Running ‘forestplot2_vtests.R’ [2s/3s]
  Running ‘test_visual_w_cochrane_mdata.R’ [1s/1s]
  Running ‘test_visual_with_Greg.R’ [0s/0s]
  Running ‘testthat.R’ [0s/0s]
  Running ‘vtest_from_vignette.R’ [3s/3s]
Running the tests in ‘tests/forestplot2_vtests.R’ failed.
Complete output:
  > library(forestplot)
  Loading required package: grid
  Loading required package: checkmate
  Loading required package: abind
  > test_data <- data.frame(
  +   coef1 = c(1, 1.59, 1.3, 1.24),
  +   coef2 = c(1, 1.7, 1.4, 1.04)
  + )
  > 
  > test_data$low1 <- test_data$coef1 - 1.96 * c(0, .2, .1, .15)
  > test_data$high1 <- test_data$coef1 + 1.96 * c(0, .2, .1, .15)
  > 
  > test_data$low2 <- test_data$coef2 - 1.96 * c(0, .1, .15, .2)
  > test_data$high2 <- test_data$coef2 + 1.96 * c(0, .1, .15, .2)
  > 
  > col_no <- grep("coef", colnames(test_data))
  > row_names <- list(
  +   list("Category 1", "Category 2", "Category 3", expression(Category >= 4)),
  +   list(
  +     "ref",
  +     substitute(
  +       expression(bar(x) == val),
  +       list(val = round(rowMeans(test_data[2, col_no]), 2))
  +     ),
  +     substitute(
  +       expression(bar(x) == val),
  +       list(val = round(rowMeans(test_data[3, col_no]), 2))
  +     ),
  +     substitute(
  +       expression(bar(x) == val),
  +       list(val = round(rowMeans(test_data[4, col_no]), 2))
  +     )
  +   )
  + )
  > 
  > coef <- with(test_data, cbind(coef1, coef2))
  > low <- with(test_data, cbind(low1, low2))
  > high <- with(test_data, cbind(high1, high2))
  > 
  > # Change all to diamonds
  > forestplot(row_names, coef, low, high,
  +   fn.ci_norm = fpDrawDiamondCI,
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   legend_args = fpLegend(
  +     title = "Group",
  +     pos = list("topright"),
  +     r = unit(.1, "snpc"),
  +     gp = gpar(col = "#CCCCCC", lwd = 1.5)
  +   ),
  +   legend = c("Treatment", "Placebo")
  + )
  > 
  > # Check colgap
  > forestplot(row_names, coef, low, high,
  +   fn.ci_norm = fpDrawDiamondCI,
  +   title = "Cool study",
  +   colgap = unit(2, "mm"),
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   legend_args = fpLegend(
  +     title = "Group",
  +     pos = list("topright"),
  +     r = unit(.1, "snpc"),
  +     gp = gpar(col = "#CCCCCC", lwd = 1.5)
  +   ),
  +   legend = c("Treatment", "Placebo")
  + )
  > 
  > forestplot(row_names, coef, low, high,
  +   fn.ci_norm = fpDrawDiamondCI,
  +   title = "Cool study",
  +   colgap = unit(20, "mm"),
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   legend_args = fpLegend(
  +     title = "Group",
  +     pos = list("topright"),
  +     r = unit(.1, "snpc"),
  +     gp = gpar(col = "#CCCCCC", lwd = 1.5)
  +   ),
  +   legend = c("Treatment", "Placebo")
  + )
  > 
  > # Change first to diamonds
  > forestplot(row_names, coef, low, high,
  +   fn.ci_norm = c(
  +     "fpDrawDiamondCI",
  +     rep("fpDrawNormalCI",
  +       times = nrow(coef) - 1
  +     )
  +   ),
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   legend = c("Treatment", "Placebo"),
  +   legend_args = fpLegend(
  +     title = "Group",
  +     pos = list("topright"),
  +     r = unit(.1, "snpc"),
  +     gp = gpar(col = "#CCCCCC", lwd = 1.5)
  +   )
  + )
  > 
  > # You can also use a list with the actual functions
  > # as long as it is formatted [[row]][[column]]
