R, Knitr, Rnw, beautiful scientific numbers

Question

I would like that all numbers generated by my knitr codes don´t look like an oldfashioned calculator.

Is there any option to get the numbers like the last one (with ·10 instead of e or E) ?

options(scipen=...) doesn't seem to have that option.

I've been searching information and I've found that it can be done directly in LaTex with the package siunitx, writing every number like this \num{1e-10}

But I'd like knitr did it automatically for all numbers, including those within tables.

PD: And how can I avoid that [1] when I print something?

PD2: Maybe something with gsub?

PD3:
I'm coming back to this problem. Imagine I don't define my own table but I get it from a regression and use xtable to produce it.

\documentclass{article}
\usepackage{siunitx}
\usepackage{booktabs}
\sisetup{     group-minimum-digits = {3},    group-separator = {,}, exponent-product = \cdot     }
\begin{document}

<<r, results='asis'>>=

library(xtable)
data(tli)
fm2 <- lm(tlimth ~ sex*ethnicty, data = tli)
xxx <- xtable(fm2)
print(xxx, booktabs = TRUE)

@
\end{document}

But it doesn't work well. What options should I use?

This is the result just with print

And this is the result with print+"booktabs=T"+my function beauty(). regards.

I don't know why it produces two tables instead of 1. And the numbers are not properly aligned. Anyway, I would like not to depend on my beauty() function but just use suintx, how can I do it?

Furl

Answer 1

---
output: pdf_document
---


```{r, results='asis'}
x <- 6.22e-21

cat(x)

cat(sfsmisc::pretty10exp(x, lab.type = 'latex')[[1]])
```

Rieger

How do you apply it to a whole table o document? – Furl

Imagine you got a table from a regression xtable(lm(...)). How would you apply your method with to that table? – Furl

@Furl in the examples I tried, xtable converted scientific notation to standard (eg pvalue 2e-16 to 0.00). since xtable does the formatting and prints out some characters, then you might have to grep the output and insert the formatting. for output that you create yourself, you can apply the format or override the print method like baptiste suggested. both of those would be more brute force than just a options(something = ...) solution – Rieger

I'm gonna submit a request on the xtable web site to ask them to add some option to do it automatically. – Furl

Answer 2

I prefer to leave the formatting to siunitx, but the pre-processing in R can get a bit fiddly,

---
output: 
  pdf_document: 
    keep_tex: yes
header-includes:
- \usepackage{siunitx}
- \usepackage{booktabs}
---

\sisetup{detect-all, tight-spacing=false, exponent-product = \cdot,
round-mode = figures,
round-precision = 3}

```{r, results='asis'}
as.sci_fy <- function(x) {class(x) <- c("sci_fy", class(x)); x}
format.sci_fy <-  function(x) sprintf("\\num{%e}", x)
print.sci_fy <- function(x) cat(format(x))


x <- 6.22e-21
as.sci_fy(x)

d <- data.frame(x=rnorm(10), y=rnorm(10), f=letters[1:10])
d <- lapply(d, function(c) if(is.numeric(c)) format(as.sci_fy(c)) else c)

library(xtable)
d <- xtable(data.frame(d, stringsAsFactors = FALSE))
 print(d, type="latex", align = c("l", "l", "l"),
        table.placement = "!htpb",
        floating.environment = "table",
        include.rownames=FALSE, 
       sanitize.text.function = function(x){x}, booktabs=TRUE)

```

Petard

What's the mining of a function that doesn't seem to do anything? "function(x){x}" – Furl

my failure to dig up ?identity. It's required when you have to pass a function, but don't want it to do anything. Here I don't want sanity. – Petard

Then whom you pass the function to? I think I understand, this is the way you execute \num{} on every cell – Furl

Imagine you got a table from a regression xtable(lm(...)). How would you apply your method with to that table? – Furl

i don't know much about xtable to be honest – Petard

I'm coming back to this problem. Imagine I don't define my own table but I get it from a regression and use xtable to produce it. <<r, results='asis'>>= library(xtable) data(tli) fm2 <- lm(tlimth ~ sex*ethnicty, data = tli) xxx <- xtable(fm2) print(xxx, booktabs = TRUE) @ What options do I need to use in my rnw file or R code to use automatically siunitx. I've tried \usepackage{siunitx} and several \sisetup{} but it doesn't seem to make any difference – Furl

Answer 3

I think the solution could be something like this

beauty <- function(xx) {cat(gsub("\\s([-+]?[0-9]*\\.?[0-9]+)([eE]([-+]?[0-9]+))\\s", " $\\1\\\\cdot{}10^{\\3}$ ", xx, perl=T)) }

d <- data.frame(x=1:10*10000, y=1:10*1e22,f=letters[1:10])

beauty(print(xtable(d, digits=5, display=c("s","G", "G", "s")), type="latex"))

It's not perfect anyway. If anybody can optimize it it would be great. Anyway I've sent a request to xtable to add this feature but it doesn't seem to be much development lately.

Another option would be to use the sanitize option with gsub.

Furl