Hi if I have a list of list like so,
List of 5
$ 1:List of 2
..$ a: Named num [1:36] 3.29 3.25 3.36 3.26 3.34 ...
.. ..- attr(*, "names")= chr [1:36] "V1" "V2" "V3" "V4" ...
..$ b: Named num [1:36] 0.659 0.65 0.672 0.652 0.669 ...
say its called l, is there a way I can extract all the 'a' element of the list of list? Currently I can extract a single 'a' element as such, l[[5]] [['sr']] but when I try something like
l[[1:5]] [['sr']] or l[[1,5]] [['sr']] it fails. Help would greatly appreciated thanks!
Is this what you want?
l <- list(list(a=1:3, b=1:3),
list(a=3:1, b=3:1))
lapply(l, function(x) x[["a"]])
[[1]]
[1] 1 2 3
[[2]]
[1] 3 2 1
Related
The data is from
datasetname="riboflavin"
data(riboflavin, package = "hdi")
Y=as.numeric(riboflavin$y)-1
mydata=data.frame(Y,X)
#X now is 71*4088
str(X)
'AsIs' num [1:71, 1:4088] 8.49 7.64 8.09 7.89 6.81 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:71] "b_Fbat107PT24.CEL" "b_Fbat107PT30.CEL" "b_Fbat107PT48.CEL" "b_Fbat107PT52.CEL" ...
..$ : chr [1:4088] "AADK_at" "AAPA_at" "ABFA_at" "ABH_at" ...
#71*1
str(Y)
num [1:71] -7.64 -7.95 -8.93 -9.29 -8.31 ...
dim(mydata)
[1] 71 2
why dim(mydata) is not 71*4089? How to obtain a data.frame of (X,Y) with a dimensionality with 71*4089？
Thanks
num [1:71, 1:4088] means riboflavin$x is a matrix. cbinding modified column y to matrix x should solve the problem.
res <- as.data.frame(cbind(Y=riboflavin$y - 1, X=riboflavin$x))
dim(res)
# [1] 71 4089
I would like to use rollapply or rollapplyr to apply the modwt function to my time series data.
I'm familiar with how rollapply/r works but I need some help setting up the output so that I can correctly store my results when using rollapply.
The modwt function in the waveslim package takes a time series and decomposes it into J levels, for my particular problem J = 4 which means I will have 4 sets of coefficients from my single time series stored in a list of 5. Of this list I am only concerned with d1,d2,d3 & d4.
The output of the modwt function looks as follows
> str(ar1.modwt)
List of 5
$ d1: num [1:200] -0.223 -0.12 0.438 -0.275 0.21 ...
$ d2: num [1:200] 0.1848 -0.4699 -1.183 -0.9698 -0.0937 ...
$ d3: num [1:200] 0.5912 0.6997 0.5416 0.0742 -0.4989 ...
$ d4: num [1:200] 1.78 1.86 1.85 1.78 1.65 ...
$ s4: num [1:200] 4.64 4.42 4.19 3.94 3.71 ...
- attr(*, "class")= chr "modwt"
- attr(*, "wavelet")= chr "la8"
- attr(*, "boundary")= chr "periodic"
In the example above I have applied the modwt function to the full length time series of length 200 but I wish to apply it to a small rolling window of 30 using rollapply.
I have already tried the following but the output is a large matrix and I cannot easily identify which values belong to d1,d2,d3 or d4
roller <- rollapplyr(ar1, 30,FUN=modwt,wf="la8",n.levels=4,boundary="periodic")
The output of this is a large matrix with the following structure:
> str(roller)
List of 855
$ : num [1:30] 0.117 -0.138 0.199 -1.267 1.872 ...
$ : num [1:30] -0.171 0.453 -0.504 -0.189 0.849 ...
$ : num [1:30] 0.438 -0.3868 0.1618 -0.0973 -0.0247 ...
$ : num [1:30] -0.418 0.407 0.639 -2.013 1.349 ...
...lots of rows omitted...
$ : num [1:30] 0.307 -0.658 -0.105 1.128 -0.978 ...
