Questions tagged [r]
R is a free, open-source programming language & software environment for statistical computing, bioinformatics, visualization & general computing. Please use minimal reproducible examples others can run using copy & paste. Show desired output entirely. Use dput() for data & specify all non-base packages with library(). Don't embed pictures for data or code, use indented code blocks instead. For statistics questions, use https://stats.stackexchange.com.
508,174
questions
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How to make a great R reproducible example
When discussing performance with colleagues, teaching, sending a bug report or searching for guidance on mailing lists and here on Stack Overflow, a reproducible example is often asked and always ...
1545
votes
14
answers
1.8m
views
How to join (merge) data frames (inner, outer, left, right)
Given two data frames:
df1 = data.frame(CustomerId = c(1:6), Product = c(rep("Toaster", 3), rep("Radio", 3)))
df2 = data.frame(CustomerId = c(2, 4, 6), State = c(rep("Alabama", 2), rep("Ohio", 1)))
...
- 24.7k
1499
votes
21
answers
1.4m
views
Sort (order) data frame rows by multiple columns
I want to sort a data frame by multiple columns. For example, with the data frame below I would like to sort by column 'z' (descending) then by column 'b' (ascending):
dd <- data.frame(b = factor(c(...
- 43.2k
1154
votes
12
answers
441k
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Grouping functions (tapply, by, aggregate) and the *apply family
Whenever I want to do something "map"py in R, I usually try to use a function in the apply family.
However, I've never quite understood the differences between them -- how {sapply, lapply, etc.} ...
- 30.3k
1083
votes
20
answers
2.4m
views
Remove rows with all or some NAs (missing values) in data.frame
I'd like to remove the lines in this data frame that:
a) contain NAs across all columns. Below is my example data frame.
gene hsap mmul mmus rnor cfam
1 ENSG00000208234 0 NA NA ...
- 12k
1043
votes
25
answers
1.9m
views
Drop data frame columns by name
I have a number of columns that I would like to remove from a data frame. I know that we can delete them individually using something like:
df$x <- NULL
But I was hoping to do this with fewer ...
- 39.7k
975
votes
30
answers
2.1m
views
How do I replace NA values with zeros in an R dataframe?
I have a data frame and some columns have NA values.
How do I replace these NA values with zeroes?
- 36.2k
956
votes
9
answers
377k
views
What are the differences between "=" and "<-" assignment operators?
What are the differences between the assignment operators = and <- in R?
I know that operators are slightly different, as this example shows
x <- y <- 5
x = y = 5
x = y <- 5
x <- y = ...
- 60.1k
914
votes
5
answers
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data.table vs dplyr: can one do something well the other can't or does poorly?
Overview
I'm relatively familiar with data.table, not so much with dplyr. I've read through some dplyr vignettes and examples that have popped up on SO, and so far my conclusions are that:
data....
- 52.4k
912
votes
8
answers
1.6m
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Rotating and spacing axis labels in ggplot2
I have a plot where the x-axis is a factor whose labels are long. While probably not an ideal visualization, for now I'd like to simply rotate these labels to be vertical. I've figured this part out ...
- 43.2k
768
votes
7
answers
93k
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How can we make xkcd style graphs?
Apparently, folk have figured out how to make xkcd style graphs in Mathematica and in LaTeX. Can we do it in R? Ggplot2-ers? A geom_xkcd and/or theme_xkcd?
I guess in base graphics, par(xkcd=TRUE)? ...
- 9,222
716
votes
19
answers
1.0m
views
How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?
I tried to install a package, using
install.packages("foobarbaz")
but received the warning
Warning message:
package 'foobarbaz' is not available (for R version x.y.z)
Why doesn't R think that the ...
- 120k
708
votes
14
answers
1.1m
views
How to convert a factor to integer\numeric without loss of information?
When I convert a factor to a numeric or integer, I get the underlying level codes, not the values as numbers.
f <- factor(sample(runif(5), 20, replace = TRUE))
## [1] 0.0248644019011408 0....
- 9,931
694
votes
14
answers
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How can I view the source code for a function?
I want to look at the source code for a function to see how it works. I know I can print a function by typing its name at the prompt:
> t
function (x)
UseMethod("t")
<bytecode: 0x2332948>
&...
- 176k
690
votes
17
answers
1.9m
views
Plot two graphs in a same plot
I would like to plot y1 and y2 in the same plot.
x <- seq(-2, 2, 0.05)
y1 <- pnorm(x)
y2 <- pnorm(x, 1, 1)
plot(x, y1, type = "l", col = "red")
plot(x, y2, type = "l", col = "green")
But ...
