## Install R packages (if not already installed)
#   install.packages("netmeta")
#   install.packages("dplyr")


options(width = 70, prompt="R> ", continue = "+ ")


## Data set 1: adjuvant treatments in Parkinson's disease
##
data("Stowe2010", package = "netmeta")
library("dplyr")
Stowe2010 %>% slice(18:20)


## Data set 2: antithrombotics to prevent strokes
##
data("Dogliotti2014", package = "netmeta")
head(Dogliotti2014, 7)


## Data set 3: treatments for chronic obstructive pulmonary disease
##
data("Baker2009", package = "netmeta")
subset(Baker2009, study == "Mahler 2002")


## Network meta-analysis in practice -- overview of netmeta
##
library("netmeta")
settings.meta(digits = 2, digits.se = 3)


## Example 1: adjuvant treatments in Parkinson's disease
##
pw1 <- pairwise(treat = list(t1, t2, t3), n = list(n1, n2, n3),
  mean = list(y1, y2, y3), sd = list(sd1, sd2, sd3),
  studlab = study, data = Stowe2010)

dim(pw1)
names(pw1)

selstudy1 <- c("COMTI(E) INT-OZ", "LARGO", "COMTI(E) Nomecomt")
subset(pw1, studlab %in% selstudy1) %>%
  select(TE, seTE, studlab, treat1, treat2, mean1, mean2)

net1 <- netmeta(TE, seTE, treat1, treat2, studlab, data = pw1,
  common = FALSE, ref = "plac")

net1 <- netmeta(pw1, common = FALSE, ref = "plac")

# pdf("Figures/netgraph1.pdf", width = 7, height = 6)
netgraph(net1, plastic = FALSE, multiarm = TRUE,
  cex = 1.25, offset = ifelse(trts != "MAOBI", 0.025, 0.01),
  number.of.studies = TRUE, cex.number = 1, pos.number.of.studies = 0.3)
# invisible(dev.off())


## Auxiliary commands to determine and set values for argument 'adj'
## in netgraph.netmeta()

nodes1 <- netgraph(net1, iterate = TRUE)$nodes

nodes1 %>% select(adj.x, adj.y)

nodes1 <- nodes1 %>%
  mutate(adj.x = replace(adj.x, trts == "Placebo", 0.9))
nodes1 %>% select(adj.x, adj.y)

# pdf("Figures/netgraph2.pdf", width = 7, height = 6)
netgraph(net1, plastic = FALSE, multiarm = TRUE,
  iterate = TRUE, col = "black",
  cex = 1.25, offset = ifelse(trts == "Placebo", 0.04, 0.02),
  adj = nodes1 %>% select(adj.x, adj.y),
  number.of.studies = TRUE, cex.number = 1)
# invisible(dev.off())

net1

print(summary(net1), truncate = studlab %in% selstudy1, nchar.trts = 4,
  nma = FALSE)

# pdf("Figures/forest1.pdf", width = 7, height = 2)
forest(net1)
# invisible(dev.off())

# pdf("Figures/forest2.pdf", width = 7, height = 4)
forest(net1, ref = c("C", "D", "M"), baseline = FALSE, drop = TRUE)
# invisible(dev.off())

netrank(net1)

set.seed(1909)
ran1 <- rankogram(net1)
ran1

# pdf("Figures/rankogram.pdf")
plot(ran1)
# invisible(dev.off())

netrank(ran1)

netleague(net1, seq = netrank(net1), ci = FALSE)

decomp.design(net1)

netsplit(net1)

# pdf("Figures/netheat.pdf")
netheat(net1, nchar.trts = 4)
# invisible(dev.off())

## Example 2: antithrombotics to prevent strokes

cilayout("(", "-")

pw2 <- pairwise(treat = treatment, n = total, event = stroke,
  studlab = study, data = Dogliotti2014, sm = "OR")

head(pw2, 5) %>% select(studlab, treat1, treat2, TE, seTE)

net2 <- netmeta(pw2, ref = "plac")

subset(pw2, studlab == "WASPO, 2007") %>%
  select(studlab, event1, n1, event2, n2)

# pdf("Figures/netgraph3.pdf")
netgraph(net2, seq = "optimal",
  plastic = FALSE, number = TRUE, cex.points = n.trts,
  offset =
    ifelse(trts == "VKAs", 0.05,
      ifelse(trts %in% c("Aspirin", "Apixaban"), 0.035, 0.025)),
  labels = paste0(trts, "\n(n=", round(n.trts), ")"))
# invisible(dev.off())

net2.mh <- netmetabin(pw2, ref = "plac")

nb2 <- netbind(net2, net2.mh, random = FALSE,
  name = c("Inverse variance", "Mantel-Haenszel"))

# pdf("Figures/forest3.pdf", width = 6, height = 7)
forest(nb2, xlim = c(0.15, 2), at = c(0.2, 0.5, 1, 2))
# invisible(dev.off())


## Example 3: treatments for chronic obstructive pulmonary disease

pw3 <- pairwise(treat = treatment, n = total, event = exac,
  studlab = paste(study, year), data = Baker2009, sm = "OR")

net3 <- netmeta(pw3, common = FALSE, ref = "plac")

selvars3 <- c("studlab", "event1", "n1", "event2", "n2")
subset(pw3, studlab == "DalNegro 2003 2008")[, selvars3]

# pdf("Figures/netgraph4.pdf")
netgraph(net3, seq = "optimal",
  plastic = FALSE, number = TRUE, cex.points = n.trts,
  offset = ifelse(n.trts < 1500, 0.025, 0.05),
  labels = paste0(gsub("+", " +\n", trts, fixed = TRUE),
    "\n(n=", round(n.trts), ")"),
  rotate = -3 * 45)
# invisible(dev.off())

net3

nc3 <- netcomb(net3, inactive = "plac")
nc3

nb3 <- netbind(net3, nc3, name = c("Standard NMA", "Additive CNMA"))

# pdf("Figures/forest4.pdf", width = 6, height = 7)
forest(nb3)
# invisible(dev.off())

netrank(nc3)

netrank(net3)

sessionInfo()