Re: [ESS] run R code upon starting each ESS session

[Manuel Teodoro via ESS-help]

Thanks a lot Tyler,

The hook  is exactly what I was looking for. I checked
the documentation but I guess I should search better next time.

In case somebody else is interested, I am sending the code directly from
within emacs, init file so, no need for extra R scripts. It is a wonderful
way to set up R sessions for me. It looks something like this:

(defvar my-r-profile "message(\"Welcome from Emacs\")")

(defun my-r-ess-init ()
  "Sends variable `tt-r-profile' to an ESS process"
  (let ((proc (ess-get-process)))
(ess-send-string proc tt-r-profile)))

(add-hook 'ess-r-post-run-hook 'my-r-ess-init)

In this way, whatever you place in  variable is executed upon
startup of the inferior R process.

Cheers!
Manuel

On Tue, Oct 3, 2023 at 9:10 PM Tyler Smith via ESS-help <
ess-help@r-project.org> wrote:

> On Tue, Oct 3, 2023, at 12:52 PM, Manuel Teodoro via ESS-help wrote:
> > Is there a way to run R code upon starting each ESS session?
> >
>
> Hi Manuel,
>
> ESS provides a hook you can use for this purpose. This is described in the
> manual:
>
> https://ess.r-project.org/Manual/ess.html#Customizing-startup
>
> To run a custom script each time ESS starts, use something like the
> following:
>
> (add-hook 'ess-r-post-run-hook (lambda () (ess-load-file "foo.R")))
>
> - ty
>
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>

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Re: [R] Problems Structuring My Data

[Bert Gunter]

I'll make an attempt to answer your question, but the results seems
extremely wasteful, as there appears to be only one REMNAME for each
FAILDATE. This means for my "solution", almost all of the entries are
empty (NULL, actually). So I assume I must misunderstand your
specification, but maybe showing you my misunderstanding will help you
and/or others to clarify or it.

Anyway, calling the data frame you provided, d, my "solution" is
simply (I changed your variable names to fdate, name, and fdays to
save typing):

w <- with(d, tapply(fdays, list(factor(fdate), name), I))
## that's an I = "eye" at the end not an "ell"

w is a *matrix* of the fdays, with the rownames of the matrix your
dates, and the colnames your remnames.  The dimension of w is 640 x
43.  As I said, most of the entries are NULL.

If this *is* perchance what you want, then I suggest you stay with
your original data frame and rethink how to work with it more
efficiently. You should *not* be guided by imitating what one does in
Excel.

However, as is more likely, I've just misunderstood what you want, so
a bit of clarification might get you the answer you seek.

Bon chance.

