In windyzn/urinaryDBP:

# Only set if the Rmd file is not in the parent directory (ie. 'projectname/')
knitr::opts_knit$set(root.dir = '../')

knitr::opts_chunk$set(collapse = TRUE, echo = FALSE, message = FALSE, warning = FALSE)
library(tidyverse)
devtools::load_all()
load_data(update = TRUE)
set_options()

ds <- project_data

ds_original <- PROMISE::PROMISE

# dm status
ds_dm <- PROMISE::PROMISE %>% 
  dplyr::mutate(dmStatus = ifelse(DM == 1, "DM",
                                  ifelse(IFG == 1, "IFG",
                                         ifelse(IGT == 1, "IGT",
                                                "NGT"))),
                # dmStatus = ifelse(is.na(dmStatus), "NGT", dmStatus),
                dmStatus = factor(dmStatus,
                                  levels = c("NGT", "IFG", "IGT", "DM"),
                                  ordered = TRUE),
                fVN = factor(
                  VN,
                  levels = c(1, 3, 6),
                  labels = c("Baseline", "3Year", "6Year"),
                  ordered = TRUE))

subchar_dm <- tableone::CreateTableOne(
  vars = c("dmStatus"),
  data = ds_dm,
  strata = "fVN",
  factorVars = c("dmStatus")) %>% 
  print()

knitr::kable(subchar_dm)

There are 43 missing measurements for glycemic status

ds_dm %>% 
  dplyr::select(SID, fVN, dmStatus, Glucose0_OGTT, Glucose120_OGTT) %>% 
  dplyr::filter(is.na(dmStatus)) %>% 
  knitr::kable()

windyzn/urinaryDBP documentation built on May 4, 2019, 6:32 a.m.