Proper proportion table and chisq.test() in R
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I am still very new to R (Version 1.1.383 on Mac), so I apologize if this question is basic. I have searched for a solution on the internet and on this page but could not find any.
What I want to do is to make a proportion table on which I can use chisq.test() to test if there is a difference between 4 patient groups in the distribution of proportion of patients with 5 different conditions.
The data I have contains percentage of patients with conditions (CHF, DM, S, MI and CHF) and the patients groups (green, yellow, orange and red). There are 238, 196, 158 and 20 patients in the 4 groups, respectively, and some patients may have more than one condition. Therefore, I use proportions and not actual number of patients.
Like this:
condition <- c("CHF", "DM", "S", "MI", "CHF")
green <- c(30,33,35,17,15)/238*100
yellow <- c(47,32,25,21,19)/196*100
orange <- c(48,24,27,27,25)/158*100
red <- c(10,2,4,1,6)/20*100
Where 30, 47, 48 and 10 patients in the four groups have CHF. 33, 32, 24 and 2 patients have DM and so on...
Using cbind() I get this matrix:
df <- cbind(condition, green, yellow, orange, red )
df
condition green yellow orange red #I only included 1 decimal.
[1,] "CHF" "12.6" "24.9" "30.4" "50"
[2,] "DM" "13.9" "16.3" "15.2" "10"
[3,] "S" "14.7" "12.8" "17.1" "20"
[4,] "MI" "7.1" "10.7" "17.1" "5"
[5,] "CHF" "6.3" "9.7" "15.8" "30"
It almost looks like what I want but "" makes me suspect that it is coded as characters and not a proper proportion table. Also this happens when I use chisq.test():
chisq.test(df)
Error in sum(x) : invalid 'type' (character) of argument
I really hope you can help. How do I make a proper proportion table and test difference in distribution of conditions in the four groups?
r rstudio chi-squared
edited Nov 23 '18 at 22:41
Brian Tompsett - 汤莱恩
4,2571339103
asked Nov 23 '18 at 17:22
Mads LumholdtMads Lumholdt
134
add a comment |
I am still very new to R (Version 1.1.383 on Mac), so I apologize if this question is basic. I have searched for a solution on the internet and on this page but could not find any.
What I want to do is to make a proportion table on which I can use chisq.test() to test if there is a difference between 4 patient groups in the distribution of proportion of patients with 5 different conditions.
The data I have contains percentage of patients with conditions (CHF, DM, S, MI and CHF) and the patients groups (green, yellow, orange and red). There are 238, 196, 158 and 20 patients in the 4 groups, respectively, and some patients may have more than one condition. Therefore, I use proportions and not actual number of patients.
Like this:
condition <- c("CHF", "DM", "S", "MI", "CHF")
green <- c(30,33,35,17,15)/238*100
yellow <- c(47,32,25,21,19)/196*100
orange <- c(48,24,27,27,25)/158*100
red <- c(10,2,4,1,6)/20*100
Where 30, 47, 48 and 10 patients in the four groups have CHF. 33, 32, 24 and 2 patients have DM and so on...
Using cbind() I get this matrix:
df <- cbind(condition, green, yellow, orange, red )
df
condition green yellow orange red #I only included 1 decimal.
[1,] "CHF" "12.6" "24.9" "30.4" "50"
[2,] "DM" "13.9" "16.3" "15.2" "10"
[3,] "S" "14.7" "12.8" "17.1" "20"
[4,] "MI" "7.1" "10.7" "17.1" "5"
[5,] "CHF" "6.3" "9.7" "15.8" "30"
It almost looks like what I want but "" makes me suspect that it is coded as characters and not a proper proportion table. Also this happens when I use chisq.test():
chisq.test(df)
Error in sum(x) : invalid 'type' (character) of argument
I really hope you can help. How do I make a proper proportion table and test difference in distribution of conditions in the four groups?
r rstudio chi-squared
edited Nov 23 '18 at 22:41
Brian Tompsett - 汤莱恩
4,2571339103
asked Nov 23 '18 at 17:22
Mads LumholdtMads Lumholdt
134
Unfortunately, this still bugs me. Ischisq.test()even the right statistical method for this problem? The summated proportions within each group (green, yellow, orange, red) is > 100% for some groups because som subjects have multiple conditions. Does this affect the the test? Could I only look at the counts of conditions and somehow tell thechisq.test()the total number of subjects within each group?
