## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight = TRUE--------------
# ## write to working directory
# library(openxlsx)
# write.xlsx(iris, file = "writeXLSX1.xlsx")
# write.xlsx(iris, file = "writeXLSXTable1.xlsx", asTable = TRUE)

## ----include = TRUE, tidy = TRUE, eval = FALSE ,highlight = TRUE--------------
# ## write a list of data.frames to individual worksheets using list names as worksheet names
# l <- list("IRIS" = iris, "MTCARS" = mtcars)
# write.xlsx(l, file = "writeXLSX2.xlsx")
# write.xlsx(l, file = "writeXLSXTable2.xlsx", asTable = TRUE)

## ----include = TRUE, tidy = TRUE, eval = FALSE ,highlight= TRUE---------------
# options("openxlsx.borderColour" = "#4F80BD")
# options("openxlsx.borderStyle" = "thin")
# options("openxlsx.dateFormat" = "mm/dd/yyyy")
# options("openxlsx.datetimeFormat" = "yyyy-mm-dd hh:mm:ss")
# options("openxlsx.numFmt" = NULL) ## For default style rounding of numeric columns
# 
# df <- data.frame("Date" = Sys.Date()-0:19, "LogicalT" = TRUE,
#                  "Time" = Sys.time()-0:19*60*60,
#                  "Cash" = paste("$",1:20), "Cash2" = 31:50,
#                  "hLink" = "https://CRAN.R-project.org/",
#                  "Percentage" = seq(0, 1, length.out=20),
#                  "TinyNumbers" = runif(20) / 1E9,  stringsAsFactors = FALSE)
# 
# class(df$Cash) <- "currency"
# class(df$Cash2) <- "accounting"
# class(df$hLink) <- "hyperlink"
# class(df$Percentage) <- "percentage"
# class(df$TinyNumbers) <- "scientific"
# 
# write.xlsx(df, "writeXLSX3.xlsx")
# write.xlsx(df, file = "writeXLSXTable3.xlsx", asTable = TRUE)
# 
# 

## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight= TRUE---------------
# hs <- createStyle(fontColour = "#ffffff", fgFill = "#4F80BD",
#                   halign = "center", valign = "center", textDecoration = "Bold",
#                   border = "TopBottomLeftRight", textRotation = 45)
# 
# write.xlsx(iris, file = "writeXLSX4.xlsx", borders = "rows", headerStyle = hs)
# write.xlsx(iris, file = "writeXLSX5.xlsx", borders = "columns", headerStyle = hs)
# 
# write.xlsx(iris, "writeXLSXTable4.xlsx", asTable = TRUE,
# headerStyle = createStyle(textRotation = 45))

## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight = TRUE--------------
# l <- list("IRIS" = iris, "colClasses" = df)
# write.xlsx(l, file = "writeXLSX6.xlsx", borders = "columns", headerStyle = hs)
# write.xlsx(l, file = "writeXLSXTable5.xlsx", asTable = TRUE, tableStyle = "TableStyleLight2")
# 
# openXL("writeXLSX6.xlsx")
# openXL("writeXLSXTable5.xlsx")

## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight = TRUE--------------
# wb <- write.xlsx(iris, "writeXLSX6.xlsx")
# setColWidths(wb, sheet = 1, cols = 1:5, widths = 20)
# saveWorkbook(wb, "writeXLSX6.xlsx", overwrite = TRUE)

## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight = TRUE--------------
# require(ggplot2)
# wb <- createWorkbook()
# options("openxlsx.borderColour" = "#4F80BD")
# options("openxlsx.borderStyle" = "thin")
# modifyBaseFont(wb, fontSize = 10, fontName = "Arial Narrow")

## ----include = TRUE,tidy = TRUE, eval = FALSE, highlight = TRUE---------------
# addWorksheet(wb, sheetName = "Motor Trend Car Road Tests", gridLines = FALSE)
# addWorksheet(wb, sheetName = "Iris", gridLines = FALSE)

## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight = TRUE--------------
# freezePane(wb, sheet = 1, firstRow = TRUE, firstCol = TRUE) ## freeze first row and column
# writeDataTable(wb, sheet = 1, x = mtcars,
# colNames = TRUE, rowNames = TRUE,
# tableStyle = "TableStyleLight9")
# 
# setColWidths(wb, sheet = 1, cols = "A", widths = 18)

## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight = TRUE--------------
# writeDataTable(wb, sheet = 2, iris, startCol = "K", startRow = 2)
# 
# qplot(data=iris, x = Sepal.Length, y= Sepal.Width, colour = Species)
# insertPlot(wb, 2, xy=c("B", 16)) ## insert plot at cell B16
# 
# means <- aggregate(x = iris[,-5], by = list(iris$Species), FUN = mean)
# vars <- aggregate(x = iris[,-5], by = list(iris$Species), FUN = var)

## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight = TRUE--------------
# headSty <- createStyle(fgFill="#DCE6F1", halign="center", border = "TopBottomLeftRight")
# writeData(wb, 2, x = "Iris dataset group means", startCol = 2, startRow = 2)
# writeData(wb, 2, x = means, startCol = "B", startRow=3, borders="rows", headerStyle = headSty)

## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight = TRUE--------------
# writeData(wb, 2, x = "Iris dataset group variances", startCol = 2, startRow = 9)
# writeData(wb, 2, x= vars, startCol = "B", startRow=10, borders="columns",
# headerStyle = headSty)
# 
# setColWidths(wb, 2, cols=2:6, widths = 12) ## width is recycled for each col
# setColWidths(wb, 2, cols=11:15, widths = 15)

## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight = TRUE--------------
# s1 <- createStyle(fontSize=14, textDecoration=c("bold", "italic"))
# addStyle(wb, 2, style = s1, rows=c(2,9), cols=c(2,2))

## ----include = TRUE, tidy = TRUE, eval = FALSE, highlight = TRUE--------------
# saveWorkbook(wb, "basics.xlsx", overwrite = TRUE) ## save to working directory