  > # Note: if you have a non-square input then
  > # the software will reformat [[col]][[row]]
  > # to [[row]][[col]]
  > forestplot(row_names, coef, low, high,
  +   fn.ci_norm = list(
  +     list(fpDrawDiamondCI, fpDrawCircleCI),
  +     list(fpDrawNormalCI, fpDrawNormalCI),
  +     list(fpDrawNormalCI, fpDrawCircleCI),
  +     list(fpDrawNormalCI, fpDrawNormalCI)
  +   ),
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   legend = c("Treatment", "Placebo"),
  +   legend_args = fpLegend(
  +     title = "Group",
  +     pos = list("topright"),
  +     r = unit(.1, "snpc"),
  +     gp = gpar(col = "#CCCCCC", lwd = 1.5)
  +   )
  + )
  > 
  > 
  > # Check with pch=1
  > forestplot(row_names, coef, low, high,
  +   pch = 1,
  +   fn.ci_norm = c("fpDrawDiamondCI", "fpDrawPointCI"),
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   legend = c("Treatment", "Placebo"),
  +   legend_args = fpLegend(
  +     title = "Group",
  +     pos = list("topright"),
  +     r = unit(.1, "snpc"),
  +     gp = gpar(col = "#CCCCCC", lwd = 1.5)
  +   )
  + )
  > # Check with pch = 2
  > forestplot(row_names, coef, low, high,
  +   pch = 2,
  +   fn.ci_norm = c("fpDrawDiamondCI", "fpDrawPointCI"),
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   legend = c("Treatment", "Placebo"),
  +   legend_args = fpLegend(
  +     title = "Group",
  +     pos = list("topright"),
  +     r = unit(.1, "snpc"),
  +     gp = gpar(col = "#CCCCCC", lwd = 1.5)
  +   )
  + )
  > 
  > # Check xlab
  > forestplot(row_names, coef, low, high,
  +   cex = 1.5,
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   legend = c("Treatment", "Placebo"),
  +   legend_args = fpLegend(title = "Group", pos = "top")
  + )
  > 
  > forestplot(row_names, coef, low, high,
  +   cex = 1,
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates"
  + )
  > 
  > 
  > # Check line-height
  > forestplot(row_names, coef, low, high,
  +   lineheight = "lines",
  +   cex = 1, # Base cex height
  +   fn.ci_norm = fpDrawDiamondCI,
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates"
  + )
  > 
  > forestplot(row_names, coef, low, high,
  +   line.margin = .1,
  +   lineheight = "lines",
  +   cex = 1.5, # Larger line height
  +   fn.ci_norm = fpDrawDiamondCI,
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   new_page = TRUE
  + )
  > 
  > 
  > my_cex <- 1.4
  > forestplot(row_names, coef, low, high,
  +   line.margin = .1,
  +   lineheight = unit(1.5 * my_cex, "lines"),
  +   cex = my_cex, # Larger line height
  +   fn.ci_norm = fpDrawDiamondCI,
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   new_page = TRUE
  + )
  > 
  > 
  > my_cex <- 1.4
  > forestplot(row_names, coef, low, high,
  +   line.margin = .1,
  +   lineheight = unit(1.5 * my_cex, "lines"),
  +   cex = my_cex, # Larger line height
  +   fn.ci_norm = fpDrawDiamondCI,
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates",
  +   new_page = TRUE
  + )
  > 
  > 
  > # Check if you can stack the plots in a grid
  > grid.newpage()
  > lv <- grid.layout(nrow = 2, heights = unit(c(.6, .4), "npc"))
  > pushViewport(viewport(layout = lv))
  > pushViewport(viewport(layout.pos.row = 1))
  > grid.rect(gp = gpar(col = "blue", fill = NA, lwd = 4))
  > forestplot(row_names, coef, low, high,
  +   new_page = FALSE,
  +   lineheight = unit(1.5 * my_cex, "lines"),