– Mads Lumholdt
Jan 31 at 15:00
add a comment |
I am still very new to R (Version 1.1.383 on Mac), so I apologize if this question is basic. I have searched for a solution on the internet and on this page but could not find any.
What I want to do is to make a proportion table on which I can use chisq.test() to test if there is a difference between 4 patient groups in the distribution of proportion of patients with 5 different conditions.
The data I have contains percentage of patients with conditions (CHF, DM, S, MI and CHF) and the patients groups (green, yellow, orange and red). There are 238, 196, 158 and 20 patients in the 4 groups, respectively, and some patients may have more than one condition. Therefore, I use proportions and not actual number of patients.
Like this:
condition <- c("CHF", "DM", "S", "MI", "CHF")
green <- c(30,33,35,17,15)/238*100
yellow <- c(47,32,25,21,19)/196*100
orange <- c(48,24,27,27,25)/158*100
red <- c(10,2,4,1,6)/20*100
Where 30, 47, 48 and 10 patients in the four groups have CHF. 33, 32, 24 and 2 patients have DM and so on...
Using cbind() I get this matrix:
df <- cbind(condition, green, yellow, orange, red )
df
condition green yellow orange red #I only included 1 decimal.
[1,] "CHF" "12.6" "24.9" "30.4" "50"
[2,] "DM" "13.9" "16.3" "15.2" "10"
[3,] "S" "14.7" "12.8" "17.1" "20"
[4,] "MI" "7.1" "10.7" "17.1" "5"
[5,] "CHF" "6.3" "9.7" "15.8" "30"
It almost looks like what I want but "" makes me suspect that it is coded as characters and not a proper proportion table. Also this happens when I use chisq.test():
chisq.test(df)
Error in sum(x) : invalid 'type' (character) of argument
I really hope you can help. How do I make a proper proportion table and test difference in distribution of conditions in the four groups?
r rstudio chi-squared
edited Nov 23 '18 at 22:41
Brian Tompsett - 汤莱恩
4,2571339103
asked Nov 23 '18 at 17:22
Mads LumholdtMads Lumholdt
134
I am still very new to R (Version 1.1.383 on Mac), so I apologize if this question is basic. I have searched for a solution on the internet and on this page but could not find any.
What I want to do is to make a proportion table on which I can use chisq.test() to test if there is a difference between 4 patient groups in the distribution of proportion of patients with 5 different conditions.
The data I have contains percentage of patients with conditions (CHF, DM, S, MI and CHF) and the patients groups (green, yellow, orange and red). There are 238, 196, 158 and 20 patients in the 4 groups, respectively, and some patients may have more than one condition. Therefore, I use proportions and not actual number of patients.
Like this:
condition <- c("CHF", "DM", "S", "MI", "CHF")
green <- c(30,33,35,17,15)/238*100
yellow <- c(47,32,25,21,19)/196*100
orange <- c(48,24,27,27,25)/158*100
red <- c(10,2,4,1,6)/20*100
Where 30, 47, 48 and 10 patients in the four groups have CHF. 33, 32, 24 and 2 patients have DM and so on...
Using cbind() I get this matrix:
df <- cbind(condition, green, yellow, orange, red )
df
condition green yellow orange red #I only included 1 decimal.
