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I'm trying to compare the prevalence of a specific lesion (binary) at the symptomatic side to the asymptomatic side within a group of patients.

I've already performed a McNemar test to compare the prevalence at the symptomatic versus asymptomatic side within patients.

However, I'm asked to also perform a conditional logistic regression. I'm not sure if my syntax is correct with respect to the stratification:

summary(clogit(ds$symp ~  ds$asymp, strata(ds$ID), data=ds, method = "exact"))

Question: Does R compare both sides of the patient (symptomatic vs asymptomatic) within the patient(s)? Or do I have to duplicate manually the patient ID (one ID for the symptomatic side AND one ID for the asymptomatic side)?

An example:

ID symp asymp
1   0   0
2   1   0
3   0   0
4   0   0
5   1   0
6   1   1
7   0   0
8   0   0
9   0   1
10  0   0

As an example: patient 2 has a lesion at the symptomatic side and patient 9 only at the asymptomatic side. Patients 6 at both sides.

A Exact McNemar test shows:

test <- table(df$symp, df$asymp)
    compare <- exact2x2(test, paired = TRUE, alternative = "two.sided", tsmethod = "central")
print(compare)
Exact McNemar test (with central confidence intervals)

data:  test
b = 1, c = 2, p-value = 1
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.00847498 9.60452988
sample estimates:
odds ratio 
       0.5

However, a conditional logistic regression model shows:

> summary(clogit(df$symp ~  df$asymp, strata(df$ID), data=df, method = "exact"))
Call:
coxph(formula = Surv(rep(1, 10L), df$symp) ~ df$asymp, data = df, 
    method = "exact")

  n= 10, number of events= 3 

        coef exp(coef) se(coef)     z Pr(>|z|)
df$symp 0.973     2.646    1.524 0.638    0.523

       exp(coef) exp(-coef) lower .95 upper .95
df$asymp 2.646      0.378    0.1334     52.46

Rsquare= 0.039   (max possible= 0.616 )
Likelihood ratio test= 0.4  on 1 df,   p=0.528
Wald test            = 0.41  on 1 df,   p=0.5232
Score (logrank) test = 0.43  on 1 df,   p=0.5127

Or should I duplicate patients and use the syntax as described above?

ID side   lesion
1   symp    0
1   asymp   1
2   symp    0
2   asymp   0
3   symp    1
3   asymp   0
4   symp    0
4   asymp   0
5   symp    1
5   asymp   1
6   symp    1
6   asymp   0
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