I'm just learning R and having a hard time wrapping my head around how to extract elements from objects in a list. I've parsed a json file into R giving me list object. But I can't figure out how, from there, to extract various json elements from the list. here's a truncated look at how my data appears after parsing the json:
> #Parse data into R objects#
> list.Json= fromJSON(,final.name, method = "C")
> head(listJson,6)
[[1]]
[[1]]$contributors
NULL
[[1]]$favorited
[1] FALSE
...[truncating]...
[[5]]
[[5]]$contributors
NULL
[[5]]$favorited
[1] FALSE
I can figure out how to extract the favorites data for one of the objects in the list
> first.object=listJson[1]
> ff=first.object[[1]]$favorited
> ff
[1] FALSE
But I'm very confused about how to extract favorited for all objects in the list. I've looked into sappily, is that the correct approach? Do I need to put the above code into a for...next loop?
sapply is going to apply some function to every element in your list. In your case, you want to access each element in a (nested) list. sapply is certainly capable of this. For instance, if you want to access the first child of every element in your list:
sapply(listJson, "[[", 1)
Or if you wanted to access the item named "favorited", you could use:
sapply(listJson, "[[", "favorited")
Note that the [ operator will take a subset of the list you're working with. So when you access myList[1], you still have a list, it's just of length 1. However, if you reference myList[[1]], you'll get the contents of the first space in your list (which may or may not be another list). Thus, you'll use the [[ operator in sapply, because you want to get down to the contents of the list.
Related
ive created a lot of character objects in R that i would like to put into a list (storing all their information).
the object looks like this and the pattern is "TMC"
str(TMCS09g10086933)
chr [1:10] "TMCS09g1008699" "TMCS09g1008610 "TMCS09g10086101" "TMCS09g10086104" "TMCS09g100864343" "TMCS09g10086434343" "TMCS09g10086994111" ...
i have hundreds of these objects. Could someone tell me how to do this?
You can use the function objects with the argument pattern to list them.
Then, you can call the function get to fetch them. If you do this with an lapply, you will get a list returned right away.
TMClist <- lapply(objects(pattern = "^TMC"), get)
First you need to find the objects, which you can do with a regex search through the list of the objects in your environment grep("^TMC", ls(), value = TRUE), then you need to get the objects using the character vector of their names. For that you use mget.
your_list <- mget(grep("^TMC", ls(), value = TRUE))
This seems to be a beginner question but I couldn't find the answer anywhere. I know how to extract an element from a list using listname[[1]] but output will always include the index number like
[1] First element of the list
Same is true for using the name like listname$name or unlist(listname$name). All I want is
First element of the list
I could of course remove the index number using regex but I doubt that this is the way it should be :-)
The reason that the [1] appears is because all atomic types in R are vectors (of type character, numeric, etc), i.e. in your case a vector of length one.
If you want to see the output without the [1] the simples way is to cat the object:
> listname <- list("This is the first list element",
"This is the second list element")
> cat(listname[[1]], "\n")
This is the first list element
>
Note: I'm aware that there are tons of post about basic deletion on R, but the conventional method doesnt work for this case:
Using R, I've built a key-value pair list, in which both key and value are the same string. (Might seem strange but that's a different discussion ..)
name <- "foo"
list[[name]] <- name
Now I want to delete an element from the list again. Using the conventional method for deletion I tried:
list[[name]] <- NULL
However, this throws the following error:
Warning: Error in <-: more elements supplied than there are to replace
Does anyone know how to delete an element in a key-value list?
Cheers
Edit: Here are the relevant parts taken directly from my code
# saving the list element
networkName <- "Simulation_1_Run_1"
.GlobalEnv$netDynListName[[networkName]] <- (networkName)
# retrieval of the element
# ...
# deletion of list element which causes an error
.GlobalEnv$netDynListName[[networkName]] <- NULL
I'm just learning R and having a hard time wrapping my head around how to extract elements from objects in a list. I've parsed a json file into R giving me list object. But I can't figure out how, from there, to extract various json elements from the list. here's a truncated look at how my data appears after parsing the json:
> #Parse data into R objects#
> list.Json= fromJSON(,final.name, method = "C")
> head(listJson,6)
[[1]]
[[1]]$contributors
NULL
[[1]]$favorited
[1] FALSE
...[truncating]...
