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.
505,558
questions
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votes
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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 ...
1540
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)))
...
- 24.6k
1498
votes
20
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(...
- 43.1k
1153
votes
12
answers
440k
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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.} ...
- 30.2k
1079
votes
20
answers
2.3m
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
1039
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 ...
- 39.4k
967
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?
- 35.8k
953
votes
9
answers
372k
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 = ...
- 59.9k
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....
- 52.2k
907
votes
8
answers
1.5m
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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 ...
- 43.1k
767
votes
7
answers
93k
views
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)? ...
- 9,202
711
votes
19
answers
999k
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....
- 9,911
694
votes
13
answers
437k
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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>
&...
- 175k
689
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 ...
- 25.6k
675
votes
11
answers
333k
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?
- 17.5k
671
votes
12
answers
564k
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 ...
- 72k
668
votes
8
answers
171k
views
What is the difference between require() and library()?
What is the difference between require() and library()?
- 9,524
655
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?
- 19.4k
642
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 ...
- 39.4k
637
votes
8
answers
953k
views
604
votes
16
answers
452k
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 ...
- 27.2k
601
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 ...
- 17.4k
570
votes
13
answers
666k
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 ...
- 11.4k
570
votes
12
answers
279k
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
545
votes
28
answers
139k
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 (...
531
votes
6
answers
554k
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",
"...
- 5,847
521
votes
14
answers
1.3m
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 =...
- 62.5k
515
votes
10
answers
408k
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 ...
- 68.3k
509
votes
19
answers
982k
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 ...
- 10.2k
501
votes
35
answers
401k
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 ...
- 21.8k
500
votes
11
answers
358k
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 ...
- 60.3k
490
votes
8
answers
426k
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,...
- 6,997
488
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 ...
- 4,883
487
votes
7
answers
663k
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
485
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 ...
- 5,375
475
votes
12
answers
923k
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 ...
- 5,425
467
votes
21
answers
1.3m
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 ...
- 27.7k
463
votes
8
answers
284k
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
450
votes
13
answers
463k
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
449
votes
14
answers
681k
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 ...
- 43.1k
446
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 dataframe 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 ...
- 6,548
446
votes
2
answers
109k
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:
...
- 88.3k
445
votes
35
answers
249k
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 ...
- 32.5k
440
votes
13
answers
680k
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?
- 9,203
439
votes
2
answers
754k
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$...
- 29.6k
435
votes
4
answers
804k
views
Is there an R function for finding the index of an element in a vector?
In R, I have an element x and a vector v. I want to find the first index of an element in v that is equal to x. I know that one way to do this is: which(x == v)[[1]], but that seems excessively ...
- 41.4k
421
votes
15
answers
385k
views
How can I trim leading and trailing white space?
I am having some trouble with leading and trailing white space in a data.frame.
For example, I look at a specific row in a data.frame based on a certain condition:
> myDummy[myDummy$country == c(&...
- 11.7k
411
votes
6
answers
426k
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 ...
- 63.1k
401
votes
18
answers
761k
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-...
- 11k