[list output truncated]
- attr(*, "dim")= int [1:2] 171 5
- attr(*, "dimnames")=List of 2
..$ : NULL
..$ : chr [1:5] "d1" "d2" "d3" "d4" ...
How can I set up a variable such that it will store the (200-30)+1 lists with lists within this for each of the scales d1,d2,d3 and d4?
For a reproducible example please use the following:
library(waveslim)
data(ar1)
ar1.modwt <- modwt(ar1, "la8", 4)
Define modwt2 which invokes modwt, takes the first 4 components and strings them out into a numeric vector. Then use rollapplyr with that giving rollr where each row of rollr is the result of one call to modwt2. Finally, reshape each row of rollr into a separate matrix and create a list, L, of those matrices:
modwt2 <- function(...) unlist(head(modwt(...), 4))
rollr <- rollapplyr(ar1, 30, FUN = modwt2, wf = "la8", n.levels = 4, boundary = "periodic")
L <- lapply(1:nrow(rollr), function(i) matrix(rollr[i,], , 4))
If a 30 x 4 x 171 array is desired then the following will simplify it into a 3d array:
simplify2array(L)
or as a list of lists:
lapply(L, function(x) as.list(as.data.frame(x)))
2) This is an alternate solution that just uses lapply directly and returns a list each of whose components is the list consisting of d1, d2, d3 and d4.
lapply(1:(200-30+1), function(i, ...) head(modwt(ar1[seq(i, length = 30)], ...), 4),
wf = "la8", n.levels = 4, boundary = "periodic")
Updates: Code improvements, expand (1) and add (2).
I do have to rename sublist titles within a main matrix list called l1. Each Name(n) is related to a value as a character string. Here is my code :
names(l1)[1] <- Name1
names(l1)[2] <- Name2
names(l1)[3] <- Name3
names(l1)[4] <- Name4
## ...
names(l1)[43] <- Name43
As you can see, I have 43 sublists. Is there a way do do that using an automated loop like for (i in 1:43) or something ? I tried to perform a loop but I am a beginner and that's very hard for now.
Edit : I would like to rename the elements of my list without having to type 43 lines manually. Here is the first three elements of my list :
str(l1)
List of 43
$ XXX : num [1:640, 1:3] -0.83 -0.925 -0.623 -0.191 0.155 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:3] "EV_BICYCLE" "HW_DISTANCE" "NO_ASSETS"
$ XXX : num [1:640, 1:2] -0.159 0.485 -0.686 -0.245 -3.361 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:2] "HOME_OWN" "METRO_DISTANCE"
$ XXX : num [1:640, 1:3] -0.79 1.15 0.224 0.388 -1.571 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:3] "BICYCLE" "HOME_OWN_SC" "POP_SC"
That is to say, I would like to replace the 43 XXX by Name1, Name2 ... to Name43
Try
names(l1) <- unlist(mget(ls(pattern="^Nom_F")))
str(l1, list.len=2)
#List of 3
# $ Accessibility : int [1:5, 1:5] 10 10 3 9 7 6 8 2 7 8 ...
# ..- attr(*, "dimnames")=List of 2
# .. ..$ : NULL
# .. ..$ : chr [1:5] "A" "B" "C" "D" ...
# $ Access : int [1:5, 1:5] 6 4 10 5 9 8 9 4 7 1 ...
#..- attr(*, "dimnames")=List of 2
# .. ..$ : NULL
# .. ..$ : chr [1:5] "A" "B" "C" "D" ...
Instead of creating separate objects, you could create a vector of real titles. For example
v1 <- LETTERS[1:3]
names(l1) <- v1
data
set.seed(42)
l1 <- setNames(lapply(1:3, function(x)
matrix(sample(1:10, 5*5, replace=TRUE), ncol=5,
dimnames=list(NULL, LETTERS[1:5]))), rep('XXX',3))
Nom_F1 <- "Accessibility"
Nom_F2 <- "Access"
Nom_F3 <- "Poverty_and_SC"
this is probably trivial but can someone help me with this?
