Hello,
To extract all but the first 2 rows, use a negative index on the rows.
I will also coerce to data.frame and add a id column, it will be needed
to plot the confidence intervals.
ORCI <- exp(cbind(OR = coef(model ), confint(model )))[-(1:2), ]
ORCI <- cbind.data.frame(ORCI, id = row.names(ORCI))
Now the base R and ggplot plots. In both cases plot the bars first, then
the points.
1. Base R
ymin <- min(apply(ORCI[2:3], 1, range)[1,])
ymax <- max(apply(ORCI[2:3], 1, range)[2,])
plot((ymin + ymax)/2,
type = "n",
xaxt = "n",
xlim = c(0.5, 5.5),
ylim = c(ymin, ymax),
xlab = "X3",
ylab = "Odds Ratio")
with(ORCI, arrows(x0 = seq_along(id),
y0 = `2.5 %`,
y1 = `97.5 %`,
code = 3,
angle = 90))
points(OR ~ seq_along(id), ORCI, pch = 16)
axis(1, at = seq_along(ORCI$id), labels = ORCI$id)
2. Package ggplot2
library(ggplot2)
ggplot(ORCI, aes(id, OR)) +
geom_errorbar(aes(ymin = `2.5 %`, max = `97.5 %`)) +
geom_point() +
theme_bw()
Hope this helps,
Rui Barradas
Às 21:01 de 14/06/2022, anteneh asmare escreveu:
sample_data =
read.table("http://freakonometrics.free.fr/db.txt",header=TRUE,sep=";";)
head(sample_data)
model = glm(Y~0+X1+X2+X3,family=binomial,data=sample_data)
summary(model)
exp(coef(model ))
exp(cbind(OR = coef(model ), confint(model )))
I have the aove sample data on logistic regression with categorical predictor
I try the above code i get the follwing out put,
OR 2.5 % 97.5 %
X1 1.67639337 1.352583976 2.09856514
X2 1.23377720 1.071959330 1.42496949
X3A 0.01157565 0.001429430 0.08726854
X3B 0.06627849 0.008011818 0.54419759
X3C 0.01118084 0.001339984 0.08721028
X3D 0.01254032 0.001545240 0.09539880
X3E 0.10654454 0.013141540 0.87369972
but i am wondering i want to extract OR and CI only for factors, My
desire out put will be
OR 2.5 % 97.5 %
X3A 0.01157565 0.001429430 0.08726854
X3B 0.06627849 0.008011818 0.54419759
X3C 0.01118084 0.001339984 0.08721028
X3D 0.01254032 0.001545240 0.09539880
X3E 0.10654454 0.013141540 0.87369972
Can any one help me the code to extact it?
additionally I want to plot the above OR with confidence interval for
the extracted one
can you also help me the code with plot,or box plot
Kind Regards,
Hana
______________________________________________
R-help@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.
______________________________________________
R-help@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.
