In Darwinita/EarthquakingLCP: Functions to process and analyze data from NOAA

knitr::opts_chunk$set(comment = NA, echo=TRUE, warning=FALSE, message=FALSE)
knitr::opts_knit$set(progress = TRUE, verbose = TRUE)

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title: "EarthquakingLCP_vignette" author: "Lorenzo Carretero" date: "r Sys.Date()" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{EarthquakingLCP_vignette} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

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Load required libraries:

# install.packages(c("dplyr","readr","lubridate","stringr","ggplot2","grid","tidyr","leaflet"))
library(dplyr)
library(readr)
library(lubridate)
library(stringr)
library(ggplot2)
library(grid)
library(tidyr)
library(leaflet)
# devtools::install()
# library(EarthquakingLCP)

The NOAA Significant Earthquake Database:

The Significant Earthquake Database contains information on 5,933 destructive earthquakes from 2150 B.C. to the present that meet at least one of the following criteria: Moderate damage (approximately $1 million or more), 10 or more deaths, Magnitude 7.5 or greater, Modified Mercalli Intensity X or greater, or the earthquake generated a tsunami. To access the raw data files the user can use the following line of code:

filename <- system.file("extdata", "signif.txt", package = "EarthquakingLCP")

Description

This is the vignette for the R package EarthquakingLCP written in R Markdown as a html_vignette document. The R package EarthquakingLCP implements seven exported useful functions (plus four internal unimported ones) to process and analyze data from the U.S. National Oceanographic and Atmospheric Administration (NOAA) on signicant earthquakes around the world. Please, visit Significant Earthquake Database for more informartion on the NOAA dataset. The functions are the following:

1. eq_clean_data(): A read data file function into a cleaned version of a data frame.
2. eq_location_clean(): A function to clean the LOCATION_NAME column from the NOAA data frame.
3. geom_timeline(): A function to plot a timeline of earthquakes.
4. geom_timeline_label(): A geom for labelling earthquake timeline plots created using geom_timeline().
5. eq_map(): A function to create a leaflet map of earthquakes and annotations.
6. eq_create_label(): A function to create labels for popups of earthquakes in leaflet maps.
7. theme_timeline: An accessory function to format the theme of geom_timeline earhtquakes plots.

Details

The R package EarthquakingLCP has the following main goals:

• Obtaining/downloading the dataset and cleaning up some of the variables.

• Visualizing some of the information in the NOAA earthquakes dataset, i.e., i) times at which earthquakes occur within certain countries, and ii) their magnitudes (i.e. Richter scale value) and the number of deaths associated with each earthquake.

• Mapping the earthquake epicenters and providing some annotations with the mapped data.

Installation

From CRAN

install.packages('EarthquakingLCP')

From GITHUB

devtools::install_github("Darwinita/EarthquakingLCP")

LOAD using

library(EarthquakingLCP)

Usage

1. eq_clean_data

eq_clean_data() reads a filename from the U.S. National Oceanographic and Atmospheric Administration (NOAA) on signicant earthquakes around the world, into a clean version of an R data frame. It stops if the file does not exist. The cleaned version of the data frame has:

i) the year, month and day converted to the Date class, after dealing with negative years (BCE). ii) EQ_PRIMARY, TOTAL_DEATHS, YEAR, LATITUDE and LONGITUDE columns converted to numeric class. iii) A clean LOCATION_NAME column by calling the eq_location_clean function.

Arguments

filename Is a character string with the file name of the input NOAA data file.

Usage

NOAAdf <- EarthquakingLCP::eq_clean_data(filename)
summary(NOAAdf)

2. eq_location_clean

eq_location_clean() cleans the LOCATION_NAME column from the NOAA data frame by stripping out the country name (including the colon) and converting names to title case.

Arguments

dataframe Is a data frame in dplyr format of the NOAA data.

Usage

NOAAdf <- EarthquakingLCP::eq_clean_data(filename)
cleanNOAAdf <- EarthquakingLCP::eq_location_clean(NOAAdf)
summary(cleanNOAAdf)

3. geom_timeline

geom_timeline() plots a timeline of earthquakes ranging from xmin to xmax dates with a point for each earthquake. Each point-earthquake is colored according to the number of fatal casualties and its size indicates the magnitudes in Richter's scale.

