presentation_meta_analyses.qmd

---
title: "Meta-analysis of non-occupational physical activity and cardiovascular disease, cancer and mortality outcomes"
subtitle: Short URL = https://t.ly/z5SO
author: "Ali Abbas"
date: 05/05/2023
date-format: long
institute: MRC-Epidemiology Unit, University of Cambridge
format: 
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    header: Access the presentation by using https://t.ly/z5SO
editor: visual
filters:
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---

# Structure

## Agenda

-   Meta-Analysis
-   Physical Activity (PA) and its relationship with diseases/mortality
-   Outcomes of interest
-   Interactive Interface
-   Code to access the dose-response curves

# Meta-Analysis

## What is meta-analysis?

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::: {.column width="60%"}
-   Statistical technique for combining data from multiple studies on a particular topic.
-   Synthesizing evidence and summarizing the results of individual studies
:::

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[![The Evidence-Based Medicine Pyramid](https://static.s4be.cochrane.org/app/uploads/2013/02/ebmpyramid.jpg)](https://s4be.cochrane.org/blog/2014/04/29/the-evidence-based-medicine-pyramid/)
:::
:::

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<https://uk.cochrane.org/news/meta-analysis-what-why-and-how>
:::

## Diseases and PA

-   Globally
    -   Cardiovascular diseases cause 17.9 million deaths per year in 2019
    -   Cancers are responsible for 9.6 million deaths in 2017
-   Physical Activity is known to reduce the risk of cardiovascular diseases, cancers and early deaths

## Physical Activity Meta-Analysis

-   The shape of the dose-response curves has not been established for a range of chronic diseases (@garcia2023non)
-   Key finding: 1 in 10 premature deaths can be avoided if everyone achieves 75 minutes of vigorous-intensity activity a week
-   Higher level of PA is associated with lower risk of all outcomes [![dose-response paper](img/paper.png)](https://bjsm.bmj.com/content/early/2023/01/23/bjsports-2022-105669)

## Eligibility Criteria

-   Prospective cohort studies with general population samples of greater than 10K adults
-   3 or more physical activity categories
-   Risk measures and Confidence Interval (CIs) for host of measures/disease end points

## Studies

-   196 studies
-   94 cohorts
-   `>` 30 Million participants

# Interactive Interface

## Outcomes - overall

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<https://shiny.mrc-epid.cam.ac.uk/meta-analyses-physical-activity/>
:::

![](img/overall_health_outcomes.svg)

## Outcomes - Level 1

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<https://shiny.mrc-epid.cam.ac.uk/meta-analyses-physical-activity/>
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![](img/overall_health_outcomes_L1.svg)

## Outcomes - Level 2

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<https://shiny.mrc-epid.cam.ac.uk/meta-analyses-physical-activity/>
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![](img/overall_health_outcomes_L2.svg)

## Outcomes - Level 3

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<https://shiny.mrc-epid.cam.ac.uk/meta-analyses-physical-activity/>
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![](img/overall_health_outcomes_L3.svg)

## Outcome category and type

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<https://shiny.mrc-epid.cam.ac.uk/meta-analyses-physical-activity/>
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|                                 |                                       |
|---------------------------------|---------------------------------------|
| ![](img/outcome-categories.png) | ![](img/outcome-n-pop-categories.png) |

## Meta-analysis and dose-range

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<https://shiny.mrc-epid.cam.ac.uk/meta-analyses-physical-activity/>
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|                                   |
|-----------------------------------|
| ![](img/dose-re.png){width="590"} |
| ![](img/MA.png){width="590"}      |

## Dose distribution and Potential Impact Fraction (PIF)

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<https://shiny.mrc-epid.cam.ac.uk/meta-analyses-physical-activity/>
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|                                      |                   |
|--------------------------------------|-------------------|
| ![](img/dose-distr.png){width="812"} | ![](img/PIFs.png) |

# Code

## R Package {auto-animate="true"}

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<https://meta-analyses.github.io/drpa/drpa.html>
:::

-   An R package called `dose-response physical activity (drpa)` is created
-   It is open source and hosted on GitHub
-   You may need to install it used `remotes::install_github("meta-analyses/drpa")`

. . .

``` r
# Specify the cause, outcome_type and the dose
rr <- drpa::dose_response(cause = cause_name, 
        outcome_type = outcome_type, 
        dose = float)
```

## R Package use {auto-animate="true"}

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<https://meta-analyses.github.io/drpa/drpa.html>
:::

::: nonincremental
-   An R package called `dose-response physical activity` is created
-   It is open source and hosted on GitHub . . .
-   You may need to install it used `remotes::install_github("meta-analyses/drpa")`
:::

. . .

``` r
# Specify the cause, outcome_type, dose and the confidence interval
rr <- drpa::dose_response(cause = "all-cause-mortality", 
        outcome_type = "fatal", 
        dose = 40,
        confidence_interval = TRUE)
```

. . .

```{r, echo=FALSE}

#| tbl-cap: "Cars"
#| tbl-colwidths: [60,40]
#| tbl-cap-location: margin

rr <- drpa::dose_response(cause = "all-cause-mortality", 
        outcome_type = "fatal", 
        dose = 15,
        confidence_interval = TRUE)

names(rr) <- c("Relative Risk", "Lower Bound", "Upper Bound")

library(knitr)
knitr::kable(rr, align = "lccrr", caption = "An example output", digits = 2)

```

## R Package arguments {auto-animate="true"}

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<https://meta-analyses.github.io/drpa/drpa.html>
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[![Arguments for the dose_response function](img/drpa-args.png)](https://meta-analyses.github.io/drpa/drpa.html)

# Lookup tables

# Download from the Interactive Interface


![Lookup table for All-cause mortality](img/lookup_table.png)

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<https://shiny.mrc-epid.cam.ac.uk/meta-analyses-physical-activity/>
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# Lookup on GitHub repo

![Lookup tables for all the outcomes](img/drpa_lookup_tables.png)

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<https://github.com/meta-analyses/drpa/tree/master/inst/extdata>
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# Lookup on GitHub repo for All-cause-mortality


![Lookup tables for all the outcomes](img/drpa_lookup_acm.png)

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<https://github.com/meta-analyses/drpa/blob/master/inst/extdata/all-cause-mortality-fatal.csv>
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