looking for some help with data manipulation in R. I have data in the following format;
ID L1 L2 L3
1 BBCBCACCBCB CBCBBBB BEBBBAAB
2 BBCBCCCCBCB CBCCCBC BBAACCCB
3 BBCBCACCBCB CBCBBBB BEBBBAAB
4 BBCBCACCBCB CBCBBBB BEBBBAAB
5 BBCBACBCCCB BBCCCBC BBCBAAAAB
6 BBCBBCCBBCB BBCBCEB BBBBCAACB
7 BBCBBCCBBCB BBCBCEB BBBBCAACB
8
9 BBCBCACCBCB CBCBBBB BEBBBAAB
10 BBCBBCCBBCB BBCBCEB BBBBCAACB
11 BBCBBCCBBCB BBCBCEB BBBBCAACB
The values in each column will be strings of varying length. I want an R function that for each column above, will
1) generate a dynamic number of columns based on the maximum length of any string in the column e.g. L1 max length = 11, therefore 11 new columns each labelled L1_1:L1_11
2) then split the strings into triplets, e.g.
ID L1 L2 L3 L1_1 L1_2 L1_3 L1_4 L1_5 L1_6 L1_7 L1_8 L1_9
1 BBCBCACCBCB CBCBBBB BEBBBAAB BBC BCB CBC BCA CAC ACC CCB CBC BCB
3) perform a calculation on this triplet i.e. (number of 'a' * 1) + (number of 'b' * 3) + (number of 'c'*7) in the triplet.
4) return the value of this calculation in the new column.
I have found that the code suggested does exactly what I need when run for columns L1, L2 but does not work for L3. The error I receive is 'Error in as.data.frame.matrix(passed.args[[i]], stringsAsFactors = st : missing value where TRUE/FALSE needed'
Any ideas? Thanks very much.
EDIT
dput(df):
structure(list(ID = 1:11, L1 = structure(c(4L, 5L, 4L, 4L, 2L, 3L, 3L, 1L, 4L, 3L, 3L), .Label = c("", "BBCBACBCCCB","BBCBBCCBBCB","BBCBCACCBCB", "BBCBCCCCBCB"), class = "factor"), L2 = structure(c(4L, 5L, 4L, 4L, 3L, 2L, 2L, 1L, 4L, 2L, 2L), .Label = c("","BBCBCEB","BBCCCBC", "CBCBBBB", "CBCCCBC"), class = "factor"), L3 = structure(c(5L,2L, 5L, 5L, 4L, 3L, 3L, 1L, 5L, 3L, 3L), .Label = c("", "BBAACCCB", "BBBBCAACB", "BBCBAAAAB", "BEBBBAAB"), class = "factor")), .Names = c("ID", "L1", "L2", "L3"), class = "data.frame", row.names = c(NA,-11L))
structure(list(ID = 1:11, L1 = structure(c(4L, 5L, 4L, 4L, 2L, 3L, 3L, 1L, 4L, 3L, 3L), .Label = c("", "BBCBACBCCCB","BBCBBCCBBCB","BBCBCACCBCB", "BBCBCCCCBCB"), class = "factor"), L2 = structure(c(4L, 5L, 4L, 4L, 3L, 2L, 2L, 1L, 4L, 2L, 2L), .Label = c("","BBCBCEB","BBCCCBC", "CBCBBBB", "CBCCCBC"), class = "factor"), L3 = structure(c(5L,2L, 5L, 5L, 4L, 3L, 3L, 1L, 5L, 3L, 3L), .Label = c("", "BBAACCCB", "BBBBCAACB", "BBCBAAAAB", "BEBBBAAB"), class = "factor")), .Names = c("ID", "L1", "L2", "L3"), class = "data.frame", row.names = c(NA,-11L))
#DATA
df = structure(list(ID = 1:4, L1 = c("abbbcc", "aabacd", "abbda",
"bbad")), .Names = c("ID", "L1"), class = "data.frame", row.names = c(NA,
-4L))
#Go through the strings and split into subgroups of 3 characters.
#Put the substrings in a list
temp = lapply(df$L1, function(x) sapply(3:nchar(x), function(i) substr(x, i-2, i)))
#Obtain the length of the subgroup with the most triplets
temp_l = max(lengths(temp))
#Subset the subgroups from 1 to temp_l so that remianing values are NA
cbind(df, setNames(data.frame(do.call(rbind, lapply(temp, function(a)
a[1:temp_l]))), nm = paste0("L1_",1:temp_l)))
# ID L1 L1_1 L1_2 L1_3 L1_4
#1 1 abbbcc abb bbb bbc bcc
#2 2 aabacd aab aba bac acd
#3 3 abbda abb bbd bda <NA>
#4 4 bbad bba bad <NA> <NA>
If you want calculation based on triplets, run the following before doing the cbind step
temp_L1 = lapply(df$L1, function(x) sapply(3:nchar(x), function(i) substr(x, i-2, i)))
temp_L1_length = max(lengths(temp_L1))
temp_L1 = lapply(temp_L1, function(x)
sapply(x, function(y){
num_a = unlist(gregexpr(pattern = "a", text = y))
num_a = sum(num_a > 0) #length of positive match
num_b = unlist(gregexpr(pattern = "b", text = y))
num_b = sum(num_b > 0)
num_c = unlist(gregexpr(pattern = "c", text = y))
num_c = sum(num_c > 0)
num_a * 1 + num_b * 3 + num_c * 7
})
)
temp_L1 = setNames(data.frame(do.call(rbind, lapply(temp_L1, function(a)
a[1:temp_L1_length]))), nm = paste0("L1_",1:temp_L1_length))
#REPEAT FOR L2, L3, ...
cbind(df, temp_L1) #Run cbind(df, temp_L1, temp_L2, ...)
# ID L1 L1_1 L1_2 L1_3 L1_4
#1 1 abbbcc 7 9 13 17
#2 2 aabacd 5 5 11 8
#3 3 abbda 7 6 4 NA
#4 4 bbad 7 4 NA NA
UPDATE
You could create a function and use it like shown below
#FUNCTION
foo = function(data, column){
temp_L1 = lapply(as.character(data[[column]]), function(x) sapply(3:nchar(x), function(i) substr(x, i-2, i)))
temp_L1_length = max(lengths(temp_L1))
temp_L1 = lapply(temp_L1, function(x)
sapply(x, function(y){
num_a = unlist(gregexpr(pattern = "a", text = y, ignore.case = TRUE))
num_a = sum(num_a > 0) #length of positive match
num_b = unlist(gregexpr(pattern = "b", text = y, ignore.case = TRUE))
num_b = sum(num_b > 0)
num_c = unlist(gregexpr(pattern = "c", text = y, ignore.case = TRUE))
num_c = sum(num_c > 0)
num_a * 1 + num_b * 3 + num_c * 7
})
)
temp_L1 = setNames(data.frame(do.call(rbind, lapply(temp_L1, function(a)
a[1:temp_L1_length]))), nm = paste0(column,"_",1:temp_L1_length))
return(temp_L1)
}
#USING ON NEW DATA
cbind(df, do.call(cbind, lapply(colnames(df)[-1], function(x) foo(data = df, column = x))))