## ----eval = FALSE, include = TRUE---------------------------------------------
# ## inspired by xtable gallery
# #https://CRAN.R-project.org/package=xtable/vignettes/xtableGallery.pdf
# 
# ## Create a new workbook
# wb <- createWorkbook()
# data(tli, package = "xtable")
# 
# ## data.frame
# test.n <- "data.frame"
# my.df <- tli[1:10, ]
# addWorksheet(wb = wb, sheetName = test.n)
# writeData(wb = wb, sheet = test.n, x = my.df, borders = "n")
# 
# ## matrix
# test.n <- "matrix"
# design.matrix <- model.matrix(~ sex * grade, data = my.df)
# addWorksheet(wb = wb, sheetName = test.n)
# writeData(wb = wb, sheet = test.n, x = design.matrix)
# 
# ## aov
# test.n <- "aov"
# fm1 <- aov(tlimth ~ sex + ethnicty + grade + disadvg, data = tli)
# addWorksheet(wb = wb, sheetName = test.n)
# writeData(wb = wb, sheet = test.n, x = fm1)
# 
# ## lm
# test.n <- "lm"
# fm2 <- lm(tlimth ~ sex*ethnicty, data = tli)
# addWorksheet(wb = wb, sheetName = test.n)
# writeData(wb = wb, sheet = test.n, x = fm2)
# 
# ## anova 1
# test.n <- "anova"
# my.anova <- anova(fm2)
# addWorksheet(wb = wb, sheetName = test.n)
# writeData(wb = wb, sheet = test.n, x = my.anova)
# 
# ## anova 2
# test.n <- "anova2"
# fm2b <- lm(tlimth ~ ethnicty, data = tli)
# my.anova2 <- anova(fm2b, fm2)
# addWorksheet(wb = wb, sheetName = test.n)
# writeData(wb = wb, sheet = test.n, x = my.anova2)
# 
# ## glm
# test.n <- "glm"
# fm3 <- glm(disadvg ~ ethnicty*grade, data = tli, family = binomial())
# addWorksheet(wb = wb, sheetName = test.n)
# writeData(wb = wb, sheet = test.n, x = fm3)
# 
# ## prcomp
# test.n <- "prcomp"
# pr1 <- prcomp(USArrests)
# addWorksheet(wb = wb, sheetName = test.n)
# writeData(wb = wb, sheet = test.n, x = pr1)
# 
# ## summary.prcomp
# test.n <- "summary.prcomp"
# addWorksheet(wb = wb, sheetName = test.n)
# writeData(wb = wb, sheet = test.n, x = summary(pr1))
# 
# ## simple table
# test.n <- "table"
# data(airquality)
# airquality$OzoneG80 <- factor(airquality$Ozone > 80,
# levels = c(FALSE, TRUE),
# labels = c("Oz <= 80", "Oz > 80"))
# airquality$Month <- factor(airquality$Month,
# levels = 5:9,
# labels = month.abb[5:9])
# my.table <- with(airquality, table(OzoneG80,Month) )
# addWorksheet(wb = wb, sheetName = test.n)
# writeData(wb = wb, sheet = test.n, x = my.table)
# 
# ## survdiff 1
# library(survival)
# test.n <- "survdiff1"
# addWorksheet(wb = wb, sheetName = test.n)
# x <- survdiff(Surv(futime, fustat) ~ rx, data = ovarian)
# writeData(wb = wb, sheet = test.n, x = x)
# 
# ## survdiff 2
# test.n <- "survdiff2"
# addWorksheet(wb = wb, sheetName = test.n)
# expect <- survexp(futime ~ ratetable(age=(accept.dt - birth.dt),
#       sex=1,year=accept.dt,race="white"), jasa, cohort=FALSE,
#       ratetable=survexp.usr)
# x <- survdiff(Surv(jasa$futime, jasa$fustat) ~ offset(expect))
# writeData(wb = wb, sheet = test.n, x = x)
# 
# ## coxph 1
# test.n <- "coxph1"
# addWorksheet(wb = wb, sheetName = test.n)
# bladder$rx <- factor(bladder$rx, labels = c("Pla","Thi"))
# x <- coxph(Surv(stop,event) ~ rx, data = bladder)
# writeData(wb = wb, sheet = test.n, x = x)
# 
# ## coxph 2
# test.n <- "coxph2"
# addWorksheet(wb = wb, sheetName = test.n)
# x <- coxph(Surv(stop,event) ~ rx + cluster(id), data = bladder)
# writeData(wb = wb, sheet = test.n, x = x)
# 
# ## cox.zph
# test.n <- "cox.zph"
# addWorksheet(wb = wb, sheetName = test.n)
# x <- cox.zph(coxph(Surv(futime, fustat) ~ age + ecog.ps,  data=ovarian))
# writeData(wb = wb, sheet = test.n, x = x)
# 
# ## summary.coxph 1
# test.n <- "summary.coxph1"
# addWorksheet(wb = wb, sheetName = test.n)
# x <- summary(coxph(Surv(stop,event) ~ rx, data = bladder))
# writeData(wb = wb, sheet = test.n, x = x)
# 
# ## summary.coxph 2
# test.n <- "summary.coxph2"
# addWorksheet(wb = wb, sheetName = test.n)
# x <- summary(coxph(Surv(stop,event) ~ rx + cluster(id), data = bladder))
# writeData(wb = wb, sheet = test.n, x = x)
# 
# ## view without saving
# openXL(wb)
# 