Cheers,
Bert

On Tue, Oct 3, 2023 at 4:25 PM Bert Gunter  wrote:
>
> I won't attempt to answer your post here, but:
>
> #I don´t know why R is showing the dates as numbers
>
> Please read the Help files!
> You say FAILDATE has "type" = S3 class, "Date".
> The first thing ?Dates tells you in the "Details" is:
>
> "Dates are represented as the number of days since 1970-01-01, with
> negative values for earlier dates. They are always printed following
> the rules of the current Gregorian calendar, even though that calendar
> was not in use long ago (it was adopted in 1752 in Great Britain and
> its colonies)."
>
> That answers your question without ever needing to post here.
>
> Cheers,
> Bert
>
>
>
> On Tue, Oct 3, 2023 at 3:18 PM Paul Bernal  wrote:
> >
> > Dear friends,
> >
> > Hope you are all doing great. I am working with a dataset which is a subset
> > of the original one, that has the following columns: FAILDATE, REM_NAME,
> > and Days_At_Failure.
> >
> > I want to structure the data in such a way that I have the unique FAILDATE
> > in "%Y-%m-%d" format, then a column for each REM_NAME and then the
> > Days_At_Failure displayed for each REM_NAME and FAILDATE (just as if I was
> > using a pivot table).
> >
> > The structure I want is the following:
> > FAILDATE  REM1 REM2  REM3  REM N
> > 2000-01-01 # days at failure #days at
> > failure
> > 2000-01-02 # days at failure #days at
> > failure
> > 2000-01-03 # days at failure #days at
> > failure
> >
> > Here is the dput() of my dataframe:
> > #I don´t know why R is showing the dates as numbers
> > #when I do str, it actually shows that FAIL date has type Date
> >  dput(head(failure_subset2, n=1000))
> > structure(list(FAILDATE = structure(c(17597, 17597, 17347, 17334,
> > 17148, 17168, 17299, 17402, 17406, 17347, 17505, 17449, 17352,
> > 17931, 17424, 17439, 17406, 17292, 17390, 17373, 17259, 17561,
> > 17563, 17550, 17723, 17814, 17564, 17299, 17307, 17296, 17483,
> > 17644, 17394, 17360, 17850, 17744, 17719, 17712, 17710, 18048,
> > 18069, 17876, 17506, 17821, 18041, 17586, 18069, 18069, 18048,
> > 17899, 17899, 17759, 17732, 17822, 17771, 17821, 17837, 17824,
> > 17469, 17483, 17582, 17613, 18016, 18036, 18030, 17862, 17871,
> > 17899, 17651, 17684, 17844, 17632, 17784, 17855, 17764, 17915,
> > 18245, 18260, 18166, 18295, 18094, 18062, 18083, 18223, 18237,
> > 18197, 18284, 18289, 18218, 18218, 18298, 18297, 18299, 17910,
> > 18089, 18304, 18141, 18272, 18387, 18183, 18184, 18422, 18422,
> > 18422, 18038, 17988, 18413, 17836, 18328, 18230, 18011, 18011,
> > 17991, 18041, 18041, 18070, 18432, 18031, 18165, 18345, 18386,
> > 17899, 18374, 18427, 18098, 18416, 18397, 18458, 18126, 18126,
> > 18123, 18286, 17827, 18069, 18081, 18505, 18508, 18086, 18468,
> > 18482, 18107, 18146, 18371, 18368, 18186, 18270, 17772, 18054,
> > 17959, 18106, 18148, 18380, 18398, 17921, 18265, 18273, 18030,
> > 18473, 18166, 18006, 18006, 18006, 18000, 17938, 18155, 18175,
> > 18047, 18503, 18042, 18072, 17964, 18223, 17850, 17871, 18071,
> > 18174, 18154, 18153, 18344, 18384, 18512, 18112, 18131, 18085,
> > 18094, 18096, 18100, 18477, 17967, 17752, 17964, 18491, 18124,
> > 18115, 18166, 17912, 18489, 18087, 18130, 18170, 18169, 18175,
> > 18177, 18226, 18376, 18374, 18217, 18226, 18135, 18136, 17942,
> > 18099, 18031, 18032, 18107, 18041, 18062, 18078, 18087, 18249,
> > 18081, 18231, 18195, 18192, 18213, 18209, 18156, 18157, 18157,
> > 18158, 18159, 18053, 18221, 18185, 18311, 18239, 18258, 18390,
> > 18390, 17997, 18197, 18095, 18145, 18101, 18194, 18260, 18260,
> > 18202, 18447, 18450, 18088, 18249, 18206, 18290, 17995, 18270,
> > 18282, 18251, 18157, 18094, 18437, 18299, 18333, 18035, 18146,
> > 18010, 18395, 18204, 

Re: [R] Question about R software and output

[Richard O'Keefe]

R is open source software, available from CRAN servers, but also
packaged for various Linux distributions.  On this machine,
running Ubuntu, R was installed using the 'apt' package manager.

R is a complete programming language with built-in support for
reading and writing over the network.  Packages -- whether on CRAN
or elsewhere -- extend R with code written in a mixture of Fortran,
C, C++, and R.  Base R behaves itself, but a package loaded from
some random GitHub site could do anything.

