There are more than 50 exposure variables and a total of 16,000 data.
I need to analyze the association between all exposure variables and outcome.
I would like to repeat the following formula.
example.data <- data.frame(outcome = c(0,0,0,1,0,1,0,0,1,0),
exposure_1 = c(2.03, 2.13, 0.15, -0.14, 0.32,2.03, 2.13, 0.15, -0.14, 0.32),
exposure_2 = c(-0.11, 0.93, -1.26, -0.95, 0.24,-0.11, 0.93, -1.26, -0.95, 0.24),
age = c(20, 25, 30, 35, 40, 50, 55, 60, 65, 70),
bmi = c(20, 23, 21, 20, 25, 18, 20, 25, 26, 27))
logit_1 <- glm(outcome ~exposure_1, family = binomial, data = example.data)
logit_2 <- glm(outcome~ exposure_2 + age+ bmi, family = binomial, data = example.data)
I made a formula like this.
Model1 <- function(x) {
temp <- glm(reformulate(x,response="outcome"), data=example.data, family=binomial)
c(exp(summary(temp)$coefficients[2,1]), # OR
exp(confint(temp)[2,1]), # CI 2.5
exp(confint(temp)[2,2]), # CI 97.5
summary(temp)$coefficients[2,4], # P-value
colAUC(predict(temp, type = "response"),example.data$outcome)) #AUC
Model1.data <- as.data.frame(t(sapply(setdiff(names(example.data),"outcome"), Model1)))
}
Model2 <- function(x) {
temp <- glm(reformulate(x + age + bmi, response="outcome"), data=example.data, family=binomial)
c(exp(summary(temp)$coefficients[2,1]), # OR
exp(confint(temp)[2,1]), # CI 2.5
exp(confint(temp)[2,2]), # CI 97.5
summary(temp)$coefficients[2,4], # P-value
colAUC(predict(temp, type = "response"),example.data$outcome)) #AUC
}
Model2.data <- as.data.frame(t(sapply(setdiff(names(example.data),"outcome"), Model2)))
However, function "Model2" is not working.
The code that I made only operates single binary logistic regression, but can not be analyzed by adding multiple confounders.
Use c()
not +
in reformulate
. In both your functions, x
takes the value of column names. I'll use mtcars
column names to illustrate:
## Model1 works
reformulate("hp", response = "mpg")
# mpg ~ hp
## Model2 doesn't work
reformulate("hp" + wt + cyl, response = "mpg")
# Error in reformulate("hp" + wt + cyl, response = "mpg") :
# object 'wt' not found
## Fix it with `c()` and quoted column names
reformulate(c("hp", "wt", "cyl"), response = "mpg")
# mpg ~ hp + wt + cyl
## Showing it works with a mix of variables and quoted column names
x = "hp"
reformulate(c(x, "wt", "cyl"), response = "mpg")
# mpg ~ hp + wt + cyl
So in your Model2
, change to reformulate(c(x, "age", "bmi"), response="outcome")
You have additional problems - you are running Model2
on all columns except for outcome
(setdiff(names(example.data),"outcome")
), but you should also exclude bmi
and age
since they are included inside the function.