R: table frequencies of letters in string based on Alphabet - r

I need to compute letter frequencies of a large list of words. For each of the locations in the word (first, second,..), I need to find how many times each letter (a-z) appeared in the list and then table the data according to the word positon.
For example, if my word list is: words <- c("swims", "seems", "gills", "draws", "which", "water")
then the result table should like that:
letter
first position
second position
third position
fourth position
fifth position
a
0
1
1
0
0
b
0
0
0
0
0
c
0
0
0
1
0
d
1
0
0
0
0
e
0
1
1
1
0
f
0
0
0
0
0
...continued until z
...
...
...
...
...
All words are of same length (5).
What I have so far is:
alphabet <- letters[1:26]
words.df <- data.frame("Words" = words)
words.df <- words.df %>% mutate("First_place" = substr(words.df$words,1,1))
words.df <- words.df %>% mutate("Second_place" = substr(words.df$words,2,2))
words.df <- words.df %>% mutate("Third_place" = substr(words.df$words,3,3))
words.df <- words.df %>% mutate("Fourth_place" = substr(words.df$words,4,4))
words.df <- words.df %>% mutate("Fifth_place" = substr(words.df$words,5,5))
x1 <- words.df$First_place
x1 <- table(factor(x1,alphabet))
x2 <- words.df$Second_place
x2 <- table(factor(x2,alphabet))
x3 <- words.df$Third_place
x3 <- table(factor(x3,alphabet))
x4 <- words.df$Fourth_place
x4 <- table(factor(x4,alphabet))
x5 <- words.df$Fifth_place
x5 <- table(factor(x5,alphabet))
My code is not effective and gives tables to each letter position sepretely. All help will be appreicated.

in base R use table:
table(let = unlist(strsplit(words,'')),pos = sequence(nchar(words)))
pos
let 1 2 3 4 5
a 0 1 1 0 0
c 0 0 0 1 0
d 1 0 0 0 0
e 0 1 1 1 0
g 1 0 0 0 0
h 0 1 0 0 1
i 0 1 2 0 0
l 0 0 1 1 0
m 0 0 0 2 0
r 0 1 0 0 1
s 2 0 0 0 4
t 0 0 1 0 0
w 2 1 0 1 0
Note that if you need all the values from a-z then use
table(factor(unlist(strsplit(words,'')), letters), sequence(nchar(words)))
Also to get a dataframe you could do:
d <- table(factor(unlist(strsplit(words,'')), letters), sequence(nchar(words)))
cbind(letters = rownames(d), as.data.frame.matrix(d))

Here is a tidyverse solution using dplyr, purrr, and tidyr:
strsplit(words.df$Words, "") %>%
map_dfr(~setNames(.x, seq_along(.x))) %>%
pivot_longer(everything(),
values_drop_na = T,
names_to = "pos",
values_to = "letter") %>%
count(pos, letter) %>%
pivot_wider(names_from = pos,
names_glue = "pos{pos}",
id_cols = letter,
values_from = n,
values_fill = 0L)
Output
letter pos1 pos2 pos3 pos4 pos5 pos6 pos7 pos8 pos9 pos10 pos11
1 a 65 127 88 38 28 17 14 5 3 0 0
2 b 58 4 7 9 2 4 2 0 1 0 0
3 c 83 14 45 37 20 19 8 3 2 0 0
4 C 2 0 0 0 0 0 0 0 0 0 0
5 d 43 8 33 47 21 22 9 3 1 1 0
6 e 45 156 81 132 114 69 48 23 14 2 2
7 f 54 11 18 10 5 2 1 0 0 0 0
8 g 23 7 27 21 15 8 7 1 0 0 0
9 h 38 56 6 28 21 10 3 3 1 1 0
10 i 25 106 51 58 38 28 8 4 1 0 0
11 j 6 0 2 2 0 0 0 0 0 0 0
12 k 9 1 6 22 12 0 0 0 0 0 0
13 l 45 41 54 54 36 9 7 6 0 2 0
14 m 45 8 31 19 8 8 4 2 0 0 0
15 n 23 42 75 53 34 41 16 16 4 2 0
16 o 28 167 76 41 38 9 11 2 1 0 0
17 p 72 20 34 30 8 3 1 1 1 0 0
18 q 7 2 1 0 0 0 0 0 0 0 0
19 r 46 74 92 59 56 45 12 9 1 1 0
20 s 119 8 67 35 31 22 18 4 1 0 0
21 t 65 30 73 83 57 42 31 9 6 3 1
22 u 12 66 39 36 20 7 7 2 0 0 0
23 v 8 7 20 12 5 5 1 0 0 0 0
24 w 53 8 13 10 2 3 0 1 0 0 0
25 y 6 4 16 15 17 15 10 5 6 1 1
26 x 0 12 5 0 0 0 0 0 0 0 0
27 z 0 0 1 0 0 0 1 1 0 0 0

Related

Summing up different elements in a matrix in R

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

How to deal with longitudinal symptom data in R using lag/lead and ifelse/case_when (or other solution)?