Data processed by R need not have been anywhere near Excel or any
kind of spreadsheet.  I don't even *have* Excel on any of the machines
I run R on.  Most of the data I process is not in .csv or .xslx format.
R is able to read data in many formats as described in the
R Data Import/Export
manual, which is fairly brief.  If there is a data exchange format
with a significant community, chances are there's an R package that
can read and/or write it.  Indeed, it is even possible to extract
information from PDFs in R using the pdftools package.

It sounds as though your primary concern is data protection, and
there's good news and bad news.  The good news is that if you stick
with R and with packages from a trusted repository, you're safe.
The bad news is that a programming language that can do anything
can do ANYTHING, and you are not safe from a malicious programmer
in your own organisation sending data anywhere she wants to.
% R
> system("some possibly dangerous command goes here")
Of course, this doesn't let anyone do something they couldn't already
do *without* R.

And this gets us to the real bad news.  I think you are trying
to achieve security by a method that cannot work.  You're trying to
limit yourself to safe software.  But you ALSO need to plug ALL the
USB ports, ALL the Thunderbolt ports, snip the wires to the Wifi and
Bluetooth modules,If a system is capable enough to install
R (or anything else), it is insecure *without* R.  You have to limit
the internet connections that can possibly be established by ANY
program, and that means several levels of firewalls.  It also means
no "work from home".

On Wed, 4 Oct 2023 at 03:18, Ferguson Charity (CEMINFERGUSON) <
charity.eminfergu...@gstt.nhs.uk> wrote:

> To whom it may concern,
>
>
>
> My understanding is that the R software is downloaded from a CRAN network
> and data is imported into it using Microsoft Excel for example. Could I
> please just double check whether any data or results from the output is
> held on external servers or is it just held on local files on the computer?
>
>
>
> Many thanks,
>
>
>
> Charity
>
>
>
> *
>
> The information contained in this message and or attachments is intended
> only for the
> person or entity to which it is addressed and may contain confidential
> and/or
> privileged material. Unless otherwise specified, the opinions expressed
> herein do not
> necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or
> any of its subsidiaries. The information contained in this e-mail may be
> subject to
> public disclosure under the Freedom of Information Act 2000. Unless the
> information
> is legally exempt from disclosure, the confidentiality of this e-mail and
> any replies
> cannot be guaranteed.
>
> Any review, retransmission,dissemination or other use of, or taking of any
> action in
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> intended
> recipient is prohibited. If you received this in error, please contact the
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> and delete the material from any system and destroy any copies.
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> We make every effort to keep our network free from viruses. However, it is
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>

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Problems Structuring My Data

[Bert Gunter]

I won't attempt to answer your post here, but:

#I don´t know why R is showing the dates as numbers

Please read the Help files!
You say FAILDATE has "type" = S3 class, "Date".
The first thing ?Dates tells you in the "Details" is:

"Dates are represented as the number of days since 1970-01-01, with
negative values for earlier dates. They are always printed following
the rules of the current Gregorian calendar, even though that calendar
was not in use long ago (it was adopted in 1752 in Great Britain and
its colonies)."

That answers your question without ever needing to post here.

