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Luigi Marongiu

2020-Jul-06 13:01 UTC

[R] how to calculate odd ratios with R?

Hello,
Is it possible to calculate with a single function the odd ratios?
Now I can use this implement:
```
or <- (De/He)/(Dn/Hn) # Disease exposed, Healthy non-exposed
logo <- log(or)
x <- sqrt(((1/De) + (1/He) + (1/Dn) + (1/Hn)))
lower_ci = exp(logo - 1.96*x)
upper_ci = exp(logo + 1.96*x)
cat("OR:", round(or, 3), "(", round(lower_ci, 3),
"-", round(upper_ci, 3), ")",
    spe = "")
```
for instance,
```
De <-6
Dn <-3
He <-4
Hn <-5
or <- (De/He)/(Dn/Hn)
logo <- log(or)
x <- sqrt(((1/De) + (1/He) + (1/Dn) + (1/Hn)))
lower_ci = exp(logo - 1.96*x)
upper_ci = exp(logo + 1.96*x)
cat("OR:", round(or, 3), "(", round(lower_ci, 3),
"-", round(upper_ci, 3), ")",
    spe = "")> OR: 2.5 ( 0.37 - 16.889 )```
Is there a simple function from some package that can also add a
p-value to this test? Or how can I calculate the p-value on my own?
-- 
Best regards,
Luigi

Sorkin, John

2020-Jul-06 13:17 UTC

head link

[R] how to calculate odd ratios with R?

Luigi,
Odds ratios can be produced using a logistic regression, which can be performed
using the glm function. The following has a detailed description of how logistic
regression can be performed using R:

https://stats.idre.ucla.edu/r/dae/logit-regression/

John


John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric
Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)


________________________________
From: R-help <r-help-bounces at r-project.org> on behalf of Luigi Marongiu
<marongiu.luigi at gmail.com>
Sent: Monday, July 6, 2020 9:01 AM
To: r-help <r-help at r-project.org>
Subject: [R] how to calculate odd ratios with R?

Hello,
Is it possible to calculate with a single function the odd ratios?
Now I can use this implement:
```
or <- (De/He)/(Dn/Hn) # Disease exposed, Healthy non-exposed
logo <- log(or)
x <- sqrt(((1/De) + (1/He) + (1/Dn) + (1/Hn)))
lower_ci = exp(logo - 1.96*x)
upper_ci = exp(logo + 1.96*x)
cat("OR:", round(or, 3), "(", round(lower_ci, 3),
"-", round(upper_ci, 3), ")",
    spe = "")
```
for instance,
```
De <-6
Dn <-3
He <-4
Hn <-5
or <- (De/He)/(Dn/Hn)
logo <- log(or)
x <- sqrt(((1/De) + (1/He) + (1/Dn) + (1/Hn)))
lower_ci = exp(logo - 1.96*x)
upper_ci = exp(logo + 1.96*x)
cat("OR:", round(or, 3), "(", round(lower_ci, 3),
"-", round(upper_ci, 3), ")",
    spe = "")> OR: 2.5 ( 0.37 - 16.889 )```
Is there a simple function from some package that can also add a
p-value to this test? Or how can I calculate the p-value on my own?
--
Best regards,
Luigi

______________________________________________
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and provide commented, minimal, self-contained, reproducible code.

	[[alternative HTML version deleted]]

Michael Dewey

2020-Jul-06 13:21 UTC

head link

[R] how to calculate odd ratios with R?

Dear Luigi

You could try the epitools package which gives a large number of ways of 
doing this. I would have thought that using Wald intervals for the log 
odds ration was not optimal with small frequencies.

