sjPlot function for specific terms for zeroinflated (ZINF) regression model
Question
i need to plot specific terms (from both conditional and zeroinflated model) from zero inflated negitve binomial regression in plot_model function using https://cran.r-project.org/web/packages/sjPlot/vignettes/plot_model_estimates.html . but i get an error (copied below) when i use term function but when i use rm.terms function it do not remove the variables from plot that i dont need. any help would be much appreciated
library(sjPlot)
library(sjlabelled)
library(sjmisc)
library(ggplot2)
library(MASS)
library(pscl)
library(boot)
zinb <- zeroinfl(ivdays~age+sex+edu,
link="logit",
dist = "negbin",
data=caterpillor)
summary(zinb)
plot_model(zinb)
plot_model(zinb, terms = c("age [b]", "age [c]"))
Error in .axisPars(usr, log = log, nintLog = nint) :
non-finite axis extents [GEPretty(inf,nan, n=5)]
In addition: Warning messages:
1: In min(new_value, na.rm = TRUE) :
no non-missing arguments to min; returning Inf
2: In min(dat$conf.low) : no non-missing arguments to min; returning Inf
3: In min(dat$estimate) : no non-missing arguments to min; returning Inf
4: In max(dat$conf.high) : no non-missing arguments to max; returning -Inf
5: In max(dat$estimate) : no non-missing arguments to max; returning -Inf
6: In axis_limits_and_ticks(axis.lim = axis.lim, min.val = min(dat$conf.low), :
NaNs produced
here is dummy data
structure(list(id = 1:100, age = structure(c(1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L ), levels = c("a", "b", "c"), class = "factor"), sex = structure(c(2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L), levels = c("F", "M"), class = "factor"), country = structure(c(1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L), levels = c("eng", "scot", "wale"), class = "factor"), edu = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L ), levels = c("x", "y", "z"), class = "factor"), lungfunction = c(45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 25L, 45L, 70L, 69L, 90L), ivdays = c(15L, 26L, 36L, 34L, 2L, 4L, 5L, 8L, 9L, 15L, 26L, 36L, 34L, 2L, 4L, 5L, 8L, 9L, 15L, 26L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 5L, 8L, 9L, 36L, 34L, 2L, 4L, 5L, 8L, 9L, 36L, 34L, 2L, 4L, 5L), no2_quintile = structure(c(1L, 1L, 1L, 1L, 1 L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L), levels = c("q1", "q2", "q3", "q4", "q5"), class = "factor")), class = "data.frame", row.names = c(NA, -100L))
1 answers
solution1
0 2022-08-30 16:38:35
Suppose you only want to show age[b] and age[c]. Try the code below:
library(sjPlot)
library(sjlabelled)
library(sjmisc)
library(ggplot2)
library(MASS)
library(pscl)
library(boot)
caterpillor=structure(list(id = 1:100,
age = structure(c(1L, 1L, 2L, 1L,
2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L,
1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L,
2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L,
2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L,
3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L,
2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 3L, 3L, 3L),
.Label = c("a", "b", "c"), class = "factor"),
sex = structure(c(2L,
1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L,
1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L,
1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L,
2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L,
2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L,
2L, 1L, 1L),
.Label = c("F", "M"), class = "factor"),
country = structure(c(1L,
1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L,
1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L,
2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L,
3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L,
1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 3L,
2L, 2L, 2L),
.Label = c("eng", "scot", "wale"), class = "factor"),
edu = structure(c(1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L,
1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L,
1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L,
1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L,
2L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 3L),
.Label = c("x", "y", "z"), class = "factor"),
lungfunction = c(45L,
23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L,
70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L,
50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L,
23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L,
70L, 69L, 90L, 50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L,
50L, 62L, 45L, 23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 45L,
23L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 25L, 45L, 70L, 69L,
90L, 50L, 62L, 25L, 45L, 70L, 69L, 90L, 50L, 62L, 25L, 45L,
70L, 69L, 90L),
ivdays = c(15L, 26L, 36L, 34L, 2L, 4L, 5L,
8L, 9L, 15L, 26L, 36L, 34L, 2L, 4L, 5L, 8L, 9L, 15L, 26L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L, 0L,
0L, 0L, 0L, 0L, 0L, 5L, 8L, 9L, 36L, 34L, 2L, 4L, 5L, 8L,
9L, 36L, 34L, 2L, 4L, 5L),
no2_quintile = structure(c(1L,
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L,
3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L,
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L),
.Label = c("q1", "q2",
"q3", "q4", "q5"), class = "factor")),
class = "data.frame", row.names = c(NA,
-100L))
zinb <- zeroinfl(ivdays~age+sex+edu,
link="logit",
dist = "negbin",
data=caterpillor)
summary(zinb)
plot_model(zinb, type="est")
# See the names of the coeffs, use this for the specification
print(coef(zinb))
plot_model(zinb, type="est", terms = c("count_ageb", "count_agec", "zero_ageb", "zero_agec"))
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