Nothing
## ---- echo = FALSE-------------------------------------------------------
knitr::opts_chunk$set(include = TRUE, echo = TRUE, eval = TRUE, message = FALSE, warning = FALSE,
fig.width = 8, fig.asp = 0.618, out.width = "100%", fig.align = "center",
cache = T)
## ------------------------------------------------------------------------
library(metaviz)
## ---- dpi = 300----------------------------------------------------------
viz_forest(x = mozart[1:10, c("d", "se")], study_labels = mozart[1:10, c("study_name")],
summary_label = "Summary effect", xlab = "Cohen d")
## ---- dpi = 300----------------------------------------------------------
viz_forest(x = mozart[1:10, c("d", "se")], study_labels = mozart[1:10, c("study_name")],
summary_label = "Summary effect", xlab = "Cohen d", variant = "rain")
## ---- dpi = 300----------------------------------------------------------
viz_forest(x = mozart[1:10, c("d", "se")], study_labels = mozart[1:10, c("study_name")],
summary_label = "Summary effect", xlab = "Cohen d", variant = "thick", method = "FE")
## ---- dpi = 300----------------------------------------------------------
viz_forest(x = mozart[1:10, c("d", "se")], study_labels = mozart[1:10, c("study_name")],
summary_label = "Summary effect", xlab = "Cohen d", variant = "rain", method = "DL")
## ---- dpi = 300----------------------------------------------------------
viz_forest(x = mozart[1:10, c("d", "se")],
group = mozart[1:10, "rr_lab"],
study_labels = mozart[1:10, "study_name"],
summary_label = c("Summary (rr_lab = no)", "Summary (rr_lab = yes)"),
xlab = "Cohen d",
col = "Greys",
variant = "rain")
## ---- dpi = 300----------------------------------------------------------
viz_forest(x = mozart[, c("d", "se")],
group = mozart[, "rr_lab"],
study_labels = mozart[, "study_name"],
summary_label = c("Summary (rr_lab = no)", "Summary (rr_lab = yes)"),
xlab = "Cohen d",
variant = "thick",
type = "cumulative")
## ---- dpi = 300----------------------------------------------------------
viz_forest(x = mozart[1:5, c("d", "se")],
study_labels = mozart[1:5, "study_name"],
xlab = "Cohen d",
variant = "rain",
type = "sensitivity")
## ---- dpi = 300----------------------------------------------------------
viz_forest(x = mozart[1:10, c("d", "se")],
group = mozart[1:10, "rr_lab"],
study_labels = mozart[1:10, "study_name"],
summary_label = c("Summary (rr_lab = no)", "Summary (rr_lab = yes)"),
xlab = "Cohen d",
variant = "thick",
annotate_CI = TRUE)
## ------------------------------------------------------------------------
study_table <- data.frame(
name = exrehab[, "study_name"],
eventsT = paste(exrehab$ai, "/", exrehab$ai + exrehab$bi, sep = ""),
eventsC = paste(exrehab$ci, "/", exrehab$ci + exrehab$di, sep = ""))
head(study_table)
## ------------------------------------------------------------------------
summary_table <- data.frame(
name = "Summary",
eventsT = paste(sum(exrehab$ai), "/", sum(exrehab$ai + exrehab$bi), sep = ""),
eventsC = paste(sum(exrehab$ci), "/", sum(exrehab$ci + exrehab$di), sep = ""))
head(summary_table)
## ---- fig.asp = 0.5, fig.width = 10, dpi = 300---------------------------
viz_forest(x = exrehab[, c("logrr", "logrr_se")], variant = "classic",
col = "Greys", xlab = "logRR", annotate_CI = T,
study_table = study_table,
summary_table = summary_table,
table_headers = c("ID", "Events (T)", "Events (C)"))
## ---- dpi = 300----------------------------------------------------------
viz_forest(x = exrehab[, c("logrr", "logrr_se")], variant = "classic",
col = "Greys", xlab = "logRR", x_limit = c(-0.35, 0.05),
annotate_CI = T, type = "sensitivity",
study_table = data.frame(left_out = exrehab[, "study_name"],
remaining_N = sum(exrehab[, "n1i"] + exrehab[, "n2i"]) -
(exrehab[, "n1i"] + exrehab[, "n2i"])),
summary_table = "None",
table_headers = c("Study left out", "N remaining", "log Risk Ratio [95% CI]"),
table_layout = matrix(c(1, 2, 3), nrow = 1))
## ---- fig.asp = 0.5, fig.width = 10, dpi = 300---------------------------
viz_forest(x = exrehab[, c("logrr", "logrr_se")], variant = "thick",
study_labels = exrehab[, "study_name"], col = "Greys",
study_table = study_table,
summary_table = summary_table,
annotate_CI = T,
table_headers = c("ID", "Events (T)", "Events (C)"),
x_trans_function = exp, xlab = "RR")
## ---- dpi = 300----------------------------------------------------------
viz_forest(x = mozart[1:10, c("d", "se")],
group = mozart[1:10, "rr_lab"],
study_labels = mozart[1:10, "study_name"],
summary_label = c("Summary (rr_lab = no)", "Summary (rr_lab = yes)"),
xlab = "Cohen d",
col = c("firebrick", "steelblue4")[mozart[1:10, "rr_lab"]],
summary_col = c("firebrick", "steelblue4"))
## ---- echo = FALSE-------------------------------------------------------
knitr::opts_chunk$set(include = TRUE, echo = TRUE, eval = TRUE, message = FALSE, warning = FALSE,
fig.width = 6, fig.asp = 0.85, out.width = "80%", fig.align = "center",
cache = T)
## ---- dpi = 300----------------------------------------------------------
viz_funnel(brainvol[, c("z", "z_se")])
## ---- dpi = 300----------------------------------------------------------
viz_funnel(brainvol[, c("z", "z_se")],
method = "DL",
contours_col = "Greys",
xlab = "r", x_trans_function = tanh,
x_breaks = atanh(c(-0.9, -0.7, -0.3, 0, 0.3, 0.7, 0.9)))
## ---- dpi = 300----------------------------------------------------------
viz_funnel(exrehab[, c("logrr", "logrr_se")],
contours_col = "Greys",
trim_and_fill = TRUE, trim_and_fill_side = "right",
egger = TRUE)
## ---- dpi = 300----------------------------------------------------------
viz_funnel(mozart[1:10, c("d", "se")], sig_contours = FALSE, addev_contours = TRUE)
## ---- dpi = 300----------------------------------------------------------
viz_sunset(homeopath[, c("d", "se")])
## ---- dpi = 300----------------------------------------------------------
viz_sunset(homeopath[, c("d", "se")], true_effect = -0.3, sig_level = 0.1, power_contours = "continuous")
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