I'm wondering whether there is a way to do in-place modification of objects in a list without using a for loop. This would be useful, for example, if the individual objects in the list are large and complex, so that we want to avoid making a temporary copy of the entire object. As an example, consider the following code, which creates a list of three data frames, then calculates the vector of maximums across all three data frames for one column of the data, and then assigns that vector to each original data frame. (Code like this is needed when aligning plots in ggplot2.)
data_list <- lapply(1:3, function(x) data.frame(x=rnorm(10), y=rnorm(10), z=rnorm(10)))
max_x <- do.call(pmax, lapply(data_list, function(d){d$x}))
for( i in 1:length(data_list))
{
data_list[[i]]$x <- max_x
}
Is there any way to write the final part without a for loop?
Answers to some of the questions I'm getting:
What makes me think a copy would be made? I don't know for sure whether a copy would or would not be made. The actual scenario I'm working with deals with entire ggplot graphs (see e.g. here). Since they are rather large and complex, it's critical that no copy be made.
What's the problem with a for loop? I just would rather iterate directly over a list than have to introduce a counter. I don't like counters.
Why not use data.table? Because I'm actually manipulating ggplot graphs, not data frames. The code provided here is just a simplified example.
Base R data structures are copy-on-modify with sharing. Take your example of a data.frame with three numeric columns. Each data.frame is a length 3 "list" vector, each containing a reference to the numeric vectors of the underlying columns. If we modify/replace the first column, R creates a new length 3 data.frame "list" containing references to the new(ly modified) column and the other two unmodified columns.
Let's take a look using the address function*
set.seed(1)
data_list <- lapply(1:3, function(x) data.frame(x=rnorm(10), y=rnorm(10), z=rnorm(10)))
before <- rapply(data_list,address)
Now you want to replace the first column with
max_x <- do.call(pmax, lapply(data_list, function(d){d$x}))
How you do this doesn't much matter, but here's one way without an explicit loop-with-counter
data_list <- lapply(data_list,`[<-`,"x",value=max_x)
after <- rapply(data_list,address)
Now compare the addresses before and after. Note that the addresses for the y and z columns have not changed. Furthermore, all "after" x columns have the same address -- the address of max_x!
address(max_x)
[1] "05660600"
cbind(before,after)
before after
x "0565F530" "05660600"
y "0565F400" "0565F400"
z "05660AC0" "05660AC0"
x "05660A28" "05660600"
y "05660990" "05660990"
z "05660860" "05660860"
x "056607C8" "05660600"
y "05660730" "05660730"
z "05660698" "05660698"
This means you don't have to worry as much as you might think about making a change to a large data structure. In general, only the modified piece and the skeleton of the data structure will have to be replaced. In this example, the max_x vector had to be created anyway, so the only overhead is creating a new 3 cell data.frame "list" and populating it with 3 references**. This, however, could start to become inefficient if you are iteratively "banging on" changes or working with subvectors rather than entire columns. These are use cases for data.table that are not applicable to this example.
* The address function used here is exported from the data.table package.
** And, of course, in this example, the 3 cell outer list "list" containing the 3 data.frames themselves.
Related
I am very new to r and am working on developing code to simulate a set of equations for my job.
I want to create multiple empty data frames based on an input variable. That is, if n=4, I want to create 4 separate data frames with separate names such as x1, x2, x3, x4. If n=10, i want 10 data frames, etc.
I want to be able to see these data frames in the global environment (that open up looking similar to an excel sheet).
Code
To make the answer generic, since that seems to be what you want, I would make a list, then populate that list with dataframes.
my_list <- list()
for (i in seq(10)) {
my_list[[i]] = data.frame(x=runif(100), y=rnorm(100))
}
Explanation
Upon execution of this code, you will have a list with 10 items, labelled 1 - 10. Each of those items is its own dataframe, with 2 columns: one containing 100 uniform random numbers, and another containing 100 Gaussian random numbers (chosen from a standard normal distribution).
