R Programming/Working with data frames

In this section, we deal with methods to read, manage and clean-up a data frame.

In R, a dataframe is a list of vectors of the same length. They don't have to be of the same type. For instance, you can combine in one dataframe a logical, a character and a numerical vector.

Reading and saving dataEdit

If data are already in an R format (.Rda or .Rdata), you can load them in memory using load(). You can save data to the R format using save().

load("mydata.Rda")
save(mydata,file="mydata.Rda")

Example DatasetsEdit

  • Most packages include example datasets to test the functions.
  • The data() function without argument gives the list of all example datasets in all the loaded packages.
  • If you want to load them in memory, you just need to use the data function and include the name of the dataset as an argument.
  • str_data() (sfsmisc) gives the structure of all datasets in a package.
> data() # lists all the datasets in all the packages in memory
> data(package="datasets") # lists all the datasets in the "datasets" package
> data(Orange) # loads the orange dataset in memory
> ?Orange # Help for the "Orange" Datasets
> str_data("datasets") # gives the structure of all the datasets in the datasets package.
  • Some packages includes lots of datasets.
    • The datasets package
    • The AER package [1] includes replication datasets for some important textbooks in econometrics.
    • The EcDat package [2] includes replication archive for the Journal of Applied Econometrics, the Journal of Business and Economic Statistics, etc

Building your own data framesEdit

You can create a dataframe using vectors.

u <- rnorm(N)
x1 <- rnorm(N)
x2 <- rnorm(N)
y <- 1 + x1 + x2 + u
mydat <- data.frame(y,x1,x2)

R has a spreadsheet-style data editor. One can use it to enter the data into a spreadsheet.

mydat <- edit(data.frame())

Read table from the clipboard :

> mydat <- read.table("clipboard")

You can also read space delimited tables in your code using gsource() (Zelig). Here is an example with Yule 1899 data[3].

mydat <- gsource(var.names = "id union pauperism out old  pop", 
variables = "
1 Kensington 27 5 104 136
2 Paddington  47 12 115 111
3 Fulham 31 21 85 174
")

Describing a data frameEdit

  • str() gives a very brief description of the data.
  • names() gives the name of each variables
  • summary() gives some very basic summary statistics for each variable

Browsing dataEdit

  • You can browse your data in a spreadsheet using View(). Depending on your operating system, this option is not always available and the result is not always the same.
  • You can print the first lines using head() and the last lines using tail().
View(mydata)
head(mydata, n = 20) # n = 20 means  that the first 20 lines are printed in the R console
  • RStudio has a nice data browser (View(mydata)).
  • RKward has also a nice data browser
  • Paul Murrell is currently developping the rdataviewer package (pdf).

Attaching dataEdit

One of the big advantage of R over Stata is that you can deal with multiple datasets at the same time. You just need to specify the name of the dataset and a "$" symbol before each variable name ( for instance mydat1$var1 and mydat2$var1). If you only work with one dataset and you don't want to write again and again the name of the dataset as a prefix for each variable, you can use attach().

mydata$var1
attach(mydata)
var1
detach(mydata)

Detecting duplicatesEdit

When you want to clean up a data set, it is very often useful to check if you don't have the same information twice in the data. R provides some functions to detect duplicates.

  • duplicated() looks at duplicated elements and return a logical vector. You can use table() to summarize this vector.
  • Duplicated() (sfsmisc) generalizes this command. Duplicated() only marks unique values with "NA".
  • remove.dup.rows() (cwhmisc).
  • unique() keep only the unique lines in a dataset.
library("Zelig")
mydat <- gsource(
variables = "
1 1 1 1
1 1 1 1
1 2 3 4
1 2 3 4
1 2 2 2
1 2 3 2")
unique(mydat) # keep unique rows
library(cwhmisc)
remove.dup.rows(mydat) # similar to unique()
table(duplicated(mydat)) # table duplicated lines
mydat$dups <- duplicated(mydat) # add a logical variable for duplicates

