In Grandez/jggEarthquake: Capstone for Mastering Software Development in R

jggEarthquake package

The functions provided by this package use data from the U.S. National Oceanographic and Atmospheric Administration (NOAA) Significant Earthquake Database.

Required set-up for this package

Currently, this package exists in a development version on GitHub. To use the package, you need to install it directly from GitHub using the install_github function from devtools.

You can use the following code to install the development version of jggEarthquake:

library(devtools)
install_github("grandez/jggEarthquake")
library(jggEarthquake)

Sample data included with the package

Users may access a sample dataframe by running the code below.

eq_data_raw

The raw data file for this data frame is in tab delimited format can be accessed (and saved to your currrent working directory) by running the following:

data_raw <-system.file("extdata", "signif.txt", package = "jggEarthquake")
file.copy(from=c(data_raw),to=getwd())
data_raw_wd <- fread("./signif.txt")

Functions

Basic functions

According the requirements of project, following functions are available:

• Data tidying functions:
  • eq_get_data
  • eq_clean_data
  • eq_location_clean
• Geom for creating visualisations:
  • geom_timeline
  • geom_timeline_label

Wrapper functions

But to simplify the use some wrappers has been added:

• eq_load_data: Load and prepare data for visualizations
• eq_geom_timeline: Generate the plot associated using geom_timeline
• eq_geom_timeline_label: Generate the plot associated using Use of these functions are shown below.

Functions detail

eq_get_data

Takes the raw data set from NOAA server or from local system

# Download data set from Server
data_raw <- eq_get_data()

# Load data set from local
data_raw_wd <- eq_get_data("inst/extdata/signif.txt")

eq_clean_data

Takes the raw data set and make it tidy. Include new fields; DATE, LATITUDE, LONGITUDE and RITCHER as primary magnitude

data_clean <- eq_clean_data(data_raw)

eq_location_clean

Takes the raw data set and modified the column LOCATION_NAME to strip out country names and reformats to title case. It is automatically called from eq_clean_data

data_loc = eq_location_clean(data_raw)

````

#### eq_load_data

Wrapper to eq_get_data + eq_clean_data

```R
# Download data set from Server
data_clean <- eq_load_data()
# Load data set from local
data_clean <- eq_load_data("inst/extdata/signif.txt")

geom_timeline

A ggplot2 graphical function to plot a timeline of earthquakes from cleaned data. The plot indicates the magnitude of each earthquake and number of deaths.

Aesthetics supported:

• x = DATE (Mandatory)
• y = List of countries, by default no countries
• xmin = Begin of year starting at 0 (Default)
• xmax = End of year, by default the last Earthquake in data set

ggplot(data_clean) +
     geom_timeline(aes(x=DATE,colour=DEATHS,fill=DEATHS,size=RITCHER,
                       xmin = 2000,xmax = 2016
                      )
                  )

geom_timeline_label

A ggplot2 graphical function to plot a timeline of earthquakes from cleaned data adding labels to n-largest earthquakes by magnitude.

Aesthetics supported:

• x = DATE (Mandatory)
• nmax = Number of labels to show according its magnitude (Mandatory)
• y = List of countries, by default no countries
• xmin = Begin of year starting at 0 (Default)
• xmax = End of year, by default the last Earthquake in data set

ggplot(data_clean) +
     geom_timeline_label(aes(x=DATE, colour=DEATHS, fill=DEATHS, size=RITCHER,
                             xmin = 2000, xmax = 2016,nmax = 5)
                  )

eq_geom_timeline

A wrapper function to help generate timeline visualisations easier. Parameters:

• Data frame (Mandatory)
• xmin
• xmax
• countries

eq_geom_timeline(eq_data_clean, xmin=0, xmax=2016, countries=c("USA", "CHINA"))

eq_geom_timeline_label

A wrapper function to help generate timeline with labels visualisations easier.

Parameters:

• Data frame (Mandatory)
• n_max (Mandatory)
• xmin
• xmax
• countries

eq_geom_timeline_label(eq_data_clean
                      ,xmin=0
                      ,xmax=2016
                      ,n_max=5
                      ,countries=c("USA", "CHINA"))

eq_map

A function to generate an interactive map showing earthquakes for a particular country. The user specifies a column from the data which the earthquake is to be annotated by eg date.

eq_clean_data(eq_data_raw) %>% 
     dplyr::filter(COUNTRY == "MEXICO" & lubridate::year(date) >= 2000) %>% 
     eq_map(annot_col="date")

eq_create_label

A function to generate a custom popup box for a selected earthquake showing location, magnitude and total deaths.

eq_clean_data(eq_data_raw) %>% 
     eq_location_clean() %>% 
     dplyr::filter(COUNTRY == "MEXICO" & lubridate::year(date) >= 2000) %>% 
     dplyr::mutate(popup_text = eq_create_label(.)) %>% 
     eq_map(annot_col="popup_text")

Miscellaneous

The package also contains a new theme theme_timeline for use with geom_timeline and geom_timeline_label. It is applied automatically when using get_timeline and get_timeline_label.

There are two custom grobs and a custom stat included with the package which are used by the geom_ functions. These are geomTimeline, geomTimelineLabel and StatTimeline.

Grandez/jggEarthquake documentation built on May 14, 2019, 2:36 p.m.