If you want to access, say, the third dataframe in the list, you'd simply type
my_list[[3]]
to get the contents of that dataframe.
(Lists use the double bracket notation in R, and you just have to "get used to it". It's fairly easy to figure out how to use them properly, though. E.g., my_list[3] will return a list with only 1 item in it, which is that third dataframe. But my_list[[3]] - notice the extra bracket - will return a dataframe, the third dataframe.)
Use R Studio to run R and to get an Excel-spreadsheety look at your data:
View (name.of.your.list [[n]])
where name.of.your.list is the name of your list of data.frames, and n is the n'th data.frame you want to view.
If you will have a list of lists of data.frames, then just keep tagging [[n's]]
View (name.of.your.list [[n]][[n2]])
As an example:
dat.all = list ()
dat.all [[1]] = list ()
dat.all [[1]][[1]] = data.table ("lol" = 1:5, "whatever" = 6:10)
View (dat.all [[1]][[1]])
Also, if you are new to R like me, then I suggest learning data.table instead of data.frame, it is much more powerful, and will probably prevent you from having to make lists of lists of data.frames.
Cheers.
Consider the following simulation snippet:
k <- 1:5
x <- seq(0,10,length.out = 100)
dsts <- lapply(1:length(k), function(i) cbind(x=x, distri=dchisq(x,k[i]),i) )
dsts <- do.call(rbind,dsts)
why does this code throws an error (dsts is matrix):
subset(dsts,i==1)
#Error in subset.matrix(dsts, i == 1) : object 'i' not found
Even this one:
colnames(dsts)[3] <- 'iii'
subset(dsts,iii==1)
But not this one (matrix coerced as dataframe):
subset(as.data.frame(dsts),i==1)
This one works either where x is already defined:
subset(dsts,x> 500)
The error occurs in subset.matrix() on this line:
else if (!is.logical(subset))
Is this a bug that should be reported to R Core?
The behavior you are describing is by design and is documented on the ?subset help page.
From the help page:
For data frames, the subset argument works on the rows. Note that subset will be evaluated in the data frame, so columns can be referred to (by name) as variables in the expression (see the examples).
In R, data.frames and matrices are very different types of objects. If this is causing a problem, you are probably using the wrong data structure for your data. Matrices are really only necessary if you meed matrix arithmetic. If you are thinking of your columns as different attributes for a row observations, then you should be storing your data in a data.frame in the first place. You could store all your values in a simple vector where every three values represent one observation, but that would also be a poor choice of data structure for your data. I'm not sure if you were trying to be more efficient by choosing a matrix but it seems like just the wrong choice.
A data.frame is stored as a named list while a matrix is stored as a dimensioned vector. A list can be used as an environment which makes it easy to evaluate variable names in that context. The biggest difference between the two is that data.frames can hold columns of different classes (numerics, characters, dates) while matrices can only hold values of exactly one data.type. You cannot always easily convert between the two without a loss of information.
Thinks like $ only work with data.frames as well.
dd <- data.frame(x=1:10)
dd$x
mm <- matrix(1:10, ncol=1, dimnames=list(NULL, "x"))
mm$x # Error
If you want to subset a matrix, you are better off using standard [ subsetting rather than the sub setting function.
dsts[ dsts[,"i"]==1, ]
This behavior has been a part of R for a very long time. Any changes to this behavior is likely to introduce breaking changes to existing code that relies on variables being evaluated in a certain context. I think the problem lies with whomever told you to use a matrix in the first place. Rather than cbind(), you should have used data.frame()
I am a naive user of R and am attempting to come to terms with the 'apply' series of functions which I now need to use due to the complexity of the data sets.
I have large, ragged, data frame that I wish to reshape before conducting a sequence of regression analyses. It is further complicated by having interlaced rows of descriptive data(characters).
