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11-writing-data.md

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R for reproducible scientific analysis
Reading data
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Learning Objectives {.objectives}

  • To be able to write out data from R

Writing data

At some point, you'll want to write out data from R.

We can use the write.table function for this, which is very similar to read.table from before.

Let's create a data-cleaning script, for this analysis, we only want to focus on the gapminder data for Australia:

write.table(
  gapminder[gapminder$country == "Australia",],
  file="cleaned-data/gapminder-aus.csv",
  sep=","
)

Let's switch back to the shell to take a look at the data to make sure it looks ok:

cd ~/gapminder/cleaned-data/
head gapminder-aus.csv

"country","year","pop","continent","lifeExp","gdpPercap"
"61","Australia",1952,8691212,"Oceania",69.12,10039.59564
"62","Australia",1957,9712569,"Oceania",70.33,10949.64959
"63","Australia",1962,10794968,"Oceania",70.93,12217.22686
"64","Australia",1967,11872264,"Oceania",71.1,14526.12465
"65","Australia",1972,13177000,"Oceania",71.93,16788.62948
"66","Australia",1977,14074100,"Oceania",73.49,18334.19751
"67","Australia",1982,15184200,"Oceania",74.74,19477.00928
"68","Australia",1987,16257249,"Oceania",76.32,21888.88903
"69","Australia",1992,17481977,"Oceania",77.56,23424.76683

Hmm, that's not quite what we wanted. Where did all these quotation marks come from? Also the row numbers are meaningless.

Let's look at the help file to work out how to change this behaviour.

?write.table

By default R will wrap character vectors with quotation marks when writing out to file. It will also write out the row and column names.

Let's fix this:

write.table(
  gapminder[gapminder$country == "Australia",],
  file="cleaned-data/gapminder-aus.csv",
  sep=",", quote=FALSE, row.names=FALSE
)

Now lets look at the data again using our shell skills:

head gapminder-aus.csv

country,year,pop,continent,lifeExp,gdpPercap
Australia,1952,8691212,Oceania,69.12,10039.59564
Australia,1957,9712569,Oceania,70.33,10949.64959
Australia,1962,10794968,Oceania,70.93,12217.22686
Australia,1967,11872264,Oceania,71.1,14526.12465
Australia,1972,13177000,Oceania,71.93,16788.62948
Australia,1977,14074100,Oceania,73.49,18334.19751
Australia,1982,15184200,Oceania,74.74,19477.00928
Australia,1987,16257249,Oceania,76.32,21888.88903
Australia,1992,17481977,Oceania,77.56,23424.76683

That looks better!

Challenge {.challenge}

Write a data-cleaning script file that subsets the gapminder data to include only data points collected since 1990.

Use this script to write out the new subset to a file in the cleaned-data/ directory.