Michael

On 06/07/2020 14:01, Luigi Marongiu wrote:> Hello,
> Is it possible to calculate with a single function the odd ratios?
> Now I can use this implement:
> ```
> or <- (De/He)/(Dn/Hn) # Disease exposed, Healthy non-exposed
> logo <- log(or)
> x <- sqrt(((1/De) + (1/He) + (1/Dn) + (1/Hn)))
> lower_ci = exp(logo - 1.96*x)
> upper_ci = exp(logo + 1.96*x)
> cat("OR:", round(or, 3), "(", round(lower_ci, 3),
"-", round(upper_ci, 3), ")",
>      spe = "")
> ```
> for instance,
> ```
> De <-6
> Dn <-3
> He <-4
> Hn <-5
> or <- (De/He)/(Dn/Hn)
> logo <- log(or)
> x <- sqrt(((1/De) + (1/He) + (1/Dn) + (1/Hn)))
> lower_ci = exp(logo - 1.96*x)
> upper_ci = exp(logo + 1.96*x)
> cat("OR:", round(or, 3), "(", round(lower_ci, 3),
"-", round(upper_ci, 3), ")",
>      spe = "")
>> OR: 2.5 ( 0.37 - 16.889 )
> ```
> Is there a simple function from some package that can also add a
> p-value to this test? Or how can I calculate the p-value on my own?
> 
-- 
Michael
http://www.dewey.myzen.co.uk/home.html

Stefan Evert

2020-Jul-06 20:28 UTC

head link

[R] how to calculate odd ratios with R?

fisher.test() computes exact confidence intervals for the odds ratio.
> On 6 Jul 2020, at 15:01, Luigi Marongiu <marongiu.luigi at gmail.com>
wrote:
> 
> Is there a simple function from some package that can also add a
> p-value to this test? Or how can I calculate the p-value on my own?

Minato Nakazawa

2020-Jul-07 05:57 UTC

head link

[R] how to calculate odd ratios with R?

A review (sorry in Japanese) on the calculation of odds ratios 
with confidence intervals using several packages in R is given
by Prof. Okumura, Mie Univ.

https://oku.edu.mie-u.ac.jp/~okumura/stat/2by2.html

x <- matrix(c(6, 3, 4, 5), 2)
# using vcd
library(vcd)
res <- oddsratio(x)
exp(confint(res))
summary(res)
# Note: summary(oddsratio(x, log=FALSE)) gives inappropriate p-value.
# using fmsb
library(fmsb)
oddsratio(x, p.calc.by.independence=FALSE)

Best,
Minato Nakazawa

On Mon, 6 Jul 2020 15:01:34 +0200
Luigi Marongiu <marongiu.luigi at gmail.com> wrote:
> Hello,
> Is it possible to calculate with a single function the odd ratios?
> Now I can use this implement:
> ```
> or <- (De/He)/(Dn/Hn) # Disease exposed, Healthy non-exposed
> logo <- log(or)
> x <- sqrt(((1/De) + (1/He) + (1/Dn) + (1/Hn)))
> lower_ci = exp(logo - 1.96*x)
> upper_ci = exp(logo + 1.96*x)
> cat("OR:", round(or, 3), "(", round(lower_ci, 3),
"-", round(upper_ci, 3), ")",
>     spe = "")
> ```
> for instance,
> ```
> De <-6
> Dn <-3
> He <-4
> Hn <-5
> or <- (De/He)/(Dn/Hn)
> logo <- log(or)
> x <- sqrt(((1/De) + (1/He) + (1/Dn) + (1/Hn)))
> lower_ci = exp(logo - 1.96*x)
> upper_ci = exp(logo + 1.96*x)
> cat("OR:", round(or, 3), "(", round(lower_ci, 3),
"-", round(upper_ci, 3), ")",
>     spe = "")
> > OR: 2.5 ( 0.37 - 16.889 )
> ```
> Is there a simple function from some package that can also add a
> p-value to this test? Or how can I calculate the p-value on my own?
> -- 
> Best regards,
> Luigi
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
> 

-- 
Minato Nakazawa <minato-nakazawa at umin.net>
Professor, Division of Global Health, Department of Public Health,
Kobe University Graduate School of Health Sciences
[web] http://minato.sip21c.org/
[phone] +81-78-796-4551
[mobile e-mail] minatonakazawa at gmail.com

R help - Jul 2020 - how to calculate odd ratios with R?

[R] how to calculate odd ratios with R?

[R] how to calculate odd ratios with R?

[R] how to calculate odd ratios with R?

[R] how to calculate odd ratios with R?

[R] how to calculate odd ratios with R?