Fitting Weibull distribution to the censored data - r

I would like to estimate Maximum Likelihood parameters of the Weibull distribution by applying to the following data with a given censoring vector in R:
data= 9 2 11 49 7 5 3 36 30 6 62 5 3 29 29 1 13 1 24 11 9 4 7 15 11 15 1 1 1 1 1 2 6 12 12 28 14 14 57 17 4 2 3 6 21 6 16 19 28 18 19 9 59 12 3 27 8 26 19 47 68 17 15 25 25 6 54 1 2 11 4 1 36 2 5 5 3 38 3 1 10 69 1 8 3 17 21 19 11 1 6 1 1 18 2 51 6 12 11 13 3 19 16 18 28 10 26 32 6 25 1 44
cens= 1 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 1
I would be very thankful if anyone could help me.


Use the Abrem package:
install.packages("abrem", repos="http://R-Forge.R-project.org")
You may need to manually install an older version of RccpArmadillo if you have issues like I did:
install.packages("https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/RcppArmadillo_0.6.100.0.0.tar.gz", repos=NULL, type="source")
Then have at it:
library(abrem)
a = Abrem(fail = c(2, 11, 49, ...), susp = c(9, 44))
a = abrem.fit(a, dist = 'weibull', method.fit = 'mle')
a = abrem.conf(a) # add 90% confidence bands
plot.abrem(a) # plot the points and fit distribution
print.abrem(a) # print the results, which includes the fitted parameters
I may have confused your failures vs. suspensions data, but hopefully the example makes it clear where each goes.

Related

Calculate weighted mean from matrix in R

I have a matrix that looks like the following. For rows 1:23, I would like to calculate the weighted mean, where the data in rows 1:23 are the weights and row 24 is the data.
1 107 33 41 22 12 4 122 44 297 123 51 16 7 9 1 1 0
10 5 2 2 1 0 3 4 6 12 3 3 0 1 1 0 0 0
11 1 3 1 0 0 0 4 2 8 3 4 0 0 0 0 0 0
12 2 1 1 0 0 0 2 1 5 6 3 1 0 0 0 0 0
13 1 0 1 0 0 0 3 1 3 5 2 2 0 1 0 0 0
14 3 0 0 0 0 0 3 1 2 3 0 1 0 0 0 0 0
15 0 0 0 0 0 0 2 0 0 1 0 1 0 0 0 0 0
16 0 0 0 0 1 0 0 0 2 0 0 0 0 0 0 0 0
17 1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
18 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
19 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
2 80 27 37 5 6 4 97 48 242 125 44 27 7 8 8 0 2
20 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
21 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
22 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
23 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
3 47 12 33 12 6 1 63 42 200 96 45 19 6 6 9 2 0
4 45 14 21 9 4 2 54 26 130 71 36 17 8 5 1 0 2
5 42 10 14 6 3 2 45 19 89 45 26 7 4 8 2 1 0
6 17 3 12 5 2 0 18 21 51 41 19 15 5 1 1 0 0
7 16 2 6 0 0 1 14 9 37 23 17 7 3 0 3 0 0
8 9 4 4 2 1 0 7 9 30 15 8 3 3 1 1 0 1
9 12 2 3 1 1 1 6 5 14 12 5 1 2 0 0 1 0
24 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
As an example using the top two rows, there would have an additional column at the end indicated the weighted mean.
1 107 33 41 22 12 4 122 44 297 123 51 16 7 9 1 1 0 6.391011
10 5 2 2 1 0 3 4 6 12 3 3 0 1 1 0 0 0 6.232558
I'm a little new to coding so I wasn't too sure how to do it - any advice would be appreciated!

You can do:
apply(df[-nrow(df), ], 1, function(row) weighted.mean(df[nrow(df), ], row))

I'm assuming your first columns is some kind of index and not used for the weighted mean (and the data is stored in matr_dat):
apply(matr_dat[-nrow(matr_dat), -1], 1,
function(row) weighted.mean(matr_dat[nrow(matr_dat), -1], row))
Using apply and setting the margin to 1, the function defined in the third argument of apply to each row of the data; to calculate the weighted mean, you can use weighted.mean and set the weights to the values of the row.

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 add elements to a vector based on another vector position wise in R

I have a positive integer value vector C which is of length 192. I want to generate another vector based on this vector C. The new vector to be created is called B (same length as C). The algorithm for creation is:
Whenever a value above 0 is observed in C, add the same value 12 places back in the vector B. For example, if the first 15 entries of C are 0 and the 16th entry is 3, then I want to add the value 3, 12 positions back (which is 16-12=position 4) in vector B. The vector B would be generated in this way over all values of C.
Any help would be greatly appreciated! The vector C can be obtained by the R library "outbreaks" and the data file from that package is ebola_kikwit_1995$onset.

It doesn't seem to be very tricky. An index vector and a for loop will do what the question asks for.
library("outbreaks")
i <- which(ebola_kikwit_1995$onset > 0)
i <- i[i > 12]
ebola_kikwit_1995$B <- 0L
for(j in i){
ebola_kikwit_1995$B[j] <- ebola_kikwit_1995$onset[j] + ebola_kikwit_1995$B[j - 12]
}
ebola_kikwit_1995$B
# [1] 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
# [28] 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
# [55] 0 0 0 0 0 1 1 1 0 0 0 0 3 0 0 0 1 2 0 2 0 2 0 1 0 0 0
# [82] 0 0 0 0 4 0 3 1 3 1 0 1 1 1 1 1 5 3 0 5 7 2 2 5 3 2 8
#[109] 5 9 5 4 10 10 13 14 20 10 9 16 7 14 13 10 18 13 17 21 31 13 21 21 15 17 16
#[136] 18 22 18 18 24 35 16 22 23 18 18 19 21 26 21 23 26 37 17 0 25 0 0 21 0 0 0
#[163] 25 28 0 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
#[190] 0 0 0

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 get a square table?

I've got the following code to create a classification table in R:
> table(class = class1, truth = valid[,1])
1 2 3 4 5 6 7 8 9 10 11 12
1 357 73 0 0 47 0 5 32 20 0 4 7
2 25 71 0 0 23 4 1 0 2 1 8 3
3 1 2 120 1 5 0 1 0 0 0 0 0
4 0 0 0 77 0 0 0 0 1 0 0 0
5 15 27 0 0 67 6 7 0 4 1 5 7
6 1 2 0 0 2 44 0 0 0 7 7 0
7 1 1 0 0 10 0 66 0 1 0 1 7
9 1 0 0 0 3 0 0 2 8 0 0 2
10 1 1 0 0 1 6 0 0 0 17 0 0
11 0 7 0 0 3 1 0 0 0 4 10 2
12 0 1 0 0 1 0 0 0 0 0 0 1
However, I need this table to be a square (line 8 is missing in this example), i.e. the number of rows should equal the number of columns, and I need the rownames and colnames to be preserved. The missing line should be filled with zeros. Any way of doing this?

The problem most probably comes from a difference in levels.
Try copying the levels from valid to class1:
class1 <- factor(class1, levels=levels(valid[,1])
table(class = class1, truth = valid[,1])

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