I been using the apply to call a function that returns a list, as such
l <- apply(df, 1, manydo); manydo function returns a list list("a" = a, "b" = b)
the output l appears to be a list of list, because when I type str(l) it returns
List of 5
$ 1:List of 2
..$ a: Named num [1:36] 3.29 3.25 3.36 3.26 3.34 ...
.. ..- attr(*, "names")= chr [1:36] "V1" "V2" "V3" "V4" ...
..$ b: Named num [1:36] 0.659 0.65 0.672 0.652 0.669 ...
I tried to access it many ways such as
l[1][1]
or l[1]['a']
unlist(l[1][1]['a'])
but nothing works. What I want is to be able to get for example, the first element and 'a' variable?
in addition, if I just call the function directly say:
l <- manydo(c(1:36)) # I can access this
l['a'] # this works, so I'm confuse ;(
thanks!
[ returns a list containing the selected elements. [[ returns a single element (not wrapped in a list), so that's what you want to use here.
l <- list(list(a=1:10, b=10:22), list(), list(), list(), list())
str(l)
## List of 5
## $ :List of 2
## ..$ a: int [1:10] 1 2 3 4 5 6 7 8 9 10
## ..$ b: int [1:13] 10 11 12 13 14 15 16 17 18 19 ...
...
Now to retrieve a:
l[[1]][['a']]
[1] 1 2 3 4 5 6 7 8 9 10
l[[1]] is the list containing a. l[[1]][['a']] is the value of a itself.
I am trying to use the penalizedLDA package to run a penalized linear discriminant analysis in order to select the "most meaningful" variables. I have searched here and on other sites for help in accessing the the output from the penalized model to no avail.
My data comprises of 400 varaibles and 44 groups. Code I used and results I got thus far:
yy.m<-as.matrix(yy) #Factors/groups
xx.m<-as.matrix(xx) #Variables
cv.out<-PenalizedLDA.cv(xx.m,yy.m,type="standard")
## aplly the penalty
out <- PenalizedLDA(xx.m,yy.m,lambda=cv.out$bestlambda,K=cv.out$bestK)
Too get the structure of the output from the anaylsis:
> str(out)
List of 10
$ discrim: num [1:401, 1:4] -0.0234 -0.0219 -0.0189 -0.0143 -0.0102 ...
$ xproj : num [1:100, 1:4] -8.31 -14.68 -11.07 -13.46 -26.2 ...
$ K : int 4
$ crits :List of 4
..$ : num [1:4] 2827 2827 2827 2827
..$ : num [1:4] 914 914 914 914
..$ : num [1:4] 162 162 162 162
..$ : num [1:4] 48.6 48.6 48.6 48.6
$ type : chr "standard"
$ lambda : num 0
$ lambda2: NULL
$ wcsd.x : Named num [1:401] 0.0379 0.0335 0.0292 0.0261 0.0217 ...
..- attr(*, "names")= chr [1:401] "R400" "R405" "R410" "R415" ...
$ x : num [1:100, 1:401] 0.147 0.144 0.145 0.141 0.129 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:401] "R400" "R405" "R410" "R415" ...
$ y : num [1:100, 1] 2 2 2 2 2 1 1 1 1 1 ...
- attr(*, "class")= chr "penlda"
I am interested in obtaining a list or matrix of the top 20 variables for feature selection, more than likely based on the coefficients of the Linear discrimination.
I realized I would have to sort the coefficients in descending order, and get the variable names matched to it. So the output I would expect is something like this imaginary example
V1 V2
R400 0.34
R1535 0.22...
Can anyone provide any pointers (not necessarily the R code). Thanks in advance.
Your out$K is 4, and that means you have 4 discriminant vectors. If you want the top 20 variables according to, say, the 2nd vector, try this:
# get the data frame of variable names and coefficients
var.coef = data.frame(colnames(xx.m), out$discrim[,2])
# sort the 2nd column (the coefficients) in decreasing order, and only keep the top 20
var.coef.top = var.coef[order(var.coef[,2], decreasing = TRUE)[1:20], ]
var.coef.top is what you want.