Re: [R] Extracting Comments from Functions/Packages
On Thu, 07 Oct 2021, Leonard Mada via R-help writes:
> Dear R Users,
>
>
> I wrote a minimal parser to extract strings and
> comments from the function definitions.
>
>
> The string extraction works fine. But there are no comments:
>
> a.) Are the comments stripped from the compiled packages?
>
> b.) Alternatively: Is the deparse() not suited for this task?
>
> b.2.) Is deparse() parsing the function/expression itself?
>
> [see code for extract.str.fun() function below]
>
>
> ### All strings in "base"
> extract.str.pkg("base")
> # type = 2 for Comments:
> extract.str.pkg("base", type=2)
> extract.str.pkg("sp", type=2)
> extract.str.pkg("NetLogoR", type=2)
>
> The code for the 2 functions (extract.str.pkg &
> extract.str.fun) and the code for the parse.simple()
> parser are below.
>
>
> Sincerely,
>
>
> Leonard
>
> ===
>
> The latest code is on GitHub:
>
> https://github.com/discoleo/R/blob/master/Stat/Tools.Formulas.R
>
>
> ### Code to process functions in packages:
> extract.str.fun = function(fn, pkg, type=1, strip=TRUE) {
> fn = as.symbol(fn); pkg = as.symbol(pkg);
> fn = list(substitute(pkg ::: fn));
> # deparse
> s = paste0(do.call(deparse, fn), collapse="");
> npos = parse.simple(s);
> extract.str(s, npos[[type]], strip=strip)
> }
> extract.str.pkg = function(pkg, type=1, exclude.z = TRUE, strip=TRUE) {
> nms = ls(getNamespace(pkg));
> l = lapply(nms, function(fn) extract.str.fun(fn,
> pkg, type=type, strip=strip));
> if(exclude.z) {
> hasStr = sapply(l, function(s) length(s) >= 1);
> nms = nms[hasStr];
> l = l[hasStr];
> }
> names(l) = nms;
> return(l);
> }
>
> ### minimal Parser:
> # - proof of concept;
> # - may be useful to process non-conformant R "code", e.g.:
> # "{\"abc\" + \"bcd\"} {FUN}"; (still TODO)
> # Warning:
> # - not thoroughly checked &
> # may be a little buggy!
>
> parse.simple = function(x, eol="\n") {
> len = nchar(x);
> n.comm = list(integer(0), integer(0));
> n.str = list(integer(0), integer(0));
> is.hex = function(ch) {
> # Note: only for 1 character!
> return((ch >= "0" && ch <= "9") ||
> (ch >= "A" && ch <= "F") ||
> (ch >= "a" && ch <= "f"));
> }
> npos = 1;
> while(npos <= len) {
> s = substr(x, npos, npos);
> # State: COMMENT
> if(s == "#") {
> n.comm[[1]] = c(n.comm[[1]], npos);
> while(npos < len) {
> npos = npos + 1;
> if(substr(x, npos, npos) == eol) break;
> }
> n.comm[[2]] = c(n.comm[[2]], npos);
> npos = npos + 1; next;
> }
> # State: STRING
> if(s == "\"" || s == "'") {
> n.str[[1]] = c(n.str[[1]], npos);
> while(npos < len) {
> npos = npos + 1;
> se = substr(x, npos, npos);
> if(se == "\\") {
> npos = npos + 1;
> # simple escape vs Unicode:
> if(substr(x, npos, npos) != "u") next;
> len.end = min(len, npos + 4);
> npos = npos + 1;
> isAllHex = TRUE;
> while(npos <= len.end) {
> se = substr(x, npos, npos);
> if( ! is.hex(se)) { isAllHex = FALSE; break; }
> npos = npos + 1;
> }
> if(isAllHex) next;
> }
> if(se == s) break;
> }
> n.str[[2]] = c(n.str[[2]], npos);
> npos = npos + 1; next;
> }
> npos = npos + 1;
> }
> return(list(str = n.str, comm = n.comm));
> }
>
>
> extract.str = function(s, npos, strip=FALSE) {
> if(length(npos[[1]]) == 0) return(character(0));
> strip.FUN = if(strip) {
> function(id) {
> if(npos[[1]][[id]] + 1 < npos[[2]][[id]]) {
> nStart = npos[[1]][[id]] + 1;
> nEnd = npos[[2]][[id]] - 1; # TODO:
> Error with malformed string
> return(substr(s, nStart, nEnd));
> } else {
> return("");
> }
> }
> } else function(id) substr(s, npos[[1]][[id]], npos[[2]][[id]]);
> sapply(seq(length(npos[[1]])), strip.FUN);
> }
>
On a.) There is an option "keep.source" that controls
this behaviour. When you install a package via
R CMD INSTALL, you can specify the option; see
R CMD INSTALL --help .
There is also the "remindR" package on CRAN which
(I think) does something similar.
