Re: [R] Use of geometric mean .. in good data analysis
I've advised people consulting me that if their data is loaded with
zeros, while they are absolutely certain that something should be where
the zeros are, then they either need a better measuring tool, or to
carefully document the results of limits on detectability and then note
what fraction of the data is really below instrument limits. It's
important information as it stands, but they don't want to go writing
fairy tales based on things not seen.
On 1/22/24 12:57, Jeff Newmiller via R-help wrote:
> Still OT... but here is my own (I think previously mentioned here) rant on
> people thrashing about with log transformation and an all-too-common kludge
> to deal with zeros mixed among small
> numbers...https://gist.github.com/jdnewmil/99301a88de702ad2fcbaef33326b08b4
>
> OP perhaps posting a link here to your question posed wherever you end up
> with it will help shorten this thread.
>
> On January 22, 2024 12:23:20 PM PST, Bert Gunter
> wrote:
>> Ah LOD's, typically LLOD's ("lower limits of detection").
>>
>> Disclaimer: I am *NOT* in any sense an expert on such matters. What follows
>> are just some comments based on my personal experience. Please filter
>> accordingly. Also, while I kept it on list as Martin suggested it might be
>> useful to do so, most folks probably can safely ignore the rant that
>> follows as off topic and not of interest. So you've been warned!!
>>
>> The rant:
>> My experience is: data that contain a "bunch" of values that are, e.g.
>> below a LLOD, are frequently reported and/or analyzed by various ad hoc,
>> and imho, uniformly bad methods. e.g.:
>>
>> 1) The censored values are recorded and analyzed as at the LLOD;
>> 2) The censored values are recorded and analyzed at some arbitrary value
>> below the LLOD, like LLOD/2;
>> 3) The censored values are are "imputed" by ad hoc methods, e.g. uniform
>> random values between 0 and the LLOD for left censoring.
>>
>> To repeat, *IMO*, all of this is junk and will produced misleading
>> statistical results. Whether they mislead enough to substantively affect
>> the science or regulatory decisions depend on the specifics of the
>> circumstances. I accept no general claim as to their innocuousness.
>>
>> Further:
>>
>> a) When you have a "lot" of values -- 50%? 75%?, 25%? -- face facts: you
>> have (practically) no useful information from the values that you do have
>> to infer what the distribution of values that you don't have looks like.
>> All one can sensibly do is say that x% of the values are below a LOD and
>> here's the distribution of what lies above. Presumably, if you have such
>> data conditional on covariates with the obvious intent to determine the
>> relationship to those covariates, you could analyze the percentages of
>> LLOD's and known values separately. There are undoubtedly more
>> sophisticated methods out there, so this is where you need to go to the
>> literature to see what might suit; though I think it will still have to
>> come down to looking at these separately (e.g. with extra parameters to
>> account for unmeasurable values). Another way of saying this is: any
>> analysis which treats all the data as arising from a single distribution
>> will depend more on the assumptions you make than on the data. So good luck
>> with that!
>>
>> b) If you have a "modest" amount of (known) censoring -- 5%?, 20%? 10%? --
>> methods for the analysis of censored data should be useful. My
>> understanding is that MI (multiple imputation) is regarded as a generally
>> useful approach, and there are many R packages that can do various flavors
>> of this. Again, you should consult the literature: there are very likely
>> nontechnical reviews of this topic, too, as well as online discussions and
>> tutorials.
>>
>> So if you are serious about dealing with this and have a lot of data with
>> these issues, my advice would be to stop looking for ad hoc advice and dig
>> into the literature: it's one of the many areas of "data science" where
>> seemingly simple but pervasive questions require complex answers.
>>
>> And, again, heed my personal caveats.
>>
>> Thus endeth my rant.
>>
>> Cheers to all,
>> Bert
>>
>>
>>
>> On Mon, Jan 22, 2024 at 9:29 AM Rich Shepard
>> wrote:
>>
>>> On Mon, 22 Jan 2024, Martin Maechler wrote:
>>>
I think it is a good question, not really only about geo-chemistry, but
about statistics in applied sciences (and engineering for that matter).
