[R] plot.hclust point to older version

Jeff Newmiller
2014-11-26T19:09:05Z

Short answer to your question is "R files" and original data from
external sources.

I tend to keep my projects in separate directories. I make a core R file that I
can run from beginning to end using source() to generate my primary analysis
objects. I then make another file to keep my source() function call in, as well
as a few exploratory plot commands. Recently I have been also sourcing the
analysis script in Rmd or Rnw files to "knit" my observations with the
output.

Some people complain that their analysis takes too long to be sourcing it all
the time. When I have that problem I set up a variable outside my analysis
script that I test in my analysis script. If the variable indicates it is time
to recalculate, then I do all of that and then save the data in sn rds or rda
file. If the variable indicates that I should reuse the cached data, then it
skips the calculations and just loads the data. This way I always load the right
libraries along with the data, and I don't accidentally save data that I
changed outside the analysis script... keeping my results reproducible. (Rds
files can be convenient if I have several different slow analyses to compare and
I want to only work on one at a time. I set up one control variable for each
analysis.)

Some people (smarter than me?) like to build their analysis into an Sweave or
knitr file. They can then strip out an analysis R file to use the way I have
described if they choose to do so ("literate programming") but I have
not picked up that habit yet.

The key is keeping a record of how every object that is in your save file was
originally created. If you tolerate auto saving and loading of the environment
then you lose that record, and pernicious errors can creep into your environment
from who knows where, and you might as well be using Excel if that is how you
work. (Note that this means I hardly ever copy data straight from Excel via the
clipboard as that is not reproducible. Usually this means Save As CSV in Excel
to start my R analysis if that is the data source.)
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Sent from my phone. Please excuse my brevity.

On November 26, 2014 2:05:54 AM PST, PIKAL Petr <petr.pikal at
precheza.cz> wrote:
>Hi
>
>You say
>
>> in other words, experienced R users do not let their workspace be
>saved
>> automatically (to '.RData') and hence do not load any .RData
>> automatically at startup.
>
>I save/load .RData for years without any issues (except of not
>installed packages when working on different PCs).I usually keep each
>project in separated .RData (and separated folder, together with all
>stuff belonging to that project), which prevent to mess things
>together.
>
>There is no such warning as "do not use .RData" in books I have
>available.
>
>I wonder how experienced useR keep track of several projects without
>using startup loading .RData?
>What would you recommend for keeping track of commands and created
>objects instead of .RData?
>
>Petr
>
>
>> -----Original Message-----
>> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of
>Martin
>> Maechler
>> Sent: Wednesday, November 26, 2014 10:03 AM
>> To: Michael Mason
>> Cc: R help
>> Subject: Re: [R] plot.hclust point to older version
>>
>>
>> > Thanks! That worked
>>
>> Of course: As in about 99.99% of all cases where Bill Dunlap  helps.
>>
>>
>> > You probably have a local copy of an old version of plot.hclust or
>> plot.dendrogram in your global environmenet or another package that
>> masks the one in package:stats.  E.g., I fired up R-2.14.2 and copied
>> those 2 plot methods to .GlobalEnv and then saved by workspace when
>> quitting R.  I then fired up R-3.1.1, which loads the workspace saved
>> by the older version of R.  I get:
>>
>> > > objects()
>> > [1] "plot.dendrogram" "plot.hclust"
>> > > plot(hclust(dist(c(2,3,5,7,11,13,17,19))))
>> > Error in .Internal(dend.window(n, merge, height, hang, labels,
>...))
>> :
>> >   there is no .Internal function 'dend.window'
>> > > traceback()
>> > 2: plot.hclust(hclust(dist(c(2, 3, 5, 7, 11, 13, 17, 19))))
>> > 1: plot(hclust(dist(c(2, 3, 5, 7, 11, 13, 17, 19))))
>>
>> > Note how calling traceback() after an error gives more information
>> about the source of the error.
>>
>> > To fix this, get rid of the .RData file that is being loaded when
R
>> starts.
>>
>> In the spirit of the old -- now politically incorrect -- sayings  ``
>> Real men don't ..... '''
>> I'd like to emphasize my own view that
>>  "Real useRs don't use .RData"
>>
>> in other words, experienced R users do not let their workspace be
>saved
>> automatically (to '.RData') and hence do not load any .RData
>> automatically at startup.
>>
>> Consequently, use R with the '--no-save' command line argument
(maybe
>> also with '--no-restore').
>>
>> ESS (Emacs Speaks Statistics) users can put
>>
>> (custom-set-variables
>>  '(inferior-R-args "--no-restore-history --no-save ")
>> )
>>
>> into their ~/.emacs
>> {and I'd like to see a way to do this easily with RStudio...}
>>
>> Martin Maechler,
>> ETH Zurich and R Core Team
>>
>> > Bill Dunlap
>> > TIBCO Software
>> > wdunlap tibco.com<http://tibco.com>
>>
>> > On Tue, Nov 25, 2014 at 12:18 PM, Rolf Turner
>> <r.turner at auckland.ac.nz<mailto:r.turner at
auckland.ac.nz>> wrote:
>> > On 26/11/14 08:53, Michael Mason wrote:
>> > Here you are. I expect most folks won't get the error.
>>
>> > N   = 100; M = 1000
>> > mat = matrix(1:(N*M) + rnorm(N*M,0,.5),N,M)
>> > h   = hclust(as.dist(1-cor(mat)))
>> > plot(h)
>>
>> > Error in .Internal(dend.window(n, merge, height2, hang, labels,
>...))
>> :
>> >    there is no .Internal function 'dend.window'
>>
>>
>>
>> > Thanks again
>>
>>
>> > On 11/25/14 11:29 AM, "Rolf Turner"
>> <r.turner at auckland.ac.nz<mailto:r.turner at
auckland.ac.nz>> wrote:
>>
>>
>>
>> > Reproducible example???
>>
>> > (I know from noddink about hclust, but I tried the example from
the
>> > help page and it plotted without any problem.)
>>
>> > cheers,
>>
>> > Rolf Turner
>>
>> > On 26/11/14 06:13, Michael Mason wrote:
>> > Hello fellow R users,
>>
>> > I have recently updated to R 3.1.2. When trying to plot an hclust
>> > object to generate the dendrogram I get the following error:
>>
>> > Error in .Internal(dend.window(n, merge, height2, hang, labels,
>...))
>> :
>> >     there is no .Internal function 'dend.window'
>>
>>
>> > I am indeed using R3.1.2 but my understanding is that the
.Internal
>> > API to the C code is no longer used. I have tried detaching the
>stats
>> > package and restarting R to no avail.
>> > I would love any help from any wiser guRus.
>>
>> > Please keep communications on-list; there are others on the list
>far
>> more likely to be able to help you than I.  I am cc-ing this reply to
>> the list.
>>
>> > For what it's worth, I can run your example without error.
>>
>> > As to how to track down what is going wrong on your system,
I'm
>> afraid I have no idea.  Someone on the list may have some thoughts.
>>
>> > cheers,
>>
>> > Rolf Turner
>>
>> > --
>> > Rolf Turner
>> > Technical Editor ANZJS
>>
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