--
Enrico Schumann
Lucerne, Switzerland
http://enricoschumann.net
__
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Re: [R] How to use ifelse without invoking warnings
Dear Ravi, It's already been suggested that you could disable warnings, but that's risky in case there's a warning that you didn't anticipate. Here's a different approach: > kk <- k[k >= -1 & k <= n] > ans <- numeric(length(k)) > ans[k > n] <- 1 > ans[k >= -1 & k <= n] <- pbeta(p, kk + 1, n - kk, lower.tail=FALSE) > ans [1] 0.0 0.006821826 0.254991551 1.0 BTW, I don't think that you mentioned that p = 0.3, but that seems apparent from the output you showed. I hope this helps, John -- John Fox, Professor Emeritus McMaster University Hamilton, Ontario, Canada web: https://socialsciences.mcmaster.ca/jfox/ On 2021-10-07 12:29 p.m., Ravi Varadhan via R-help wrote: Hi, I would like to execute the following vectorized calculation: ans <- ifelse (k >= -1 & k <= n, pbeta(p, k+1, n-k, lower.tail = FALSE), ifelse (k < -1, 0, 1) ) For example: k <- c(-1.2,-0.5, 1.5, 10.4) n <- 10 ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), ifelse (k < -1, 0, 1) ) Warning message: In pbeta(p, k + 1, n - k, lower.tail = FALSE) : NaNs produced print(ans) [1] 0.0 0.006821826 0.254991551 1.0 The answer is correct. However, I would like to eliminate the annoying warnings. Is there a better way to do this? Thank you, Ravi [[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 use ifelse without invoking warnings
Bert's approach is much less risky! On Thu, Oct 7, 2021 at 1:37 PM Bert Gunter wrote: > > ?suppressWarnings > > > p <- .05 > > k <- c(-1.2,-0.5, 1.5, 10.4) > > n <- 10 > > > > ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), > ifelse (k < -1, 0, 1) ) > Warning message: > In pbeta(p, k + 1, n - k, lower.tail = FALSE) : NaNs produced > > > > suppressWarnings(ans <- ifelse (k >= -1 & k <= n, > pbeta(p,k+1,n-k,lower.tail=FALSE), ifelse (k < -1, 0, 1) )) > ## no warnings > > Bert Gunter > > "The trouble with having an open mind is that people keep coming along and > sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Thu, Oct 7, 2021 at 10:21 AM Ravi Varadhan via R-help < > r-help@r-project.org> wrote: > > > Hi, > > I would like to execute the following vectorized calculation: > > > > ans <- ifelse (k >= -1 & k <= n, pbeta(p, k+1, n-k, lower.tail = FALSE), > > ifelse (k < -1, 0, 1) ) > > > > For example: > > > > > > > k <- c(-1.2,-0.5, 1.5, 10.4) > > > n <- 10 > > > ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), > > ifelse (k < -1, 0, 1) ) > > Warning message: > > In pbeta(p, k + 1, n - k, lower.tail = FALSE) : NaNs produced > > > print(ans) > > [1] 0.0 0.006821826 0.254991551 1.0 > > > > The answer is correct. However, I would like to eliminate the annoying > > warnings. Is there a better way to do this? > > > > Thank you, > > Ravi > > > > > > [[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. > > > > [[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. -- Sarah Goslee (she/her) http://www.sarahgoslee.com __ 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 use ifelse without invoking warnings
If you are positive the warnings don't matter for your application, you can disable them: see ?options for details of warn. But that can be dangerous, so be careful! Sarah On Thu, Oct 7, 2021 at 1:21 PM Ravi Varadhan via R-help wrote: > > Hi, > I would like to execute the following vectorized calculation: > > ans <- ifelse (k >= -1 & k <= n, pbeta(p, k+1, n-k, lower.tail = FALSE), > ifelse (k < -1, 0, 1) ) > > For example: > > > > k <- c(-1.2,-0.5, 1.5, 10.4) > > n <- 10 > > ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), ifelse > > (k < -1, 0, 1) ) > Warning message: > In pbeta(p, k + 1, n - k, lower.tail = FALSE) : NaNs produced > > print(ans) > [1] 0.0 0.006821826 0.254991551 1.0 > > The answer is correct. However, I would like to eliminate the annoying > warnings. Is there a better way to do this? > > Thank you, > Ravi > > > [[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. -- Sarah Goslee (she/her) http://www.sarahgoslee.com __ 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 use ifelse without invoking warnings
?suppressWarnings > p <- .05 > k <- c(-1.2,-0.5, 1.5, 10.4) > n <- 10 > > ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), ifelse (k < -1, 0, 1) ) Warning message: In pbeta(p, k + 1, n - k, lower.tail = FALSE) : NaNs produced > > suppressWarnings(ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), ifelse (k < -1, 0, 1) )) ## no warnings Bert Gunter "The trouble with having an open mind is that people keep coming along and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Thu, Oct 7, 2021 at 10:21 AM Ravi Varadhan via R-help < r-help@r-project.org> wrote: > Hi, > I would like to execute the following vectorized calculation: > > ans <- ifelse (k >= -1 & k <= n, pbeta(p, k+1, n-k, lower.tail = FALSE), > ifelse (k < -1, 0, 1) ) > > For example: > > > > k <- c(-1.2,-0.5, 1.5, 10.4) > > n <- 10 > > ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), > ifelse (k < -1, 0, 1) ) > Warning message: > In pbeta(p, k + 1, n - k, lower.tail = FALSE) : NaNs produced > > print(ans) > [1] 0.0 0.006821826 0.254991551 1.0 > > The answer is correct. However, I would like to eliminate the annoying > warnings. Is there a better way to do this? > > Thank you, > Ravi > > > [[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. > [[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] How to use ifelse without invoking warnings
Hi, I would like to execute the following vectorized calculation: ans <- ifelse (k >= -1 & k <= n, pbeta(p, k+1, n-k, lower.tail = FALSE), ifelse (k < -1, 0, 1) ) For example: > k <- c(-1.2,-0.5, 1.5, 10.4) > n <- 10 > ans <- ifelse (k >= -1 & k <= n, pbeta(p,k+1,n-k,lower.tail=FALSE), ifelse (k > < -1, 0, 1) ) Warning message: In pbeta(p, k + 1, n - k, lower.tail = FALSE) : NaNs produced > print(ans) [1] 0.0 0.006821826 0.254991551 1.0 The answer is correct. However, I would like to eliminate the annoying warnings. Is there a better way to do this? Thank you, Ravi [[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] Extracting Comments from Functions/Packages
Dear R Users,
I wrote a minimal parser to extract strings and comments from the
function definitions.
The string extraction works fine. But there are no comments:
a.) Are the comments stripped from the compiled packages?
b.) Alternatively: Is the deparse() not suited for this task?
b.2.) Is deparse() parsing the function/expression itself?
[see code for extract.str.fun() function below]
### All strings in "base"
extract.str.pkg("base")
# type = 2 for Comments:
extract.str.pkg("base", type=2)
extract.str.pkg("sp", type=2)
extract.str.pkg("NetLogoR", type=2)
The code for the 2 functions (extract.str.pkg & extract.str.fun) and the
code for the parse.simple() parser are below.