[1,] "CHF" "12.6" "24.9" "30.4" "50"
[2,] "DM" "13.9" "16.3" "15.2" "10"
[3,] "S" "14.7" "12.8" "17.1" "20"
[4,] "MI" "7.1" "10.7" "17.1" "5"
[5,] "CHF" "6.3" "9.7" "15.8" "30"
It almost looks like what I want but "" makes me suspect that it is coded as characters and not a proper proportion table. Also this happens when I use chisq.test():
chisq.test(df)
Error in sum(x) : invalid 'type' (character) of argument
I really hope you can help. How do I make a proper proportion table and test difference in distribution of conditions in the four groups?
r rstudio chi-squared
r rstudio chi-squared
edited Nov 23 '18 at 22:41
Brian Tompsett - 汤莱恩
4,2571339103
asked Nov 23 '18 at 17:22
Mads LumholdtMads Lumholdt
134
edited Nov 23 '18 at 22:41
Brian Tompsett - 汤莱恩
4,2571339103
asked Nov 23 '18 at 17:22
Mads LumholdtMads Lumholdt
134
edited Nov 23 '18 at 22:41
Brian Tompsett - 汤莱恩
4,2571339103
edited Nov 23 '18 at 22:41
Brian Tompsett - 汤莱恩
4,2571339103
edited Nov 23 '18 at 22:41
Brian Tompsett - 汤莱恩
4,2571339103
4,2571339103
asked Nov 23 '18 at 17:22
Mads LumholdtMads Lumholdt
134
asked Nov 23 '18 at 17:22
Mads LumholdtMads Lumholdt
134
asked Nov 23 '18 at 17:22
Mads LumholdtMads Lumholdt
134
134
Unfortunately, this still bugs me. Ischisq.test()even the right statistical method for this problem? The summated proportions within each group (green, yellow, orange, red) is > 100% for some groups because som subjects have multiple conditions. Does this affect the the test? Could I only look at the counts of conditions and somehow tell thechisq.test()the total number of subjects within each group?
– Mads Lumholdt
Jan 31 at 15:00
add a comment |
Unfortunately, this still bugs me. Ischisq.test()even the right statistical method for this problem? The summated proportions within each group (green, yellow, orange, red) is > 100% for some groups because som subjects have multiple conditions. Does this affect the the test? Could I only look at the counts of conditions and somehow tell thechisq.test()the total number of subjects within each group?
– Mads Lumholdt
Jan 31 at 15:00
Unfortunately, this still bugs me. Is
chisq.test() even the right statistical method for this problem? The summated proportions within each group (green, yellow, orange, red) is > 100% for some groups because som subjects have multiple conditions. Does this affect the the test? Could I only look at the counts of conditions and somehow tell the chisq.test() the total number of subjects within each group?– Mads Lumholdt
Jan 31 at 15:00
Unfortunately, this still bugs me. Is
chisq.test() even the right statistical method for this problem? The summated proportions within each group (green, yellow, orange, red) is > 100% for some groups because som subjects have multiple conditions. Does this affect the the test? Could I only look at the counts of conditions and somehow tell the chisq.test() the total number of subjects within each group?– Mads Lumholdt
Jan 31 at 15:00
add a comment |
1 Answer
1
active
oldest
votes
We created a matrix with cbind and matrix can have only single class. Having 'condition' as a column changes the numeric columns to character and this creates the issue in chisq.test.
According to ?chisq.test, the input argument 'x' can be vector or matrix, but the permitted class is numeric or factor.
x - a numeric vector or matrix. x and y can also both be factors.
So, create the matrix with only numeric vectors and keep the 'condition' as row names.
df <- cbind(green, yellow, orange, red)
row.names(df) <- condition
chisq.test(df)
answered Nov 23 '18 at 17:24
akrunakrun
421k13209284
1
Oh my god. Such an elegant solution. Thank you. I have been struggling with this problem for hours now.
– Mads Lumholdt
Nov 23 '18 at 17:29
@MadsLumholdt Glad to know that the solution is useful.
– akrun
Nov 23 '18 at 17:30
add a comment |
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1 Answer
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1 Answer
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active
oldest
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oldest
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active
oldest
votes
We created a matrix with cbind and matrix can have only single class. Having 'condition' as a column changes the numeric columns to character and this creates the issue in chisq.test.
According to ?chisq.test, the input argument 'x' can be vector or matrix, but the permitted class is numeric or factor.
x - a numeric vector or matrix. x and y can also both be factors.
