title	output
Lab 05 - Data Wrangling Amei_Hao	html_document

Learning goals

• Use the merge() function to join two datasets.
• Deal with missings and impute data.
• Identify relevant observations using quantile().
• Practice your GitHub skills.

Lab description

For this lab we will be, again, dealing with the meteorological dataset downloaded from the NOAA, the met. In this case, we will use data.table to answer some questions regarding the met dataset, while at the same time practice your Git+GitHub skills for this project.

This markdown document should be rendered using github_document document.

Part 1: Setup the Git project and the GitHub repository

1. Go to your documents (or wherever you are planning to store the data) in your computer, and create a folder for this project, for example, "PM566-labs"

2. In that folder, save this template as "README.Rmd". This will be the markdown file where all the magic will happen.

3. Go to your GitHub account and create a new repository, hopefully of the same name that this folder has, i.e., "PM566-labs".

4. Initialize the Git project, add the "README.Rmd" file, and make your first commit.

5. Add the repo you just created on GitHub.com to the list of remotes, and push your commit to origin while setting the upstream.

Most of the steps can be done using command line:

# Step 1
cd ~/Documents
mkdir PM566-labs
cd PM566-labs

# Step 2
wget https://raw.githubusercontent.com/USCbiostats/PM566/master/content/assignment/05-lab.Rmd 
mv 05-lab.Rmd README.md

# Step 3
# Happens on github

# Step 4
git init
git add README.Rmd
git commit -m "First commit"

# Step 5
git remote add origin [email protected]:[username]/PM566-labs
git push -u origin master

You can also complete the steps in R (replace with your paths/username when needed)

# Step 1
setwd("~/Documents")
dir.create("PM566-labs")
setwd("PM566-labs")

# Step 2
download.file(
  "https://raw.githubusercontent.com/USCbiostats/PM566/master/content/assignment/05-lab.Rmd",
  destfile = "README.Rmd"
  )

# Step 3: Happens on Github

# Step 4
system("git init && git add README.Rmd")
system('git commit -m "First commit"')

# Step 5
system("git remote add origin [email protected]:[username]/PM566-labs")
system("git push -u origin master")

Once you are done setting up the project, you can now start working with the MET data.

Setup in R

1. Load the data.table (and the dtplyr and dplyr packages if you plan to work with those).

library(data.table)
library(dplyr)

 met <- fread("https://raw.githubusercontent.com/USCbiostats/data-science-data/master/02_met/met_all.gz")

2. Load the met data from https://raw.githubusercontent.com/USCbiostats/data-science-data/master/02_met/met_all.gz, and also the station data. For the later, you can use the code we used during lecture to pre-process the stations data:

 # Download the data
 stations <- fread("ftp://ftp.ncdc.noaa.gov/pub/data/noaa/isd-history.csv")
 stations[, USAF := as.integer(USAF)]

 # Dealing with NAs and 999999
 stations[, USAF   := fifelse(USAF == 999999, NA_integer_, USAF)]
 stations[, CTRY   := fifelse(CTRY == "", NA_character_, CTRY)]
 stations[, STATE  := fifelse(STATE == "", NA_character_, STATE)]

 # Selecting the three relevant columns, and keeping unique records
 stations <- unique(stations[, list(USAF, CTRY, STATE)])

 # Dropping NAs
 stations <- stations[!is.na(USAF)]

 # Removing duplicates
 stations[, n := 1:.N, by = .(USAF)]
 stations <- stations[n == 1,][, n := NULL]

3. Merge the data as we did during the lecture.

met = merge(
   x = met, y = stations, 
   by.x = "USAFID", by.y = "USAF",
   all.x = TRUE, all.y = FALSE
   )

 met[1:5, .(USAFID,WBAN,STATE)]

Question 1: Representative station for the US

What is the median station in terms of temperature, wind speed, and atmospheric pressure? Look for the three weather stations that best represent continental US using the quantile() function. Do these three coincide?

met_stations = met [, .(
      wind.sp = mean(wind.sp,na.rm = TRUE),
    atm.press = mean(atm.press, na.rm = TRUE),
     temp     =  mean(temp, na.rm =  TRUE)
 ), by = USAFID]

 met_stations[, temp50 := quantile(temp,probs = .5, na.rm = TRUE)]
 met_stations[, atmp50 := quantile(atm.press,probs = .5, na.rm = TRUE)]
 met_stations[, windsp50 := quantile(wind.sp,probs = .5, na.rm = TRUE)]

 met_stations[which.min(abs(temp - temp50))]
 met_stations[which.min(abs(atm.press - atmp50))]
 met_stations[which.min(abs(wind.sp - windsp50))]

No, these three do not coincide.