Sincerely,
Leonard
===
The latest code is on GitHub:
https://github.com/discoleo/R/blob/master/Stat/Tools.Formulas.R
### Code to process functions in packages:
extract.str.fun = function(fn, pkg, type=1, strip=TRUE) {
fn = as.symbol(fn); pkg = as.symbol(pkg);
fn = list(substitute(pkg ::: fn));
# deparse
s = paste0(do.call(deparse, fn), collapse="");
npos = parse.simple(s);
extract.str(s, npos[[type]], strip=strip)
}
extract.str.pkg = function(pkg, type=1, exclude.z = TRUE, strip=TRUE) {
nms = ls(getNamespace(pkg));
l = lapply(nms, function(fn) extract.str.fun(fn, pkg, type=type,
strip=strip));
if(exclude.z) {
hasStr = sapply(l, function(s) length(s) >= 1);
nms = nms[hasStr];
l = l[hasStr];
}
names(l) = nms;
return(l);
}
### minimal Parser:
# - proof of concept;
# - may be useful to process non-conformant R "code", e.g.:
# "{\"abc\" + \"bcd\"} {FUN}"; (still TODO)
# Warning:
# - not thoroughly checked &
# may be a little buggy!
parse.simple = function(x, eol="\n") {
len = nchar(x);
n.comm = list(integer(0), integer(0));
n.str = list(integer(0), integer(0));
is.hex = function(ch) {
# Note: only for 1 character!
return((ch >= "0" && ch <= "9") ||
(ch >= "A" && ch <= "F") ||
(ch >= "a" && ch <= "f"));
}
npos = 1;
while(npos <= len) {
s = substr(x, npos, npos);
# State: COMMENT
if(s == "#") {
n.comm[[1]] = c(n.comm[[1]], npos);
while(npos < len) {
npos = npos + 1;
if(substr(x, npos, npos) == eol) break;
}
n.comm[[2]] = c(n.comm[[2]], npos);
npos = npos + 1; next;
}
# State: STRING
if(s == "\"" || s == "'") {
n.str[[1]] = c(n.str[[1]], npos);
while(npos < len) {
npos = npos + 1;
se = substr(x, npos, npos);
if(se == "\\") {
npos = npos + 1;
# simple escape vs Unicode:
if(substr(x, npos, npos) != "u") next;
len.end = min(len, npos + 4);
npos = npos + 1;
isAllHex = TRUE;
while(npos <= len.end) {
se = substr(x, npos, npos);
if( ! is.hex(se)) { isAllHex = FALSE; break; }
npos = npos + 1;
}
if(isAllHex) next;
}
if(se == s) break;
}
n.str[[2]] = c(n.str[[2]], npos);
npos = npos + 1; next;
}
npos = npos + 1;
}
return(list(str = n.str, comm = n.comm));
}
extract.str = function(s, npos, strip=FALSE) {
if(length(npos[[1]]) == 0) return(character(0));
strip.FUN = if(strip) {
function(id) {
if(npos[[1]][[id]] + 1 < npos[[2]][[id]]) {
nStart = npos[[1]][[id]] + 1;
nEnd = npos[[2]][[id]] - 1; # TODO: Error with
malformed string
return(substr(s, nStart, nEnd));
} else {
return("");
}
}
} else function(id) substr(s, npos[[1]][[id]], npos[[2]][[id]]);
sapply(seq(length(npos[[1]])), strip.FUN);
}
__
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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] Unusual Error Loading tidyverse
My experience is that the combination of OneDrive and R leads to lack of
productivity.
--
W. Michael Conklin
EVP Marketing & Data Sciences
GfK
M +1 612 567 8287
-Original Message-
From: R-help On Behalf Of Kevin Thorpe
Sent: Thursday, October 7, 2021 10:50 AM
To: Jeff Newmiller
Cc: R Help Mailing List
Subject: Re: [R] Unusual Error Loading tidyverse
Nice fortune.
In retrospect, maybe it would have worked to re-build the user library. Things
were acting so strangely to me I opted for the direct, if more dangerous
approach. :-)
> On Oct 7, 2021, at 11:37 AM, Jeff Newmiller wrote:
>
> Sad, more like.
>
> fortunes::fortune(337)
>
> You would have done just as well to delete the user library and let R prompt
> you to re-create it if things were that bad. Note that the default R
> configuration always looks first in the user library and only falls back to
> the system library if the desired package is not found in the user library.
> In most user-administered R installations you are better off acting as though
> the system library wasn't there.
>
> On October 7, 2021 7:56:05 AM PDT, Kevin Thorpe
> wrote:
>> I thought I would close the loop on this. It was really weird and I don’t
>> understand everything that went on.
>>
>> First, it was indeed the case that the main library was not writeable so
>> packages were being installed in a user library.
>>
>> Here is where it gets confusing to me. Both library paths did appear in
>> .libPaths(). I could not figure out where that was being set since there was
>> no user .Rprofile and Rprofile.site was not modified. To start over I got
>> the user to delete the local library and started R as an administrator and
>> forced installation in the main library with the lib argument. However, even
>> with dependencies=TRUE in install.packages() everything was not getting
>> installed. I then had the user start RStudio as an admin and use the install
>> packages from the menu, again specifying the main library and asking for
>> dependencies. When this was done, many additional packages were then
>> installed that were not installed when running the native R application.
>> Eventually, after that, tidyverse loaded (I realize it is a wrapper to load
>> a bunch of other packages). I also had the user install rms (which we use)
>> and again, various bits did not get installed and had to be manually
>> requested (I don’t remember which ones).
>>
>> Anyway, in the end we got his system functioning. I realize that running as
>> admin to install packages is probably not best practice, but it was the only
>> way I saw to get things working. I _think_ some of the problems were because
>> his home directory is synced with OneDrive and the user library path was to
>> a OneDrive folder.
>>
>> I am often shocked by the difficulties students have installing packages.
>> They manage to get errors that I have never seen in all my user of using R.
>> On a Win10 box of my own, I installed R and packages with no difficulties
>> so, naturally am surprised when things go this haywire with an installation.
>>
>> That’s my story. Hope it was entertaining. :-)
>>
>> Kevin
>>
>>
>>> On Sep 24, 2021, at 3:26 PM, Duncan Murdoch
>>> wrote:
>>>
>>> It is worth checking that the library where things were most recently
>>> installed is the first place R looks, i.e. the first entry in .libPaths().
