[R] Making TIFF images with rtiff

Inman, Brant A. M.D. Inman.Brant at mayo.edu
Fri Jan 12 15:16:52 CET 2007

Thanks to all the responders.  Here are some replies to the comments:

1) Concerning the term TIFF "format".
It may be that the journals are misusing the term TIFF, but it would
also appear that wikipedia is as well. The first sentence in the wiki
link sent below states:

"Tagged Image File FORMAT (abbreviated TIFF) is a file FORMAT for mainly
storing images, including photographs and line art."

Either way, the semantics of the word TIFF are probably not that
important for the current query.  If a publisher wants images in TIFF, I
would like to provide them in that format, regardless of whether or not
I deem the request proper.  After all they are the publishing experts!

2) Converting PNGs to TIFFs with Photoshop.
This is principally what I have done in the past that has given the poor
results that I have noted. I thought that it could be something that I
was specifically doing wrong so I consulted the medical imaging and
design department of my institution (Mayo Clinic) which informed me that
there is often a loss of information, some times quite large, in these
types of image format conversions. They suggested that it is best to
work with the TIFFs from the start if possible, which is why I am trying
to explore this option in R.  It is interesting that my imaging
department was able to convert the WMF format to TIFF with much better
success.  However, since Photoshop does not support WMFs, I am unable to
do this myself.  I have downloaded ImageMagick and will try that.

3)Lack of gratitude by R users.
It is interesting to note upon reviewing the R-help files that many
queries (perhaps even the majority?) do, in fact, convey gratitude.
Unfortunately, I have also noted that there are several messages from R
developers that appear to feel underappreciated. I suspect that one
reason that R is experiencing an explosion of users is precisely that
people appreciate and value the donation of free time provided by
statistical experts--such as Harrell, Weigand, Ripley and Kort in this
thread--for the development of accurate and powerful statistical
software.  Furthermore, the support provided for the software in the
form of R-help is outstanding, again something that I think is part of
the package deal that is attracting new users to R.  In other words, one
should not assume a general lack of gratitude on behalf of R-help users
but should see the growth of R as evidence that the software and its
developpers/supporters are indeed greatly valued.  I do not think that R
would be used much if people did not appreciate the nice packages,
functions and help provided.  Indeed, those of us that have access to
multiple software programs (I have access to JMP, SPSS, SPLUS and SAS)
choose R as our primary method of analysis because we feel that the
sharing environment supported by CRAN is a better way of doing
statistical computing.  Enough said.

4)Flexible journal policies.
Of 4 papers that I have submitted in the last 3 months for publication
in 3 journals (all to cancer related journals), all were subjected to
online file checkers that forced me to upload TIFF files instead of
PDFs.  Not only do they check the format, but also various other
resolution related items. In other words, I would not have even made it
past the online submission stage if I only PDFs to work with. 

5)Using the bitmap function to make TIFFs.
This sounds like a very attractive option.  I have tried this option
using the simple code below:

plot(speed ~ dist)	# Simple plot to test
bitmap(file='C:\\...\\test.tif',type = "tifflzw", res = 1200)

Error in system(paste(gsexe, "-help"), intern = TRUE, invisible = TRUE)
        gswin32c.exe not found


Despite what the error message suggests, I do have a functional
Ghostscript 8.54 program installed on my Windows XP machine with the
executable found in the directory: C:\Program
Files\gs\gs8.54\bin\gswin32c.  I am not sure why R is not finding the
program.  I tried making a Windows environmental variable, R_GSCMD, with
this system address but that did not have any success.  Does the
gswin32c file need to be in my R PATH?

Brant Inman
Mayo Clinic

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