I'm trying to perform calculations on different elements in a matrix in R. My Matrix is 18x18 and I would like to get e.g. the mean of each 6x6 array (which makes 9 arrays in total). My desired arrays would be:
A1 <- df[1:6,1:6]
A2 <- df[1:6,7:12]
A3 <- df[1:6,13:18]
B1 <- df[7:12,1:6]
B2 <- df[7:12,7:12]
B3 <- df[7:12,13:18]
C1 <- df[13:18,1:6]
C2 <- df[13:18,7:12]
C3 <- df[13:18,13:18]
The matrix looks like this:
5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90
5 14 17 9 10 8 4 10 12 18 9 13 14 NA NA 19 15 10 10
10 30 32 23 27 17 28 25 12 28 29 28 26 19 25 34 24 11 17
15 16 16 16 9 17 27 17 16 30 13 18 13 15 13 19 8 7 9
20 15 12 18 18 18 6 4 6 9 11 10 10 13 11 8 10 15 15
25 7 13 21 7 3 5 2 5 5 4 3 2 3 5 2 1 5 6
30 5 9 1 7 7 4 4 12 8 9 2 0 5 2 1 0 2 6
35 3 0 2 0 0 4 4 7 4 4 5 2 0 0 1 0 0 0
40 0 4 0 0 0 1 3 9 10 10 1 0 0 0 1 0 1 0
45 0 0 0 0 0 3 10 9 17 9 1 0 0 0 0 0 0 0
50 0 0 2 0 0 0 2 8 20 0 0 0 0 0 1 0 0 0
55 0 0 0 0 0 0 7 3 21 0 0 0 0 0 0 0 0 0
60 0 0 0 0 3 4 10 2 2 0 0 1 0 0 0 0 0 0
65 0 0 0 0 0 4 8 4 8 11 0 0 0 0 0 0 0 0
70 0 0 0 0 0 6 2 5 14 0 0 0 0 0 0 0 0 0
75 0 0 0 0 0 4 0 5 9 0 0 0 0 0 0 0 0 0
80 0 0 0 0 0 4 4 0 4 2 0 0 0 0 0 0 0 0
85 0 0 0 0 0 0 0 4 1 1 0 0 0 0 0 0 0 0
90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Is there a clean way to solve this issue with a loop?
Thanks a lot in advance,
Paul
Given your matrix, e.g.
x <- matrix(1:(18*18), ncol=18)
Try, for example for sub matrices of 6
step <- 6
nx <- nrow(x)
if((nx %% step) != 0) stop("nx %% step should be 0")
indI <- seq(1, nx, by=step)
nbStep <- length(indI)
for(Col in 1:nbStep){
for(Row in 1:nbStep){
name <- paste0(LETTERS[Col],Row)
theCol <- indI[Col]:(indI[Col]+step-1)
theRow <- indI[Row]:(indI[Row]+step-1)
assign(name, sum(x[theCol, theRow]))
}
}
You'll get your results in A1, A2, A3...
This is the idea. Twist the code for non square matrices, different size of sub matrices, ...
Here's one way:
# generate fake data
set.seed(47)
n = 18
m = matrix(rpois(n * n, lambda = 5), nrow = n)
# generate starting indices
n_array = 6
start_i = seq(1, n, by = n_array)
arr_starts = expand.grid(row = start_i, col = start_i)
# calculate sums
with(arr_starts, mapply(function(x, y) sum(m[(x + 1:n_array) - 1, (y + 1:n_array) - 1]), row, col))
# [1] 158 188 176 201 188 201 197 206 204
Hi stack overflow community,
I'm relatively new to R (9 months) and this is my first stack overflow question with reprex and would really appreciate any help. I mainly use tidyverse although I am open to base R solutions.
Problem:
I have ~21,000 rows of symptom data with >10 variables per day. I would like to be able to classify "exacerbations" of a disease (in this case chest infections in lung disease) by using rules to define the start and end of the episode so that I can later calculate duration of episodes, type of episode (this depends on the combination of symptoms) and treatment received. As with any data set involving patients there are missing values. I have imputed from the most recent day if less than 2 days of data is missing.
The below code is a simplified, made up example involving only 1 symptom.
Exacerbation Rule:
Start of exacerbation = 2 days of worse symptoms (>= 3)
Resolution of exacerbation = 5 days with normal breathing (<=2)
I would ideally want to be able to identify all days when an exacerbation is happening too.