>>> Often R is installed by an administrator, and users can't write to the main
>>> library, so when they install packages they go somewhere else. If
>>> "somewhere else" isn't first in .libPaths(), R won't see the new installs.
>>>
>>> Duncan Murdoch
>>>
>>> On 24/09/2021 2:04 p.m., Kevin Thorpe wrote:
I did try installing xml2 and it appeared to complete. I will ask him to
try again and send me the output.
> On Sep 24, 2021, at 1:58 PM, Jeff Newmiller
> wrote:
>
> Seems like they should install the xml2 package before proceeding to load
> whatever (tidyverse).
>
> This kind of "dependency missing" problem tends to be a recurring problem
> particularly on Windows but in general when some deeply-embedded
> dependency fails to load or is removed in preparation for upgrading.
>
> On September 24, 2021 10:40:41 AM PDT, Kevin Thorpe
> wrote:
>> Below is some output from one of my students. I have never seen this
>> error and tried a few things (updating packages for one) but am at a
>> loss to help further. Would appreciate suggestions that I can pass along.
>>
>> Here is the error. I tried an install.packages(“xml2”) which appeared to
>> complete but the error persists.
>>
>>> library("tidyverse")
>> Error: package or namespace load failed for ‘tidyverse’ in
>> library.dynam(lib, package, package.lib):
>> DLL ‘xml2’ not found: maybe not installed for this architecture?
>>
>> Here is the sessionInfo()
>>
>>> sessionInfo()
>> R
Re: [R] Unusual Error Loading tidyverse
Nice fortune.
In retrospect, maybe it would have worked to re-build the user library. Things
were acting so strangely to me I opted for the direct, if more dangerous
approach. :-)
> On Oct 7, 2021, at 11:37 AM, Jeff Newmiller wrote:
>
> Sad, more like.
>
> fortunes::fortune(337)
>
> You would have done just as well to delete the user library and let R prompt
> you to re-create it if things were that bad. Note that the default R
> configuration always looks first in the user library and only falls back to
> the system library if the desired package is not found in the user library.
> In most user-administered R installations you are better off acting as though
> the system library wasn't there.
>
> On October 7, 2021 7:56:05 AM PDT, Kevin Thorpe
> wrote:
>> I thought I would close the loop on this. It was really weird and I don’t
>> understand everything that went on.
>>
>> First, it was indeed the case that the main library was not writeable so
>> packages were being installed in a user library.
>>
>> Here is where it gets confusing to me. Both library paths did appear in
>> .libPaths(). I could not figure out where that was being set since there was
>> no user .Rprofile and Rprofile.site was not modified. To start over I got
>> the user to delete the local library and started R as an administrator and
>> forced installation in the main library with the lib argument. However, even
>> with dependencies=TRUE in install.packages() everything was not getting
>> installed. I then had the user start RStudio as an admin and use the install
>> packages from the menu, again specifying the main library and asking for
>> dependencies. When this was done, many additional packages were then
>> installed that were not installed when running the native R application.
>> Eventually, after that, tidyverse loaded (I realize it is a wrapper to load
>> a bunch of other packages). I also had the user install rms (which we use)
>> and again, various bits did not get installed and had to be manually
>> requested (I don’t remember which ones).
>>
>> Anyway, in the end we got his system functioning. I realize that running as
>> admin to install packages is probably not best practice, but it was the only
>> way I saw to get things working. I _think_ some of the problems were because
>> his home directory is synced with OneDrive and the user library path was to
>> a OneDrive folder.
>>
>> I am often shocked by the difficulties students have installing packages.
>> They manage to get errors that I have never seen in all my user of using R.
>> On a Win10 box of my own, I installed R and packages with no difficulties
>> so, naturally am surprised when things go this haywire with an installation.
>>
>> That’s my story. Hope it was entertaining. :-)
>>
>> Kevin
>>
>>
>>> On Sep 24, 2021, at 3:26 PM, Duncan Murdoch
>>> wrote:
>>>
>>> It is worth checking that the library where things were most recently
>>> installed is the first place R looks, i.e. the first entry in .libPaths().
>>> Often R is installed by an administrator, and users can't write to the main
>>> library, so when they install packages they go somewhere else. If
>>> "somewhere else" isn't first in .libPaths(), R won't see the new installs.
>>>
>>> Duncan Murdoch
>>>
>>> On 24/09/2021 2:04 p.m., Kevin Thorpe wrote:
I did try installing xml2 and it appeared to complete. I will ask him to
try again and send me the output.
> On Sep 24, 2021, at 1:58 PM, Jeff Newmiller
> wrote:
>
> Seems like they should install the xml2 package before proceeding to load
> whatever (tidyverse).
>
> This kind of "dependency missing" problem tends to be a recurring problem
> particularly on Windows but in general when some deeply-embedded
> dependency fails to load or is removed in preparation for upgrading.
>
> On September 24, 2021 10:40:41 AM PDT, Kevin Thorpe
> wrote:
>> Below is some output from one of my students. I have never seen this
>> error and tried a few things (updating packages for one) but am at a
>> loss to help further. Would appreciate suggestions that I can pass along.
>>
>> Here is the error. I tried an install.packages(“xml2”) which appeared to
>> complete but the error persists.
>>
>>> library("tidyverse")
>> Error: package or namespace load failed for ‘tidyverse’ in
>> library.dynam(lib, package, package.lib):
>> DLL ‘xml2’ not found: maybe not installed for this architecture?
>>
>> Here is the sessionInfo()
>>
>>> sessionInfo()
>> R version 4.1.1 (2021-08-10)
>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>> Running under: Windows 10 x64 (build 19042)
>>
>> Matrix products: default
>>
>> locale:
>> [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
>> LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
>> [5]
Re: [R] Unusual Error Loading tidyverse
Sad, more like.
fortunes::fortune(337)
You would have done just as well to delete the user library and let R prompt
you to re-create it if things were that bad. Note that the default R
configuration always looks first in the user library and only falls back to the
system library if the desired package is not found in the user library. In most
user-administered R installations you are better off acting as though the
system library wasn't there.
