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R Code - Producing Automated Outputs

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16 views

R Code - Producing Automated Outputs

Uploaded by

nhanvlh23414b
Copyright
© © All Rights Reserved
Available Formats
Download as DOCX, PDF, TXT or read online on Scribd
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This code is part of NCRM Online Tutorial:

Producing Automated Outputs (using R) https://www.ncrm.ac.uk/resources/online/all/?


id=20832

#Install and load required packages


install.packages("gtsummary")
install.packages("flextable")
install.packages("officer")
install.packages("car")
library(gtsummary)
library(flextable)
library(officer)
library(car)

#Create a dataset called 'cars' by loading the built-in 'mtcars' dataset


#Some variables are then removed to create a smaller dataset
cars <- mtcars
head(cars)
cars$drat<-NULL
cars$qsec<-NULL
cars$hp<-NULL
cars$gear<-NULL
cars$carb<-NULL
cars$disp<-NULL
head(cars)
summary(cars)

#Examine distribution of variables


hist(cars$mpg) # Approximately normally distributed
table(cars$cyl) # Values of 4, 6, 8
hist(cars$wt) # Continuous, not normally distributed
table(cars$vs) # Values of 0, 1
table(cars$am) # Values of 0, 1

#Convert weight from 1000s of pounds to tonnes


cars$wt <- cars$wt * 0.454

#Declare categorical variables as factor variables and label the categories


cars$vs <- factor(cars$vs, levels = c(0,1), labels = c("V-shaped", "Straight"))
cars$am <- factor(cars$am, levels = c(0,1), labels = c("Automatic", "Manual"))
cars$cyl <- factor(cars$cyl, levels = c(4,6,8))

#Re-order dataset columns and examine final dataset


cars <- cars[, c("am", "wt", "vs", "cyl", "mpg")]
head(cars)
summary(cars)

#Base this table on the 'cars' dataset


#Specify which variables are continuous and categorical
#Specify the name to use in the table for each variable
#State the descriptive statistics to use for each variable
#Specify the file path and file name for the Word document
tbl_summary(cars,
type = list(c(wt, mpg) ~ "continuous", c(am, vs, cyl) ~ "categorical"),
label = list(
am ~ "Transmission type",
wt ~ "Weight (tonnes)",
vs ~ "Engine configuration",
cyl ~ "Number of cylinders",
mpg ~ "Fuel economy (miles per gallon)"),
statistic = list(
c(mpg) ~ "{mean} ({sd})",
c(wt) ~ "{median} ({p25}, {p75})",
c(am, vs, cyl) ~ "{n} ({p}%)")
) %>%
as_flex_table() %>%
flextable::save_as_docx(path="C:/Users/ldw1c13/Documents/Descriptives Table 1.docx")

#Stratify the above table according to transmission type


#Specify the stratification variable using ‘by = am’
tbl_summary(cars,
by = am,
type = list(c(wt, mpg) ~ "continuous", c(vs, cyl) ~ "categorical"),
label = list(
wt ~ "Weight (tonnes)",
vs ~ "Engine configuration",
cyl ~ "Number of cylinders",
mpg ~ "Fuel economy (miles per gallon)"),
statistic = list(
c(mpg) ~ "{mean} ({sd})",
c(wt) ~ "{median} ({p25}, {p75})",
c(vs, cyl) ~ "{n} ({p}%)")
) %>%
as_flex_table() %>%
flextable::save_as_docx(path="C:/Users/ldw1c13/Documents/Descriptives Table 2.docx")

#Define the model ‘m1’ and use it in the regression table


#Specify the name to use in the table for each exposure
#Do not display the intercept in the table
#Only show one row for the binary exposure engine configuration
#Modify column headings and footnotes
m1 <- lm(mpg ~ wt + vs + relevel(cyl, ref = "8"), data=cars)
tbl_regression(m1,
label = list(
wt ~ "Weight (tonnes)",
vs ~ "Engine configuration (straight vs v-shaped)",
'relevel(cyl, ref = "8")' ~ "Number of cylinders"),
intercept = FALSE,
show_single_row = c(vs)
) %>%
modify_header(label = "**Exposure**", estimate = "**Estimate**", ci = "**95% CI**", p.value = "**P-value**") %>
%
modify_footnote(ci = "CI: Confidence interval", abbreviation = TRUE) %>%
modify_footnote(estimate ~ "Difference in fuel economy (miles per gallon) according to exposure; exposures were
included simultaneously in the model") %>%
as_flex_table() %>%
flextable::save_as_docx(path="C:/Users/ldw1c13/Documents/Regression Table 1.docx")

#Define the logistic regression model ‘m2’ and use it in the regression table
#Display exponentiated coefficients (odds ratios) in the table
m2 <- glm(am ~ mpg + vs, data=cars, family=binomial)
tbl_regression(m2, exponentiate=TRUE,
label = list(
mpg ~ "Fuel economy (miles per gallon)",
vs ~ "Engine configuration (straight vs v-shaped)"),
intercept = FALSE,
show_single_row = c(vs)
) %>%
modify_header(label = "**Exposure**", estimate = "**OR**", ci = "**95% CI**", p.value = "**P-value**") %>%
modify_footnote(estimate = "OR: Odds ratio", abbreviation = TRUE) %>%
modify_footnote(ci = "CI: Confidence interval", abbreviation = TRUE) %>%
modify_footnote(estimate ~ "Odds ratios for manual transmission according to exposures; exposures were included
simultaneously in the model") %>%
as_flex_table() %>%
flextable::save_as_docx(path="C:/Users/ldw1c13/Documents/Regression Table 2.docx")

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