Here is the data:
#load packages
library(tidyverse)
#load data
id <- "A"
day <- c(1:50)
symptom <- c(2,2,2,2,2,2,2,2,2,2,2,3,2,2,2,2,NA,NA,NA,2,2,2,3,3,3,4,4,3,3,2,3,2,2,3,3,2,2,2,2,2,2,3,2,2,2,2,2,3,2,2)
df <- data.frame(id,day,symptom)
#Data Dictionary
#Symptom: 1 = Better than usual, 2 = Normal/usual, 3 = Worse than usual, 4 = Much worse than usual
What I have tried:
I have tried to approach this by using a combination of lag() and lead() with conditional statements case_when() and ifelse().
df %>%
mutate_at(vars("symptom"), #used for more variables within vars() argument
.funs = list(lead1 = ~ lead(., n = 1),
lead2 = ~ lead(., n = 2),
lead3 = ~ lead(., n = 3),
lead4 = ~ lead(., n = 4),
lead5 = ~ lead(., n = 5),
lag1 = ~ lag(., n = 1),
lag2 = ~ lag(., n = 2),
lag3 = ~ lag(., n = 3))) %>%
mutate(start = case_when(symptom <= 2 ~ 0,
symptom >= 3 ~
ifelse(symptom >= lag2 & symptom <= lag1,1,0)),
end = case_when(symptom >=3 ~
ifelse(lead1 <=2 &
lead2 <=2 &
lead3 <=2 &
lead4 <=2 &
lead5 <=2,1,0)))
My main issue is that of complexity. As I build in more symptoms and rules I have to refer to different variables that have ifelse()/case_when() statements within it. I am sure there is a more elegant solution to my problem.
The other issue is that during an "exacerbation" the exacerbation_start variable should only be used at the start and not during the episode. Similarly for exacerbation_end it would only be applicable when an exacerbation is already happening. I have tried using ifelse() statements to refer to when an exacerbation is happening but not been able to get this to work and obey the rule I desire.
The output I would like is:
id day symptom start end exacerbation
1 A 1 2 0 0 0
2 A 2 2 0 0 0
3 A 3 2 0 0 0
4 A 4 2 0 0 0
5 A 5 2 0 0 0
6 A 6 2 0 0 0
7 A 7 2 0 0 0
8 A 8 2 0 0 0
9 A 9 2 0 0 0
10 A 10 2 0 0 0
11 A 11 2 0 0 0
12 A 12 3 0 0 0
13 A 13 2 0 0 0
14 A 14 2 0 0 0
15 A 15 2 0 0 0
16 A 16 2 0 0 0
17 A 17 NA 0 0 0
18 A 18 NA 0 0 0
19 A 19 NA 0 0 0
20 A 20 2 0 0 0
21 A 21 2 0 0 0
22 A 22 2 0 0 0
23 A 23 3 0 0 0
24 A 24 3 1 0 1
25 A 25 3 0 0 1
26 A 26 4 0 0 1
27 A 27 4 0 0 1
28 A 28 3 0 0 1
29 A 29 3 0 0 1
30 A 30 2 0 0 1
31 A 31 3 0 0 1
32 A 32 2 0 0 1
33 A 33 2 0 0 1
34 A 34 3 0 0 1
35 A 35 3 0 1 1
36 A 36 2 0 0 0
37 A 37 2 0 0 0
38 A 38 2 0 0 0
39 A 39 2 0 0 0
40 A 40 2 0 0 0
41 A 41 2 0 0 0
42 A 42 3 0 0 0
43 A 43 2 0 0 0
44 A 44 2 0 0 0
45 A 45 2 0 0 0
46 A 46 2 0 0 0
47 A 47 2 0 0 0
48 A 48 3 0 0 0
49 A 49 2 0 0 0
50 A 50 2 0 0 0
I look forward to your replies!
