I have a dataframe with ~9000 rows of human coded data in it, two coders per item so about 4500 unique pairs. I want to break the dataset into each of these pairs, so ~4500 dataframes, run a kripp.alpha on the scores that were assigned, and then save those into a coder sheet I have made. I cannot get the loop to work to do this.
I can get it to work individually, using this:
example.m <- as.matrix(example.m)
s <- kripp.alpha(example.m)
example$alpha <- s$value
However, when trying a loop I am getting either "Error in get(v) : object 'NA' not found" when running this:
for (i in items) {
v <- i
v <- v[c("V1","V2")]
v <- assign(v, as.matrix(get(v)))
s <- kripp.alpha(v)
i$alpha <- s$value
}
Or am getting "In i$alpha <- s$value : Coercing LHS to a list" when running:
for (i in items) {
i.m <- i[c("V1","V2")]
i.m <- as.matrix(i.m)
s <- kripp.alpha(i.m)
i$alpha <- s$value
}
Here is an example set of data. Items is a list of individual dataframes.
l <- as.data.frame(matrix(c(4,3,3,3,1,1,3,3,3,3,1,1),nrow=2))
t <- as.data.frame(matrix(c(4,3,4,3,1,1,3,3,1,3,1,1),nrow=2))
items <- c("l","t")
I am sure this is a basic question, but what I want is for each file, i, to add a column with the alpha score at the end. Thanks!
Your problem is with scoping and extracting names from objects when referenced through strings. You'd need to eval() some of your object to make your current approach work.
Here's another solution
library("irr") # For kripp.alpha
# Produce the data
l <- as.data.frame(matrix(c(4,3,3,3,1,1,3,3,3,3,1,1),nrow=2))
t <- as.data.frame(matrix(c(4,3,4,3,1,1,3,3,1,3,1,1),nrow=2))
# Collect the data as a list right away
items <- list(l, t)
Now you can sapply() directly over the elements in the list.
sapply(items, function(v) {
kripp.alpha(as.matrix(v[c("V1","V2")]))$value
})
which produces
[1] 0.0 -0.5
Related
I'm trying to split a 2 level deep list of characters into a 1 level list using a suffix.
More precisely, I have a list of genes, each containing 6 lists of probes corresponding to 6 bins. The architecture looks like :
feat_indexed_probes_bin$HSPB6$bin1
[1] "cg14513218" "cg22891287" "cg20713852" "cg04719839" "cg27580050" "cg18139462" "cg02956481" "cg26608795" "cg15660498" "cg25654926" "cg04878216"
I'm trying to get a list "bins_indexed_probes" with the following architecture :
bins_indexed_probes$HSPB6_bin6 containing the same probes so I can pass it to my map-reducing function.
I tried many solutions such as melt(), for loop, etc but I can't figure how to perform a double nested loop ( on genes and on bins) and get a list output with only 1 level depth.
For the moment, my func to do so is the following :
create_map <- function(indexes = feat_indexed_probes_bin, binlist = c("bin1", "bin2", "bin3", "bin4", "bin5", "bin6"), genes = features) {
map <- list()
ret <- lapply(binlist, function(bin) {
lapply(rownames(features), function(gene) {
map[[paste(gene, "_", bin, sep = "")]] <- feat_indexed_probes_bin[[gene]][[bin]]
tmp_names <<- paste(gene, "_", bin, sep = "")
return(map)
})
names(map) <- tmp_names
rm(tmp_names)
})
return(ret)
}
it returns:
[[6]][[374]]
GDF10_bin6
"cg13565300"
[[6]][[375]]
NULL
[[6]][[376]]
[[6]][[376]]$HNF1B_bin6
[1] "cg03433642" "cg09679923" "cg17652435" "cg03348978" "cg02435495" "cg02701059" "cg05110178" "cg11862993" "cg09463047"
[[6]][[377]]
[[6]][[377]]$GPIHBP1_bin6
[1] "cg01953797" "cg00152340"
instead, I would expect something like
$GPIHBP1_bin1
"cg...." "cg...."
...
$GPIHBP1_bin6
"someotherprobe"
$someothergene_bin1
"probe" "probe"
...
I hope I'm being clear, and since this is my first time asking question, I already apologise if I didn't follow the stackoverflow protocol.
