How can I create a parallel analysis scree in R?
Dataset Dput
structure(list(V1 = structure(c(4, 4, 2, 2, 2, 2, 2, 2, 4, 4,
2, 3, 2, 3, 4, 2, 2, 2, 3, 3, 2, 3, 1, 3, 3, 3, 3, 4, 1, 2, 4,
1, 2, 3, 2, 3, 1, 1, 2, 2, 4, 3, 2, 1, 2, 3, 3, 4, 3, 3, 2, 3,
1, 4, 3, 2, 3, 4, 1, 3, 3, 3, 2, 2, 1, 2, 3, 4, 4, 2, 4, 3, 2,
3, 3, 3, 3, 2, 4, 3, 3, 3, 2, 2, 3, 4, 2, 4, 4, 2, 2, 3, 3), format.spss = "F8.0"),
V2 = structure(c(4, 4, 3, 4, 3, 4, 3, 2, 4, 1, 3, 3, 3, 4,
3, 3, 2, 3, 4, 3, 1, 4, 2, 3, 4, 2, 4, 3, 3, 2, 3, 2, 3,
3, 4, 3, 3, 3, 3, 3, 3, 2, 4, 2, 2, 2, 4, 3, 4, 4, 2, 4,
2, 3, 3, 3, 3, 3, 4, 3, 3, 3, 3, 4, 3, 3, 4, 4, 4, 4, 4,
3, 4, 3, 3, 3, 4, 2, 4, 3, 4, 3, 3, 2, 3, 3, 4, 3, 4, 3,
4, 4, 3), format.spss = "F8.0"), V3 = structure(c(4, 4, 4,
4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3,
3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,
4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4), format.spss = "F8.0"),
V4 = structure(c(4, 4, 3, 4, 3, 4, 2, 1, 3, 2, 3, 1, 4, 4,
2, 3, 2, 2, 2, 4, 1, 2, 2, 2, 3, 2, 3, 2, 2, 1, 3, 1, 1,
2, 4, 1, 1, 2, 3, 2, 2, 1, 1, 1, 3, 2, 4, 3, 3, 3, 3, 3,
3, 4, 3, 1, 4, 3, 4, 3, 2, 3, 2, 1, 4, 1, 4, 1, 2, 4, 4,
4, 3, 3, 3, 2, 2, 1, 4, 3, 2, 3, 2, 1, 3, 4, 1, 2, 4, 3,
4, 2, 2), format.spss = "F8.0"), V5 = structure(c(3, 3, 3,
4, 3, 4, 3, 1, 1, 1, 1, 2, 1, 2, 2, 2, 1, 2, 2, 2, 3, 2,
2, 2, 2, 4, 2, 3, 2, 3, 4, 1, 4, 2, 3, 3, 2, 2, 3, 2, 2,
3, 3, 2, 3, 3, 3, 2, 2, 2, 3, 2, 3, 3, 2, 2, 3, 3, 2, 3,
2, 2, 3, 3, 3, 2, 3, 3, 3, 4, 3, 2, 3, 3, 3, 3, 3, 3, 4,
3, 3, 3, 3, 3, 3, 3, 3, 2, 3, 3, 4, 3, 3), format.spss = "F8.0"),
V6 = structure(c(4, 4, 3, 4, 3, 4, 4, 1, 3, 3, 3, 3, 2, 3,
4, 2, 4, 3, 3, 3, 3, 4, 4, 3, 3, 3, 4, 4, 4, 3, 4, 4, 3,
3, 3, 4, 2, 2, 3, 3, 3, 4, 2, 4, 3, 4, 4, 4, 3, 4, 2, 4,
3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 3, 1, 4, 4, 4, 4, 4, 4,
4, 3, 4, 4, 4, 4, 2, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 3,
4, 4, 4), format.spss = "F8.0"), V7 = structure(c(4, 4, 2,
4, 2, 4, 4, 3, 3, 3, 2, 2, 4, 4, 3, 3, 1, 4, 3, 3, 1, 2,
4, 3, 4, 2, 4, 4, 3, 3, 2, 2, 3, 2, 4, 3, 3, 3, 3, 3, 3,
1, 4, 3, 2, 2, 4, 3, 4, 4, 2, 4, 2, 3, 4, 3, 3, 3, 4, 3,
4, 4, 3, 4, 4, 3, 4, 4, 4, 4, 3, 4, 4, 4, 3, 3, 4, 3, 4,
3, 3, 3, 3, 2, 2, 4, 4, 4, 4, 2, 4, 4, 3), format.spss = "F8.0"),
V8 = structure(c(4, 4, 2, 1, 2, 1, 1, 1, 3, 3, 2, 3, 2, 3,
4, 2, 2, 2, 3, 3, 2, 3, 1, 3, 3, 3, 3, 4, 1, 2, 4, 1, 2,
3, 2, 3, 1, 1, 2, 2, 3, 1, 1, 1, 2, 3, 3, 4, 3, 3, 2, 3,
1, 3, 4, 2, 3, 4, 1, 3, 3, 3, 2, 2, 1, 2, 3, 4, 4, 2, 4,
3, 4, 4, 4, 4, 3, 2, 4, 3, 3, 3, 2, 2, 3, 4, 2, 4, 4, 2,
1, 3, 4), format.spss = "F8.0"), V9 = structure(c(4, 4, 4,
4, 4, 4, 4, 4, 3, 3, 2, 3, 3, 3, 3, 2, 3, 3, 2, 3, 4, 4,
4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 4, 3, 2, 4, 3, 4,
4, 4, 4, 4, 4, 3, 3, 3, 3, 4, 4, 4, 4, 4, 3, 4, 3, 2, 4,
3, 3, 4, 4, 4, 3, 4, 4, 4, 4, 4, 3, 4, 3, 4, 3, 4, 4, 4,
4, 3, 4, 4, 4, 4, 4, 3, 2, 4, 4, 4, 4, 4), format.spss = "F8.0"),
V10 = structure(c(4, 4, 2, 4, 2, 4, 3, 2, 3, 3, 3, 2, 4,
4, 2, 2, 1, 3, 4, 4, 1, 4, 2, 3, 3, 2, 4, 3, 2, 3, 3, 1,
3, 2, 4, 3, 2, 3, 3, 3, 3, 1, 2, 4, 2, 3, 4, 4, 3, 3, 2,
4, 2, 4, 3, 3, 4, 3, 4, 3, 4, 4, 4, 1, 4, 3, 3, 4, 3, 4,