EDIT
I have added 50 more rows of data to simulate multiple exacerbations and the issue with right censoring and NAs. I have also included a second participant "B" to see if this is a reason for issues.
id <- c("A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A",
"A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A",
"A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A","A",
"B","B","B","B","B","B","B","B","B","B","B","B","B","B","B","B",
"B","B","B","B","B","B","B","B","B","B","B","B","B","B","B","B",
"B","B","B","B","B","B","B","B","B","B","B","B","B","B","B","B","B","B")
day <- c(1:50,1:50)
symptom <- c(2,3,3,3,3,2,2,2,2,2,2,3,2,2,2,2,NA,NA,NA,2,2,2,3,3,3,4,4,3,3,2,3,2,2,3,3,2,2,2,2,2,2,3,2,2,2,2,2,3,2,2, 2,2,2,2,2,2,3,2,3,3,2,3,2,3,2,2,2,2,2,2,3,3,3,3,NA,NA,NA,2,2,2,3,2,2,2,2,2,3,2,2,3,NA,NA,NA,3,3,3,3,3,3,2)
df <- data.frame(id,day,symptom)
id day symptom start end exacerbation censor
1 A 1 2 0 0 0 0
2 A 2 3 1 0 1 0
3 A 3 3 0 0 1 0
4 A 4 3 0 0 1 0
5 A 5 3 0 1 1 0
6 A 6 2 0 0 0 0
7 A 7 2 0 0 0 0
8 A 8 2 0 0 0 0
9 A 9 2 0 0 0 0
10 A 10 2 0 0 0 0
11 A 11 2 0 0 0 0
12 A 12 3 0 0 0 0
13 A 13 2 0 0 0 0
14 A 14 2 0 0 0 0
15 A 15 2 0 0 0 0
16 A 16 2 0 0 0 0
17 A 17 NA 0 0 0 0
18 A 18 NA 0 0 0 0
19 A 19 NA 0 0 0 0
20 A 20 2 0 0 0 0
21 A 21 2 0 0 0 0
22 A 22 2 0 0 0 0
23 A 23 3 1 0 1 0
24 A 24 3 0 0 1 0
25 A 25 3 0 0 1 0
26 A 26 4 0 0 1 0
27 A 27 4 0 0 1 0
28 A 28 3 0 0 1 0
29 A 29 3 0 0 1 0
30 A 30 2 0 0 1 0
31 A 31 3 0 0 1 0
32 A 32 2 0 0 1 0
33 A 33 2 0 0 1 0
34 A 34 3 0 0 1 0
35 A 35 3 0 0 1 0
36 A 36 2 0 0 1 0
37 A 37 2 0 0 1 0
38 A 38 2 0 0 1 0
39 A 39 2 0 0 1 0
40 A 40 2 0 0 1 0
41 A 41 2 0 1 1 0
42 A 42 3 0 0 0 0
43 A 43 2 0 0 0 0
44 A 44 2 0 0 0 0
45 A 45 2 0 0 0 0
46 A 46 2 0 0 0 0
47 A 47 2 0 0 0 0
48 A 48 3 0 0 0 0
49 A 49 2 0 0 0 0
50 A 50 2 0 0 0 0
51 B 1 2 0 0 0 0
52 B 2 2 0 0 0 0
53 B 3 2 0 0 0 0
54 B 4 2 0 0 0 0
55 B 5 2 0 0 0 0
56 B 6 2 0 0 0 0
57 B 7 3 0 0 0 0
58 B 8 2 0 0 0 0
59 B 9 3 0 0 0 0
60 B 10 3 1 0 1 0
61 B 11 2 0 0 1 0
62 B 12 3 0 0 1 0
63 B 13 2 0 0 1 0
64 B 14 3 0 0 1 0
65 B 15 2 0 0 1 0
66 B 16 2 0 0 1 0
67 B 17 2 0 0 1 0
68 B 18 2 0 0 1 0
69 B 19 2 0 1 1 0
70 B 20 2 0 0 0 0
71 B 21 3 1 0 1 0
72 B 22 3 0 0 1 0
73 B 23 3 0 0 1 0
74 B 24 3 0 0 1 0
75 B 25 NA 0 0 0 1
76 B 26 NA 0 0 0 1
77 B 27 NA 0 0 0 1
78 B 28 2 0 0 0 1
79 B 29 2 0 0 0 1
80 B 30 2 0 0 0 1
81 B 31 3 0 0 0 1
82 B 32 2 0 0 0 1
83 B 33 2 0 0 0 1
84 B 34 2 0 0 0 1
85 B 35 2 0 0 0 1
86 B 36 2 0 0 0 1
87 B 37 3 0 0 0 0
88 B 38 2 0 0 0 0
89 B 39 2 0 0 0 0
90 B 40 3 0 0 0 0
91 B 41 NA 0 0 0 0
92 B 42 NA 0 0 0 0
93 B 43 NA 0 0 0 0
94 B 44 3 1 0 1 0
95 B 45 3 0 0 1 0
96 B 46 3 0 0 1 0
97 B 47 3 0 0 1 0
98 B 48 3 0 0 1 0
99 B 49 3 0 0 1 0
100 B 50 2 0 0 1 0
>
Here is a try for a more elegant and scalable way to write your algorithm:
First, you do not have to compute the lead and lag calls before you can use case_when. Of note, I find it good practice to explicitly write the TRUE option of case_when. Here is some code.
