In meta-analyses/drpa: Dose-response for Physical Activity and various causes and diseases

knitr::opts_chunk$set(collapse = T, comment = "#>", root.dir = 'vignettes')
options(tibble.print_min = 4L, tibble.print_max = 4L, rmarkdown.html_vignette.check_title = FALSE)

Last updated on: r format(Sys.Date(), '%d %B, %Y')

Installation from GitHub

The package is not available at CRAN. It needs to be installed from GitHub. Please use this command to install it.

remotes::install_github("meta-analyses/drpa")

You may need to install the remotes package first.

List of diseases/cause and their upper limit

The first column disease specifies the supported diseases in the package. The other three columns, which are outcome types (fatal, non-fatal and fatal-and-non-fatal), show the last knot (based on the available data points) for the specific disease. We don't have confidence that our meta-analysis is reliable after this point, and assumes an onward flat relationship. Whenever a disease such as all-cause-cvd doesn't have an outcome type non-fatal, it will be NA. More will follow in the next section.

library(magrittr)
require(kableExtra)

dtable <- readr::read_csv('../inst/extdata/75p_diseases.csv')

kbl(dtable) %>%
  kable_styling(bootstrap_options = c("striped", "hover", "condensed", "responsive"))

Setup

Load the package

library(drpa)

Get dose response relationship

Get response for dose 40 for all-cause-cvd with the default quantile 0.5 and censoring at doubling of WHO's recommended level of physical activity for adults (17.5 MMETs hours per week).

The quantile's value is between 0 and 1 [excluding the boundary values]

drpa::dose_response(cause = 'all-cause-cvd', outcome_type = 'fatal-and-non-fatal', dose = 40, 
                    quantile = 0.5, confidence_intervals = T, censor_method = 'WHO-DRL')

Arguments

Description of the arguments are mentioned below:

| Argument | Description | |-----------------|-------------------------------------------------------| | cause | All-cause-mortality or disease name | | outcome_type | Either one of the three possibilities for outcome type: fatal, non-fatal or fatal-and-non-fatal | | dose | Dose (all-cause or disease) | | quantile | Numeric value between 0 and 1 - default is 0.5. This captures the range of dose values between lower and upper confidence levels. | | censor_method | This determines whether any censor method applies to the dose-response relationship. There are four possibilities: none, 75thPercentile(to use 75th percentile using person years), WHO-DRL (WHO's recommended physical activity per week 8.75 when doubled, so 17.5 MMETs hours per week) or WHO-QRL (WHO's recommended physical activity per week 8.75 when quadrupled, so 35 MMETs hours per week) . The default value is WHO-DRL - a fixed censor point at 17.5 after which the relationship remains the same. | | confidence_intervals | Boolean variable to determine whether confidence intervals are returned or not - default false |

meta-analyses/drpa documentation built on Nov. 6, 2023, 5:06 a.m.