On October 7, 2021 7:56:05 AM PDT, Kevin Thorpe
wrote:
>I thought I would close the loop on this. It was really weird and I don’t
>understand everything that went on.
>
>First, it was indeed the case that the main library was not writeable so
>packages were being installed in a user library.
>
>Here is where it gets confusing to me. Both library paths did appear in
>.libPaths(). I could not figure out where that was being set since there was
>no user .Rprofile and Rprofile.site was not modified. To start over I got the
>user to delete the local library and started R as an administrator and forced
>installation in the main library with the lib argument. However, even with
>dependencies=TRUE in install.packages() everything was not getting installed.
>I then had the user start RStudio as an admin and use the install packages
>from the menu, again specifying the main library and asking for dependencies.
>When this was done, many additional packages were then installed that were not
>installed when running the native R application. Eventually, after that,
>tidyverse loaded (I realize it is a wrapper to load a bunch of other
>packages). I also had the user install rms (which we use) and again, various
>bits did not get installed and had to be manually requested (I don’t remember
>which ones).
>
>Anyway, in the end we got his system functioning. I realize that running as
>admin to install packages is probably not best practice, but it was the only
>way I saw to get things working. I _think_ some of the problems were because
>his home directory is synced with OneDrive and the user library path was to a
>OneDrive folder.
>
>I am often shocked by the difficulties students have installing packages. They
>manage to get errors that I have never seen in all my user of using R. On a
>Win10 box of my own, I installed R and packages with no difficulties so,
>naturally am surprised when things go this haywire with an installation.
>
>That’s my story. Hope it was entertaining. :-)
>
>Kevin
>
>
>> On Sep 24, 2021, at 3:26 PM, Duncan Murdoch wrote:
>>
>> It is worth checking that the library where things were most recently
>> installed is the first place R looks, i.e. the first entry in .libPaths().
>> Often R is installed by an administrator, and users can't write to the main
>> library, so when they install packages they go somewhere else. If
>> "somewhere else" isn't first in .libPaths(), R won't see the new installs.
>>
>> Duncan Murdoch
>>
>> On 24/09/2021 2:04 p.m., Kevin Thorpe wrote:
>>> I did try installing xml2 and it appeared to complete. I will ask him to
>>> try again and send me the output.
On Sep 24, 2021, at 1:58 PM, Jeff Newmiller
wrote:
Seems like they should install the xml2 package before proceeding to load
whatever (tidyverse).
This kind of "dependency missing" problem tends to be a recurring problem
particularly on Windows but in general when some deeply-embedded
dependency fails to load or is removed in preparation for upgrading.
On September 24, 2021 10:40:41 AM PDT, Kevin Thorpe
wrote:
> Below is some output from one of my students. I have never seen this
> error and tried a few things (updating packages for one) but am at a loss
> to help further. Would appreciate suggestions that I can pass along.
>
> Here is the error. I tried an install.packages(“xml2”) which appeared to
> complete but the error persists.
>
>> library("tidyverse")
> Error: package or namespace load failed for ‘tidyverse’ in
> library.dynam(lib, package, package.lib):
> DLL ‘xml2’ not found: maybe not installed for this architecture?
>
> Here is the sessionInfo()
>
>> sessionInfo()
> R version 4.1.1 (2021-08-10)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows 10 x64 (build 19042)
>
> Matrix products: default
>
> locale:
> [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
> LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Canada.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> loaded via a namespace (and not attached):
> [1] Rcpp_1.0.7 cellranger_1.1.0 pillar_1.6.2 compiler_4.1.1 dbplyr_2.1.1
> forcats_0.5.1 tools_4.1.1
> [8] jsonlite_1.7.2 lubridate_1.7.10 lifecycle_1.0.0 tibble_3.1.4
> gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.11
>
Re: [R] RSQLite slowness
Dear Martin Morgan,
Thanks for all those links! Yes, my
question can be characterized like that
I think, traditional way writing
a temporary table into the database and
left JOINing the others vs.
parameterized query.
A relevant example would be to first
create the database from the compressed
tsv files:
for i in gene_info gene2refseq; do
wget -c https://ftp.ncbi.nlm.nih.gov/gene/DATA/$i.gz
gzip -d $i.gz
sqlite3 gene_info.sqlite ".mode tabs" ".import $i $i"
rm $i; done
then run this R code:
H <- data.frame(Group = c(1, 1, 2, 2),
NM = c("NM_001267695", "NM_001007636",
"NM_001003706", "NM_001353612"))
conn <- DBI::dbConnect(RSQLite::SQLite(), "gene_info.sqlite")
DBI::dbWriteTable(conn, "H", H, overwrite=T)
statement.1 <-
"SELECT * FROM gene2refseq R
LEFT JOIN gene_info I ON I.GeneID = R.GeneID
WHERE R.`RNA_nucleotide_accession.version`
LIKE '%' || ? || '%'"
time.1 <- proc.time()
x1 <- DBI::dbGetQuery(
conn=conn,
statement=statement.1,
param=list(H$NM))
time.1 <- proc.time() - time.1
statement.2 <-
"SELECT * FROM H
LEFT JOIN gene2refseq R ON
R.`RNA_nucleotide_accession.version`
LIKE '%' || H.NM || '%'
LEFT JOIN gene_info I ON I.GeneID = R.GeneID"
time.2 <- proc.time()
x2 <- DBI::dbGetQuery(
conn=conn,
statement=statement.2)
time.2 <- proc.time() - time.2
DBI::dbDisconnect(conn)
saveRDS(object=x1, file="ex1_x1.rds", compress="xz")
saveRDS(object=x2, file="ex1_x2.rds", compress="xz")
saveRDS(object=list("Time x1"=list(time.1),
"Time x2"=list(time.2)),
file="ex1_t.rds", compress="xz")
I got these timings in the ex1_t.rds
file:
$`Time x1`
user system elapsed
571.731 182.006 772.199
$`Time x2`
user system elapsed
200.068 90.529 295.086
As you can see, statement.1 takes a lot
longer to process compared to
statement.2 ... When I add the rest of
the 31 search terms, the difference gets
a lot bigger like I pointed out
initially, beyond the full hour vs. only
a few minutes.
