Good afternoon,
Can someone help me with this problem? I am trying to create a linear regression with this data and in some variables I have the following problem:
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Can you please help me? Thank you very much for your help.
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library(tidyverse)
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library(dplyr)
library(tibble)
library(psych)
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library(flextable)
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library(Gmisc)
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library(Hmisc)
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library(kableExtra)
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library(knitr)
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library(prettydoc)
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library(gtsummary)
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library(eeptools)
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library(rstudioapi)
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library(htmlTable)
library(lubridate)
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library(nnet)
library(questionr)
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library(sjPlot)
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library(readr)
de <- read_csv("C:/Users/juanp/Desktop/de.csv",
col_types = cols(status.dead = col_factor(levels = c("1",
"0")), status.icu = col_factor(levels = c("1",
"0"))))
#> Warning: Missing column names filled in: 'X1' [1]
structure(de)
#> # A tibble: 981 x 9
#> X1 PATIENT.NUMBER status status.icu status.dead lockdown_date Age_category
#> <dbl> <dbl> <chr> <fct> <fct> <chr> <chr>
#> 1 1 0 Disch~ 0 0 Before lockd~ (50 to 59 y~
#> 2 2 1 Disch~ 0 0 After lockdo~ (50 to 59 y~
#> 3 3 2 Disch~ 0 0 After lockdo~ [18 to 40 y~
#> 4 4 3 Disch~ 0 0 After lockdo~ Above 80 ye~
#> 5 5 3 Disch~ 0 0 After lockdo~ Above 80 ye~
#> 6 6 4 Disch~ 0 0 After lockdo~ [18 to 40 y~
#> 7 7 5 Disch~ 0 0 After lockdo~ (50 to 59 y~
#> 8 8 6 Disch~ 0 0 After lockdo~ [18 to 40 y~
#> 9 9 7 Disch~ 0 0 After lockdo~ (50 to 59 y~
#> 10 10 8 Disch~ 0 0 After lockdo~ (60 to 69 y~
#> # ... with 971 more rows, and 2 more variables: OBESITY <dbl>, morbidity <chr>
t3.2 <-
glm(de$status.dead ~ de$Age_category , data= de, family = binomial) %>%
tbl_regression(exponentiate = TRUE) %>%
bold_p(t = 0.10) %>%
bold_labels() %>%
italicize_levels()
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
#> Warning in regularize.values(x, y, ties, missing(ties)): collapsing to unique
#> 'x' values
t3.2
| Characteristic | OR 1 | 95% CI 1 | p-value |
|---|---|---|---|
| de$Age_category | |||
| (40 to 49 years] | — | — | |
| (50 to 59 years] | 9.18 | 1.54, 175 | 0.042 |
| (60 to 69 years] | 4.41 | 0.99, 30.5 | 0.073 |
| (70 to 79 years] | 0.55 | 0.19, 1.45 | 0.2 |
| [18 to 40 years) | 6.09 | 1.38, 42.1 | 0.029 |
| Above 80 years | 0.10 | 0.04, 0.22 | <0.001 |
| Under 18 years | 958247 | 0.00, 3558377584379648918482064260406646080066682662420688868642226602864626064426646442264480046204228684402864062280648644 | > 0.9 > > |
| 1 OR = Odds Ratio, CI = Confidence Interval |