Thank you already for reading me
Consider a nested lapply with extract, [[, and setNames calls, all wrapped in do.call using c to bind return elements together.
bins_indexed_probes <- do.call(c,
lapply(1:6, function(i)
setNames(lapply(feat_indexed_probes_bin, `[[`, i),
paste0(names(feat_indexed_probes_bin), "_bin", i))
)
)
# RE-ORDER ELEMENTS BY NAME
bins_indexed_probes <- bins_indexed_probes[sort(names(bins_indexed_probes))]
Rextester Demo
I am trying to compile two vectors from my for loop, to then cbind into a table. (I was trying to do this all in one step, but because of the below issue I'm trying to simplify.)
I set three vectors, id_name, count_rows, and id_test.
Going through my new_dat (a pre-exiting data frame), I'm setting vector result to be the number of the rows where the ID is i.
I'm then printing the output, which works fine.
But when I try to push the values into the vectors, I get Error: object 'id_name' not found. And the same for the other two.
Here's my code:
id_name <- c()
count_rows <- c()
id_test <- c()
for (i in id) {
result <- sum(new_dat$ID == i)
id_test <- c("hello", "world")
id_name <- c(id_name, i)
count_rows <-c(count_rows, result)
print(result)
print(i)
}
Initialize your vectors differently. See below; you may need to change numeric if your data aren't numeric, and substitute the data's actual length for N (if you know it beforehand).
id_name <- vector('numeric', length=N)
What you are doing now creates a NULL variable, of class NULL.
I have a list called "scenbase" that contains 40 data frames, which are each 326 rows by 68 columns. I would like to use lapply() to subset the data frames so they only retain rows 33-152. I've written a simple function called trim() (below), and am attempting to apply it to the list of data frames but am getting an error message. The function and my attempt at using it with lapply is below:
trim <- function(i)
{ (i <- i[33:152,]) }
lapply(scenbase, trim)
Error in i[33:152, ] : incorrect number of dimensions
When I try to do the same thing to one of the individual data frames (soil11base.txt) that are included in the list (below), it works as expected:
soil11base.txt <- soil11base.txt[33:152,]
Any idea what I need to do to get the dimensions correct?
You have 2 solutions. You can either
(a) assign to a new list newList = lapply(scenbase, function(x) { x[33:152,,drop=F]} )
(b) use the <<- operator will assign your trimmed data in place lapply(1:length(scenbase), function(x) { scenbase[[x]] <<- scenbase[[x]][33:152,,drop=F]} ).
Your call does not work because the i is not in the global scope. You can work your way around that by using calls to the <<- operator which assigns to the first variable it finds in successive parent environments. Or by creating a new trimmed list.
Here is some code that reproduces solution (a):
listOfDfs = list()
for(i in 1:10) { listOfDfs[[i]] = data.frame("x"=sample(letters,200,replace=T),"y"=sample(letters,200,replace=T)) }
choppedList = lapply(listOfDfs, function(x) { x[33:152,,drop=F]} )
Here is some code that reproduces solution (b):
listOfDfs = list()
for(i in 1:10) { listOfDfs[[i]] = data.frame("x"=sample(letters,200,replace=T),"y"=sample(letters,200,replace=T)) }
lapply(1:length(listOfDfs), function(x) { listOfDfs[[x]] <<- listOfDfs[[x]][33:152,,drop=F]} )
I have in my environment a series of data frames called EOG. There is one for each year between 2006 and 2012. Like, EOG2006, EOG2007...EOG2012. I would like to add them as elements of a list.
First, I am trying to know if this is possible. I read the official R guide and a couple of R programming manuals but I didn't find explicit examples about that.
Second, I would like to do this using a for loop. Unfortunately, the code I used to do the job is wrong and I am going crazy to fix it.
for (j in 2006:2012){
z<-j
sEOG<-paste("EOG", z, sep="")
dEOG<-get(paste("EOG", z, sep=""))
lsEOG<-list()
lsEOG[[sEOG]]<-dEOG
}
This returns a list with one single element. Where is the mistake?
You keep reinitializing the list inside the loop. You need to move lsEOG<-list() outside the for loop.