Best,
Rasmus
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Unusual Error Loading tidyverse
I thought I would close the loop on this. It was really weird and I don’t
understand everything that went on.
First, it was indeed the case that the main library was not writeable so
packages were being installed in a user library.
Here is where it gets confusing to me. Both library paths did appear in
.libPaths(). I could not figure out where that was being set since there was no
user .Rprofile and Rprofile.site was not modified. To start over I got the user
to delete the local library and started R as an administrator and forced
installation in the main library with the lib argument. However, even with
dependencies=TRUE in install.packages() everything was not getting installed. I
then had the user start RStudio as an admin and use the install packages from
the menu, again specifying the main library and asking for dependencies. When
this was done, many additional packages were then installed that were not
installed when running the native R application. Eventually, after that,
tidyverse loaded (I realize it is a wrapper to load a bunch of other packages).
I also had the user install rms (which we use) and again, various bits did not
get installed and had to be manually requested (I don’t remember which ones).
Anyway, in the end we got his system functioning. I realize that running as
admin to install packages is probably not best practice, but it was the only
way I saw to get things working. I _think_ some of the problems were because
his home directory is synced with OneDrive and the user library path was to a
OneDrive folder.
I am often shocked by the difficulties students have installing packages. They
manage to get errors that I have never seen in all my user of using R. On a
Win10 box of my own, I installed R and packages with no difficulties so,
naturally am surprised when things go this haywire with an installation.
That’s my story. Hope it was entertaining. :-)
Kevin
> On Sep 24, 2021, at 3:26 PM, Duncan Murdoch wrote:
>
> It is worth checking that the library where things were most recently
> installed is the first place R looks, i.e. the first entry in .libPaths().
> Often R is installed by an administrator, and users can't write to the main
> library, so when they install packages they go somewhere else. If "somewhere
> else" isn't first in .libPaths(), R won't see the new installs.
>
> Duncan Murdoch
>
> On 24/09/2021 2:04 p.m., Kevin Thorpe wrote:
>> I did try installing xml2 and it appeared to complete. I will ask him to try
>> again and send me the output.
>>> On Sep 24, 2021, at 1:58 PM, Jeff Newmiller
>>> wrote:
>>>
>>> Seems like they should install the xml2 package before proceeding to load
>>> whatever (tidyverse).
>>>
>>> This kind of "dependency missing" problem tends to be a recurring problem
>>> particularly on Windows but in general when some deeply-embedded dependency
>>> fails to load or is removed in preparation for upgrading.
>>>
>>> On September 24, 2021 10:40:41 AM PDT, Kevin Thorpe
>>> wrote:
Below is some output from one of my students. I have never seen this error
and tried a few things (updating packages for one) but am at a loss to
help further. Would appreciate suggestions that I can pass along.
Here is the error. I tried an install.packages(“xml2”) which appeared to
complete but the error persists.
> library("tidyverse")
Error: package or namespace load failed for ‘tidyverse’ in
library.dynam(lib, package, package.lib):
DLL ‘xml2’ not found: maybe not installed for this architecture?
Here is the sessionInfo()
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 cellranger_1.1.0 pillar_1.6.2 compiler_4.1.1 dbplyr_2.1.1
forcats_0.5.1 tools_4.1.1
[8] jsonlite_1.7.2 lubridate_1.7.10 lifecycle_1.0.0 tibble_3.1.4
gtable_0.3.0 pkgconfig_2.0.3 rlang_0.4.11
[15] reprex_2.0.1 DBI_1.1.1 haven_2.4.3 withr_2.4.2 dplyr_1.0.7 httr_1.4.2
fs_1.5.0
[22] generics_0.1.0 vctrs_0.3.8 hms_1.1.0 grid_4.1.1 tidyselect_1.1.1
glue_1.4.2 R6_2.5.1
[29] fansi_0.5.0 readxl_1.3.1 tzdb_0.1.2 tidyr_1.1.3 ggplot2_3.3.5
purrr_0.3.4 readr_2.0.1
[36] modelr_0.1.8 magrittr_2.0.1 backports_1.2.1 scales_1.1.1
ellipsis_0.3.2 assertthat_0.2.1 colorspace_2.0-2
[43] utf8_1.2.2 munsell_0.5.0 broom_0.7.9 crayon_1.4.1
>>>
>>> --
>>> Sent from my phone. Please excuse my brevity.
>
--
Kevin E. Thorpe
Head of Biostatistics, Applied Health
Re: [R] RSQLite slowness
On 2021-10-06 12:11 -0700, Jeff Newmiller wrote: > FWIW all SQL implementations work > better with indexes An index seems to be a good way to improve sql performance, I'll look into it. Best, Rasmus signature.asc Description: PGP signature __ 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] RSQLite slowness
Dear Ivan, Thanks for that explaination! I think it explains the slowness clearly. It is possible to use carray is in Rust [1] so it might be available in R in the future(?) I'll look into rusqlite some time at least. sqlite is supposed to be one of the fastest sql implementations. Realm [2] might be faster, but I don't know how to use it in R so ... I thought someone might suggest Redis, but I think it is way slower. sqlite with indexes and the traditional way of doing that by writing in a temporary table might just be it ... Best, Rasmus [1] https://docs.rs/rusqlite/0.24.2/rusqlite/vtab/array/index.html [2] https://en.wikipedia.org/wiki/Realm_(database) [3] https://en.wikipedia.org/wiki/Redis signature.asc Description: PGP signature __ 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] adding results to plot
Hallo Rui.
I finally tested your function and it seems to me that it should propagate
to the core R or at least to the stats package.
Although it is a bit overkill for my purpose, its use is straightforward and
simple. I checked it for several *test functions and did not find any
problem.
Thanks and best regards.
Petr
> -Original Message-
> From: Rui Barradas
> Sent: Friday, September 17, 2021 9:56 PM
> To: PIKAL Petr ; r-help
> Subject: Re: [R] adding results to plot
>
> Hello,
>
> *.test functions in base R return a list of class "htest", with its own
> print method.
> The method text.htest for objects of class "htest" below is a hack. I
> adapted the formating part of the code of print.htest to plot text().