Cheers,
Bert



On Tue, Oct 3, 2023 at 3:18 PM Paul Bernal  wrote:
>
> Dear friends,
>
> Hope you are all doing great. I am working with a dataset which is a subset
> of the original one, that has the following columns: FAILDATE, REM_NAME,
> and Days_At_Failure.
>
> I want to structure the data in such a way that I have the unique FAILDATE
> in "%Y-%m-%d" format, then a column for each REM_NAME and then the
> Days_At_Failure displayed for each REM_NAME and FAILDATE (just as if I was
> using a pivot table).
>
> The structure I want is the following:
> FAILDATE  REM1 REM2  REM3  REM N
> 2000-01-01 # days at failure #days at
> failure
> 2000-01-02 # days at failure #days at
> failure
> 2000-01-03 # days at failure #days at
> failure
>
> Here is the dput() of my dataframe:
> #I don´t know why R is showing the dates as numbers
> #when I do str, it actually shows that FAIL date has type Date
>  dput(head(failure_subset2, n=1000))
> structure(list(FAILDATE = structure(c(17597, 17597, 17347, 17334,
> 17148, 17168, 17299, 17402, 17406, 17347, 17505, 17449, 17352,
> 17931, 17424, 17439, 17406, 17292, 17390, 17373, 17259, 17561,
> 17563, 17550, 17723, 17814, 17564, 17299, 17307, 17296, 17483,
> 17644, 17394, 17360, 17850, 17744, 17719, 17712, 17710, 18048,
> 18069, 17876, 17506, 17821, 18041, 17586, 18069, 18069, 18048,
> 17899, 17899, 17759, 17732, 17822, 17771, 17821, 17837, 17824,
> 17469, 17483, 17582, 17613, 18016, 18036, 18030, 17862, 17871,
> 17899, 17651, 17684, 17844, 17632, 17784, 17855, 17764, 17915,
> 18245, 18260, 18166, 18295, 18094, 18062, 18083, 18223, 18237,
> 18197, 18284, 18289, 18218, 18218, 18298, 18297, 18299, 17910,
> 18089, 18304, 18141, 18272, 18387, 18183, 18184, 18422, 18422,
> 18422, 18038, 17988, 18413, 17836, 18328, 18230, 18011, 18011,
> 17991, 18041, 18041, 18070, 18432, 18031, 18165, 18345, 18386,
> 17899, 18374, 18427, 18098, 18416, 18397, 18458, 18126, 18126,
> 18123, 18286, 17827, 18069, 18081, 18505, 18508, 18086, 18468,
> 18482, 18107, 18146, 18371, 18368, 18186, 18270, 17772, 18054,
> 17959, 18106, 18148, 18380, 18398, 17921, 18265, 18273, 18030,
> 18473, 18166, 18006, 18006, 18006, 18000, 17938, 18155, 18175,
> 18047, 18503, 18042, 18072, 17964, 18223, 17850, 17871, 18071,
> 18174, 18154, 18153, 18344, 18384, 18512, 18112, 18131, 18085,
> 18094, 18096, 18100, 18477, 17967, 17752, 17964, 18491, 18124,
> 18115, 18166, 17912, 18489, 18087, 18130, 18170, 18169, 18175,
> 18177, 18226, 18376, 18374, 18217, 18226, 18135, 18136, 17942,
> 18099, 18031, 18032, 18107, 18041, 18062, 18078, 18087, 18249,
> 18081, 18231, 18195, 18192, 18213, 18209, 18156, 18157, 18157,
> 18158, 18159, 18053, 18221, 18185, 18311, 18239, 18258, 18390,
> 18390, 17997, 18197, 18095, 18145, 18101, 18194, 18260, 18260,
> 18202, 18447, 18450, 18088, 18249, 18206, 18290, 17995, 18270,
> 18282, 18251, 18157, 18094, 18437, 18299, 18333, 18035, 18146,
> 18010, 18395, 18204, 18259, 18311, 18335, 18444, 18444, 18453,
> 18453, 18192, 18098, 17969, 17680, 18147, 18147, 17977, 17996,
> 18001, 18399, 18432, 18354, 18147, 17912, 17995, 17995, 18221,
> 18428, 18447, 18452, 18264, 18321, 18334, 18386, 18156, 18371,
> 18345, 18156, 18164, 18029, 18433, 17602, 17931, 18290, 18339,
> 18424, 18052, 18052, 18166, 18540, 18783, 18166, 18607, 18606,
> 18606, 18594, 18592, 18805, 18648, 18768, 18887, 1, 18648,
> 18630, 18812, 18812, 18845, 18932, 18418, 18950, 18166, 18702,
> 18684, 18812, 18589, 18597, 18611, 18648, 18577, 19024, 19041,
> 19043, 18768, 19216, 18787, 19159, 18529, 18589, 18646, 18166,
> 18571, 18637, 18624, 18716, 18166, 18568, 18527, 18535, 18542,
> 18494, 18846, 18166, 18877, 18548, 18659, 18839, 18905, 18632,
> 18804, 18648, 18892, 18921, 18718, 18805, 18805, 18561, 18682,
> 18943, 18949, 18542, 18927, 18409, 19047, 19059, 18524, 18941,
> 18941, 18941, 18648, 19044, 18758, 19034, 18609, 18788, 18812,
> 18676, 19194, 18740, 18812, 18842, 18659, 19042, 18230, 19036,
> 19144, 19032, 18542, 19097, 18564, 18166, 18552, 18557, 18467,
> 19002, 19174, 18624, 18828, 18542, 18542, 18686, 18628, 18702,
> 19227, 19239, 19264, 17597, 17470, 17401, 17344, 17562, 17578,
> 17476, 17539, 17348, 17326, 17420, 17423, 17427, 17347, 17359,
> 17372, 17385, 17365, 17365, 17598, 17977, 17977, 17736, 17684,
> 17612, 17792, 17220, 17310, 