Arguments

dataframe A cleaned version of a NOAA data frame stat Statistical transformation. No data transformation if "identity". xmin (optional): minimum date for earthquakes xmax (optional): maximum date for earthquakes

Usage

xmin = lubridate::ymd_hm("1016-01-01",truncated = 2)
xmax = lubridate::ymd_hm("2016-01-01",truncated = 2)
NOAAdf <- EarthquakingLCP::eq_clean_data(filename)
NOAAdfSp <- NOAAdf %>%
   dplyr::filter(COUNTRY %in% c("SPAIN", "IRAN", "BELGIUM"))
 ggplot2::ggplot(data = NOAAdfSp, ggplot2::aes(x = DATE,
                             y = COUNTRY)
                 ) +
   EarthquakingLCP::geom_timeline(ggplot2::aes(size = EQ_PRIMARY,
                     fill = TOTAL_DEATHS),
                 xmin = xmin, xmax = xmax) +
   EarthquakingLCP::theme_timeline() +
   ggplot2::labs(size = "Richter scale value", color = "# deaths")

4. geom_timeline_label

geom_timeline_label() adds a vertical line to each earthquake data point with a text label (e.g. LOCATION_NAME). There should be an option to subset to n_max number of earthquakes,sorted by any measure of magnitude (e.g. EQ_PRIMARY).

Arguments

n_max: An integer corresponding to the number of top earthquakes to label, sorted by measure of magnitude.

Usage

xmin = lubridate::ymd_hm("1016-01-01",truncated = 2)
xmax = lubridate::ymd_hm("2016-01-01",truncated = 2)
NOAAdf <- EarthquakingLCP::eq_clean_data(filename)
NOAAdfSp <- NOAAdf %>%
   dplyr::filter(COUNTRY %in% c("SPAIN", "IRAN", "BELGIUM"))
 ggplot2::ggplot(data = NOAAdfSp, ggplot2::aes(x = DATE,
                             y = COUNTRY)
                 ) +
   EarthquakingLCP::geom_timeline(ggplot2::aes(size = EQ_PRIMARY,
                     fill = TOTAL_DEATHS),
                 xmin = xmin, xmax = xmax) +
   EarthquakingLCP::geom_timeline_label(aes(label = LOCATION_NAME, measure = EQ_PRIMARY),
        xmin = xmin, xmax = xmax, n_max = 5) +
   EarthquakingLCP::theme_timeline() +
   ggplot2::labs(size = "Richter scale value", color = "# deaths")

5. eq_map

eq_map() creates a map with the epicenters (LATITUDE & LONGITUDE) of selected earthquakes and annotates each point with a pop up window containing annotation data stored in a column of the data frame (e.g. DATE)

Arguments

dataframe A cleaned version of a NOAA data frame annot_col A character. The column of the data frame for which to annotate the pop up window for the selected earthquake.

Usage

NOAAdf <- EarthquakingLCP::eq_clean_data(filename)
NOAAdf %>%
         dplyr::filter(COUNTRY == "MEXICO" & lubridate::year(DATE) >= 2000) %>%
         EarthquakingLCP::eq_map(annot_col = "DATE")

6. eq_create_label

eq_create_label() pust together a character string for each earthquake that will show the cleaned location LOCATION_NAME, as cleaned by eq_location_clean(), the magnitude (e.g., EQ_PRIMARY), and the total number of deaths (e.g., TOTAL_DEATHS), with boldface labels for each. If an earthquake has missing values for any of these, both the label and the value should be skipped.

Arguments

dataframe A cleaned version of a NOAA data frame

Usage

NOAAdf <- EarthquakingLCP::eq_clean_data(filename)
NOAAdf %>%
         dplyr::filter(COUNTRY == "MEXICO" & lubridate::year(DATE) >= 2000) %>%
         dplyr::mutate(popup_text = EarthquakingLCP::eq_create_label(.)) %>%
         EarthquakingLCP::eq_map(annot_col = "popup_text")

Darwinita/EarthquakingLCP documentation built on May 12, 2019, 8:40 a.m.