> I find it maybe too complicated but it seems to work.
>
> Warning: Not debugged at all.
>
>
>
> text.htest <- function (ht, x, y = NULL, digits = getOption("digits"),
> prefix = "", adj = NULL, ...) {
>out <- list()
>i_out <- 1L
>out[[i_out]] <- paste(strwrap(ht$method, prefix = prefix), sep = "\n")
>i_out <- i_out + 1L
>out[[i_out]] <- paste0("data: ", ht$data.name)
>
>stat_line <- NULL
>i_stat_line <- 0L
>if (!is.null(ht$statistic)) {
> i_stat_line <- i_stat_line + 1L
> stat_line[[i_stat_line]] <- paste(names(ht$statistic), "=",
>format(ht$statistic, digits =
> max(1L, digits - 2L)))
>}
>if (!is.null(ht$parameter)) {
> i_stat_line <- i_stat_line + 1L
> stat_line[[i_stat_line]] <- paste(names(ht$parameter), "=",
>format(ht$parameter, digits =
> max(1L, digits - 2L)))
>}
>if (!is.null(ht$p.value)) {
> fp <- format.pval(ht$p.value, digits = max(1L, digits - 3L))
> i_stat_line <- i_stat_line + 1L
> stat_line[[i_stat_line]] <- paste("p-value",
>if (startsWith(fp, "<")) fp else
> paste("=", fp))
>}
>if(!is.null(stat_line)){
> i_out <- i_out + 1L
> #out[[i_out]] <- strwrap(paste(stat_line, collapse = ", "))
> out[[i_out]] <- paste(stat_line, collapse = ", ")
>}
>if (!is.null(ht$alternative)) {
> alt <- NULL
> i_alt <- 1L
> alt[[i_alt]] <- "alternative hypothesis: "
> if (!is.null(ht$null.value)) {
>if (length(ht$null.value) == 1L) {
> alt.char <- switch(ht$alternative, two.sided = "not equal to",
> less = "less than", greater = "greater than")
> i_alt <- i_alt + 1L
> alt[[i_alt]] <- paste0("true ", names(ht$null.value), " is ",
> alt.char,
> " ", ht$null.value)
>}
>else {
> i_alt <- i_alt + 1L
> alt[[i_alt]] <- paste0(ht$alternative, "\nnull values:\n")
>}
> }
> else {
>i_alt <- i_alt + 1L
>alt[[i_alt]] <- ht$alternative
> }
> i_out <- i_out + 1L
> out[[i_out]] <- paste(alt, collapse = " ")
>}
>if (!is.null(ht$conf.int)) {
> i_out <- i_out + 1L
> out[[i_out]] <- paste0(format(100 * attr(ht$conf.int, "conf.level")),
> " percent confidence interval:\n", " ",
> paste(format(ht$conf.int[1:2], digits =
> digits), collapse = " "))
>}
>if (!is.null(ht$estimate)) {
> i_out <- i_out + 1L
> out[[i_out]] <- paste("sample estimates:", round(ht$estimate,
> digits = digits), sep = "\n")
>}
>i_out <- i_out + 1L
>out[[i_out]] <- "\n"
>names(out)[i_out] <- "sep"
>out <- do.call(paste, out)
>if(is.null(adj)) adj <- 0L
>text(x, y, labels = out, adj = adj, ...)
>invisible(out)
> }
>
>
> res <- shapiro.test(rnorm(100))
> plot(1,1, ylim = c(0, length(res) + 1L))
> text(res, 0.6, length(res) - 1)
> res
>
> res2 <- t.test(rnorm(100))
> plot(1,1, ylim = c(0, length(res2) + 1L))
> text(res2, 0.6, length(res2) - 1L)
> res2
>
>
> Hope this helps,
>
> Rui Barradas
>
>
>
> Às 15:12 de 16/09/21, PIKAL Petr escreveu:
> > Dear all
> >
> > I know I have seen the answer somewhere but I am not able to find it.
> Please
> > help
> >
> >> plot(1,1)
> >> res <- shapiro.test(rnorm(100))
> >> res
> >
> > Shapiro-Wilk normality test
> >
> > data: rnorm(100)
> > W = 0.98861, p-value = 0.5544
> >
> > I would like to add whole res object to the plot.
> >
> > I can do it one by one
> >> text(locator(1), res$method)
> >> text(locator(1), as.character(res$p.value))
> > ...
> > But it is quite inconvenient
> >
> > I could find some way in ggplot world but not in plain plot world.
> >
> > Best regards
> > Petr
> >
> >
> > __
> > 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] Tidygrraph example not working
Hi, I am trying to learn more about tidygraph, so i am following this blog: https://www.data-imaginist.com/2017/introducing-tidygraph/ Few months ago the examples in the blog worked very well, but today they do not. I just installed R x64 4.1.1, so i should be up and running with the latest on a Windows machine. >From the blog: iris_clust <- hclust(dist(iris[1:4])) iris_tree <- as_tbl_graph(iris_clust) iris_tree <- iris_tree %>% activate(nodes) %>% mutate(Species = ifelse(leaf, as.character(iris$Species)[label], NA)) %>% activate(edges) %>% mutate(to_setose = .N()$Species[to] == 'setosa') iris_tree#> # A tbl_graph: 299 nodes and 298 edges#> ##> # A rooted tree#> ##> # Edge Data: 298 x 3 (active)#>fromto to_setose#> #> 1 3 1 TRUE#> 2 3 2 TRUE#> 3 7 5 TRUE#> 4 7 6 TRUE#> 5 8 4 TRUE#> 6 8 7NA#> # ... with 292 more rows#> ##> # Node Data: 299 x 5#> height leaf label members Species#> #> 1 0.000 TRUE108 1 setosa#> 2 0.000 TRUE131 1 setosa#> 3 0.2645751 FALSE 2#> # ... with 296 more rows Now from my R session: library(tidygraph) Attaching package: ‘tidygraph’ The following object is masked from ‘package:stats’: filter iris_clust <- hclust(dist(iris[1:4])) iris_tree <- as_tbl_graph(iris_clust) iris_tree <- iris_tree %>% activate(nodes) %>% mutate(Species = ifelse(leaf, as.character(iris$Species)[label], NA)) %>% activate(edges) %>% mutate(to_setose = .N()$Species[to] == "setosa") iris_tree # A tbl_graph: 299 nodes and 298 edges # # A rooted tree # # Edge Data: 298 x 3 (active) fromto to_setose 1 3 1 NA 2 3 2 NA 3 7 5 NA 4 7 6 NA 5 8 4 NA 6 8 7 NA # ... with 292 more rows # # Node Data: 299 x 5 height leaf label members Species 1 0 TRUE "108" 1 2 0 TRUE "131" 1 3 0.265 FALSE "" 2 # ... with 296 more rows As you see the attributes from the Species column are not added to the table, and all are NA. It is not clear to me where i made my mistake. Any help is very much appreciated. Thanks, Monica [[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.