[R] Problems Structuring My Data

[Paul Bernal]

Dear friends,

Hope you are all doing great. I am working with a dataset which is a subset
of the original one, that has the following columns: FAILDATE, REM_NAME,
and Days_At_Failure.

I want to structure the data in such a way that I have the unique FAILDATE
in "%Y-%m-%d" format, then a column for each REM_NAME and then the
Days_At_Failure displayed for each REM_NAME and FAILDATE (just as if I was
using a pivot table).

The structure I want is the following:
FAILDATE  REM1 REM2  REM3  REM N
2000-01-01 # days at failure #days at
failure
2000-01-02 # days at failure #days at
failure
2000-01-03 # days at failure #days at
failure

Here is the dput() of my dataframe:
#I don´t know why R is showing the dates as numbers
#when I do str, it actually shows that FAIL date has type Date
 dput(head(failure_subset2, n=1000))
structure(list(FAILDATE = structure(c(17597, 17597, 17347, 17334,
17148, 17168, 17299, 17402, 17406, 17347, 17505, 17449, 17352,
17931, 17424, 17439, 17406, 17292, 17390, 17373, 17259, 17561,
17563, 17550, 17723, 17814, 17564, 17299, 17307, 17296, 17483,
17644, 17394, 17360, 17850, 17744, 17719, 17712, 17710, 18048,
18069, 17876, 17506, 17821, 18041, 17586, 18069, 18069, 18048,
17899, 17899, 17759, 17732, 17822, 17771, 17821, 17837, 17824,
17469, 17483, 17582, 17613, 18016, 18036, 18030, 17862, 17871,
17899, 17651, 17684, 17844, 17632, 17784, 17855, 17764, 17915,
18245, 18260, 18166, 18295, 18094, 18062, 18083, 18223, 18237,
18197, 18284, 18289, 18218, 18218, 18298, 18297, 18299, 17910,
18089, 18304, 18141, 18272, 18387, 18183, 18184, 18422, 18422,
18422, 18038, 17988, 18413, 17836, 18328, 18230, 18011, 18011,
17991, 18041, 18041, 18070, 18432, 18031, 18165, 18345, 18386,
17899, 18374, 18427, 18098, 18416, 18397, 18458, 18126, 18126,
18123, 18286, 17827, 18069, 18081, 18505, 18508, 18086, 18468,
18482, 18107, 18146, 18371, 18368, 18186, 18270, 17772, 18054,
17959, 18106, 18148, 18380, 18398, 17921, 18265, 18273, 18030,
18473, 18166, 18006, 18006, 18006, 18000, 17938, 18155, 18175,
18047, 18503, 18042, 18072, 17964, 18223, 17850, 17871, 18071,
18174, 18154, 18153, 18344, 18384, 18512, 18112, 18131, 18085,
18094, 18096, 18100, 18477, 17967, 17752, 17964, 18491, 18124,
18115, 18166, 17912, 18489, 18087, 18130, 18170, 18169, 18175,
18177, 18226, 18376, 18374, 18217, 18226, 18135, 18136, 17942,
18099, 18031, 18032, 18107, 18041, 18062, 18078, 18087, 18249,
18081, 18231, 18195, 18192, 18213, 18209, 18156, 18157, 18157,
18158, 18159, 18053, 18221, 18185, 18311, 18239, 18258, 18390,
18390, 17997, 18197, 18095, 18145, 18101, 18194, 18260, 18260,
18202, 18447, 18450, 18088, 18249, 18206, 18290, 17995, 18270,
18282, 18251, 18157, 18094, 18437, 18299, 18333, 18035, 18146,
18010, 18395, 18204, 18259, 18311, 18335, 18444, 18444, 18453,