My approach to date has been to use a factor to split the data frame into sets with equal row lengths (i.e. a list), then attempt to remove the trailing empty columns, make two new, matching lists, one of data and one of chars and then use reshape to produce a common column number, then recombine the sets in each list. e.g. a simplified example:
myDF <- as.data.frame(rbind(c("v1",as.character(1:10)),
c("v1",letters[1:10]),
c("v2",c(as.character(1:6),rep("",4))),
c("v2",c(letters[1:6], rep("",4)))))
myDF[,1] <- as.factor(myDF[,1])
myList <- split(myDF, myDF[,1])
myList[[1]]
I can remove the empty columns for an individual set and can split the data frame into two sets from the interlacing rows but have been stumped with the syntax in writing a function to apply the following function to the list - though 'lapply' with 'seq_along' should do it?
Thus for the individual set:
DF <- myList[[2]]
DF <- DF[,!sapply(DF, function(x) all(x==""))]
DF
(from an earlier answer to a similar, but simpler example on this site). I have a large data set and would like an elegant solution (I could use a loop but that would not use the capabilities of R effectively). Once I have done that I ought to be able to use the same rationale to reshape the frames and then recombine them.
regards
jac
Try
lapply(split(myDF, myDF$V1), function(x) x[!colSums(x=='')])
I am trying to restructure an enormous dataframe (about 12.000 cases): In the old dataframe one person is one row and has about 250 columns (e.g. Person 1, test A1, testA2, testB, ...)and I want all the results of test A (1 - 10 A´s overall and 24 items (A-Y) for that person in one column, so one person end up with 24 columns and 10 rows. There is also a fixed dataframe part before the items A-Y start (personal information like age, gender etc.), which I want to keep as it is (fixdata).
The function/loop works for 30 cases (I tried it in advance) but for the 12.000 it is still calculating, for nearly 24hours now. Any ideas why?
restructure <- function(data, firstcol, numcol, numsets){
out <- data.frame(t(rep(0, (firstcol-1)+ numcol)) )
names(out) <- names(daten[0:(firstcol+numcol-1)])
for(i in 1:nrow(daten)){
fixdata <- (daten[i, 1:(firstcol-1)])
for (j in (seq(firstcol, ((firstcol-1)+ numcol* numsets), by = numcol))){
flexdata <- daten[i, j:(j+numcol-1)]
tmp <- cbind(fixdata, flexdata)
names(tmp) <- names(daten[0:(firstcol+numcol-1)])
out <- rbind(out,tmp)
}
}
out <- out[2:nrow(out),]
return(out)
}
Thanks in advance!
Idea why: you rbind to out in each iteration. This will take longer each iteration as out grows - so you have to expect more than linear growth in run time with increasing data sets.
So, as Andrie tells you can look at melt.
Or you can do it with core R: stack.
Then you need to cbind the fixed part yourself to the result, (you need to repeat the fixed columns with each = n.var.cols
A third alternative would be array2df from package arrayhelpers.
I agree with the others, look into reshape2 and the plyr package, just want to add a little in another direction. Particularly melt, cast,dcast might help you. Plus, it might help to make use of smart column names, e.g.:
As<-grep("^testA",names(yourdf))
# returns a vector with the column position of all testA1 through 10s.
Besides, if you 'spent' the two dimensions of a data.frame on test# and test type, there's obviously none left for the person. Sure, you identify them by an ID, that you could add an aesthetic to when plotting, but depending on what you want to do you might want to store them in a list. So you end up with a list of persons with a data.frame for every person. I am not sure what you are trying to do, but still hope this helps though.