John W Tukey (and several other of the grands of the time) had the log
transform among the "First aid transformations":
If the data for a continuous variable must all be positive it is also
typically the case that the distribution is considerably skewed to the
right. In such a case behave as a good human who sees another human in
health distress: apply First Aid -- do the things you learned to do
quickly without too much thought, because things must happen fast ---to
hopefully save the other's
Re: [R] Inappropriate color name
On Thu, 19 Nov 2020 23:27:29 +0100 Heinz Tuechler wrote: > One may remember that people who might feel offended by "Indian Red" > (Native Americans) make up less than 0.5 percent of all "Indians". > It is hardly the fault of the people of India that Native Americans > were called Indians by an Italian navigator who thought he had landed > in India. I have worked with and know or knew probably somewhere near 100 American Indians. None of them were "offended" by "Indian," most referred to themselves as "Indian," particularly when few outsiders could even pronounce their tribal names. Several of them referred me to the works and words of Russel Means, Ogalala Lakota, an actor and activist, who mocked the use of phrases such as "Native American" as silly, and easily as offensive and racist in its failure to distinguish among tribal peoples as any such sweeping label could be. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Inappropriate color name
On Sun, 15 Nov 2020 17:35:41 -0900 Lainey Gallenberg wrote: Lainey, Assumptions are always fraught. Your assumption about the "meaning" of Indian Red is simply wrong. Indian red is named for a lateritic soil in India. It isn't racist, and I have American Indian friends who have expressed disappointment at the historical facts. They also prefer "American Indian" to "Native American." So, what to do??? JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to understand the mentality behind tidyverse and ggplot2?
On Tue, 17 Nov 2020 12:43:21 -0500 C W wrote: > Dear R list, > > I am an old-school R user. I use apply(), with(), and which() in base > package instead of filter(), select(), separate() in Tidyverse. The > idea of pipeline (i.e. %>%) my code was foreign to me for a while. It > makes the code shorter, but sometimes less readable? > > With ggplot2, I just don't understand how it is organized. Take this > code: > > > ggplot(diamonds, aes(x=carat, y=price)) + > > geom_point(aes(color=cut)) + > geom_smooth() > > There are three plus signs. How do you know when to "add" and what to > "add"? I've seen more plus signs. > > To me, aes() stands for aesthetic, meaning looks. So, anything > related to looks like points and smooth should be in aes(). > Apparently, it's not the case. > > So, how does ggplot2 work? Could someone explain this for an > old-school R user? > > Thank you! > A really short form is to consider that ggplot2 syntax defines an object, and then additional simply adds to it, which is what all the plus signs are. Ideally, you can start a ggplot call with a designation of a target: Instead of: ggplot(diamonds, aes(x=carat, y=price)) + ... use something like" fig1 <- ggplot(diamonds, aes(x=carat, y=price)) + ... This creates an environment object that can then be further modified. Learning the syntax is a chore, but the output tends to be fine, especially for publications and final graphics. One the other hand it's slower and fussier than some of the more traditional approaches, which are what I would prefer for EDA. JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] FREDR and R 3.6
On Thu, 29 Oct 2020 13:29:41 -0400 H wrote: > I tried to install the fredr package yesterday to access the data > series hosted by the St. Louis Fed but my installation of R, version > 3.6, tells me it is not available from a cran repository. > > I could not find any information on this on the fredr information > package and was wondering if anyone here might know? > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html and provide commented, > minimal, self-contained, reproducible code. If you check, the response is correct. The package is available on Github. JWdougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why does a 2 GB RData file exceed my 16GB memory limit when reading it in?