18453, 18192, 18098, 17969, 17680, 18147, 18147, 17977, 17996,
18001, 18399, 18432, 18354, 18147, 17912, 17995, 17995, 18221,
18428, 18447, 18452, 18264, 18321, 18334, 18386, 18156, 18371,
18345, 18156, 18164, 18029, 18433, 17602, 17931, 18290, 18339,
18424, 18052, 18052, 18166, 18540, 18783, 18166, 18607, 18606,
18606, 18594, 18592, 18805, 18648, 18768, 18887, 1, 18648,
18630, 18812, 18812, 18845, 18932, 18418, 18950, 18166, 18702,
18684, 18812, 18589, 18597, 18611, 18648, 18577, 19024, 19041,
19043, 18768, 19216, 18787, 19159, 18529, 18589, 18646, 18166,
18571, 18637, 18624, 18716, 18166, 18568, 18527, 18535, 18542,
18494, 18846, 18166, 18877, 18548, 18659, 18839, 18905, 18632,
18804, 18648, 18892, 18921, 18718, 18805, 18805, 18561, 18682,
18943, 18949, 18542, 18927, 18409, 19047, 19059, 18524, 18941,
18941, 18941, 18648, 19044, 18758, 19034, 18609, 18788, 18812,
18676, 19194, 18740, 18812, 18842, 18659, 19042, 18230, 19036,
19144, 19032, 18542, 19097, 18564, 18166, 18552, 18557, 18467,
19002, 19174, 18624, 18828, 18542, 18542, 18686, 18628, 18702,
19227, 19239, 19264, 17597, 17470, 17401, 17344, 17562, 17578,
17476, 17539, 17348, 17326, 17420, 17423, 17427, 17347, 17359,
17372, 17385, 17365, 17365, 17598, 17977, 17977, 17736, 17684,
17612, 17792, 17220, 17310, 17452, 17641, 17813, 17407, 17712,
17697, 17752, 17694, 17724, 17862, 17865, 17633, 18048, 17815,
17911, 17753, 17818, 17784, 17619, 17697, 17381, 17641, 17449,
17456, 17555, 17564, 17574, 17793, 17889, 17869, 17885, 17890,
17903, 17912, 17809, 17891, 17846, 17916, 18019, 18234, 18180,
18181, 18292, 18140, 18036, 18289, 18278, 18298, 18297, 18295,
18319, 18313, 17936, 17939, 18109, 18340, 18166, 18206, 18204,
17904, 17998, 18269, 18165, 18120, 18349, 18368, 18416, 18416,
18025, 18322, 17989, 17830, 17845, 17869, 18065, 18328, 18324,
17944, 17920, 18433, 17962, 18169, 18170, 18171, 18340, 18393,
18070, 18083, 18087, 18108, 18116, 18142, 18386, 18425, 18464,
18498, 18400, 17931, 18459, 18126, 18124, 18310, 18228, 17828,
17851, 18143, 18028, 18425, 18416, 18482, 18482, 18396, 18428,
18414, 18441, 

Re: [ESS] run R code upon starting each ESS session

[Tyler Smith via ESS-help]

On Tue, Oct 3, 2023, at 12:52 PM, Manuel Teodoro via ESS-help wrote:
> Is there a way to run R code upon starting each ESS session?
>

Hi Manuel,

ESS provides a hook you can use for this purpose. This is described in the 
manual: 

https://ess.r-project.org/Manual/ess.html#Customizing-startup

To run a custom script each time ESS starts, use something like the following:

(add-hook 'ess-r-post-run-hook (lambda () (ess-load-file "foo.R")))

- ty

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Re: [R] Question about R software and output

[CALUM POLWART]

Charity

There is OFTEN confusion what we mean when we say "R".