So, create the matrix with only numeric vectors and keep the 'condition' as row names.
df <- cbind(green, yellow, orange, red)
row.names(df) <- condition
chisq.test(df)
answered Nov 23 '18 at 17:24
akrunakrun
421k13209284
1
Oh my god. Such an elegant solution. Thank you. I have been struggling with this problem for hours now.
– Mads Lumholdt
Nov 23 '18 at 17:29
@MadsLumholdt Glad to know that the solution is useful.
– akrun
Nov 23 '18 at 17:30
add a comment |
We created a matrix with cbind and matrix can have only single class. Having 'condition' as a column changes the numeric columns to character and this creates the issue in chisq.test.
According to ?chisq.test, the input argument 'x' can be vector or matrix, but the permitted class is numeric or factor.
x - a numeric vector or matrix. x and y can also both be factors.
So, create the matrix with only numeric vectors and keep the 'condition' as row names.
df <- cbind(green, yellow, orange, red)
row.names(df) <- condition
chisq.test(df)
answered Nov 23 '18 at 17:24
akrunakrun
421k13209284
1
Oh my god. Such an elegant solution. Thank you. I have been struggling with this problem for hours now.
– Mads Lumholdt
Nov 23 '18 at 17:29
@MadsLumholdt Glad to know that the solution is useful.
– akrun
Nov 23 '18 at 17:30
add a comment |
We created a matrix with cbind and matrix can have only single class. Having 'condition' as a column changes the numeric columns to character and this creates the issue in chisq.test.
According to ?chisq.test, the input argument 'x' can be vector or matrix, but the permitted class is numeric or factor.
x - a numeric vector or matrix. x and y can also both be factors.
So, create the matrix with only numeric vectors and keep the 'condition' as row names.
df <- cbind(green, yellow, orange, red)
row.names(df) <- condition
chisq.test(df)
answered Nov 23 '18 at 17:24
akrunakrun
421k13209284
We created a matrix with cbind and matrix can have only single class. Having 'condition' as a column changes the numeric columns to character and this creates the issue in chisq.test.
According to ?chisq.test, the input argument 'x' can be vector or matrix, but the permitted class is numeric or factor.
x - a numeric vector or matrix. x and y can also both be factors.
So, create the matrix with only numeric vectors and keep the 'condition' as row names.
df <- cbind(green, yellow, orange, red)
row.names(df) <- condition
chisq.test(df)
answered Nov 23 '18 at 17:24
akrunakrun
421k13209284
answered Nov 23 '18 at 17:24
akrunakrun
421k13209284
answered Nov 23 '18 at 17:24
akrunakrun
421k13209284
answered Nov 23 '18 at 17:24
akrunakrun
421k13209284
421k13209284
1
Oh my god. Such an elegant solution. Thank you. I have been struggling with this problem for hours now.
– Mads Lumholdt
Nov 23 '18 at 17:29
@MadsLumholdt Glad to know that the solution is useful.
– akrun
Nov 23 '18 at 17:30
add a comment |
1
Oh my god. Such an elegant solution. Thank you. I have been struggling with this problem for hours now.
– Mads Lumholdt
Nov 23 '18 at 17:29
@MadsLumholdt Glad to know that the solution is useful.
– akrun
Nov 23 '18 at 17:30
1
1
Oh my god. Such an elegant solution. Thank you. I have been struggling with this problem for hours now.
– Mads Lumholdt
Nov 23 '18 at 17:29
Oh my god. Such an elegant solution. Thank you. I have been struggling with this problem for hours now.
– Mads Lumholdt
Nov 23 '18 at 17:29
@MadsLumholdt Glad to know that the solution is useful.
– akrun
Nov 23 '18 at 17:30
@MadsLumholdt Glad to know that the solution is useful.
– akrun
Nov 23 '18 at 17:30
add a comment |
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Unfortunately, this still bugs me. Is
chisq.test()even the right statistical method for this problem? The summated proportions within each group (green, yellow, orange, red) is > 100% for some groups because som subjects have multiple conditions. Does this affect the the test? Could I only look at the counts of conditions and somehow tell thechisq.test()the total number of subjects within each group?– Mads Lumholdt
Jan 31 at 15:00