggplot2::draw_key_blank,
setup_data = function(data, params) {
if (!is.null(params$n_max)) {
if (!("size" %in% colnames(data))) {
stop(paste("'size' aesthetics needs to be",
"provided when 'n_max' is defined."))
}
data <- data %>%
dplyr::group_by_("group") %>%
dplyr::top_n(params$n_max, size) %>%
dplyr::ungroup()
}
data
},
draw_panel = function(data, panel_scales, coord, n_max) {
if (!("y" %in% colnames(data))) {
data$y <- 0.15
}
coords <- coord$transform(data, panel_scales)
n_grp <- length(unique(data$group))
offset <- 0.2 / n_grp
lines <- grid::polylineGrob(
x = unit(c(coords$x, coords$x), "npc"),
y = unit(c(coords$y, coords$y + offset), "npc"),
id = rep(1:dim(coords)[1], 2),
gp = grid::gpar(
col = "grey"
)
)
names <- grid::textGrob(
label = coords$label,
x = unit(coords$x, "npc"),
y = unit(coords$y + offset, "npc"),
just = c("left", "bottom"),
rot = 45
)
grid::gList(lines, names)
}
)
#' Theme for a correct visualization
#'
#' @description This is a theme to configure the look of the geom
#'
#' @importFrom ggplot2 theme element_blank element_line
#'
#' @examples
#' \dontrun{
#' data %>% eq_clean_data() %>%
#' dplyr::filter(Date >= "1980-01-01" & Date <="2014-01-01" & COUNTRY == c("ITALY","USA", "JORDAN")) %>%
#' ggplot(aes(x = Date,
#' y = COUNTRY,
#' color = DEATHS,
#' size = EQ_MAG_ML
#' )) +
#' geom_timeline() +
#' theme_timeline()
#'
#' }
#'
#' @export
theme_timeline <- function() {
ggplot2::theme(
plot.background = ggplot2::element_blank(),
panel.background = ggplot2::element_blank(),
legend.key = ggplot2::element_blank(),
axis.title.y = ggplot2::element_blank(),
axis.line.x = ggplot2::element_line(size = 1),
axis.ticks.y = ggplot2::element_blank(),
legend.position = "bottom"
)
}
#' Map of earthquakes
#'
#' @description The function maps the epicenters (LATITUDE/LONGITUDE) and annotates
#' each point with in pop up window containing annotation data stored
#' in a column of the data frame
#'
#' @importFrom leaflet leaflet addTiles addCircleMarkers
#' @importFrom dplyr %>%
#'
#' @param data A data frame with the earthquake data
#' @param annot_col A string with the name of the column to show in the pop up
#'
#' @return A Map with earthquakes and annotations.
#'
#' @examples
#' \dontrun{
#' eq_map(data, annot_col = "Date")
#' }
#' @export
eq_map <- function(data, annot_col) {
map <- leaflet::leaflet() %>%
leaflet::addTiles() %>%
leaflet::addCircleMarkers(lng = data$LONGITUDE, lat = data$LATITUDE,
radius = data$EQ_MAG_ML, weight = 1,
popup = data[[annot_col]])
map
}
#' Creates a label for leaflet map
#'
#' @description This function takes the dataset as an argument and
#' creates an HTML label that can be used as the annotation text in the leaflet map
#'
#' @param data A data frame with the earthquake data
#'
#' @return A vector with labels
#'
#' @export
#'
#' @examples
#' \dontrun{
#' eq_create_label(data)
#' }
eq_create_label <- function(data) {
popup_text <- with(data, {
part1 <- ifelse(is.na(LOCATION_NAME), "",
paste("<strong>Location:</strong>",
LOCATION_NAME))
part2 <- ifelse(is.na(EQ_MAG_ML), "",
paste("<br><strong>Magnitude</strong>",
EQ_MAG_ML))
part3 <- ifelse(is.na(DEATHS), "",
paste("<br><strong>Total deaths:</strong>",
DEATHS))
paste0(part1, part2, part3)
})
}
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