[R] plot.hclust point to older version

PIKAL Petr
2014-11-27T13:40:36Z

Hm

> -----Original Message-----
> From: Jeff Newmiller [mailto:jdnewmil at dcn.davis.CA.us]
> Sent: Wednesday, November 26, 2014 8:09 PM
> To: PIKAL Petr; Martin Maechler
> Cc: R help
> Subject: Re: [R] plot.hclust point to older version
>
> 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

I do the same.

> 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

Not exactly. All commands are saved in .Rhistory, which from time to time I
rename and keep for further use. And sometimes I also make a separate file with
commands used, especially when I am at the end of my work on a project.


> 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.)

As I understand you do more sophisticated version what I am doing. The key is to
keep projects in separate directories and do not polute them with unrelated
objects. The problem in my way is when I accidentaly destroy an object and I
need to restore it, which can sometimes be tedious work. OTOH it keeps me
focused on what I am doing :-)

Anyway, I shall consider save and saveRDS to keep copy of important objects
outside .RData environment, if something went wrong.

Thanks for idea.

Best regards.
Petr


> -----------------------------------------------------------------------
> ----
> Jeff Newmiller                        The     .....       .....  Go
> Live...
> DCN:<jdnewmil at dcn.davis.ca.us>        Basics: ##.#.       ##.#.
Live
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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


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