- 25.7k
679
votes
11
answers
337k
views
The difference between bracket [ ] and double bracket [[ ]] for accessing the elements of a list or dataframe
R provides two different methods for accessing the elements of a list or data.frame: [] and [[]].
What is the difference between the two, and when should I use one over the other?
- 17.6k
675
votes
12
answers
576k
views
How to unload a package without restarting R
I'd like to unload a package without having to restart R (mostly because restarting R as I try out different, conflicting packages is getting frustrating, but conceivably this could be used in a ...
- 72.3k
672
votes
8
answers
174k
views
What is the difference between require() and library()?
What is the difference between require() and library()?
- 9,564
660
votes
7
answers
1.1m
views
Run R script from command line
I have a file, called a.r, it has a chmod of 755,
sayHello <- function(){
print('hello')
}
sayHello()
How can I run this via command-line?
- 19.5k
643
votes
27
answers
1.2m
views
Convert a list to a data frame
I have a nested list of data. Its length is 132 and each item is a list of length 20. Is there a quick way to convert this structure into a data frame that has 132 rows and 20 columns of data?
Here is ...
- 39.7k
638
votes
8
answers
960k
views
606
votes
16
answers
454k
views
Drop unused factor levels in a subsetted data frame
I have a data frame containing a factor. When I create a subset of this dataframe using subset or another indexing function, a new data frame is created. However, the factor variable retains all of ...
- 27.3k
604
votes
17
answers
1.2m
views
Create an empty data.frame
I'm trying to initialize a data.frame without any rows. Basically, I want to specify the data types for each column and name them, but not have any rows created as a result.
The best I've been able ...
- 17.5k
575
votes
13
answers
687k
views
How to find out which package version is loaded in R?
I am in a process of figuring out how to use my university cluster. It has 2 versions of R installed. System wide R 2.11 (Debian 6.0) and R 2.14.2 in non-standard location.
I am trying to use MPI ...
- 11.5k
570
votes
12
answers
281k
views
Quickly reading very large tables as dataframes
I have very large tables (30 million rows) that I would like to load as a dataframes in R. read.table() has a lot of convenient features, but it seems like there is a lot of logic in the ...
- 6,035
547
votes
28
answers
140k
views
Tricks to manage the available memory in an R session
What tricks do people use to manage the available memory of an interactive R session? I use the functions below [based on postings by Petr Pikal and David Hinds to the r-help list in 2004] to list (...
534
votes
6
answers
568k
views
How to use the tryCatch() function?
I want to write code using tryCatch to deal with errors downloading data from the web.
url <- c(
"http://stat.ethz.ch/R-manual/R-devel/library/base/html/connections.html",
"...
- 5,877
532
votes
14
answers
1.4m
views
How to change legend title in ggplot
I have the following plot like below. It was created with this command:
library(ggplot2)
df <- data.frame(cond = factor(rep(c("A", "B"), each = 200)),
rating =...
- 63.1k
525
votes
11
answers
418k
views
Folder management with r : Check existence of directory and create it if it doesn't exist
I often find myself writing R scripts that generate a lot of output. I find it cleaner to put this output into its own directory(s). What I've written below will check for the existence of a directory ...
- 68.6k
516
votes
19
answers
997k
views
How to sum a variable by group
I have a data frame with two columns. First column contains categories such as "First", "Second", "Third", and the second column has numbers that represent the number of times I saw the specific ...
- 10.3k
503
votes
36
answers
408k
views
How to find the statistical mode?
In R, mean() and median() are standard functions which do what you'd expect. mode() tells you the internal storage mode of the object, not the value that occurs the most in its argument. But is there ...
- 21.9k
501
votes
11
answers
367k
views
Combine a list of data frames into one data frame by row
I have code that at one place ends up with a list of data frames which I really want to convert to a single big data frame.
I got some pointers from an earlier question which was trying to do ...
- 60.5k
493
votes
8
answers
435k
views
How to add leading zeros?
I have a set of data which looks something like this:
anim <- c(25499,25500,25501,25502,25503,25504)
sex <- c(1,2,2,1,2,1)
wt <- c(0.8,1.2,1.0,2.0,1.8,1.4)
data <- data.frame(anim,sex,...