Re: [R] RSQLite slowness
On Wed, 6 Oct 2021 16:23:15 + Rasmus Liland wrote: >"SELECT * FROM gene2refseq > LEFT JOIN gene_info ON > gene_info.GeneID = gene2refseq.GeneID > WHERE gene2refseq.`RNA_nucleotide_accession.version` > LIKE ?" <...> > x1 <- DBI::dbGetQuery(conn=conn, > statement=statement, > param=list(Håkan20210914$RNANucleotideAccession)) I think that the problem here is that you pass a vector as a bound parameter to LIKE, when parameter placeholders usually expect a scalar. DBI transparently handles this: >> The elements of the `params` argument do not need to be scalars, >> vectors of arbitrary length (including length 0) are supported. For >> queries, calling dbFetch() binding such parameters returns >> concatenated results, equivalent to binding and fetching for each >> set of values and connecting via rbind(). I think this means that DBI runs a SELECT for each value in Håkan20210914$RNANucleotideAccession, which is understandably slower than a single query. Unfortunately, it's hard to pass vectors of values to queries with bound parameters; the SQL engines I know don't have a syntax for "WHERE param IN (:multi_placeholder:)". SQLite comes with carray [1], but I don't know whether it's exposed by RSQLite (could be hard to do in a pointer-safe way), and you're already aware of the traditional way of doing that: create a temporary table, populate it and JOIN with the rest of the query. -- Best regards, Ivan [1] https://www.sqlite.org/carray.html __ 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] Strange behavior of 2-d array within function
Hi I would print/save iteration number to see at what time this occured and probably traceback() could give you some hint. Alternatively you could make a function from your code see ?function and use debug to trace the error. Without some working example it is impossible to see where is the problem. Cheers Petr > -Original Message- > From: R-help On Behalf Of Gabriel Toro > Sent: Wednesday, October 6, 2021 8:32 PM > To: r-help@r-project.org > Subject: [R] Strange behavior of 2-d array within function > > Hi, > > I have a function, which defines an array of dimensions 5000 by 60, calculates > the values within that array and then returns the array on exit. > > I get an error: Error in my_simulated[ir, 1:it] : incorrect number of dimensions > > For some strange reason, the array is somehow being changed from >mode "numeric" and attributes $dim=6000 by 50 >to >mode "list" and attributes NULL > > This change occurs at more or less random iterations within a loop (all within > the same function call). I am not explicitly manipulating the mode or > attributes of the array after it is created. > > I would appreciate any suggestions on what may be causing this problem. I > have stared at the code for a long time, run the debugger, etc. > > Thanks, > > Gabriel > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting- > guide.html > and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R-es] Respuestas múltiples en una sola columna
Hola:
Otra posibilidad sería la que aparece a continuación.
Saludos,
Marcelino
library(readxl)
library(reshape2)
datin <- read_excel("Ejes formativos.xlsx")
datin_long <- melt(datin, id.vars=c("ID", "area_pertenencia"))[,c("ID",
"value", "area_pertenencia")]
names(datin_long) <- c("ID", "ejes", "area")
datin_long <- datin_long[!is.na(datin_long$ejes),]
El 07/10/2021 a las 4:40, juan manuel dias escribió:
Muchas gracias a ambos!
El mié., 6 de octubre de 2021 15:52, Carlos Ortega
escribió:
Hola,
Sí, otra alternativa para dejarlo como has comentado y leyendo
directamente de Excel...
#---
library(dplyr)
library(tidyr)
library(readr)
library(readxl)
datin <- read_excel("Ejes formativos.xlsx")
datin_long <- datin %>%
pivot_longer(
cols = starts_with("eje"),
values_to = "ejes"
) %>%
rename( area = area_pertenencia) %>%
select(-name) %>%
relocate(ejes, .before = area)
#---
Saludos,
Carlos Ortega
www.qualityexcellence.es
El mié, 6 oct 2021 a las 20:17, juan manuel dias ()
escribió:
Hola, cómo andan!
Tengo una base de una encuesta sobre formación profesional realizada a un
conjunto de empleados de una institución.
Una de las preguntas es de respuesta múltiple, eje_tem_1,eje_tem_2,
eje_tem_3hasta eje_tem_17.
Necesitaría que las respuestas de cada persona que están en esas
distintas columnas (eje_tem a eje_tem_17) queden en una misma columna, y
asimismo que se repita el "ID" y el "area_pertenencia" tantas veces como
opciones haya marcado cada caso/persona/"ID".
Estuve intentando con pivot_longer pero sin resultados!
Actualmente está así
*id | eje_tem_1 | eje_tem_2 | eje_tem_3 | eje_tem_4area*
1 rh sist comunfilos
admin
2 rh arte
medic
3 sistmatem empre comun
asist
4 arte matem empre sist
asist
Y necesitaría que quede así:
*id | ejes| area*
1 rh admin
1 sist admin
1 comunadmin
1 filosadmin
1 admin admin
2 rh medic
2 arte medic
.. .
Adjunto un recorte de la base!
Muchas gracias!
Saludos, Juan.
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--
Saludos,
Carlos Ortega
www.qualityexcellence.es
[[alternative HTML version deleted]]
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.
--
Marcelino de la Cruz Rot
Depto. de Biología y Geología
Física y Química Inorgánica
Universidad Rey Juan Carlos
Móstoles España
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