I am doing some describtive sequence analysis using the "TraMineR" library. I want to report my findings via R-Markdown in html format. For formating tables I use "kable" and "kableExtra".
To get the frequency and propotions of the most common sequences I use seqtab()
. The result is an stslist.freq
object. When I try to coerce it to a dataframe, the dataframe is not containing any frequencies and proportions.
I tried to print the results of seqtab()
and store this result again. This gives me the dataframe I desire. However there are two "problems" with that: (1) I don't understand what is happening here and it seems like a "dirty" trick, (2) as a result I also get the output of the print command in my final html document if I don't split the code in multiple chunks and disable the ouput in the specific chunk.
Here is some code to replicate the problem:
library("TraMineR")
#Data creation
data.long <- data.frame(
id=rep(1:50, each=4),
time = c(0,1,2,3),
status = sample(letters[1:2], 200, replace = TRUE),
weight=rep(runif(50, 0, 1), each=4)
)
#reshape
data.wide <- reshape(data.long, v.names = "status", idvar="id", direction="wide", timevar="time")
#sequence
sequence <- seqdef(data.wide,
var=c("status.0", "status.1", "status.2", "status.3"),
weights=data.wide$weight)
#frequencies of sequences
##doesn't work:
seqtab.df1 <- as.data.frame(seqtab(sequence))
##works:
seqtab.df2 <- print(seqtab(sequence))
I expect the dataframe to be the same as the one saved in seqtab.df2
, however either without using the print command or with "silently" (no output printed) using the print command.
Thank you very much for your help and let me know if I forgot something to make answering the question possible!
If you look at the class()
of the object returned by seqtab
, it has the type
class(seqtab(sequence))
# [1] "stslist.freq" "stslist" "data.frame"
so if we look at exactly, what's happening in the print statement for such an object we can get a clue what's going on
TraMineR:::print.stslist.freq
# function (x, digits = 2, width = 1, ...)
# {
# table <- attr(x, "freq")
# print(table, digits = digits, width = width, ...)
# }
# <bytecode: 0x0000000003e831f8>
# <environment: namespace:TraMineR>
We see that what it's really giving you is the "freq" attribute. You can extract this directly and skip the print()
attr(seqtab(sequence), "freq")
# Freq Percent
# a/3-b/1 4.283261 20.130845
# b/1-a/1-b/2 2.773341 13.034390
# a/2-b/1-a/1 2.141982 10.067073
# a/1-b/1-a/1-b/1 1.880359 8.837476
# a/1-b/2-a/1 1.723489 8.100203
# b/1-a/2-b/1 1.418302 6.665861
# b/2-a/1-b/1 1.365099 6.415813
# a/1-b/3 1.241644 5.835586
# a/1-b/1-a/2 1.164434 5.472710
# a/2-b/2 1.092656 5.135360