## knitr configuration: http://yihui.name/knitr/options#chunk_options library(knitr) showMessage <- FALSE showWarning <- TRUE set_alias(w = "fig.width", h = "fig.height", res = "results") opts_chunk$set(comment = "##", error= TRUE, warning = showWarning, message = showMessage, tidy = FALSE, cache = FALSE, echo = TRUE, fig.width = 7, fig.height = 7, fig.path = "man/figures")
The package require all variables to be numerical. So a multi-categorical factor needs to be converted to dummy variables or multiple dichotomous indicators. For survival outcome models, the indicator variable is for the event (1 = event, 0 = censored).
library(regmedint) library(tidyverse) ## Prepare dataset data(vv2015)
regmedint
objectFollowing typical modeling workflow in R (e.g., lm
and glm
), a constructor function is used to create a model fit object. The summary
method is the main user function for examining the results in the object. Lower-level methods such as coef
, vcov
, and confint
are also provided for flexibility. The print
method is mainly for meaningful implicit printing when only the object name is evaluated. All methods for the regmedint
object has arguments a0
, a1
, m_cde
, and c_cond
. These are used to re-evaluate the results without re-fitting the underlying models.
regemedint()
object constructorregmedint_obj <- regmedint(data = vv2015, ## Variables yvar = "y", avar = "x", mvar = "m", cvar = c("c"), eventvar = "event", ## Values at which effects are evaluated a0 = 0, a1 = 1, m_cde = 1, c_cond = 0.5, ## Model types mreg = "logistic", yreg = "survAFT_weibull", ## Additional specification interaction = TRUE, casecontrol = FALSE)
summary()
for regmedint
summary(regmedint_obj) summary(regmedint_obj, exponentiate = TRUE) summary(regmedint_obj, m_cde = 0, c_cond = 1) summary(regmedint_obj, m_cde = 0, c_cond = 1, level = 0.99)
coef()
for regmedint
coef(regmedint_obj) coef(regmedint_obj, m_cde = 0, c_cond = 1)
vcov()
for regmedint
vcov(regmedint_obj) vcov(regmedint_obj, m_cde = 0, c_cond = 1)
confint()
for regmedint
confint(regmedint_obj) confint(regmedint_obj, m_cde = 0, c_cond = 1) confint(regmedint_obj, m_cde = 0, c_cond = 1, level = 0.99)
print()
for regmedint
regmedint_obj # Implicit printing print(regmedint_obj) print(regmedint_obj, m_cde = 0, c_cond = 1)
summary_regmedint
The summary
method for the regmedint
object returns an object of class summary_regmedint
. To extract the mediation analysis result table as a matrix, use the coef
method.
coef()
for summary_regmedint
coef(summary(regmedint_obj))
print()
for summary_regmedint
regmedint_summary_obj <- summary(regmedint_obj) regmedint_summary_obj # Implicit printing print(regmedint_summary_obj)
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