On Wed, 2 Sep 2020 16:31:53 -0500 David Jones wrote: > Thank you Uwe, John, and Bert - this is very helpful context. > > If it helps inform the discussion, to address John and Bert's > questions - I actually had less memory free when I originally ran the > analyses and saved the workspace, than when I read in the data back in > later on (I rebooted in an attempt to free all possible memory before > rereading the workspace back in). > I assumed that, though I shouldn't have. Nice to know. Were you working from a terminal or through a GUI like RStudio? You will need to provide a really clear description of the initial and later conditions. Your step to reboot and then load is exactly what I would have done, I would also have killed any network connection temporarily to see if there are other things going on that caused the problem out side of R. You should also let any potential helper know what OS you are using, and what hardware configuration you have. Since you rebooted you are probably not working across a network, but ... JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Why does a 2 GB RData file exceed my 16GB memory limit when reading it in?
On Wed, 2 Sep 2020 13:36:43 +0200 Uwe Ligges wrote: > On 02.09.2020 04:44, David Jones wrote: > > I ran a number of analyses in R and saved the workspace, which > > resulted in a 2GB .RData file. When I try to read the file back > > into R > > Compressed in RData but uncompressed in main memory > > > > later, it won't read into R and provides the error: "Error: cannot > > allocate vector of size 37 Kb" > > > > This error comes after 1 minute of trying to read things in - I > > presume a single vector sends it over the memory limit. But, > > memory.limit() shows that I have access to a full 16gb of ram on my > > machine (12 GB are free when I try to load the RData file). > > But the data may need more > > > > gc() shows the following after I receive this error: > > > > used (Mb) gc trigger (Mb) max used (Mb) > > Ncells 623130 33.3 4134347 220.8 5715387 305.3 > > Vcells 1535682 11.8 883084810 6737.5 2100594002 16026.3 > > So 16GB were used when R gave up. > > Best, > Uwe Ligges For my own part, looking at the OP's question, it does seem curious that R could write that .RData file, but on the same system not be able to reload something it created. How would that work. Wouldn't the memory limit have been exceeded BEFORE the the .RData file was written the FIRST time? JDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] grid and lattice packages not working
On Mon, 27 Jul 2020 10:12:33 -0700 Abhai Sawkar wrote: It might help if you provided an example of what happens when you invoke one of the routines. As it stands, this could be due to several different causes. JWdougherty > Hi R support team, > > I downloaded R from the Internet and tried to use the grid GUI > package but it seems like the graphical functions can't be found. > > I did a quick search() and despite the presence of the grid and > lattice packages in my R folder, it doesn't seem to be there either. > > Any help would be appreciated. > > Thank you and kind regards > Abhai > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html and provide commented, > minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to stack two Stack manhattan plots?
On Wed, 10 Jun 2020 15:36:11 -0500
Ana Marija wrote:
> Hello,
>
> I have a data frame like this:
>
> > head(tmp1)
> CHR BP PoldPnew
> 1 1 785989 0.9521 0.09278
> 2 1 1130727 0.4750 0.19010
> 3 1 1156131 0.5289 0.48520
> 4 1 1158631 0.2554 0.18140
> 5 1 1211292 0.2954 0.48590
> 6 1 1478153 0.5542 0.68790
> ...
>
> I did:
> tmp.tidy <- tmp1 %>% gather(key, value, -BP, -CHR)
> jpeg("over.jpeg")
> ggplot(tmp.tidy, aes(BP, value, color=key)) + geom_point() +
> facet_wrap(~CHR, nrow=1)
> dev.off()
>
> but I got this plot in attach which doesn't make sense. Can you please
> advise how to make this plot?
>
> thanks
> Ana
If you would, the str() output might help people understand what is
happening, and also how many records you're looking at. The head()
output is a bit thin on information. There are various manhattan plot
packages for R including a specialized package for ggplot2.