- 7,057
490
votes
21
answers
1.6m
views
Counting the number of elements with the values of x in a vector
I have a vector of numbers:
numbers <- c(4,23,4,23,5,43,54,56,657,67,67,435,
453,435,324,34,456,56,567,65,34,435)
How can I have R count the number of times a value x appears in the ...
- 4,903
490
votes
7
answers
675k
views
How do I install an R package from source?
A friend sent me along this great tutorial on webscraping The New York Times with R. I would really love to try it. However, the first step is to install a package called [RJSONIO][2] from source.
I ...
Madjoro
487
votes
19
answers
1.9m
views
Changing column names of a data frame
I have a data frame called "newprice" (see below) and I want to change the column names in my program in R.
> newprice
Chang. Chang. Chang.
1 100 36 136
2 120 -33 ...
- 5,395
477
votes
12
answers
937k
views
How can two strings be concatenated?
How can I concatenate (merge, combine) two values?
For example I have:
tmp = cbind("GAD", "AB")
tmp
# [,1] [,2]
# [1,] "GAD" "AB"
My goal is to concatenate the two values in "tmp" to one ...
- 5,445
471
votes
21
answers
1.4m
views
How to rename a single column in a data.frame?
I know if I have a data frame with more than 1 column, then I can use
colnames(x) <- c("col1","col2")
to rename the columns. How to do this if it's just one column?
Meaning a ...
- 27.9k
463
votes
8
answers
285k
views
Cluster analysis in R: determine the optimal number of clusters
How can I choose the best number of clusters to do a k-means analysis. After plotting a subset of below data, how many clusters will be appropriate? How can I perform cluster dendro analysis?
n = 1000
...
- 4,667
455
votes
12
answers
1.7m
views
Extracting specific columns from a data frame
I have an R data frame with 6 columns, and I want to create a new data frame that only has three of the columns.
Assuming my data frame is df, and I want to extract columns A, B, and E, this is the ...
- 6,630
454
votes
13
answers
470k
views
Write lines of text to a file in R
In the R scripting language, how do I write lines of text, e.g., the following two lines
Hello
World
to a file named "output.txt"?
- 24.8k
451
votes
35
answers
256k
views
Elegant way to check for missing packages and install them?
I seem to be sharing a lot of code with coauthors these days. Many of them are novice/intermediate R users and don't realize that they have to install packages they don't already have.
Is there an ...
- 32.7k
450
votes
14
answers
693k
views
Side-by-side plots with ggplot2
I would like to place two plots side by side using the ggplot2 package, i.e. do the equivalent of par(mfrow=c(1,2)).
For example, I would like to have the following two plots show side-by-side with ...
- 43.2k
448
votes
2
answers
110k
views
Why is `[` better than `subset`?
When I need to filter a data.frame, i.e., extract rows that meet certain conditions, I prefer to use the subset function:
subset(airquality, Month == 8 & Temp > 90)
Rather than the [ function:
...
- 88.7k
444
votes
13
answers
690k
views
Sample random rows in dataframe
I am struggling to find the appropriate function that would return a specified number of rows picked up randomly without replacement from a data frame in R language? Can anyone help me out?
- 9,263
441
votes
4
answers
812k
views
Is there an R function for finding the index of an element in a vector?
In R, I have an element x and a vector v. I want to find the first index of an element in v that is equal to x. I know that one way to do this is: which(x == v)[[1]], but that seems excessively ...
- 41.6k
440
votes
2
answers
767k
views
How to set limits for axes in ggplot2 R plots?
I plot the following:
library(ggplot2)
carrots <- data.frame(length = rnorm(500000, 10000, 10000))
cukes <- data.frame(length = rnorm(50000, 10000, 20000))
carrots$veg <- 'carrot'
cukes$...
- 29.7k
423
votes
15
answers
391k
views
How can I trim leading and trailing white space?
I am having some trouble with leading and trailing white space in a data.frame.
For example, I look at a specific row in a data.frame based on a certain condition:
> myDummy[myDummy$country == c(&...
- 11.7k
413
votes
6
answers
429k
views
How to find the length of a string in R
How to find the length of a string (i.e., number of characters in a string) without splitting it in R? I know how to find the length of a list but not of a string.
And what about Unicode strings? How ...
- 63.6k
403
votes
18
answers
765k
views
Convert data.frame columns from factors to characters
I have a data frame. Let's call him bob:
> head(bob)
phenotype exclusion
GSM399350 3- 4- 8- 25- 44+ 11b- 11c- 19- NK1.1- Gr1- TER119-
GSM399351 3- 4- 8- 25-...
- 11.1k