Maybe you're not getting the plyr or other functions for reshaping the data component. How about something more direct and low level. If you currently just have one line that goes A1, A2, A3... A10, B1-B10, etc. then extract that lump of stuff from your data frame, I'm guessing columns 11-250, and then just make that section the shape you want and put them back together.
yDat <- data[, 11:250]
yDF <- lapply( 1:nrow(data), function(i) matrix(yDat[i,], ncol = 24) )
yDF <- do.call(rbind, y) #combine the list of matrices returned above into one
yDF <- data.frame(yDF) #get it back into a data.frame
names(yDF) <- LETTERS[1:24] #might as well name the columns
That's the fastest way to get the bulk of your data in the shape you want. All the lapply function did was add dimension attributes to each row so that they were in the shape you wanted and then return them as a list, which was massaged with the subsequent rows. But now it doesn't have any of your ID information from the main data.frame. You just need to replicate each row of the first 10 columns 10 times. Or you can use the convenience function merge to help with that. Make a common column that is already in your first 10 rows one of the columns of the new data.frame and then just merge them.
yInfo <- data[, 1:10]
ID <- yInfo$ID
yDF$ID <- rep( yInfo$ID, each = 10 )
newDat <- merge(yInfo, yDF)
And now you're done... mostly, you might want to make an extra column that names the new rows
newDat$condNum <- rep(1:10, nrow(newDat)/10)
This will be very fast running code. Your data.frame really isn't that big at all and much of the above will execute in a couple of seconds.
This is how you should be thinking of data in R. Not that there aren't convenience functions to handle the bulk of this but you should be doing this that avoid looping as much as possible. Technically, what happened above only had one loop, the lapply used right at the start. It had very little in that loop as well (they should be compact when you use them). You're writing in scalar code and it is very very slow in R... even if you weren't really abusing memory and growing data while doing it. Furthermore, keep in mind that, while you can't always avoid a loop of some kind, you can almost always avoid nested loops, which is one of your biggest problems.
(read this to better understand your problems in this code... you've made most of the big errors in there)
My dataframe(m*n) has few hundreds of columns, i need to compare each column with all other columns (contingency table) and perform chisq test and save the results for each column in different variable.
Its working for one column at a time like,
s <- function(x) {
a <- table(x,data[,1])
b <- chisq.test(a)
}
c1 <- apply(data,2,s)
The results are stored in c1 for column 1, but how will I loop this over all columns and save result for each column for further analysis?
If you're sure you want to do this (I wouldn't, thinking about the multitesting problem), work with lists :
Data <- data.frame(
x=sample(letters[1:3],20,TRUE),
y=sample(letters[1:3],20,TRUE),
z=sample(letters[1:3],20,TRUE)
)
# Make a nice list of indices
ids <- combn(names(Data),2,simplify=FALSE)
# use the appropriate apply
my.results <- lapply(ids,
function(z) chisq.test(table(Data[,z]))
)
# use some paste voodoo to give the results the names of the column indices
names(my.results) <- sapply(ids,paste,collapse="-")
# select all values for y :
my.results[grep("y",names(my.results))]
Not harder than that. As I show you in the last line, you can easily get all tests for a specific column, so there is no need to make a list for each column. That just takes longer and takes more space, but gives the same information. You can write a small convenience function to extract the data you need :
extract <- function(col,l){
l[grep(col,names(l))]
}
extract("^y$",my.results)
Which makes you can even loop over different column names of your dataframe and get a list of lists returned :
lapply(names(Data),extract,my.results)
I strongly suggest you get yourself acquainted with working with lists, they're one of the most powerful and clean ways of doing things in R.
PS : Be aware that you save the whole chisq.test object in your list. If you only need the value for Chi square or the p-value, select them first.
Fundamentally, you have a few problems here:
You're relying heavily on global arguments rather than local ones.
This makes the double usage of "data" confusing.
Similarly, you rely on a hard-coded value (column 1) instead of
passing it as an argument to the function.
You're not extracting the one value you need from the chisq.test().
This means your result gets returned as a list.
You didn't provide some example data. So here's some:
m <- 10
n <- 4
mytable <- matrix(runif(m*n),nrow=m,ncol=n)
Once you fix the above problems, simply run a loop over various columns (since you've now avoided hard-coding the column) and store the result.