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Mastering Software Development in R Specialization Capstone

Tags

  • Author : AH Uyekita
  • Date : 21/fev/2019
  • Course : Mastering Software Development in R Specialization Capstone
  • Project : Capstone Project
    • COD : MSDR
    • Instructor: Roger D. Peng
    • Instructor: Brooke Anderson

Installation

You can use this package installing it by the use of devtools library from R.

# Downloading the package
devtools::install_github("AndersonUyekita/JHU_MSDR_Capstone")

# Loading the library
library(msdr)

Vignettes

I have disclosed the principal Vignette in the RPubs.

Bookdown

The Bookdown is a compendium of all functions of this package.


Introduction

This package is the outcome of the Mastering Software Development in R Capstone.

Description

The package is tailored to work with the NOAA (National Oceanic Atmospheric Administration) Earthquake database.

This database has 6,086 observations and 47 features (database downloaded in 20/feb/2019), which 4,283 observations are about earthquake and 1,803 with FLAG_TSUNAMI as true.

From this 4,283 observations, there are 27 with negative YEAR and 4,256 with positives values. Finally, from this last subset 1,305 observations have no EQ_PRIMARY (Magnitude in Richter Scale), which means they are recorded as NA, so there are only 2,951 valid observations.

Objectivies

Development a new package capable to plot a timeline using the ggplot2 as bedrock. I have also created a function to deal with maps (OpenStreet maps) and earthquake information.

Functionalities

The package has 6 functions, which could be easily used, 2 functions with some restrictions of use (because it is not so easy to use), and 1 theme.

eq_clean_data

This function loads a given file_name and then performs the data cleaning. Undercover of this process these functions call the eq_location_clean to creates a new column called LOCATION.

Have in mind, this function also perfoms the conversion of data to the proper class type.

eq_create_label

Combines three columns to creates a new one with HTML structure, this is necessary because the Leaflet package requires the data to be displayed inside of the popup as HTML format.

eq_location_clean

Adds the LOCATION column. The dataset must have the LOCATION_NAME. If not the function will not work properly.

eq_map

Draw an OpenStreet Map and circles representing the earthquake's location. The popups show the date of the event. All this feature built over the Leaflet package.

geom_timeline

Plot a timeline based on magnitude (EQ_PRIMARY) and total deaths (TOTAL_DEATHS).

geom_timeline_label

Given a plot of geom_timeline, this function annotates labels to the n_max earthquakes with the highest magnitude (EQ_PRIMARY).

theme_msdr

A theme to remove the background, grid, axis ticks, etc. Aims to increase the ink ratio of the plot.

There are two more functions, but these two has its works "hidden".

GeomTimeline

Creates all visuals to be plotted by the geom_timeline.

GeomTimelineLabel

Creates all visuals to be plotted by the geom_timeline_label.

Examples

Some simple examples using the package.

Timeline

This example shows how to use eq_clean_data, geom_timeline, geom_timeline_label, and theme_msdr.

# Loading the data.
df_clean <- eq_clean_data(file_name = raw_data_path)

# Subsetting the df_clean to select some countries in Asia.
df_asia <- df_clean %>%
       dplyr::filter(COUNTRY %in% c("INDONESIA","THAILAND", "MYANMAR (BURMA)", "JAPAN"),
                     YEAR > 2000 & YEAR <= 2019)

# Plotting.
df_asia %>%
       ggplot2::ggplot() +

              # Defining the aes.
              msdr::geom_timeline(ggplot2::aes(x     = DATE,
                                               y     = COUNTRY,
                                               size  = EQ_PRIMARY,
                                               color = TOTAL_DEATHS) +
       # Adding theme
       msdr::theme_msdr() +

              # Editing the legends' titles
              ggplot2::labs(color = "# deaths",
                            size  = "Richter scale value") +

       # Adding annotations
       msdr::geom_timeline_label(ggplot2::aes(x     = DATE,
                                              label = LOCATION,
                                              y     = COUNTRY,
                                              mag   = EQ_PRIMARY,
                                              n_max = 10))

You can find more examples of use in the vignette or in the Bookdown.

OpenStreet Maps and Annotations

This example makes use of eq_map and eq_create_label.

# Creating a new data.
df_america <- df_clean %>% dplyr::filter(COUNTRY %in% c('USA','MEXICO','CANADA'),
                                         YEAR > 1990 & YEAR < 2019)

# Creating a complex text using the eq_create_label.
df_america %>%
       dplyr::mutate(popup_text = msdr::eq_create_label(.)) %>%
              msdr::eq_map(annot_col = 'popup_text')

You can also find more examples in the vignette or in the Bookdown.

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