## ----eval = FALSE, include = TRUE, tidy = TRUE, highlight= TRUE---------------
# require(ggplot2)
# 
# wb <- createWorkbook()
# 
# ## read historical prices from yahoo finance
# ticker <- "CBA.AX"
# csv.url <- paste0("https://query1.finance.yahoo.com/v7/finance/download/",
# ticker, "?period1=1597597610&period2=1629133610&interval=1d&events=history&includeAdjustedClose= TRue")
# prices <- read.csv(url(csv.url), as.is = TRUE)
# prices$Date <- as.Date(prices$Date)
# close <- prices$Close
# prices$logReturns = c(0, log(close[2:length(close)]/close[1:(length(close)-1)]))
# 
# ## Create plot of price series and add to worksheet
# ggplot(data = prices, aes(as.Date(Date), as.numeric(Close))) +
# geom_line(colour="royalblue2") +
# labs(x = "Date", y = "Price", title = ticker) +
# geom_area(fill = "royalblue1",alpha = 0.3) +
# coord_cartesian(ylim=c(min(prices$Close)-1.5, max(prices$Close)+1.5))
# 
# ## Add worksheet and write plot to sheet
# addWorksheet(wb, sheetName = "CBA")
# insertPlot(wb, sheet = 1, xy = c("J", 3))
# 
# ## Histogram of log returns
# ggplot(data = prices, aes(x = logReturns)) + geom_histogram(binwidth=0.0025) +
# labs(title = "Histogram of log returns")
# 
# ## currency
# class(prices$Close) <- "currency" ## styles as currency in workbook
# 
# ## write historical data and  histogram of returns
# writeDataTable(wb, sheet = "CBA", x = prices)
# insertPlot(wb, sheet = 1, startRow=25, startCol = "J")
# 
# ## Add conditional formatting to show where logReturn > 0.01 using default style
# conditionalFormat(wb, sheet = 1, cols = seq_len((prices)), rows = 2:(nrow(prices)+1),
# rule = "$H2 > 0.01")
# 
# ## style log return col as a percentage
# logRetStyle <- createStyle(numFmt = "percentage")
# 
# addStyle(wb, 1, style = logRetStyle, rows = 2:(nrow(prices) + 1),
# cols = "H", gridExpand = TRUE)
# 
# setColWidths(wb, sheet=1, cols = c("A", "F", "G", "H"), widths = 15)
# 
# ## save workbook to working directory
# saveWorkbook(wb, "stockPrice.xlsx", overwrite = TRUE)
# openXL("stockPrice.xlsx")