Creating and removing variablesEdit

To create a new variable

mydata$newvar <- oldvar

If you want to delete a variable in a dataset, you can assign NULL to that variable :

# Delete the x variable in the df data frame.
df$x <- NULL

Renaming variablesEdit

  • It is possible to rename variable by redefining the vector of names of a data frame.
  • There is also a rename() function in the reshape package.
df <- data.frame(x = 1:10, y = 21:30)
names(df)
names(df) <- c("toto","tata")
names(df)
names(df)[2] <- "titi"
names(df)

Creating a subset of the dataEdit

One can subset the data using subset(). The first argument is the name of the dataset, the second argument is a logical condition which say which lines will be included in the new dataset and the last argument is the list of variable which will be included in the new dataset.

In the following example, we generate a fake dataset and we use the subset() command to select the lines and columns of interest. We choose the lines such that x1 > 0 and x2 < 0 and we only keep x1 and x2 as variables.

N <- 100
x1 <- rnorm(N)
x2 <- 1 + rnorm(N) + x1
x3 <- rnorm(N) + x2
mydat <- data.frame(x1,x2,x3)
subset(x = mydat, subset = x1 > 0 & x2 < 0, select = c(x1,x2))
subset(x = mydat, subset = x1 > 0 & x2 < 0, select = - x3) # the same.

It is also possible to reorder the columns using the select option.

subset(x = mydat, subset = x1 > 0 & x2 < 0, select = c(x1,x2))
subset(x = mydat, subset = x1 > 0 & x2 < 0, select = c(x2,x1))

Sorting and orderingEdit

  • order()
mydat[order(var1,var2),]

Suppose you want to randomize the order in a data set. You just need to generate a vector from a uniform distribution and to sort following that vector.

df[order(runif(nrow(df))),]

Detecting missing valuesEdit

  • is.na() returns a logical vector equal to TRUE if any of the variable in a dataset is missing and to FALSE otherwise.
  • complete.cases() returns a logical vector indicating TRUE if all cases are complete and FALSE otherwise.
> table(complete.cases(df))

Reshaping a dataframeEdit

This topic is important if you deal with panel data. Panel data can be stored in a wide format with one observation per unit and a variable for each time period or in a long format with one observation per unit and time period. reshape() reshapes a dataset in a wide or long format.

> country <- c("'Angola'","'UK'","'France'")
> gdp.1960 <- c(1,2,3)
> gdp.1970 <- c(2,4,6)
> mydat <- data.frame(country,gdp.1960,gdp.1970)
> mydat # wide format
  country gdp.1960 gdp.1970
1  Angola       1       2
2      UK       2       4
3  France       3       6
> reshape( data = mydat, varying = list(2:3) , v.names = "gdp", direction = "long") # long format
    country time gdp id
1.1  Angola    1   1  1
2.1      UK    1   2  2
3.1  France    1   3  3
1.2  Angola    2   2  1
2.2      UK    2   4  2
3.2  France    2   6  3
  • varying gives the numbers of the columns which are time-varying
  • v.names gives the prefix of the time-varying variables
  • direction gives the direction, either "long" or "wide".
  • See also :
    • reShape() (Hmisc)
    • See Hadley Wickham's reshape package[4]
    • See Duncan Murdoch's tables package [5]

External linksEdit

Expanding a datasetEdit

Sometimes we need to duplicate some lines in a dataset. For instance, if we want to generate a fake dataset with a panel data structure. In that case, we would first generate time invariant variables and then duplicate each line by a given scalar in order to create time-varying variables.

It is possible to use the expand() function in the epicalc package. This will multiply each line by a given number.

