## ---- 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")