Looping through variable names in R - r

Question

I'm having a looping issue. It should be simple to solve, but "R for Stata Users" (I've coded in Stata for a couple of years), Roger Peng's videos, and Google don't seem to be helping me. Can one of you please explain to me what I'm doing wrong?
I'm trying to write a loop that run through the 'thresholds' dataframe to pull out information from three sets of columns. I can do what I want to do by writing the same segment of code three times, but as the code gets more complicated, this will become quite cumbersome.
Here is a sample of 'thresholds' (see dput output below, added by a friendly reader):
threshold_1_name threshold_1_dir threshold_1_value
1 overweight > 25
2 possible malnutrition < 31
3 Q1 > 998
4 Q1 > 998
5 Q1 > 998
6 Q1 > 998
threshold_1_units threshold_2_name threshold_2_dir threshold_2_value threshold_2_units
1 kg/m^2 obese > 30 kg/m^2
2 cm <NA> > NA
3 <NA> Q3 > 998
4 Q3 > 998
5 Q3 > 998
6 Q3 > 998
This code does what I want to do:
newvars1 <- paste(thresholds$varname, thresholds$threshold_1_name, sep = "_")
noval <- is.na(thresholds$threshold_1_value)
newvars1 <- newvars1[!noval]
newvars2 <- paste(thresholds$varname, thresholds$threshold_2_name, sep = "_")
noval <- is.na(thresholds$threshold_2_value)
newvars2 <- newvars2[!noval]
newvars3 <- paste(thresholds$varname, thresholds$threshold_3_name, sep = "_")
noval <- is.na(thresholds$threshold_3_value)
newvars3 <- newvars3[!noval]
And here is how I am trying to loop:
variables <- NULL
for (i in 1:3) {
valuevar <- paste("threshold", i, "value", sep = "_")
namevar <- paste("threshold", i, "name", sep = "_")
newvar <- paste("varnames", i, sep = "")
for (j in 1:length(thresholds$varname)) {
check <- is.na(thresholds[valuevar[j]])
if (check == FALSE) {
newvars <- paste(thresholds$varname, thresholds[namevar], sep = "_")
}
}
variables <- c(variables, newvars)
}
And here is the error I am receiving:
Error: unexpected '}' in "}"
I think something about the way I am calling the 'i' is messing things up, but I'm not sure how to do it correctly. My Stata habits using locals are really biting me in the butt as I switch to R.
EDIT to add dput output, by a friendly reader:
thresholds <- structure(list(varname = structure(1:6, .Label = c("varA", "varB",
"varC", "varD", "varE", "varF"), class = "factor"), threshold_1_name = c("overweight",
"possible malnutrition", "Q1", "Q1", "Q1", "Q1"), threshold_1_dir = c(">",
"<", ">", ">", ">", ">"), threshold_1_value = c(25L, 31L, 998L,
998L, 998L, 998L), threshold_1_units = c("kg/m^2", "cm", NA,
NA, NA, NA), threshold_2_name = c("obese", "<NA>", "Q3", "Q3",
"Q3", "Q3"), threshold_2_dir = c(">", ">", ">", ">", ">", ">"
), threshold_2_value = c(30L, NA, 998L, 998L, 998L, 998L), threshold_2_units = c("kg/m^2",
"cm", NA, NA, NA, NA)), .Names = c("varname", "threshold_1_name",
"threshold_1_dir", "threshold_1_value", "threshold_1_units",
"threshold_2_name", "threshold_2_dir", "threshold_2_value", "threshold_2_units"
), row.names = c(NA, -6L), class = "data.frame")

Answer 1

The first problem I see is in if(check = "FALSE") that's an assignment = if you're testing a condition it needs to be ==. Also, quoting the word "FALSE" means you're testing a variable for the string value (literally the word FALSE), not the logical value, which is FALSE without the quotations.
The second problem has been rightly pointed out by #BlueMagister, you're missing ) at the end of for (j in 1:length(...)) {
See # bad!
for (j in 1:length(thresholds$varname)) {
check <- is.na(thresholds[valuevar[j]])
if (check = "FALSE") { # bad!
newvars <- paste(thresholds$varname, thresholds[namevar], sep = "_")
}
}
See # good!
for (j in 1:length(thresholds$varname)) {
check <- is.na(thresholds[valuevar[j]])
if (check == FALSE) { # good!
newvars <- paste(thresholds$varname, thresholds[namevar], sep = "_")
}
}
But because it's an if statement you can use really simple logic, especially on logicals (TRUE / FALSE values).
See # better!
for (j in 1:length(thresholds$varname)) {
check <- is.na(thresholds[valuevar[j]])
if (!check) { # better!
newvars <- paste(thresholds$varname, thresholds[namevar], sep = "_")
}
}

Answer 2

There is obviously a missing bracket in you for loop. You should consider to use an editor that supports brace matching to avoid those kind of errors.

Answer 3

I think the easiest thing to do would be to just write a function that does what your desired non-looping code does. For reference, here's the output from that code, using the dput output from the edit to your question.
> newvars1 <- paste(thresholds$varname, thresholds$threshold_1_name, sep = "_")
> newvars1 <- newvars1[!is.na(thresholds$threshold_1_value)]
> newvars2 <- paste(thresholds$varname, thresholds$threshold_2_name, sep = "_")
> newvars2 <- newvars2[!is.na(thresholds$threshold_2_value)]
> c(newvars1, newvars2)
[1] "varA_overweight" "varB_possible malnutrition"
[3] "varC_Q1" "varD_Q1"
[5] "varE_Q1" "varF_Q1"
[7] "varA_obese" "varC_Q3"
[9] "varD_Q3" "varE_Q3"
[11] "varF_Q3"
Here's what that function would look like:
unlist(lapply(1:2, function(k) {
newvars <- paste(thresholds$varname,
thresholds[[paste("threshold", k, "name", sep="_")]], sep = "_")
newvars <- newvars[!is.na(thresholds[[paste("threshold", k, "value", sep="_")]])]
}))
# [1] "varA_overweight" "varB_possible malnutrition"
# [3] "varC_Q1" "varD_Q1"
# [5] "varE_Q1" "varF_Q1"
# [7] "varA_obese" "varC_Q3"
# [9] "varD_Q3" "varE_Q3"
#[11] "varF_Q3"
I tried to figure out what was going on in your loop but there was a lot in there that didn't make sense to me; here's how I'd write it if I was going to loop in that way.
variables <- NULL
for (i in 1:2) {
valuevar <- paste("threshold", i, "value", sep = "_")
namevar <- paste("threshold", i, "name", sep = "_")
newvars <- c()
for (j in 1:nrow(thresholds)) {
if (!is.na(thresholds[[valuevar]][j])) {
newvars <- c(newvars, paste(thresholds$varname[j],
thresholds[[namevar]][j], sep = "_"))
}
}
variables <- c(variables, newvars)
}
variables