df2=df %>%
mutate(
exacerbation_start = case_when(
is.na(symptom) ~ NA_real_,
symptom <= 2 ~ 0,
symptom >= 3 & symptom >= lag(symptom, n=2) & symptom <= lag(symptom, n=1) ~ 1,
TRUE ~ 0
),
exacerbation_end = case_when(
symptom >=3 ~ ifelse(lead(symptom, n=1) <=2 &
lead(symptom, n=2) <=2 & lead(symptom, n=3) <=2 &
lead(symptom, n=4) <=2 & lead(symptom, n=5) <=2,
1,0),
TRUE ~ NA_real_
)
)
all.equal(df1,df2) #TRUE
Alternatively, if your algorithm is the same for all symptoms, you might want to use custom functions:
get_exacerbation_start = function(x){
case_when(
is.na(x) ~ NA_real_,
x <= 2 ~ 0,
x >= 3 & x >= lag(x, n=2) & x <= lag(x, n=1) ~ 1,
TRUE ~ 0
)
}
get_exacerbation_end = function(x){
case_when(
x >=3 ~ ifelse(x >=3 & lead(x, n=1) <=2 &
lead(x, n=2) <=2 & lead(x, n=3) <=2 &
lead(x, n=4) <=2 & lead(x, n=5) <=2,
1,0),
TRUE ~ NA_real_
)
}
df3=df %>%
mutate(
exacerbation_start = get_exacerbation_start(symptom),
exacerbation_end = get_exacerbation_end(symptom)
)
all.equal(df1,df3) #also TRUE
This latter way might be even more powerful with some mutate_at calls.
EDIT: after seeing your edit, here is a try to get the exacerbation period. The code is quite ugly in my opinion, I'm not sure that row_number was supposed to be used this way.
df_final=df %>%
transmute(
id,day,symptom,
start = get_exacerbation_start(symptom),
end = get_exacerbation_end(symptom),
exacerbation = row_number()>=which(start==1)[1] & row_number()<=which(end==1)[1]
)
I may come back with a less convoluted approach, but try this:
library(dplyr)
library(tidyr)
df %>%
group_by(id,
idx = with(
rle(
case_when(symptom <= 2 ~ 'normal',
symptom >= 3 ~ 'worse',
TRUE ~ symptom %>% as.character)),
rep(seq_along(lengths), lengths)
)
) %>%
mutate(
trajectory = case_when(cumsum(symptom <= 2) == 5 ~ 2, cumsum(symptom >= 3) == 2 ~ 1)
) %>%
group_by(id) %>% fill(trajectory) %>%
mutate(
trajectory = replace_na(trajectory, 0),
start = +(trajectory == 1 & lag(trajectory) == 2),
end = +(trajectory == 2 & lag(trajectory) == 1),
exacerbation = +(trajectory == 1 | start == 1 | end == 1)
) %>%
select(-idx, -trajectory) %>% as.data.frame
Output:
id day symptom start end exacerbation
1 A 1 2 0 0 0
2 A 2 2 0 0 0
3 A 3 2 0 0 0
4 A 4 2 0 0 0
5 A 5 2 0 0 0
6 A 6 2 0 0 0
7 A 7 2 0 0 0
8 A 8 2 0 0 0
9 A 9 2 0 0 0
10 A 10 2 0 0 0
11 A 11 2 0 0 0
12 A 12 3 0 0 0
13 A 13 2 0 0 0
14 A 14 2 0 0 0
15 A 15 2 0 0 0
16 A 16 2 0 0 0
17 A 17 NA 0 0 0
18 A 18 NA 0 0 0
19 A 19 NA 0 0 0
20 A 20 2 0 0 0
21 A 21 2 0 0 0
22 A 22 2 0 0 0
23 A 23 3 0 0 0
24 A 24 3 1 0 1
25 A 25 3 0 0 1
26 A 26 4 0 0 1
27 A 27 4 0 0 1
28 A 28 3 0 0 1
29 A 29 3 0 0 1
30 A 30 2 0 0 1
31 A 31 3 0 0 1
32 A 32 2 0 0 1
33 A 33 2 0 0 1
34 A 34 3 0 0 1
35 A 35 3 0 0 1
36 A 36 2 0 0 1
37 A 37 2 0 0 1
