[英]Odds ratio and confidence intervals from glmer output
I have made a model that looks at a number of variables and the effect that has on pregnancy outcome. 我制作了一个模型,该模型着眼于许多变量及其对妊娠结局的影响。 The outcome is a grouped binary. 结果是分组二进制。 A mob of animals will have 34 pregnant and 3 empty, the next will have 20 pregnant and 4 empty and so on. 一群动物将有34个怀孕和3个空,接下来将有20个怀孕和4个空等等。
I have modelled this data using the glmer
function where y is the pregnancy outcome (pregnant or empty). 我使用glmer
函数对这些数据建模,其中y是妊娠结果(怀孕或空白)。
mclus5 <- glmer(y~adg + breed + bw_start + year + (1|farm),
data=dat, family=binomial)
I get all the usual output with coefficients etc. but for interpretation I would like to transform this into odds ratios and confidence intervals for each of the coefficients. 我得到所有通常的系数等输出但是对于解释我想将其转换为每个系数的优势比和置信区间。
In past logistic regression models I have used the following code 在过去的逻辑回归模型中,我使用了以下代码
round(exp(cbind(OR=coef(mclus5),confint(mclus5))),3)
This would very nicely provide what I want, but it does not seem to work with the model I have run. 这将很好地提供我想要的东西,但它似乎不适用于我运行的模型。
Does anyone know a way that I can get this output for my model through R? 有谁知道我可以通过R为我的模型获得此输出的方式?
The only real difference is that you have to use fixef()
rather than coef()
to extract the fixed-effect coefficients ( coef()
gives you the estimated coefficients for each group ). 唯一真正的区别是你必须使用fixef()
而不是coef()
来提取固定效应系数( coef()
给出每组的估计系数)。
I'll illustrate with a built-in example from the lme4
package. 我将用lme4
包中的内置示例进行lme4
。
library("lme4")
gm1 <- glmer(cbind(incidence, size - incidence) ~ period + (1 | herd),
data = cbpp, family = binomial)
Fixed-effect coefficients and confidence intervals, log-odds scale: 固定效应系数和置信区间,对数 - 赔率表:
cc <- confint(gm1,parm="beta_") ## slow (~ 11 seconds)
ctab <- cbind(est=fixef(gm1),cc)
(If you want faster-but-less-accurate Wald confidence intervals you can use confint(gm1,parm="beta_",method="Wald")
instead; this will be equivalent to @Gorka's answer but marginally more convenient.) (如果你想要更快但更准确的Wald置信区间,你可以使用confint(gm1,parm="beta_",method="Wald")
;这相当于@ Gorka的答案,但稍微方便一些。)
Exponentiate to get odds ratios: Exponentiate得到比值比:
rtab <- exp(ctab)
print(rtab,digits=3)
## est 2.5 % 97.5 %
## (Intercept) 0.247 0.149 0.388
## period2 0.371 0.199 0.665
## period3 0.324 0.165 0.600
## period4 0.206 0.082 0.449
A marginally simpler/more general solution: 一个稍微简单/更通用的解决方案:
library(broom.mixed)
tidy(gm1,conf.int=TRUE,exponentiate=TRUE,effects="fixed")
for Wald intervals, or add conf.method="profile"
for profile confidence intervals. 对于Wald间隔,或为配置文件置信区间添加conf.method="profile"
。
I believe there is another, much faster way (if you are OK with a less accurate result). 我相信还有另一种更快的方法(如果你的结果不太准确)。
From: http://www.ats.ucla.edu/stat/r/dae/melogit.htm 来自: http : //www.ats.ucla.edu/stat/r/dae/melogit.htm
First we get the confidence intervals for the Estimates 首先,我们得到估计的置信区间
se <- sqrt(diag(vcov(mclus5)))
# table of estimates with 95% CI
tab <- cbind(Est = fixef(mclus5), LL = fixef(mclus5) - 1.96 * se, UL = fixef(mclus5) + 1.96 * se)
Then the odds ratios with 95% CI 然后比值比为95%CI
print(exp(tab), digits=3)
Other option I believe is to just use package emmeans
: 我认为其他选择只是使用包emmeans
:
library(emmeans)
data.frame(confint(pairs(emmeans(fit, ~ factor_name,type="response"))))
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