  +   cex = my_cex, # Larger line height
  +   fn.ci_norm = fpDrawDiamondCI,
  +   zero = 1, boxsize = 0.5,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates"
  + )
  > grid.rect(gp = gpar(col = "red", fill = NA, lwd = 2))
  > popViewport()
  > pushViewport(viewport(layout.pos.row = 2))
  > grid.rect(gp = gpar(col = "blue", fill = NA, lwd = 4))
  > forestplot(row_names, coef, low, high,
  +   new_page = FALSE,
  +   lineheight = unit(1.5 * my_cex, "lines"),
  +   cex = my_cex, # Larger line height
  +   fn.ci_norm = fpDrawDiamondCI,
  +   zero = 1, boxsize = 0.5,
  +   col = fpColors(
  +     box = c("royalblue", "gold"),
  +     line = c("darkblue", "orange"),
  +     summary = c("darkblue", "red")
  +   ),
  +   xlab = "The estimates"
  + )
  > grid.rect(gp = gpar(col = "red", fill = NA, lwd = 2))
  > popViewport()
  > 
  > row_names <- list(list("test = 1", expression(test >= 2)))
  > 
  > test_data <- data.frame(
  +   coef = c(1.8, .8),
  +   low = c(1.4, 0.4),
  +   high = c(5, 1.55)
  + )
  > 
  > forestplot(row_names,
  +            test_data$coef,
  +            test_data$low,
  +            test_data$high,
  +            zero = 1,
  +            cex = 1,
  +            lineheight = "auto",
  +            xlab = "Odds",
  +            xlog = TRUE)
  > 
  > #####################
  > # Check square data #
  > #####################
  > test_data <- data.frame(
  +   coef1 = c(1, 1.59, 1.24),
  +   coef2 = c(1, 1.7, 1.04),
  +   coef3 = c(1, 1.8, .94)
  + )
  > test_data$low1 <- test_data$coef1 - 1.96 * c(0, .2, .15)
  > test_data$high1 <- test_data$coef1 + 1.96 * c(0, .2, .15)
  > 
  > test_data$low2 <- test_data$coef2 - 1.96 * c(0, .1, .2)
  > test_data$high2 <- test_data$coef2 + 1.96 * c(0, .1, .2)
  > 
  > test_data$low3 <- test_data$coef3 - 1.96 * c(0, .1, .2)
  > test_data$high3 <- test_data$coef3 + 1.96 * c(0, .1, .2)
  > 
  > coef <- with(test_data, cbind(coef1, coef2, coef3))
  > low <- with(test_data, cbind(low1, low2, low3))
  > high <- with(test_data, cbind(high1, high2, high3))
  > 
  > forestplot(1:3, coef, low, high,
  +   title = "Cool study",
  +   zero = 1, boxsize = 0.25,
  +   fn.ci_norm = c(
  +     "fpDrawDiamondCI",
  +     rep("fpDrawNormalCI",
  +       times = nrow(coef) - 1
  +     )
  +   ),
  +   col = fpColors(
  +     box = c("royalblue", "gold", "gold"),
  +     line = c("darkblue", "orange", "orange")
  +   ),
  +   xlab = "The estimates"
  + )
  > 
  > # Single row test - issue #57
  > tt <- data.frame(
  +   mean = 3, upper = 4, lower = 2, P = 0.01, gene = "XX"
  + )
  > tt |>
  +   forestplot(labeltext = c(gene,P),
  +              xlog = TRUE,
  +              xlab = "OR",boxsize = 0.25) |>
  +   fp_set_style(box = "royalblue",
  +                line = "darkblue",
  +                summary = "royalblue") |>
  +   fp_add_header(gene = c("gene"),
  +                 P = c("P")) |>
  +   fp_set_zebra_style("#EFEFEF")
  Error: The package dplyr is needed for this function to work. Please install it.
  Execution halted
Running the tests in ‘tests/test_visual_with_Greg.R’ failed.
Complete output:
  > library(Greg)
  Error in library(Greg) : there is no package called 'Greg'
  Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  Error in library("testthat") : there is no package called 'testthat'
  Execution halted