Add multiple rows based on column string R - r

Question

I have a data frame that looks like this...
patient_ID CBC CBN totindex samp index
120 1007 BLOQ BLOQ 7 8 1
121 1007 BLOQ BLOQ 8 9 1
122 1007 BLOQ BLOQ 9 10 1
123 1007 BLOQ BLOQ 10 11 1
124 1007 BLOQ BLOQ 11 12 1
125 1007 BLOQ BLOQ 12 15 4
126 1007 BLOQ BLOQ 13 16 1
127 1007 BLOQ BLOQ 14 17 1
128 1007 BLOQ BLOQ 15 18 1
129 1007 BLOQ BLOQ 16 19 1
130 1007 BLOQ BLOQ 17 20 1
I created the index column to denote any rows in the samp column to show where the previous row is not in numerical order. For example, if the numbers are a difference of one, I make the index of the row 3. In this case, there was a difference of 2 in the samp column between rows 124 and 125. So I placed a 4. I do this for other examples as well like a difference of 3 or 4 is indexed as a 5 or 6.
How can I insert 1 or 2 or 3 or 4 new blank lines in between the discrepancies?
In this example, I would like this output...
patient_ID CBC CBN totindex samp index
120 1007 BLOQ BLOQ 7 8 1
121 1007 BLOQ BLOQ 8 9 1
122 1007 BLOQ BLOQ 9 10 1
123 1007 BLOQ BLOQ 10 11 1
124 1007 BLOQ BLOQ 11 12 1
125 1007 0 0 0 13 1
126 1007 0 0 0 14 1
127 1007 BLOQ BLOQ 12 15 1
128 1007 BLOQ BLOQ 13 16 1
129 1007 BLOQ BLOQ 14 17 1
130 1007 BLOQ BLOQ 15 18 1
131 1007 BLOQ BLOQ 16 19 1
132 1007 BLOQ BLOQ 17 20 1
Thus, adding 2 rows equal to 0 before the 4 index, keep the patient_ID, remove the 4, and add the 13 and 14 to the samp column.
I have tried a for loop like this...
nidx4 <- as.numeric(rownames(df[grep("4", df$index), ]))
dfnew <- data.frame()
for (idx in 1:length(nidx4)) {
if (idx==1){
df1 = df[1:(nidx4[idx]-1),]
}
else if (idx == length(nidx4)) {
df1 = df[nidx4[idx-1]:nrow(df),]
}
else {
df1 = df[(nidx4[idx-1]):(nidx4[idx]-1),]
}
df1[nrow(df1)+1,] = 0
df1[nrow(df1)+1,] = 0
df1[nrow(df1)-1,21] = df1[nrow(df1)-2,21]+1
df1[nrow(df1),21] = df1[nrow(df1)-1,21]+1
dfnew = rbind(dfnew,df1)
}
for (row in 1:nrow(dfnew)){
if (dfnew[row,"index"] == 0) {dfnew[row,"index"] = 1}
if (dfnew[row,"index"] == 4) {dfnew[row,"index"] = 1}
}
rownames(dfnew) <- NULL
df <- dfnew
But that only accounts for the first few indices. The last iteration of 4 in the index is not accounted for. Also, I had to change the loop code to this because, before, it was stopping at the last iteration of 4 and not including the rest of the data frame.
Any help would be great.
Edit + Answer
This worked for me by adding in all of the column names that I wanted to iterate over.
dfnew <- complete(df, patient_ID, samp = full_seq(samp, period = 1),
fill = list("Sample_Name_(run_ID)" = "no_sample",
Sample_Name = "no_sample", THC = "0", OH_THC = "0",
THC_COOH = "0", THC_COO_gluc = "0", THC_gluc = "0",
CBD = "0", "6aOH_CBD" = "0", "7OH_CBD" = "0",
"6bOH_CBD" = "0", CBD_COOH = "0", CBD_gluc = "0",
CBC = "0", CBN = "0", CBG = "0", THCV = "0", CBDV = "0",
totindex = 0,
index = 1)) %>%
mutate(index = 1)

Answer 1

We may use complete
library(tidyr)
library(dplyr)
complete(df1, patient_ID, samp = full_seq(samp, period = 1),
fill = list(CBC = "0", CBN = "0", totindex = 0, index = 1)) %>%
mutate(index = 1)
-output
# A tibble: 13 × 6
patient_ID samp CBC CBN totindex index
<int> <dbl> <chr> <chr> <int> <dbl>
1 1007 8 BLOQ BLOQ 7 1
2 1007 9 BLOQ BLOQ 8 1
3 1007 10 BLOQ BLOQ 9 1
4 1007 11 BLOQ BLOQ 10 1
5 1007 12 BLOQ BLOQ 11 1
6 1007 13 0 0 0 1
7 1007 14 0 0 0 1
8 1007 15 BLOQ BLOQ 12 1
9 1007 16 BLOQ BLOQ 13 1
10 1007 17 BLOQ BLOQ 14 1
11 1007 18 BLOQ BLOQ 15 1
12 1007 19 BLOQ BLOQ 16 1
13 1007 20 BLOQ BLOQ 17 1
Or use
complete(df1, patient_ID, samp = full_seq(samp, period = 1)) %>%
mutate(across(CBC:CBN, replace_na, "0"),
totindex = replace_na(totindex, 0), index = 1)
Or use
complete(df1, patient_ID, samp = full_seq(samp, period = 1),
fill = setNames(c(as.list(rep('0', 2)), 0, 1),
names(df1)[c(2:4, 6)]))
data
df1 <- structure(list(patient_ID = c(1007L, 1007L, 1007L, 1007L, 1007L,
1007L, 1007L, 1007L, 1007L, 1007L, 1007L), CBC = c("BLOQ", "BLOQ",
"BLOQ", "BLOQ", "BLOQ", "BLOQ", "BLOQ", "BLOQ", "BLOQ", "BLOQ",
"BLOQ"), CBN = c("BLOQ", "BLOQ", "BLOQ", "BLOQ", "BLOQ", "BLOQ",
"BLOQ", "BLOQ", "BLOQ", "BLOQ", "BLOQ"), totindex = 7:17, samp = c(8L,
9L, 10L, 11L, 12L, 15L, 16L, 17L, 18L, 19L, 20L), index = c(1L,
1L, 1L, 1L, 1L, 4L, 1L, 1L, 1L, 1L, 1L)), class = "data.frame",
row.names = c("120",
"121", "122", "123", "124", "125", "126", "127", "128", "129",
"130"))