Add book example

Author: NightlordTW

bibliography.bib

@@ -20,3 +20,29 @@ @incollection{debray_principles_2025
   year      = {2026},
   note      = {In press}
 }
+
+@article{selvarajan_efficacy_2022,
+  title = {Efficacy of Pharmacological Interventions in {{COVID}}-19: {{A}} Network Meta-analysis},
+  author = {Selvarajan, Sandhiya and Anandaradje, Annuja and Shivabasappa, Santhosh and Melepurakkal Sadanandan, Deepthy and Nair, N. Sreekumaran and George, Melvin},
+  year = 2022,
+  month = sep,
+  journal = {British Journal of Clinical Pharmacology},
+  volume = {88},
+  number = {9},
+  pages = {4080--4091},
+  doi = {10.1111/bcp.15338},
+  urldate = {2023-04-12}
+}
+
+@article{siemieniuk_drug_2020,
+  title = {Drug Treatments for Covid-19: Living Systematic Review and Network Meta-Analysis},
+  author = {Siemieniuk, Reed AC and Bartoszko, Jessica J and Ge, Long and Zeraatkar, Dena and Izcovich, Ariel and Kum, Elena and {Pardo-Hernandez}, Hector and Qasim, Anila and Martinez, Juan Pablo D{\'i}az and Rochwerg, Bram and Lamontagne, Francois and Han, Mi Ah and Liu, Qin and Agarwal, Arnav and Agoritsas, Thomas and Chu, Derek K and Couban, Rachel and Cusano, Ellen and Darzi, Andrea and Devji, Tahira and Fang, Bo and Fang, Carmen and Flottorp, Signe Agnes and Foroutan, Farid and Ghadimi, Maryam and {Heels-Ansdell}, Diane and Honarmand, Kimia and Hou, Liangying and Hou, Xiaorong and Ibrahim, Quazi and Khamis, Assem and Lam, Bonnie and Loeb, Mark and Marcucci, Maura and McLeod, Shelley L and Motaghi, Sharhzad and Murthy, Srinivas and Mustafa, Reem A and Neary, John D and Rada, Gabriel and Riaz, Irbaz Bin and Sadeghirad, Behnam and Sekercioglu, Nigar and Sheng, Lulu and Sreekanta, Ashwini and Switzer, Charlotte and Tendal, Britta and Thabane, Lehana and Tomlinson, George and Turner, Tari and Vandvik, Per O and Vernooij, Robin WM and {Viteri-Garc{\'i}a}, Andr{\'e}s and Wang, Ying and Yao, Liang and Ye, Zhikang and Guyatt, Gordon H and {Brignardello-Petersen}, Romina},
+  year = 2020,
+  month = jul,
+  journal = {BMJ},
+  pages = {m2980},
+  issn = {1756-1833},
+  doi = {10.1136/bmj.m2980}
+}
+
+

covid-network-meta-analysis.qmd

@@ -0,0 +1,73 @@
+---
+title: "Comparative Effectiveness of Treatments for COVID-19: A Network Meta-Analysis Example"
+author: "Thomas Debray"
+format:
+  html:
+    toc: true
+    number-sections: true
+execute:
+  message: false
+  warning: false
+bibliography: 'bibliography.bib'
+---
+
+## Overview
+This vignette reproduces the main analyses discussed in the book chapter "Principles of meta-analysis and indirect treatment comparisons" [@debray_principles_2025].
+
+We focus on a case study assessing the comparative effectiveness of remdesivir and tocilizumab in hospitalized COVID-19 patients, using data synthesized from 21 randomized trials.
+
+## Data Source
+
+Trials were identified from two published network meta-analyses [@selvarajan_efficacy_2022; @siemieniuk_drug_2020], the COVID-NMA Initiative [Covid-NMA.com], and [clinicaltrials.gov].
+
+Inclusion criteria were:
+
+* hospitalized COVID-19 patients,
+* interventions: remdesivir or tocilizumab,
+* comparator: placebo or standard of care,
+* short-term mortality outcome available,
+* peer-reviewed publication.
+
+```{r}
+#| echo: true
+#| message: false
+#| warning: false
+library(dplyr)
+
+covid <- readRDS(file.path("data","covid.rds"))
+
+# Define abbreviations
+covid <- covid %>% mutate(
+  trt = case_when(
+    trtn == "Remdesivir" ~ "REM",
+    trtn == "Tocilizumab" ~ "TOC",
+    trtn == "Standard of care" ~ "STD"
+  )
+)
+```
+
+```{r}
+#| echo: true
+#| message: false
+#| warning: false
+library(kableExtra)
+kable(head(covid))
+```
+
+## Setting up the Network
+
+We first define the network of interventions and visualize the geometry of available evidence.
+
+```{r}
+#| echo: true
+#| message: false
+#| warning: false
+library(multinma)
+net <- set_agd_arm(data = covid,
+                   study = studlab,
+                   trt = trt,
+                   r = events,
+                   n = n)
+plot(net, weight_edges = TRUE, weight_nodes = TRUE)  +
+    theme(legend.position = "none")
+```