tab (version 4.1.1)

tabcoxph: Create Summary Table for Fitted Cox Proportional Hazards Model

Description

Creates a table summarizing a GEE fit using the coxph function.

Usage

tabcoxph(fit, columns = c("beta.se", "hr.ci", "p"), var.labels = NULL,
  factor.compression = 1, sep.char = ", ", indent.spaces = 3,
  latex = TRUE, decimals = 2, formatp.list = NULL,
  print.html = FALSE, html.filename = "table1.html")

Arguments

fit

Fitted coxph object.

columns

Character vector specifying what columns to include. Choies for each element are "events", "beta", "se", "beta.se", "beta.betaci", "betaci", "hr", "hr.hrci", "hrci", "z", and "p".

var.labels

Named list specifying labels to use for certain predictors. For example, if fit includes a predictor named "race" that you want to label "Race/ethnicity" and a predictor named "age_yrs" that you want to label "Age (years)", use var.labels = list(race = "Race/ethnicity", age_yrs = "Age (years)".

factor.compression

Integer value from 1 to 5 controlling how much compression is applied to factor predictors (higher value = more compression). If 1, rows are Variable, Level 1 (ref), Level 2, ...; if 2, rows are Variable (ref = Level 1), Level 2, ...; if 3, rows are Level 1 (ref), Level 2, ...; if 4, rows are Level 2 (ref = Level 1), ...; if 5, rows are Level 2, ...

sep.char

Character string with separator to place between lower and upper bound of confidence intervals. Typically "-" or ", ".

indent.spaces

Integer value specifying how many spaces to indent factor levels.

latex

Logical value for whether to format table so it is ready for printing in LaTeX via xtable or kable.

decimals

Numeric value specifying number of decimal places for numbers other than p-values.

formatp.list

List of arguments to pass to formatp.

print.html

Logical value for whether to write a .html file with the table to the current working directory.

html.filename

Character string specifying the name of the .html file that gets written if print.html = TRUE.

Value

Data frame which you can print in R (e.g. with xtable's xtable or knitr's kable) or export to Word, Excel, or some other program. To export the table, set print.html = TRUE. This will result in a .html file being written to your current working directory, which you can open and copy/paste into your document.

References

1. Therneau, T. (2015). A Package for Survival Analysis in S. R package version 2.38. https://cran.r-project.org/package=survival.

2. Therneau, T.M. and Grambsch, P.M. (2000). Modeling Survival Data: Extending the Cox Model. Springer, New York. ISBN 0-387-98784-3.

Examples

# NOT RUN {
# Cox PH model with age, sex, race, and treatment
library("survival")
fit <- coxph(Surv(time = time, event = delta) ~ Age + Sex + Race + Group,
             data = tabdata)
kable(tabcoxph(fit))

# Can also use piping
fit %>% tabcoxph() %>% kable()

# Same as previous, but with custom labels for Age and Race and factors
# displayed in slightly more compressed format
fit %>%
  tabcoxph(var.labels = list(Age = "Age (years)", Race = "Race/ethnicity"),
           factor.compression = 2) %>%
           kable()

# Cox PH model with some higher-order terms
fit <- coxph(Surv(time = time, event = delta) ~
             poly(Age, 2, raw = TRUE) + Sex + Race + Group + Race*Group,
             data = tabdata)
fit %>% tabcoxph() %>% kable()


# }