Re: [Orgmode] [babel] R questions

[Dan Davison]

Sébastien Vauban <address@hidden> writes:

> Hello,
>
> One of this questions is a bit border-line, but I'm still trying ;-)
>
> I have this table generated by a script:
>
> #+results: abc2008
> | "2008/1"  | -78.59 |   1627.24 |
> | "2008/2"  | -80.17 |    700.33 |
> | "2008/3"  | -80.17 |     879.8 |
> | "2008/4"  | -80.17 | -25823.17 |
> | "2008/5"  | -80.17 |   3570.75 |
> | "2008/6"  | -81.77 |    2377.8 |
> | "2008/7"  | -81.77 |    2889.4 |
> | "2008/8"  | -81.77 |   2612.92 |
> | "2008/9"  | -81.77 |   1585.21 |
> | "2008/10" |  -83.4 |   1561.42 |
> | "2008/11" |  -83.4 |   2189.17 |
> | "2008/12" |     "" |        "" |
>
> I want to draw the 12 months with the values side by side.
>
> Problem #1: the "" in the last line hinder the generation of the graph. Format
> error.

Missing values in R are represented by the value NA. If you change the
last line of your table to

| "2008/12" |     NA |        NA |

then it works [1], [2], [3].

>
> #+srcname: expenses-bar-plot(abc = abc2008)
> #+begin_src R :results file :file abc2008.pdf
>     barplot(abc[,3], col = "red", main = "Profit and Loss 2008", las = 1, xlab
>     = "Months", ylab = "EUR")
> #+end_src
>
> Problem #2: I don't know how to ask for drawing the 2 columns. I've tried

OK, so one point that is arguably relevant to this mailing list is that
when org tables are read into R, the object that is created in R is a
*data frame*. Not a matrix. (A data frame can have columns of
different types; matrices are all one type). [4]

So to solve your problem, you'd need to read the description of the
height argument in the help page for barplot (?barplot), noting that it
says "either a vector or matrix", and also noting that it says that bars
correspond to columns (not rows), thus realising that you need to
explicitly convert the relevant columns of the data frame to a matrix
and then transpose.

However, your two columns have rather different magnitude values and so
are not very well suited for plotting on the same scale. Below I
rescaled the first column by a factor of 20 so you can at least see the
bars.

#+srcname: expenses-bar-plot-two-columns(abc = abc2008)
#+begin_src R :file abc2008.png
  ## select the two columns, convert to matrix, transpose and rescale top row.
  x <- t(as.matrix(abc[,2:3])) * c(20,1)
  barplot(x, col = rep(c("red","blue"), ncol(x)), main = "Profit and Loss 
2008", las = 1, xlab= "Months", ylab = "EUR", beside=TRUE)
#+end_src

Dan



Footnotes:

[1] Note no quotes around NA here. You asked a good question about
quoting in org-babel; it will be answered.

[2] I guess one could potentially think about dealing with missing
values more explicitly in org-babel. E.g. there could be a header arg
specifying what values are to be treatyed as missing. Nothing like that
exists currently.

[3] You might think that an alternative would be to
do something like this in R

abc[abc == "\"\""] <- NA

but the trouble is that with those double quotes present, R will
interpret the column as containing character data rather than numeric,
and things will not be pretty.

[4] org-babel uses orgtbl-to-tsv followed by read.table() to convert the
org table into a data.frame in R. A source of much confusion with
R-beginners is that by default, read.table converts character columns
into the *factor* data type. Note that org-babel currently uses
'as.is=TRUE' when calling read.table and therefore does *not* convert to
factor. This may avoid some confusion among users but is
memory-inefficient and misses out on other advantages of factors.