inst/doc/eqtools_intro.md

In tcoopermont/eqtools: Earthquake Tools

title: "Intro to Eartquake Tools" author: "Tom Cooper" date: "2017-07-30" output: rmarkdown::html_vignette vignette: > %\VignetteIndexEntry{Intro to Eartquake Tools} %\VignetteEngine{knitr::rmarkdown} %\VignetteEncoding{UTF-8}

Earthquake Tools Package - eqtools

The eqtools package makes it easy for users to explore the U.S. National Oceanographic and Atmospheric Administration (NOAA) dataset on significant earthquakes around the world. This dataset contains information about 5,933 earthquakes over an approximately 4,000 year time span.

Downloading dataset

The datset is available from the NOAA Website The entire dataset can be download by clicking on the link: "Download entire significant earthquake data file in tab-delimited format."

What Eqtools includes

• Functions to clean the data to prepare for
• Geoms to create timeline plots
• Functions to create interactive html maps

Data: NOAA significant earthquake data

     library(readr)
     eqdata <- read_delim(  system.file("extdata",
                          "signif-july-2017.txt.gz",
               package = "eqtools"),delim = "\t")

## Parsed with column specification:
## cols(
##   .default = col_integer(),
##   FLAG_TSUNAMI = col_character(),
##   SECOND = col_character(),
##   EQ_PRIMARY = col_character(),
##   EQ_MAG_MW = col_character(),
##   EQ_MAG_MS = col_character(),
##   EQ_MAG_MB = col_character(),
##   EQ_MAG_ML = col_double(),
##   EQ_MAG_MFA = col_character(),
##   EQ_MAG_UNK = col_character(),
##   COUNTRY = col_character(),
##   STATE = col_character(),
##   LOCATION_NAME = col_character(),
##   LATITUDE = col_character(),
##   LONGITUDE = col_character(),
##   DEATHS = col_character(),
##   MISSING = col_character(),
##   INJURIES = col_character(),
##   DAMAGE_MILLIONS_DOLLARS = col_character(),
##   TOTAL_DEATHS = col_character(),
##   TOTAL_MISSING = col_character()
##   # ... with 2 more columns
## )

## See spec(...) for full column specifications.

    dim(eqdata)

## [1] 5952   47

Cleaning tools

eq_clean_data convert LATITUDE and LONGITUDE to numeric

    library(eqtools)
    str(eqdata$LATITUDE)

##  chr [1:5952] "  31.100" "  38.000" "  35.683" "  36.400" "  31.500" ...

    eq_data_clean <- eq_clean_data(eqdata)
    str(eq_data_clean$LATITUDE)

##  num [1:5952] 31.1 38 35.7 36.4 31.5 ...

eq_clean_location removes country from LOCATION_NAME and converts it to title case

    eqdata$LOCATION_NAME[1]

## [1] "JORDAN:  BAB-A-DARAA,AL-KARAK"

    eq_data_ready <- eq_clean_location(eq_data_clean)
    eq_data_ready$LOCATION_NAME[1]

## [1] "Bab-a-Daraa,al-Karak"

Plotting Tools

geom_timeline() creates a timeline plot of eathquakes by year

    library(dplyr)
    library(ggplot2)
    library(grid)
    minDate <- as.Date("2000-1-1","%Y-%m-%d")     
    maxDate <- as.Date("2015-12-31","%Y-%m-%d")   
    eq_us_mex_data <- mutate(eq_data_ready) %>%
          filter( DATE >= minDate,DATE <= maxDate, COUNTRY %in% c("USA","MEXICO")) %>%
      mutate(EQ_PRIMARY = as.numeric(EQ_PRIMARY))
     ggplot(eq_us_mex_data,aes(x = DATE, y = 1,
         xmin = minDate,xmax = maxDate,
         )) +
  geom_timeline(aes(size = EQ_PRIMARY))

geom_timeline_label() adds labels to the geom_timeline plot

    #library(ggplot2)
     ggplot(eq_us_mex_data,aes(x = DATE, y = 1,
         xmin = minDate,xmax = maxDate,
         )) +
  geom_timeline(aes(size = EQ_PRIMARY)) +
  geom_timeline_label(aes(label = LOCATION_NAME,size = EQ_PRIMARY,n_max = 5))

If y is set to a data column the timelines are split up. xlim and ylim can be added to adjust for labels.

    #library(ggplot2)
     ggplot(eq_us_mex_data,aes(x = DATE, y = COUNTRY,
         xmin = minDate,xmax = maxDate,
         )) +
  geom_timeline(aes(size = EQ_PRIMARY)) +
  geom_timeline_label(aes(label = LOCATION_NAME,size = EQ_PRIMARY,n_max = 5)) + 
  xlim(as.Date("1999-1-1","%Y-%m-%d"),as.Date("2017-12-31","%Y-%m-%d")  ) + 
  ylim(c(as.character(unique(eq_us_mex_data$COUNTRY)),""))

Mapping Tools

eq_map creates a leaflet map

      library(leaflet)

      #eq_map(eq_us_mex_data,annot_col = eq_us_mex_data$DATE)

eq_create_label() formats information to be used in a web popup

  popup_labels <- eq_create_label(eq_us_mex_data) 
  paste(popup_labels[1],"\n")
#> [1] "<b>Location</b> Napa <br /> <b>Magnitude:</b> 5 <br /> <b>Total deaths:</b> NA <br /> \n"

Add the labels to the map

  #eq_us_mex_data <- mutate_(eq_us_mex_data,pop = ~ popup_labels)
  #eq_map(eq_us_mex_data,annot_col = eq_us_mex_data$pop)

"He who gives up [code] safety for [code] speed deserves neither." (via)

tcoopermont/eqtools documentation built on May 30, 2019, 7:21 a.m.