Masi Masi - 29 days ago 17
R Question

How to loop subset of lists in R?

I have a list of 9 lists, see the following code where I want to loop only three lists

p
,
r
and
t
for Pearson, Spearson and Kendall correlations, respectively, instead of all 9 lists.
The current pseudocode is the following where the test function is
corrplot(M.cor, ...)
, see below the complete pseudocode

for (i in p.mat.all) {
...
}


Code with
mtcars
test data

library("psych")
library("corrplot")

M <- mtcars

M.cor <- cor(M)

p.mat.all <- psych::corr.test(M.cor, method = c("pearson", "kendall", "spearman"),
adjust = "none", ci = F)

str(p.mat.all)

str(p.mat.all$r)

str(p.mat.all$t)

str(p.mat.all$p)


Output about the list of 9 lists

List of 9
$ r : num [1:11, 1:11] 1 -0.991 -0.993 -0.956 0.939 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
.. ..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
$ n : num 11
$ t : num [1:11, 1:11] Inf -21.92 -25.4 -9.78 8.22 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
.. ..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
$ p : num [1:11, 1:11] 0.00 4.04e-09 1.09e-09 4.32e-06 1.78e-05 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
.. ..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
$ se : num [1:11, 1:11] 0 0.0452 0.0391 0.0978 0.1143 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
.. ..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
$ adjust: chr "none"
$ sym : logi TRUE
$ ci : NULL
$ Call : language psych::corr.test(x = M.cor, method = c("pearson", "kendall", "spearman"), adjust = "none", ci = F)
- attr(*, "class")= chr [1:2] "psych" "corr.test"
num [1:11, 1:11] 1 -0.991 -0.993 -0.956 0.939 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
num [1:11, 1:11] Inf -21.92 -25.4 -9.78 8.22 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
num [1:11, 1:11] 0.00 4.04e-09 1.09e-09 4.32e-06 1.78e-05 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...
..$ : chr [1:11] "mpg" "cyl" "disp" "hp" ...


My pseudocode about looping all three correlations with the test function
corrplot
, but it will not work because it goes through all 9 lists

for (i in p.mat.all) {
p.mat <- i
print("p.mat ===========")
print(i)

alpha <- 0.05
corrplot( M.cor,
method="color",
type="upper",
addCoefasPercent = TRUE,
tl.col = "black",
tl.pos = "td",
p.mat = p.mat, sig.level = alpha, insig = "blank",
order = "original"
)
}


Expected output: loop only
t
,
p
and
r
lists such that they can be passed to the test function
corrplot


R: 3.3.1

OS: Debian 8.5

Answer

Or with an *apply function:

lapply(p.mat.all[c("r","p","t")], function(x) {
  # x takes now first p.mat.all$r, then p.mat.all$p, etc
  print("p.mat ===========")
  print(x)    

  alpha <- 0.05 
  corrplot( M.cor,  
          method="color", 
          type="upper", 
          addCoefasPercent = TRUE, 
          tl.col = "black",
          tl.pos = "td", 
          p.mat = x, sig.level = alpha, insig = "blank", 
          order = "original"
  )
})