4, 3, 3, 3, 3, 3, 4, 1, 4, 3, 3, 3, 3, 2, 3, 4, 4, 2, 4,
2, 4, 4, 3), format.spss = "F8.0"), V11 = structure(c(3,
3, 1, 4, 1, 4, 1, 1, 1, 1, 2, 1, 1, 1, 3, 2, 2, 2, 2, 1,
2, 3, 1, 2, 3, 3, 2, 1, 2, 2, 2, 3, 2, 2, 3, 2, 1, 2, 2,
1, 1, 4, 3, 1, 3, 2, 3, 1, 2, 1, 2, 1, 2, 2, 1, 2, 2, 3,
2, 2, 2, 2, 2, 2, 1, 1, 1, 3, 3, 4, 2, 1, 2, 2, 3, 3, 3,
3, 4, 3, 2, 3, 3, 2, 2, 2, 2, 1, 3, 1, 4, 1, 3), format.spss = "F8.0"),
V12 = structure(c(4, 4, 3, 2, 3, 2, 3, 1, 3, 3, 3, 3, 2,
3, 3, 2, 4, 3, 3, 4, 4, 3, 3, 4, 4, 3, 3, 3, 4, 3, 4, 4,
3, 3, 3, 4, 2, 2, 3, 3, 3, 4, 2, 4, 3, 4, 4, 4, 3, 4, 2,
4, 3, 3, 3, 3, 4, 3, 3, 2, 2, 1, 1, 3, 1, 4, 4, 4, 4, 4,
4, 4, 3, 3, 2, 2, 2, 2, 4, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4,
3, 2, 3, 4), format.spss = "F8.0")), class = c("tbl_df",
"tbl", "data.frame"), row.names = c(NA, -93L))
EFA Before Scree Plot
I have done the work of performing exploratory factor analysis on the data:
fa3 <- fa(hwk2,
nfactors = 3,
n.obs = 93,
rotate = "oblimin",
max.iter = 100)
fa3
Which gives me this:
MR1 MR3 MR2 h2 u2 com
V1 0.03 0.87 -0.05 0.77 0.23 1.0
V2 0.75 0.05 0.09 0.63 0.37 1.0
V3 0.13 0.06 0.67 0.53 0.47 1.1
V4 0.50 0.07 0.08 0.31 0.69 1.1
V5 0.03 -0.06 0.88 0.77 0.23 1.0
V6 0.00 0.47 0.32 0.37 0.63 1.8
V7 0.80 -0.08 -0.04 0.60 0.40 1.0
V8 0.05 0.88 -0.03 0.80 0.20 1.0
V9 -0.22 0.02 0.58 0.34 0.66 1.3
V10 0.75 0.10 0.01 0.63 0.37 1.0
V11 0.03 0.00 0.53 0.29 0.71 1.0
V12 -0.24 0.52 0.14 0.28 0.72 1.6
MR1 MR3 MR2
SS loadings 2.18 2.09 2.03
Proportion Var 0.18 0.17 0.17
Cumulative Var 0.18 0.36 0.53
Proportion Explained 0.35 0.33 0.32
Cumulative Proportion 0.35 0.68 1.00
With factor correlations of
MR1 MR3 MR2
MR1 1.00 0.32 0.19
MR3 0.32 1.00 0.15
MR2 0.19 0.15 1.00
Basic Scree
Making a normal scree plot from there is quite simple. I just add this to my script:
scree(hwk2,
pc=T,
factors = F,
main = "Scree Plot of Eigenvalues")
Which creates this:
What I Want
However, I want to graph simulated parallel analysis with it. In Jamovi this is super easy to accomplish:
However, I don't see an option for this so far. There is another version of scree I have tried fa.parallel but the legend comes out really strange:
fa.parallel(
hwk2,
n.obs = 93,
fm = "minres",
nfactors = 3,
main = "Parallel Analysis Scree Plots",
n.iter = 100,
error.bars = FALSE,
se.bars = FALSE,
SMC = FALSE,
ylabel = NULL,
show.legend = F,
sim = TRUE,
quant = .95,
use = "pairwise",
plot = TRUE,
correct = .5
)
I get either this if I remove the legend:
Or I get this annoying one with the legend:
Basically, I just need factor analysis and don't need principal components in the plot, but I can't figure out how to remove it.
Solution
The only problem is that there are Heywood cases, so the fa analysis isn't trustworthy.
library(psych)
fa.parallel(
hwk2,
n.obs = 93,
fa = "fa", # you want only "fa", not "pc"
show.legend = TRUE, # show legend
fm = "minres",
nfactors = 3,
main = "Parallel Analysis Scree Plots",
n.iter = 100,
error.bars = FALSE,
se.bars = FALSE,
SMC = FALSE,
ylabel = NULL,
sim = TRUE,
quant = .95,
use = "pairwise",
plot = TRUE,
correct = .5
)
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