lsEOG<-list()
for (j in 2006:2012){
z <- j
sEOG <- paste("EOG", z, sep="")
dEOG <- get(paste("EOG", z, sep=""))
lsEOG[[sEOG]] <-dEOG
}
Also, you can use j directly in the paste functions:
sEOG <- paste("EOG", j, sep="")
I had the same question, but felt that the OP's initial code was a bit opaque for R beginners. So, here is perhaps a bit clearer example of how to create data frames in a loop and add them to a list which I just now figured out by playing around in the R shell:
> dfList <- list() ## create empty list
>
> for ( i in 1:5 ) {
+ x <- rnorm( 4 )
+ y <- sin( x )
+ dfList[[i]] <- data.frame( x, y ) ## create and add new data frame
+ }
>
> length( dfList ) ## 5 data frames in list
[1] 5
>
> dfList[[1]] ## print 1st data frame
x y
1 -0.3782376 -0.3692832
2 -1.3581489 -0.9774756
3 1.2175467 0.9382535
4 -0.7544750 -0.6849062
>
> dfList[[2]] ## print 2nd data frame
x y
1 -0.1211670 -0.1208707
2 -1.5318212 -0.9992406
3 0.8790863 0.7701564
4 1.4014124 0.9856888
>
> dfList[[2]][4,2] ## in 2nd data frame, print element in row 4 column 2
[1] 0.9856888
>
For R beginners like me, note that double brackets are required to access the ith data frame. Basically, double brackets are used for lists while single brackets are used for vectors.
If the data frames are saved as an object you can find them by apropos("EOG", ignore.case=FALSE) and them with a loop store them in the list:
list.EOG<- apropos("EOG", ignore.case=FALSE) #Find the objects with case sensitive
lsEOG<-NULL #Creates the object to full fill in the list
for (j in 1:length(list.EOG)){
lsEOG[i]<-get(list.EOG[i]) #Add the data.frame to each element of the list
}
to add the name of each one to the list you can use:
names(lsEOG, "names")<-list.EOG
Thanks in advance, and sorry if this question has been answered previously - I have looked pretty extensively. I have a dataset containing a row of with concatenated information, specifically: name,color code,some function expression. For example, one value may be:
cost#FF0033#log(x)+6.
I have all of the code to extract the information, and I end up with a vector of expressions that I would like to convert to a list of actual functions.
For example:
func.list <- list()
test.func <- c("x","x+1","x+2","x+3","x+4")
where test.func is the vector of expressions. What I would like is:
func.list[[3]]
To be equivalent to
function(x){x+3}
I know that I can create a function using:
somefunc <- function(x){eval(parse(text="x+1"))}
to convert a character value into a function. The problem comes when I try and loop through to make multiple functions. For an example of something I tried that didn't work:
for(i in 1:length(test.func)){
temp <- test.func[i]
f <- assign(function(x){eval(expr=parse(text=temp))})
func.list[[i]] <- f
}
Based on another post (http://stats.stackexchange.com/questions/3836/how-to-create-a-vector-of-functions) I also tried this:
makefunc <- function(y){y;function(x){y}}
for(i in 1:length(test.func)){
func.list[[i]] <- assign(x=paste("f",i,sep=""),value=makefunc(eval(parse(text=test.func[i]))))
}
Which gives the following error: Error in eval(expr, envir, enclos) : object 'x' not found
The eventual goal is to take the list of functions and apply the jth function to the jth column of the data.frame, so that the user of the script can specify how to normalize each column within the concatenated information given by the column header.
Maybe initialize your list with a single generic function, and then update them using:
foo <- function(x){x+3}
> body(foo) <- quote(x+4)
> foo
function (x)
x + 4
More specifically, starting from a character, you'd probably do something like:
body(foo) <- parse(text = "x+5")
Just to add onto joran's answer, this is what finally worked:
test.data <- matrix(data=rep(1,25),5,5)
test.data <- data.frame(test.data)
test.func <- c("x","x+1","x+2","x+3","x+4")
func.list <- list()
for(i in 1:length(test.func)){
func.list[[i]] <- function(x){}
body(func.list[[i]]) <- parse(text=test.func[i])
}
processed <- mapply(do.call,func.list,lapply(test.data,list))
Thanks again, joran.
This is what I do:
f <- list(identity="x",plus1 = "x+1", square= "x^2")
funCreator <- function(snippet){
txt <- snippet
function(x){
exprs <- parse(text = txt)
eval(exprs)
}
}
listOfFunctions <- lapply(setNames(f,names(f)),function(x){funCreator(x)}) # I like to have some control of the names of the functions
listOfFunctions[[1]] # try to see what the actual function looks like?
library(pryr)
unenclose(listOfFunctions[[3]]) # good way to see the actual function http://adv-r.had.co.nz/Functional-programming.html
# Call your funcions
listOfFunctions[[2]](3) # 3+1 = 4
do.call(listOfFunctions[[3]],list(3)) # 3^2 = 9
attach(listOfFunctions) # you can also attach your list of functions and call them by name
square(3) # 3^2 = 9
identity(7) # 7 ## masked object identity, better detach it now!
detach(listOfFunctions)