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

How to create another column in R based on whether a variable appears in another dataframe

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

How to combine rows into one row in TermDocumentMatrix?

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...

Create one column out of several columns Rstudio or Excel

I've tried to find an already existing question on this matter but I couldn't so that is why I'm asking here you:
Summary:
I want to make ONE column out of several Columns. All the values in the columns are put in the same order as they are and also, the columns should be stacked below each other.
Description and details
Below is an example of how my csv.file look like. However, note that there is >400 columns and that's why I don't want to do it manually in for example Excel. ALL columns has 24 rows each.
X1 X2 X3 X4 X5 X6 ... X470
0 1 5 10 8 0 7
0 0 0 0 0 0 0
2 3 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
0 0 0 0 0 0 0
I want to "stack" all the columns in one column, as I've shortly described in the summary:
Info: The sign "..." below implies the rest of the values from that column.
VALUE FROM COLUMN
0 X1
0 X1
2 X1
...
1 X2
0 X2
3 X2
...
5 X3
...
10 X4
...
8 X5
...
0 X6
...
7 X470
...
So in the end, instead of having 486 column where each of them have 24 rows. I will have 1 column with 11664 rows. It would be good if the origin column is written in a new column on the side (as showed above) but this is not "obligated".
OBS! Note that I've with this df just showed in general what I want to achieve, so clear and understandable commands are appreciated as I will apply it to my df.
It doesn't matter if the solution is done in R or Excel! As long as it is easy to do
I hope my description is clear, otherwise please let me know so I can try to describe again.
Many thanks for suggestions and help.
Kind regards, Elin
We can use stack to get the values in one column and the colnames in the next.
stack(df)
Or use unlist
data.frame(VALUE=unlist(df),
fromColumn= rep(names(df), each=nrow(df)))
Here's a VBA user defined function to do the job:
Function ConcatCols(Colrange As Variant) As Variant
Dim LongCol() As Variant, i As Long, j As Long, k As Long
Dim NumCols As Long, NumRows As Long, NumRows2 As Long
If TypeName(Colrange) = "Range" Then Colrange = Colrange.Value2
NumRows = UBound(Colrange)
NumCols = UBound(Colrange, 2)
NumRows2 = NumRows * NumCols
ReDim LongCol(1 To NumRows2, 1 To 1)
k = 1
For i = 1 To NumCols
For j = 1 To NumRows
LongCol(k, 1) = Colrange(j, i)
k = k + 1
Next j
Next i
ConcatCols = LongCol
End Function
Enter the code in a VBA module then enter =ConcatCols(A1:RL24) as an array function (Ctrl-Shift-Enter) in column RM (or wherever you want) to view the entire concatenated column, or call from a VBA sub to write the data to the spreadsheet.
The following is pretty simple but requires loading the reshape2 package which I think is included in base. As suggested above, stack() gives similar output, but reverses the columns.
library(reshape2)
df <- data.frame("A" = 1:21, "B" = 21:41, "C" = 40:60)
> df
A B C
1 1 21 40
2 2 22 41
3 3 23 42
4 4 24 43
5 5 25 44
6 6 26 45
7 7 27 46
8 8 28 47
9 9 29 48
10 10 30 49
11 11 31 50
12 12 32 51
13 13 33 52
14 14 34 53
15 15 35 54
16 16 36 55
17 17 37 56
18 18 38 57
19 19 39 58
20 20 40 59
21 21 41 60
melt(df)
> melt(df)
No id variables; using all as measure variables
variable value
1 A 1
2 A 2
3 A 3
4 A 4
5 A 5
6 A 6
7 A 7
8 A 8
9 A 9
10 A 10
11 A 11
12 A 12
13 A 13
14 A 14
15 A 15
16 A 16
17 A 17
18 A 18
19 A 19
20 A 20
21 A 21
22 B 21
23 B 22
24 B 23
25 B 24
26 B 25
27 B 26
28 B 27
29 B 28
30 B 29
31 B 30
32 B 31
33 B 32
34 B 33
35 B 34
36 B 35
37 B 36
38 B 37
39 B 38
40 B 39
41 B 40
42 B 41
43 C 40
44 C 41
45 C 42
46 C 43
47 C 44
48 C 45
49 C 46
50 C 47
51 C 48
52 C 49
53 C 50
54 C 51
55 C 52
56 C 53
57 C 54
58 C 55
59 C 56
60 C 57
61 C 58
62 C 59
63 C 60

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