Knit the document, commit your changes, and Save it on GitHub. Don't forget to add README.md to the tree, the first time you render it.

Question 2: Representative station per state

Just like the previous question, you are asked to identify what is the most representative, the median, station per state. This time, instead of looking at one variable at a time, look at the euclidean distance. If multiple stations show in the median, select the one located at the lowest latitude.

met_stations = met [, .(
      wind.sp = mean(wind.sp,na.rm = TRUE),
    atm.press = mean(atm.press, na.rm = TRUE),
     temp     =  mean(temp, na.rm =  TRUE)
 ), by = .(USAFID, STATE)]

 # calculate the median by state
 met_stations[, temp50s := quantile(temp,probs = .5, na.rm = TRUE), by = STATE]
 met_stations[, atmp50s := quantile(atm.press,probs = .5, na.rm = TRUE),  by = STATE]
 met_stations[, windsp50s := quantile(wind.sp,probs = .5, na.rm = TRUE),  by = STATE]

 #temperature
 met_stations[, tempdif  := which.min(abs(temp - temp50s)), by=STATE]
 met_stations[, recordid := 1:.N, by = STATE]
 met_temp = met_stations[recordid == tempdif, .(USAFID, temp, temp50s, STATE)]
 met_temp

 #ATM press
 met_stations[, tempdif  := which.min(abs(atm.press - atmp50s)), by=STATE]
 met_stations[recordid == tempdif, .(USAFID, atm.press, atmp50s, STATE)]

 #wind speed
 met_stations[, tempdif  := which.min(abs(wind.sp - windsp50s)), by=STATE]
 met_stations[recordid == tempdif, .(USAFID, wind.sp, windsp50s, STATE)]

Knit the doc and save it on GitHub.

Question 3: In the middle?

For each state, identify what is the station that is closest to the mid-point of the state. Combining these with the stations you identified in the previous question, use leaflet() to visualize all ~100 points in the same figure, applying different colors for those identified in this question.

met_stations = unique(met[, .(USAFID, STATE, lon, lat)])

 met_stations[, n := 1:.N, by=USAFID]
 met_stations <- met_stations[n == 1]

 # a short cut using the .SD keyword
 # met_stations[, .SD[1], by=USAFID]

 met_stations[, lat_mid := quantile(lat, probs = .5, na.rm = TRUE), by=STATE]
 met_stations[, lon_mid := quantile(lon, probs = .5, na.rm = TRUE), by=STATE]


 # Looking at the euclidean distances
 met_stations[, dist := sqrt((lat-lat_mid)^2+(lon-lon_mid)^2)]
 met_stations[, minrecord := which.min(dist), by=STATE]
 met_stations[, n := 1:.N, by=STATE]
 met_location = met_stations[n == minrecord, .(USAFID, STATE, lon, lat)]
 met_location
 
 all_stations = met[, .(USAFID, lat, lon, STATE)][, .SD[1], by = "USAFID"]

 # Recovering lon and lat from the original dataset
 met_temp <- merge(
   x = met_temp,
   y = all_stations,
   by = "USAFID",
   all.x = TRUE, all.y = FALSE
 )
 
 library(leaflet)

 #combine the datasets
 dat1 = met_location[, .(lon, lat)]
 dat1[, type := "Center of the state"]

 dat2 = met_temp[, .(lon, lat)]
 dat2[, type := "Center of the temperature"]

 dat = rbind(dat1,dat2)

 # drewing the map
 rh_pal <- colorFactor(c('blue', 'purple', 'red'),
                        domain = as.factor(dat$type))
 leaflet(dat) %>%
   addProviderTiles("OpenStreetMap") %>%
   addCircles(lng = ~lon, lat = ~lat, color=~rh_pal(type), opacity=1,fillOpacity=1, radius=500)

Knit the doc and save it on GitHub.

Question 4: Means of means

Using the quantile() function, generate a summary table that shows the number of states included, average temperature, wind-speed, and atmospheric pressure by the variable "average temperature level," which you'll need to create.

Start by computing the states' average temperature. Use that measurement to classify them according to the following criteria:

• low: temp < 20
• Mid: temp >= 20 and temp < 25
• High: temp >= 25

Once you are done with that, you can compute the following:

• Number of entries (records),
• Number of NA entries,
• Number of stations,
• Number of states included, and
• Mean temperature, wind-speed, and atmospheric pressure.

All by the levels described before.

Knit the document, commit your changes, and push them to GitHub. If you'd like, you can take this time to include the link of the issue of the week so that you let us know when you are done, e.g.,

git commit -a -m "Finalizing lab 5 https://github.com/USCbiostats/PM566/issues/23"