JWDougherty
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Re: [R] Package installation problem
On Fri, 29 May 2020 08:47:35 +0300 Eric Berger wrote: > Hi John, > This is a bit off-topic for this mailing list as your issue is a > linux, specifically Fedora, issue, and not R. > I don't use Fedora but I did a quick Google search on > > fedora missing package .pc file > > and that came back with a lot of hits. This one in particular should > be a good place to start. > It gives some explanation as to when installation will result in a .pc > file (seems to relate to -dev versions). > > https://stackoverflow.com/questions/33050517/supply-pc-file-for-pkg-config > > HTH, > Eric > Thanks Eric. I wasn't sure where the hick-up was (R or Fedora). The library the error message said couldn't be found was right where it belonged. The first thing I did was check that the *devel file was in the lib64 directory, and it was. The pc file was the only vagrant, and it was not on the system at all. I'm going to try to get sense out of Fedora about this because with "devel" files it should have been. When I reinstalled this latest time from the command line, the "pc" file was placed just as it should have been. The threads on stackoverflow are four years old, so this has been around in one form or another for a while. Again, thanks, JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Package installation problem
On Fri, 29 May 2020 18:36:39 +0200 Martin Møller Skarbiniks Pedersen wrote: > sudo dnf install libcurl-devel Martin, I was going to say I had already done that more than once, using both the command line and the new "dnfdragora" package manager, but then decided, "what the heck. I'll try again." This time the *.pc file appeared where it belonged. So, thank you. Evidently, I tweaked the right thing, whatever it was, right before I gave up and wrote my request, thinking that if FC32 broke my tseries installation, it would have broken others. As usual the r-list is quicker, and much more helpful. I'll pass this along to Fedora, since there seems to be a problem of some kind. libcurl-devel was already installed on my system, the first thing I ckecked. It was just the *.pc file that was the problem. Thanks, JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Package installation problem
I'm not certain just what this problem is. Trying to install the "curl" package, which "tseries" wants results in the following error: Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable Package 'libcurl', required by 'virtual:world', not found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing `libcurl.pc' to the PKG_CONFIG_PATH environment variable Package 'libcurl', required by 'virtual:world', not found Using PKG_CFLAGS= Using PKG_LIBS=-lcurl - ANTICONF ERROR --- Configuration failed because libcurl was not found. Try installing: * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc) * rpm: libcurl-devel (Fedora, CentOS, RHEL) * csw: libcurl_dev (Solaris) If libcurl is already installed, check that 'pkg-config' is in your PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config is unavailable you can set INCLUDE_DIR and LIB_DIR manually via: R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...' ERROR: configuration failed for package ‘curl’ * removing ‘/home/john/R/x86_64-redhat-linux-gnu-library/3.6/curl’ Warning in install.packages : installation of package ‘curl’ had non-zero exit status However, libcurl is installed, installed. What does seem to missing is "libcurl.pc". The ../pkgconfig directory contains a number of different *.pc files, but not that one. I'm asking here first because someone else may have already encountered and solved this. I'm running Fedora 32 with kde on a 4 X AMD system. I just updated Fedora. JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] the volcano orientation
Out of curiosity, and considering the bewildering array of projections
and grids in use for various mapping purposes, you seem to be saying in your
example 2 that the grid coordinates number south to north and east to
west. Given scale of the coordinate numbers, would that be a national
grid system employed in New Zealnd?
J. W. Dougherty
On Mon, 11 May 2020 13:56:49 +1200
"Richard O'Keefe" wrote:
> Hey, I know that volcano! It's walking distance from the Intermediate
> school I attended.
> To you it's a plot; to me it's a place.
> So I offer you four scenarios.
>
> 1. You think of it as a place you know and have been.
> In that case the "right" orientation is the one that best matches
> what you are used to seeing.
> For me, that would put the peak on the right of the plot.
>
> 2. You think of it as a patch in a map.
> In that case the "right:" orientation is the one that matches the
> map. That would put the peak at the bottom of the plot.
>
> 3. You think of it as a product of geological processes, and are
> perhaps interested in
> whether there is any connection between the orientation of the
> volcano and the
> direction the Auckland hot-spot (currently at White Island) was
> moving. In that case you'd choose south-west -> north-east as the
> primary axis. (I think. Not really sure.)