38 A 38 2 0 0 1
39 A 39 2 0 0 1
40 A 40 2 0 1 1
41 A 41 2 0 0 0
42 A 42 3 0 0 0
43 A 43 2 0 0 0
44 A 44 2 0 0 0
45 A 45 2 0 0 0
46 A 46 2 0 0 0
47 A 47 2 0 0 0
48 A 48 3 0 0 0
49 A 49 2 0 0 0
50 A 50 2 0 0 0
I have two dataframes which look similar to this:
>health
ID Stroke Diab MI Age Sex
1 1 0 0 0 65 M
2 2 0 0 0 66 M
3 3 1 0 0 78 F
4 4 0 0 0 55 M
5 5 0 0 0 67 M
6 6 1 1 1 66 M
7 7 0 0 0 79 F
8 8 0 0 0 54 M
9 9 0 0 0 65 F
10 10 1 1 1 78 F
>Asthma
ID Smoker Smoking_Status
1 12 2 0
2 15 0 1
3 24 1 0
4 2 2 1
5 8 2 0
6 53 1 1
7 10 0 0
8 32 0 0
9 1 0 0
10 5 1 1
These are the codes that I used to produce these example tables
health <- data.frame(ID=c(1,2,3,4,5,6,7,8,9,10), Stroke = factor(c(0,0,1,0,0,1,0,0,0,1)),
Diab = factor(c(0,0,0,0,0,1,0,0,0,1)), MI = factor(c(0,0,0,0,0,1,0,0,0,1)),
Age = factor(c(65,66,78,55,67,66,79,54,65,78)),
Sex = factor(c("M","M","F","M","M","M","F","M","F","F")))
Asthma <- data.frame(ID=c(12,15,24,2,8,53,10,32,1,5), Smoker = factor(c(2,0,1,2,2,1,0,0,0,1)),
Smoking_Status = factor(c(0,1,0,1,0,1,0,0,0,1)))
My question is how can I produce another column in the health dataframe which would give another column a value of 1 to show whether the ID appeared in the Asthma dataframe.
This is my expected outcome:
ID Asthma Stroke Diab MI Age Sex
1 1 1 0 0 0 65 M
2 2 1 0 0 0 66 M
3 3 0 1 0 0 78 F
4 4 0 0 0 0 55 M
5 5 1 0 0 0 67 M
6 6 0 1 1 1 66 M
7 7 0 0 0 0 79 F
8 8 0 0 0 0 54 M
9 9 0 0 0 0 65 F
10 10 1 1 1 1 78 F
One of the many probable ways:
health$asthma =match(x = health$ID,table = Asthma$ID,nomatch = 0)
health$asthma = replace(x = health$asthma,list = which(health$asthma>0),values = 1)
Using data.table:
health = as.data.table(x = health)
Asthma = as.data.table(x = Asthma)
health[,`:=`(asthma = numeric(nrow(health)))]
set(x = health,i = which(health$ID %in% Asthma$ID),j = "asthma",value = 1)
#> health
# ID Stroke Diab MI Age Sex asthma
# 1: 1 0 0 0 65 M 1
# 2: 2 0 0 0 66 M 1
# 3: 3 1 0 0 78 F 0
# 4: 4 0 0 0 55 M 0
# 5: 5 0 0 0 67 M 1
# 6: 6 1 1 1 66 M 0
# 7: 7 0 0 0 79 F 0
# 8: 8 0 0 0 54 M 1
# 9: 9 0 0 0 65 F 0
#10: 10 1 1 1 78 F 1
You can do this in one line using data.table package-
> data.table::setDT(health)[,ind:=ifelse(ID %in% Asthma$ID,1,0)]
> health
ID Stroke Diab MI Age Sex id_app ind
1: 1 0 0 0 65 M 1 1
2: 2 0 0 0 66 M 1 1
3: 3 1 0 0 78 F 0 0
4: 4 0 0 0 55 M 0 0
5: 5 0 0 0 67 M 1 1
6: 6 1 1 1 66 M 0 0
7: 7 0 0 0 79 F 0 0
8: 8 0 0 0 54 M 1 1
9: 9 0 0 0 65 F 0 0
10: 10 1 1 1 78 F 1 1
Iam trying to combine rows into on row in TermDocumentMatrix
(I know every row represents each words)
ex) cabin, staff -> crews
Because 'cabin, staff and crew' mean samething,
Iam trying to combine rows which represent 'cabin, staff'
into one row which represent 'crew.
but, it doesn't work at all.