[[5]]
[[5]]$contributors
NULL
[[5]]$favorited
[1] FALSE
I can figure out how to extract the favorites data for one of the objects in the list
> first.object=listJson[1]
> ff=first.object[[1]]$favorited
> ff
[1] FALSE
But I'm very confused about how to extract favorited for all objects in the list. I've looked into sappily, is that the correct approach? Do I need to put the above code into a for...next loop?
sapply is going to apply some function to every element in your list. In your case, you want to access each element in a (nested) list. sapply is certainly capable of this. For instance, if you want to access the first child of every element in your list:
sapply(listJson, "[[", 1)
Or if you wanted to access the item named "favorited", you could use:
sapply(listJson, "[[", "favorited")
Note that the [ operator will take a subset of the list you're working with. So when you access myList[1], you still have a list, it's just of length 1. However, if you reference myList[[1]], you'll get the contents of the first space in your list (which may or may not be another list). Thus, you'll use the [[ operator in sapply, because you want to get down to the contents of the list.
I find the following behaviour of the R person object rather unexpected:
Let's create a multi-person object:
a = c(person("Huck", "Finn"), person("Tom", "Sawyer"))
Imagine we want to update the given name of one person in the object:
a[[1]]$given <- 'Huckleberry'
Then if we inspect our object, to my surprise we have:
> a
[1] " <> [] ()" "Tom Sawyer"
Where'd Huckleberry Finn go?! (Note that if we try this with just a single person object, it works fine.) Why does this happen?
How can we do the above so that we get the more logical behavior of correcting just the first name?
The syntax you want here is
a <- c(person("Huck", "Finn"), person("Tom", "Sawyer"))
a[1]$given<-"Huckleberry"
a
#[1] "Huckleberry Finn" "Tom Sawyer"
A group of people is still a "person" and it has it's own special indexing function [.person and concat function c.person so it has perhaps different behavior than you were expecting. The problem was that [[ ]] was messing with the underlying hidden list.
Actually, it's interesting because they've overloaded nearly all the indexing methods for person but not the [<- or [[<- and that's really what's causing the error. Because up to here, we're the same
`$<-`(`[`(a,1), "given", "Huckleberry") #works
`$<-`(`[[`(a,1), "given", "Huckleberry") #works
but when we get to
`[<-`(a, 1, `$<-`(`[`(a,1), "given", "Huckleberry")) #works
`[[<-`(a, 1, `$<-`(`[[`(a,1), "given", "Huckleberry")) #no work
we see a difference. The special wrapping/unwrapping that happens during retrieval does not happen during assignment.
So what's going on is that a "person" is always a list of lists. The outer list holds all the people and the inner lists hold the data. You can think of the data like this
x<-list(
list(name="a"),list(name="b")
)
y<-list(
list(name="c")
)
where x is a collection of two people and y is a "single" person. When you do
x[1]<-y
x
you end up with
list(
list(name="c"),list(name="b")
)
since you're replacing a list with a list which is how [ indexing works with lists. But if you try to replace the element at [[1]] with a list of lists, that list will get nested. For example
x[[1]]<-y
x
becomes
x<-list(
list(list(name="c")),list(name="b")
)
And that extra level of nesting is what's confusing R when it goes to print the person in the first position. That first person won't have any named elements at the second level, so when it goes to print, it will return
emptyp <- structure(list(structure(list(), class="person")), class="person")
utils:::format.person(emptyp)
# " <> [] ()"
which gives is the symbols where it's trying to place the name, e-mail address, role, and comment.