How to prevent coercion to list in R - r

Question

I am trying to remove all NA values from two columns in a matrix and make sure that neither column has a value that the other doesn't.
code:
data <- dget(file)
dependent <- data[,"chroma"]
independent <- data[,"mass..Pantheria."]
names(independent) <- names(dependent) <- rownames(data)
for (name in rownames(data)) {
if(is.na(dependent[name])) {
independent$name <- NULL
dependent$name <- NULL
}
if(is.na(independent[name])) {
independent$name <- NULL
dependent$name <- NULL
}
}
print(dput(independent))
print(dput(dependent))
I am brand new to R and am trying to perform this task with a for loop. However, when I delete a section by assigning NULL I receive the following warning:
1: In independent$Aeretes_melanopterus <- NULL : Coercing LHS to a list
2: In dependent$name <- NULL : Coercing LHS to a list
No elements are deleted and independent and dependent retain all their original rows.
file (input):
structure(list(chroma = c(7.443501276, 10.96156313, 13.2987235,
17.58110922, 13.4991105), mass..Pantheria. = c(NA, 126.57, NA,
160.42, 250.57)), .Names = c("chroma", "mass..Pantheria."), class = "data.frame", row.names = c("Aeretes_melanopterus",
"Ammospermophilus_harrisii", "Ammospermophilus_insularis", "Ammospermophilus_nelsoni",
"Atlantoxerus_getulus"))
chroma mass..Pantheria.
Aeretes_melanopterus 7.443501 NA
Ammospermophilus_harrisii 10.961563 126.57
Ammospermophilus_insularis 13.298723 NA
Ammospermophilus_nelsoni 17.581109 160.42
Atlantoxerus_getulus 13.499111 250.57
desired output:
structure(list(chroma = c(10.96156313, 17.58110922, 13.4991105
), mass..Pantheria. = c(126.57, 160.42, 250.57)), .Names = c("chroma",
"mass..Pantheria."), class = "data.frame", row.names = c("Ammospermophilus_harrisii",
"Ammospermophilus_nelsoni", "Atlantoxerus_getulus"))
chroma mass..Pantheria.
Ammospermophilus_harrisii 10.96156 126.57
Ammospermophilus_nelsoni 17.58111 160.42
Atlantoxerus_getulus 13.49911 250.57
structure(c(126.57, 160.42, 250.57), .Names = c("Ammospermophilus_harrisii",
"Ammospermophilus_nelsoni", "Atlantoxerus_getulus"))
Ammospermophilus_harrisii Ammospermophilus_nelsoni Atlantoxerus_getulus
126.57 160.42 250.57
structure(c(10.96156313, 17.58110922, 13.4991105), .Names = c("Ammospermophilus_harrisii",
"Ammospermophilus_nelsoni", "Atlantoxerus_getulus"))
Ammospermophilus_harrisii Ammospermophilus_nelsoni Atlantoxerus_getulus
10.96156 17.58111 13.49911

Answer 1

Looks like you want to omit rows from your data where chroma or mass..Pantheria are NA. Here's a quick way to do it:
data = data[!is.na(data$chroma) & !is.na(data$mass..Pantheria.), ]
I'm not sure why you are breaking independent and dependent out separately, but after filtering out bad observations is a good time to do it.
Since those are your only two columns, this is equivalent to omitting rows from your data frame that have any NA values, so you can use a shortcut like this:
data = na.omit(data)
If you want to keep a "pristine" copy of your raw data, simply change the name of the result:
data_no_na = na.omit(data)
# or
data = data[!is.na(data$chroma) & !is.na(data$mass..Pantheria.), ]
As to what's wrong with your code, $ is used for extracting columns from a data frame, but you're trying to use it for a named vector (since you've already extracted the columns), which doesn't work. Even then, $ only works with a literal string, you can't use it with a variable. For data frames, you need to use brackets to extract columns stored in variables. For example, the built-in mtcars data has a column called "mpg":
# these work:
mtcars$mpg
mtcars[, "mpg"]
my_col = "mpg"
mtcars[, my_col]
mtcars$my_col ## does not work, need to use brackets!
You can never use $ with row names in a data frame, only column names.