>
> 4. You think of it as a picture, an illustration in a textbook. It
> might need to be cropped
> vertically so you can fit another illustration on the same page.
> For that and
> perceptual reasons you want the major linear axis of the image to
> be horizontal.
> In that case, what we have now is a perfectly reasonable choice.
>
> "Quality is fitness for use."
>
> On Sun, 10 May 2020 at 12:44, Michael Sumner
> wrote:
> >
> > Does anyone know why 'volcano' is oriented as it is?
> >
> > image(volcano) ## filled.contour is the same
> >
> > I know it's all arbitrary, but north-up is a pretty solid
> > convention. Is there any reason why the classic 'image()' example
> > data set would not default to this orientation?
> >
> > A Google map of the site (in Web Mercator):
> >
> > https://www.google.com/maps/place/Maungawhau+%2F+Mount+Eden/@-36.8763271,174.7619561,856m/data=!3m1!1e3!4m8!1m2!2m1!1smaungawhau!3m4!1s0x6d0d47db8d7bd1ff:0x8bcffe2a5c7360d2!8m2!3d-36.867!4d174.767
> >
> >
> > For image(), the north-up orientation is
> > 't(volcano[,ncol(volcano):1])'.
> >
> > If you are interested in a roughly georeferenced version I have
> > code here:
> >
> > https://gist.github.com/mdsumner/20fe3ffa04421bf8e0517c19085e5fd8
> >
> > (Also see fortunes::fortune("conventions") )
> >
> > Best, Mike
> >
> >
> > --
> > Michael Sumner
> > Software and Database Engineer
> > Australian Antarctic Division
> > Hobart, Australia
> > e-mail: mdsum...@gmail.com
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html and provide commented,
> > minimal, self-contained, reproducible code.
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> http://www.R-project.org/posting-guide.html and provide commented,
> minimal, self-contained, reproducible code.
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Re: [R] Analyzing Baseball Data With R
On Mon, 16 Mar 2020 15:35:36 -0700 "Phillip Heinrich" wrote: > Can’t get past first step of Chapter 7 page 164. > > Opened a new RStudio window. Loaded tidyverse and keyed in > library(tidyverse) which of course includes dplyr. The working > directory is: C:/Users/Owner/Documents. > > Then keyed in: db <- src_sqlite(“data/pitchrx.sqlite”,create=TRUE) > > And got the following error: Error: Could not connect to database: > unable to open database > file > > Googled everything I could think of to find the sqlite function and > the pitchrx.sqlite empty data base. Can someone give me some > direction? > > I wondering if I have configured RStudio incorrectly. Why doesn’t my > by RStudio point to the correct data file? > I get the idea that this might be homework. There's a good deal of information missing if you want help, and probably you've neglected a few steps that need to be taken before you can proceed. You also need to understand the difference between R and RStudio. What you could do is type in "??src_sqlite() and see what it tells you. For instance, have you installed the package RSQlite? If you haven't you need to install it. It also appears that you might be running Windows. Have you installed sqlite? And so on ... JWD __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] CRAN UC Berkeley link
This link https://cran.cnr.berkeley.edu/ on the "mirrors" page no longer points to a CRAN mirror. It seems to be generic to UCB. JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sample size required to estimate population variance
On Tue, 2 Jul 2019 22:23:18 + (UTC) Thomas Subia via R-help wrote: > Colleagues, > Can anyone suggest a package or code which might help me calculate > the minimum sample size required to estimate the population variance? > I can do this in Minitab but I'd rather do this in R. Thomas Subia You want to look into the capabilities of the pwr package. This page offers some information: https://www.statmethods.net/stats/power.html JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Open a file which name contains a tilde
On Wed, 5 Jun 2019 18:07:15 +0200
Frank Schwidom wrote:
In reading file names, names with spaces require escaping of the
spaces, and you are using not only a tilde but the space as spell. The
tilde is conventionally read as wild card representing the leading
portion of the file address, which is what you see here:
The long standing convention in unix and linux is that a tilde is
shorthand for your home directory, just as "./" is the local directory
and "../" is one step back up the directory tree. The output of
path.expand() varies in how your string is constructed:
1. > path.expand("ab")
[1] "ab"
2. > path.expand("a b")
[1] "a b"
3. > path.expand("a ~b")
[1] "a ~b"
4. > path.expand("a ~ b")
[1] "a /home/john b"
5. > path.expand("a ~/b")
[1] "a /home/john/b"
6. > path.expand("~/a b")
[1] "/home/john/a b"
Notice that the spaces have an effect on how the tilde is parsed in
the string. The next to last case sees a string with three elements:
"a", the local path, and "b". The last expands the tilde as the "path"
to a hypothetical file "b" in the home directory. In the sixth case the
same behaviour occurs.
