Reporting automation from R

MS formats are still ubiquitous in corporate environments

Formats and complex layouts are strong requirements

Document updates and graphical annotations are time consuming

Deploiement must be easy

An R API for creating

• MS documents
• that look like corporate documents
• with complex tables
• and editable graphics where specific annotations can be made by non R coders

Graphical and tabular objets to use (1)

library(ReporteRs)

## Loading required package: ReporteRsjars

library(magrittr)
library(ggplot2)

myplot <- ggplot(data = mtcars,
                 aes(x = wt, y = qsec,
                     color = drat)) + geom_point()
  
my_ft <- vanilla.table(mtcars)

Graphical and tabular objets to use (2)

myplot

Graphical and tabular objets to use (3)

docx() %>% 
  addTitle("Tabular example") %>% 
  addFlexTable( my_ft ) %>% 
  addTitle("Graphic example") %>% 
  addPlot(fun = print, x = myplot, vector.graphic = TRUE) %>% 
  writeDoc("docs/first_.docx")

It produces this document.

pptx() %>% 
  addSlide("Title and Content") %>% 
  addTitle("Tabular example") %>% 
  addFlexTable( my_ft ) %>% 
  addSlide("Title and Content") %>% 
  addTitle("Graphic example") %>% 
  addPlot(fun = print, x = myplot) %>% 
  writeDoc("docs/first_.pptx")

It produces this document.

• Layout
  • Free table header and footer
  • Merge cells (by rows or columns)
• Format : cells, borders, paragraphs, text
• Annotate : add text and images

• Documentated here : http://davidgohel.github.io/ReporteRs/FlexTable.html
• Sugar functions are available in package rtable.

## Source: local data frame [12 x 6]
## Groups: Status, Gender [?]
## 
##          Status Gender Ulceration     n  mean    sd
##           (chr)  (chr)      (chr) (int) (dbl) (dbl)
## 1         Alive Female     Absent    68 1.693 2.004
## 2         Alive Female    Present    23 2.972 2.593
## 3         Alive   Male     Absent    24 1.468 1.719
## 4         Alive   Male    Present    19 4.319 2.423
## 5      Melanoma Female     Absent     8 2.139 1.184
## 6      Melanoma Female    Present    20 4.724 4.128
## 7      Melanoma   Male     Absent     8 3.266 4.681
## 8      Melanoma   Male    Present    21 5.143 2.862
## 9  Non-melanoma Female     Absent     3 1.667 1.141
## 10 Non-melanoma Female    Present     4 3.302 3.713
## 11 Non-melanoma   Male     Absent     4 2.420 2.499
## 12 Non-melanoma   Male    Present     3 8.053 4.019

my_flextable = FlexTable( data ) %>%
  spanFlexTableRows(j = 1, runs = data$Status) %>% 
  spanFlexTableRows(j = 2, runs = data$Gender) %>% 
  addHeaderRow( value = c("Group by", "Statistics"), 
                colspan = c(3, 3), first = T ) %>% 
  setFlexTableWidths(widths = c(1.5, 1.5, 1.5, .75, .75, .75))

my_flextable[to = "header"] = textBold(font.size=12)
my_flextable[to = "header"] = parCenter(padding=2)

my_flextable[] = textNormal(font.size=11)

my_flextable[data$mean < 2, "mean" ] = 
  textItalic(color = "gray", font.size=11)
my_flextable[data$mean > 3, "mean" ] = 
  textBold(color = "red", font.size=11)

my_flextable[] = parCenter(padding=2)

my_flextable[data$sd > 2, "sd", 
             text.properties = textProperties(
               vertical.align = "superscript") ] = "*"
my_flextable <- addFooterRow(my_flextable, 
       value = "*", colspan = 6, 
       text.properties = textProperties(
         vertical.align = "superscript") )
my_flextable[1, 1, to = "footer"] = 
  "standard deviation is > 2"

• Use option vector.graphics=TRUE

pptx() %>% addSlide("Title and Content") %>% 
  addPlot(fun = print, x = myplot, 
    vector.graphic = TRUE) %>% 
  writeDoc("docs/evg_.pptx")

docx() %>% addPlot(fun = print, 
    x = myplot, vector.graphic = TRUE) %>% 
  writeDoc("docs/evg_.docx")

Outputs

evg_.pptx and evg_.docx .

install.packages(c( "ReporteRs", "rtable") )

rtable is complementing ReporteRs for tabular reporting.

Most common issues :

• R 32 bits and java 64 bits
• R 64 bits and java 32 bits

Getting help

stackoverflow and tag reporters: http://stackoverflow.com/questions/tagged/reporters

google-groups: https://groups.google.com/forum/#!forum/reporters-package

Issues - bugs

Github: https://github.com/davidgohel/ReporteRs/issues

Creating PowerPoint presentations

http://www.sthda.com/english/wiki/create-and-format-powerpoint-documents-from-r-software

Creating Word documents

http://www.sthda.com/english/wiki/create-and-format-word-documents-using-r-software-and-reporters-package

• Clinical reporting
  • for R users
  • shiny app for non R users
• Financial reporting