## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.width = 6 ) ## ----setup, results='hide', message=FALSE, warning=FALSE, echo=FALSE---------- library(BCEA) library(dplyr) library(reshape2) library(ggplot2) library(purrr) ## ----------------------------------------------------------------------------- data(Smoking) treats <- c("No intervention", "Self-help", "Individual counselling", "Group counselling") bcea_smoke <- bcea(eff, cost, ref = 4, interventions = treats, Kmax = 500) ## ----------------------------------------------------------------------------- # all interventions ceef.plot(bcea_smoke) # subset setComparisons(bcea_smoke) <- c(1,3) ceef.plot(bcea_smoke) # check numbering and legend setComparisons(bcea_smoke) <- c(3,1) ceef.plot(bcea_smoke) setComparisons(bcea_smoke) <- c(3,2) ceef.plot(bcea_smoke) setComparisons(bcea_smoke) <- 1 ceef.plot(bcea_smoke) # add interventions back in setComparisons(bcea_smoke) <- c(1,3) ceef.plot(bcea_smoke) ## ----error=TRUE--------------------------------------------------------------- try({ bcea_smoke <- bcea(eff, cost, ref = 4, interventions = treats, Kmax = 500) # all interventions ceef.plot(bcea_smoke, graph = "ggplot") # subset setComparisons(bcea_smoke) <- c(1,3) ceef.plot(bcea_smoke, graph = "ggplot") # check numbering and legend setComparisons(bcea_smoke) <- c(3,1) ceef.plot(bcea_smoke, graph = "ggplot") setComparisons(bcea_smoke) <- c(3,2) ceef.plot(bcea_smoke, graph = "ggplot") setComparisons(bcea_smoke) <- 1 ceef.plot(bcea_smoke, graph = "ggplot") # add interventions back in setComparisons(bcea_smoke) <- c(1,3) ceef.plot(bcea_smoke, graph = "ggplot") }) ## ----error=TRUE--------------------------------------------------------------- try({ # base R ceef.plot(bcea_smoke, pos = c(1,0)) ceef.plot(bcea_smoke, pos = c(1,1)) ceef.plot(bcea_smoke, pos = TRUE) ceef.plot(bcea_smoke, pos = FALSE) ceef.plot(bcea_smoke, pos = "topleft") ceef.plot(bcea_smoke, pos = "topright") ceef.plot(bcea_smoke, pos = "bottomleft") ceef.plot(bcea_smoke, pos = "bottomright") # ggplot2 ceef.plot(bcea_smoke, graph = "ggplot", pos = c(1,0)) ceef.plot(bcea_smoke, graph = "ggplot", pos = c(1,1)) ceef.plot(bcea_smoke, graph = "ggplot", pos = TRUE) ceef.plot(bcea_smoke, graph = "ggplot", pos = FALSE) ceef.plot(bcea_smoke, graph = "ggplot", pos = "top") ceef.plot(bcea_smoke, graph = "ggplot", pos = "bottom") ceef.plot(bcea_smoke, graph = "ggplot", pos = "left") ceef.plot(bcea_smoke, graph = "ggplot", pos = "right") }) ## ----error=TRUE--------------------------------------------------------------- try({ ceef.plot(bcea_smoke, flip = TRUE, dominance = FALSE, start.from.origins = FALSE, print.summary = FALSE, graph = "base") ceef.plot(bcea_smoke, dominance = TRUE, start.from.origins = FALSE, pos = TRUE, print.summary = FALSE, graph = "ggplot2") }) ## ----error=TRUE--------------------------------------------------------------- try({ ceef.plot(bcea_smoke, flip = TRUE, dominance = TRUE, start.from.origins = TRUE, print.summary = FALSE, graph = "base") ceef.plot(bcea_smoke, dominance = TRUE, start.from.origins = TRUE, pos = TRUE, print.summary = FALSE, graph = "ggplot2") }) ## ----error=TRUE--------------------------------------------------------------- try({ data("Smoking") cost[, 4] <- -cost[, 4] bcea_smoke <- bcea(eff, cost, ref = 3, interventions = treats, Kmax = 500) # all interventions ceef.plot(bcea_smoke, graph = "ggplot") ceef.plot(bcea_smoke, graph = "base") ceef.plot(bcea_smoke, start.from.origins = TRUE, graph = "ggplot") ceef.plot(bcea_smoke, start.from.origins = TRUE, graph = "base") setComparisons(bcea_smoke) <- c(1,2) ceef.plot(bcea_smoke, graph = "ggplot") ceef.plot(bcea_smoke, graph = "base") eff[, 3] <- -eff[, 3] bcea_smoke <- bcea(eff, cost, ref = 3, interventions = treats, Kmax = 500) ceef.plot(bcea_smoke, graph = "ggplot") ceef.plot(bcea_smoke, graph = "base") data("Smoking") eff[, 3] <- -eff[, 3] bcea_smoke <- bcea(eff, cost, ref = 3, interventions = treats, Kmax = 500) ceef.plot(bcea_smoke, graph = "ggplot") ceef.plot(bcea_smoke, graph = "base") }) ## ----eval=FALSE, echo=FALSE--------------------------------------------------- # # create output docs # rmarkdown::render(input = "vignettes/ceef.Rmd", output_format = "pdf_document", output_dir = "vignettes") # rmarkdown::render(input = "vignettes/ceef.Rmd", output_format = "html_document", output_dir = "vignettes")