R said argument "weighting" is missing, with no default
The codes I typed is below
r=GET('http://www.airlinequality.com/airline-reviews/cathay-pacific-airways/')
base_url=('http://www.airlinequality.com/airline-reviews/cathay-pacific-airways/')
h<-read_html(base_url)
all.reviews = c()
for (i in 1:10){
print(i)
url = paste(base_url, 'page/', i, '/', sep="")
r = GET(url)
h = read_html(r)
comment_area = html_nodes(h, '.tc_mobile')
comments= html_nodes(comment_area, '.text_content')
reviews = html_text(comments)
all.reviews=c(all.reviews, reviews)}
cps <- Corpus(VectorSource(all.reviews))
cps <- tm_map(cps, content_transformer(tolower))
cps <- tm_map(cps, content_transformer(stripWhitespace))
cps <- tm_map(cps, content_transformer(removePunctuation))
cps <- tm_map(cps, content_transformer(removeNumbers))
cps <- tm_map(cps, removeWords, stopwords("english"))
tdm <- TermDocumentMatrix(cps, control=list(
wordLengths=c(3, 20),
weighting=weightTf))
rows.cabin = grep('cabin|staff', row.names(tdm))
rows.cabin
# [1] 235 1594
count.cabin = as.array(rollup(tdm[rows.cabin,], 1))
count.cabin
#Docs
#Terms 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47
#1 0 1 1 0 0 2 2 0 0 1 1 0 4 0 1 0 1 0 2 1 0 0 1 3 1 4 2 0 3 0 1 1 4 0 0 2 1 0 0 2 1 0 2 1 3 3 1
#Docs
#Terms 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91
#1 0 1 0 1 2 3 2 2 1 1 0 2 0 0 0 0 0 2 0 1 0 0 4 0 2 2 1 3 1 1 1 1 0 0 0 5 3 0 2 1 0 1 0 0
#Docs
#Terms 92 93 94 95 96 97 98 99 100
#1 1 5 2 1 0 0 0 1 0
row.crews = grep('crews', row.names(tdm))
row.crews
#[1] 408
tdm[row.crews,] = count.cabin
rows.cabin = setdiff(rows.cabin, row.crews) # ok
tdm = tdm[-rows.cabin,] # ok
dtm = as.DocumentTermMatrix(tdm)
# Error in .TermDocumentMatrix(t(x), weighting) :
# argument "weighting" is missing, with no default
maybe it is not right approach to combine rows in TermDocumentMatrix
Please fix this codes or suggest better approach to solve this problem.
Thanks in advance.
Hmm I wonder why you stick to your approach, which obviously does not work, instead of just copying+pasting+adjusting* my suggestion from here?
library(tm)
library(httr)
library(rvest)
library(slam)
# [...] # your code
inspect(tdm[grep("cabin|staff|crew", Terms(tdm), ignore.case=TRUE), 1:15])
# Docs
# Terms 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
# cabin 0 0 0 0 0 1 1 0 0 1 0 0 3 0 0
# crew 0 0 0 1 1 1 1 0 2 1 0 1 0 2 0
# crews 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
# staff 0 1 1 0 0 1 1 0 0 0 1 0 1 0 1
dict <- list(
"CREW" = grep("cabin|staff|crew", Terms(tdm), ignore.case=TRUE, value = TRUE)
)
terms <- Terms(tdm)
for (x in seq_along(dict))
terms[terms %in% dict[[x]] ] <- names(dict)[x]
tdm <- slam::rollup(tdm, 1, terms, sum)
inspect(tdm[grep("cabin|staff|crew", Terms(tdm), ignore.case=TRUE), 1:15])
# Docs
# Terms 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
# CREW 0 1 1 1 1 3 3 0 2 2 1 1 4 2 1
*I only adjusted the line inside the dict definition...