## ----eval = FALSE, include = TRUE---------------------------------------------
# require(openxlsx)
# require(jpeg)
# require(ggplot2)
# 
# plotFn <- function(x, ...) {
#   colvec <- grey(x)
#   colmat <- array(match(colvec, unique(colvec)), dim = dim(x)[1:2])
#   image(x = 0:(dim(colmat)[2]), y = 0:(dim(colmat)[1]), z = t(colmat[rev(seq_len(nrow(colmat))) , ]),
#     col = unique(colvec), xlab = "", ylab = "", axes = FALSE, asp = 1,
#     bty ="n", frame.plot=FALSE, ann=FALSE)
# }
# 
# ## Create workbook and add a worksheet, hide gridlines
# wb <- createWorkbook("Einstein")
# addWorksheet(wb, "Original Image", gridLines = FALSE)
# 
# A <- readJPEG(file.path(path.package("openxlsx"), "einstein.jpg"))
# height <- nrow(A)
# width <- ncol(A)
# 
# ## write "Original Image" to cell B2
# writeData(wb, 1, "Original Image", xy = c(2,2))
# 
# ## write Object size to cell B3
# writeData(wb, 1, sprintf("Image object size: %s bytes",
#                          format(object.size(A+0)[[1]], big.mark=',')),
#           xy = c(2,3))  ## equivalent to startCol = 2, startRow = 3
# 
# ## Plot image
# par(mar=rep(0, 4), xpd = NA)
# plotFn(A)
# 
# ## insert plot currently showing in plot window
# insertPlot(wb, 1, width, height, units="px", startRow= 5, startCol = 2)
# 
# ## SVD of covariance matrix
# rMeans <- rowMeans(A)
# rowMeans <- do.call("cbind", lapply(seq_len(ncol(A)), function(X) rMeans))
# A <- A - rowMeans
# E <- svd(A %*% t(A) / (ncol(A) - 1)) # SVD on covariance matrix of A
# pve <- data.frame("Eigenvalues" = E$d,
#                   "PVE" = E$d/sum(E$d),
#                   "Cumulative PVE" = cumsum(E$d/sum(E$d)))
# 
# ## write eigenvalues to worksheet
# addWorksheet(wb, "Principal Component Analysis")
# hs <- createStyle(fontColour = "#ffffff", fgFill = "#4F80BD",
#                   halign = "CENTER", textDecoration = "Bold",
#                   border = "TopBottomLeftRight", borderColour = "#4F81BD")
# 
# writeData(wb, 2, x="Proportions of variance explained by Eigenvector" ,startRow = 2)
# mergeCells(wb, sheet=2, cols=1:4, rows=2)
# 
# setColWidths(wb, 2, cols = 1:3, widths = c(14, 12, 15))
# writeData(wb, 2, x=pve, startRow = 3, startCol = 1, borders="rows", headerStyle=hs)
# 
# ## Plots
# pve <- cbind(pve, "Ind" = seq_len(nrow(pve)))
# ggplot(data = pve[1:20,], aes(x = Ind, y = 100*PVE)) +
#   geom_bar(stat="identity", position = "dodge") +
#   xlab("Principal Component Index") + ylab("Proportion of Variance Explained") +
#   geom_line(size = 1, col = "blue") + geom_point(size = 3, col = "blue")
# 
# ## Write plot to worksheet 2
# insertPlot(wb, 2, width = 5, height = 4, startCol = "E", startRow = 2)
# 
# ## Plot of cumulative explained variance
# ggplot(data = pve[1:50,], aes(x = Ind, y = 100*Cumulative.PVE)) +
#   geom_point(size=2.5) + geom_line(size=1) + xlab("Number of PCs") +
#   ylab("Cumulative Proportion of Variance Explained")
# insertPlot(wb, 2, width = 5, height = 4, xy= c("M", 2))
# 
# 
# ## Reconstruct image using increasing number of PCs
# nPCs <- c(5, 7, 12, 20, 50, 200)
# startRow <- rep(c(2, 24), each = 3)
# startCol <- rep(c("B", "H", "N"), 2)
# 
# ## create a worksheet to save reconstructed images to
# addWorksheet(wb, "Reconstructed Images", zoom = 90)
# 
# for(i in seq_len(length(nPCs))) {
# 
#   V <- E$v[, 1:nPCs[i]]
#   imgHat <- t(V) %*% A  ## project img data on to PCs
#   imgSize <- object.size(V) + object.size(imgHat) + object.size(rMeans)
# 
#   imgHat <- V %*% imgHat + rowMeans  ## reconstruct from PCs and add back row means
#   imgHat <- round((imgHat - min(imgHat)) / (max(imgHat) - min(imgHat))*255) # scale
#   plotFn(imgHat/255)
# 
#   ## write strings to worksheet 3
#   writeData(wb, "Reconstructed Images",
#             sprintf("Number of principal components used:  %s",
#                     nPCs[[i]]), startCol[i], startRow[i])
# 
#   writeData(wb, "Reconstructed Images",
#             sprintf("Sum of component object sizes: %s bytes",
#                     format(as.numeric(imgSize), big.mark=',')), startCol[i], startRow[i]+1)
# 
#   ## write reconstruced image
#   insertPlot(wb, "Reconstructed Images", width, height, units="px",
#              xy = c(startCol[i], startRow[i]+3))
# 
# }
# 
# # hide grid lines
# showGridLines(wb, sheet = 3, showGridLines = FALSE)
# 
# ## Make text above images BOLD
# boldStyle <- createStyle(textDecoration="BOLD")
# 
# ## only want to apply style to specified cells (not all combinations of rows & cols)
# addStyle(wb, "Reconstructed Images", style=boldStyle,
#          rows = c(startRow, startRow+1), cols = rep(startCol, 2),
#          gridExpand = FALSE)
# 
# ## save workbook to working directory
# saveWorkbook(wb, "Image dimensionality reduction.xlsx", overwrite = TRUE)
# 
# 
# 
# 
# ## remove example files for cran test
# if (identical(Sys.getenv("NOT_CRAN", unset = "true"), "false")) {
#   file_list<-list.files(pattern="\\.xlsx",recursive = TRUE)
#   file_list<-fl[!grepl("inst/extdata",file_list)&!grepl("man/",file_list)]
# 
#   if(length(file_list)>0) {
#     rm(file_list)
#   }
# }

## ----cleanup, eval = FALSE, include = FALSE-----------------------------------
# xlsx_files <- dir(pattern = "*.xlsx")
# unlink(xlsx_files)