N <- 1000
T <- 5
wide <- data.frame(id = 1:N,f = rnorm(N),  rep = T)
library("epicalc")
long <- expand(wide,index.var = "rep")
long$time <- rep(1:T,N)

We can also use the do it yourself solution or create our own function. The idea is simple. We create a vector which igives for each line the number of times it should be replicated (dups in the following example). Then we use the rep() function to create a vector which repeats the line numbers according to what we want. The last step creates a new dataset which repeats lines according to the desired pattern.

expand <- function(df,dups){
	df$dups <- dups
	pattern <- rep(1:nrow(df), times=df$dups)
	df2 <- df[pattern,]
	index <- function(x){
		1:length(x)
		}
	df2$year <- unlist(tapply(df2$dups, df2$id, index))
	df2$dups <- NULL 
	return(df2)
	}
 
df <- data.frame(x = rnorm(3), id = 1:3)
dups = c(3,1,2)
expand(df,dups)

Merging dataframesEdit

Merging data can be very confusing, especially if the case of multiple merge. Here is a simple example :

We have one table describing authors :

> authors <- data.frame(
+     surname = I(c("Tukey", "Venables", "Tierney", "Ripley", "McNeil")),
+     nationality = c("US", "Australia", "US", "UK", "Australia"),
+     deceased = c("yes", rep("no", 4)))
> authors
   surname nationality deceased
1    Tukey          US      yes
2 Venables   Australia       no
3  Tierney          US       no
4   Ripley          UK       no
5   McNeil   Australia       no

and one table describing books

> books <- data.frame(
+     name = I(c("Tukey", "Venables", "Tierney",
+              "Ripley", "Ripley", "McNeil", "R Core")),
+     title = c("Exploratory Data Analysis",
+               "Modern Applied Statistics ...",
+               "LISP-STAT",
+               "Spatial Statistics", "Stochastic Simulation",
+               "Interactive Data Analysis",
+               "An Introduction to R"),
+     other.author = c(NA, "Ripley", NA, NA, NA, NA,
+                      "Venables & Smith"))
> books
      name                         title     other.author
1    Tukey     Exploratory Data Analysis             <NA>
2 Venables Modern Applied Statistics ...           Ripley
3  Tierney                     LISP-STAT             <NA>
4   Ripley            Spatial Statistics             <NA>
5   Ripley         Stochastic Simulation             <NA>
6   McNeil     Interactive Data Analysis             <NA>
7   R Core          An Introduction to R Venables & Smith

We want to merge tables books and authors by author's name ("surname" in the first dataset and "name" in the second one). We use the merge() command. We specify the name of the first and the second datasets, then by.x and by.y specify the identifier in both datasets. all.x and all.y specify if we want to keep all the observation of the first and the second dataset. In that case we want to have all the observations from the books dataset but we just keep the observations from the author dataset which match with an observation in the books dataset.

> final <- merge(books, authors, by.x = "name", by.y = "surname", sort=F,all.x=T,all.y=F)
> final
      name                         title     other.author nationality deceased
1    Tukey     Exploratory Data Analysis             <NA>          US      yes
2 Venables Modern Applied Statistics ...           Ripley   Australia       no
3  Tierney                     LISP-STAT             <NA>          US       no
4   Ripley            Spatial Statistics             <NA>          UK       no
5   Ripley         Stochastic Simulation             <NA>          UK       no
6   McNeil     Interactive Data Analysis             <NA>   Australia       no
7   R Core          An Introduction to R Venables & Smith        <NA>     <NA>

It is also possible to merge two data.frame objects while preserving the rows’ order by one of the two merged objects[6].

ResourcesEdit

ReferencesEdit

  1. The AER Package http://cran.r-project.org/web/packages/AER/index.html
  2. The EcDat Package http://cran.r-project.org/web/packages/Ecdat/index.html
  3. "An investigation into the causes of changes in pauperism in England, chiefly during the last two intercensal decades (Part I.)" - GU Yule - Journal of the Royal Statistical Society, June 1899, p 283
  4. Reshaping Data with the reshape Package : http://www.jstatsoft.org/v21/i12
  5. vignette for the tables package: http://cran.r-project.org/web/packages/tables/vignettes/tables.pdf
  6. Merging data frames while preserving the rows
  7. R Data Manual http://cran.r-project.org/doc/manuals/R-data.html
  8. Paul Murrell introduction to Data Technologies http://www.stat.auckland.ac.nz/~paul/ItDT/
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Last modified on 21 February 2014, at 03:26