lme4::glmer.nb 函数根据顺序生成 "Error in family$family : $ operator not defined for this S4 class" 运行 模型

Question

library(lme4)

dummy <- as.data.frame(cbind(speed = rpois(100, 10), pop = rep(1:4, each = 25), season = rep(1:2, each = 50), id = seq(1, 100, by = 1)))
dummy2 <- as.data.frame(cbind(speed = c(rnbinom(50, 10, 0.6), rnbinom(50, 10, 0.1)), pop = rep(1:4, each = 25), season = rep(1:2, each = 50), id = seq(1, 100, by = 1)))

poisson <- glmer(speed~pop*season + (1|id),
             data=dummy, family="poisson")
neg.bin <- glmer.nb(speed ~ pop*season + (1|id),
                data=dummy2, control=glmerControl(optimizer="bobyqa"))

当我 运行 使用 lme4 包在负二项式模型之前创建泊松模型的脚本时，运行 宁 neg.bin 模型时出现以下错误：

Error in family$family : $ operator not defined for this S4 class

但是，如果我 运行 模型的顺序相反，我不会收到错误消息。

library(lme4)
dummy <- as.data.frame(cbind(speed = rpois(100, 10), pop = rep(1:4, each = 25), season = rep(1:2, each = 50), id = seq(1, 100, by = 1)))
dummy2 <- as.data.frame(cbind(speed = c(rnbinom(50, 10, 0.6), rnbinom(50, 10, 0.1)), pop = rep(1:4, each = 25), season = rep(1:2, each = 50), id = seq(1, 100, by = 1)))
neg.bin <- glmer.nb(speed ~ pop*season + (1|id),
                data=dummy2, control=glmerControl(optimizer="bobyqa"))
poisson <- glmer(speed~pop*season + (1|id),
             data=dummy, family="poisson")

neg.bin 模型示例确实有收敛警告，但我的实际模型也出现了相同的模式，收敛良好。 运行泊松模型首先如何影响 neg.bin 模型？

Answer 1

因为你屏蔽了 R 函数 poisson。以下将正常工作（除了 neg.bin 有收敛警告）：

library(lme4)
set.seed(0)
dummy <- as.data.frame(cbind(speed = rpois(100, 10), pop = rep(1:4, each = 25), season = rep(1:2, each = 50), id = seq(1, 100, by = 1)))
dummy2 <- as.data.frame(cbind(speed = c(rnbinom(50, 10, 0.6), rnbinom(50, 10, 0.1)), pop = rep(1:4, each = 25), season = rep(1:2, each = 50), id = seq(1, 100, by = 1)))

## use a different name for your model, say `poisson_fit`
poisson_fit <- glmer(speed~pop*season + (1|id),
         data=dummy, family="poisson")

negbin_fit <- glmer.nb(speed ~ pop*season + (1|id),
            data=dummy2, control=glmerControl(optimizer="bobyqa"))

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问题来了。在 glmer.nb 的前几行中有一行：

mc$family <- quote(poisson)

因此，如果您屏蔽 poisson，则无法找到 stats 包中的正确函数 poisson。

Ben 刚刚解决了这个问题，将其替换为：

mc$family <- quote(stats::poisson)

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我最初对 family = "poisson" 和 match.fun 的观察并不是这里的真正问题。它只是解释了为什么在glm和mgcv::gam这样的例程中，传递一串family.

是合法的