If you read the help for path.expand(), the routine expects
"leading" tildes, which explains the free floating "path in the fourth
example. In the third example, where the forward slash is omitted, the
routine simply treats the tilde as part of a string.
Also note this at http://www.linfo.org/file_name.html:
"...file names only use alphanumeric characters (mostly lower case),
underscores, hyphens and periods. Other characters, such as dollar
signs, percentage signs and brackets, have special meanings to the
shell and can be distracting to work with. File names should never
begin with a hyphen."
The probable "bug" is that none of the programmers imagined that anyone
would use special characters within file names, "legal" or not, (just
not done, don't y' know). In any case the simple solution, if you
really, really need a tilde in a filename, is to avoid setting it off in
spaces, or any other character that could mislead a routine into
treating it conventionally as shorthand for you home directory.
JWDougherty
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Re: [R] Mac/PC differences in lmer results
On Wed, 29 May 2019 18:44:26 +0200 Nicolas Schuck wrote: > Dear fellow R coders, > > I am observing differences in results obtained using glmer when using > a Mac or Linux computer versus a PC Just as an aside and point of information, both the Mac and the Linux systems are PCs, just as much so as one running Windows. The designation "PC" refers to hardware. Your question demands the extra steps of thinking about what other operating system might be in use. There are others though I doubt R is implemented on any of them. JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] install R
On Wed, 8 May 2019 21:05:29 +0800 (CST) yueli wrote: > Hello, > > > I am trying to install R. > > > Thanks in advance for any help! > > > Yue > > It appears that your GCC compiler installation doesn't include all the compilers that can come with it. All those "no's" listed in your output listing should be "yes" to compile R, its help files, and various compiled material required by add-on packages (or just about anything else that needs a compiler other than vanilla C). At a minimum you should have both "gfortran" and "g++" in your /usr/bin directory. You can see from your output that the configure routine looks for several different alternatives for fortran compiler and none are found. As it stands, the only compiler you seem to have enabled appears to be the basic GNU C compiler. It looks as if you might have a minimal desktop system installed, but linux is open source, which means that to fully use it, you will want various compilers for any software that comes as source you want to compile. Your alternative with R would be to install the binary, but the lack of compilers will still be a problem with many packages you may want to use in R, since they too often use at least the Fortran compiler, and I'm pretty sure I have see g++ called as well. JDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with use RMarkdown and knitr in an rdm output to word.doc
On Mon, 8 Apr 2019 11:19:12 + Bill Poling wrote: One solution to your problem may be to use an environment like RStudio. You can maintain multiple open documents including an rmd document and using knitr and rmarkdown, add and then run code snippets the output of which becomes embedded in the generated Word document. I use this approach, but the default Word styles are a nuisance and not suitable for draft reports. So, following generation of the Word document you will need to reformat the document. This works in both Windows and Linux (where you need Libreoffice installed). JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Which dependency list to build first?
On Tue, 26 Feb 2019 05:47:38 -0800 (PST) Rich Shepard wrote: > /usr/lib/R/library/later/libs/later.so: undefined symbol: > __atomic_fetch_add_8 Stackoverflow may help at least in locating the trouble. A web search indicates the error is not unknown in other contexts than R. JWDougherty __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