R is effectively a single bit of software with a ton of other bits of
software as optional extras.  You might think of some of those optional
extras like apps on a phone. You'd say you have a phone when you can open
the box and power it on. But you might add say "Spotify" app to it. That
will then be downloading the songs. And inevitably sending some data back
(I not do Spotify - no idea what - but it must have your identification and
what songs to play as a minimum).

R packages are like apps. They interact with the R core and do sometimes
amazing things. I think the majority do all that entirely on the machine
running R. BUT some may be using external services. There is for instance a
package that can interact with the Twitter API.  It would be impossible to
do that without sending as a minimum some login data and downloading data
back.  But you'd not normally send your entire research database to Twitter
during the login!

There will be SOME R packages that may be doing some odd stuff which might
need the dataset sent to the web. I can't think of any! Then there are
packages that could accidentally send data that you may or may not consider
sensitive. Say for instance you have a postcode list for every patient in
your research study. And you wanted to geocode that to get their location
as a long/lat... you can do that in an r package - which will have to send
the post code to get the answer. You haven't identified why you want the
postcode... but it is patient identifiable data...

That's R.

Add to that R Studio (or possibly other software solutions) - which is a
development environment which sits on top of R. It's often what people mean
by programming in R but it's effectively a glorified text editor. R Studio
desktop doesn't send data anywhere. Although it has database connectors
that could (but so can excel so if IG are flipping out feel free to remind
them of that!).

R Studio can work with git which is a version management system and can
upload code to a service like GitHub. You COULD upload data in that, or you
could chose not to.

And finally...

R Studio has a cloud version. It looks 98% the same as R Studio desktop.
Now called Posit.Cloud. That's a cloud service. While it may be secure etc
-- you are processing on their server not your PC.  And if this was your
question - it's a whole different set of answers!!


You may also want to Google NHSRcommunity where you might find help if
there are IG question to address as many of us will have wrestled with an
NHS IG team at some point.



On Tue, 3 Oct 2023, 17:26 Michael Dewey,  wrote:

> Dear Charity
>
> Since your organisation is a member of King's Health Partners you might
> like to ask colleagues in KCL for local support.
>
> Michael
>
> On 02/10/2023 08:48, Ferguson Charity (CEMINFERGUSON) wrote:
> > To whom it may concern,
> >
> >
> >
> > My understanding is that the R software is downloaded from a CRAN
> network and data is imported into it using Microsoft Excel for example.
> Could I please just double check whether any data or results from the
> output is held on external servers or is it just held on local files on the
> computer?
> >
> >
> >
> > Many thanks,
> >
> >
> >
> > Charity
> >
> >
> >
> *
> >
> > The information contained in this message and or attachments is intended
> only for the
> > person or entity to which it is addressed and may contain confidential
> and/or
> > privileged material. Unless otherwise specified, the opinions expressed
> herein do not
> > necessarily represent those of Guy's and St Thomas' NHS Foundation Trust
> or
> > any of its subsidiaries. The information contained in this e-mail may be
> subject to
> > public disclosure under the Freedom of Information Act 2000. Unless the
> information
> > is legally exempt from disclosure, the confidentiality of this e-mail
> and any replies
> > cannot be guaranteed.
> >
> > Any review, retransmission,dissemination or other use of, or taking of
> any action in
> > reliance upon, this information by persons or entities other than the
> intended
> > recipient is prohibited. If you received this in error, please contact
> the sender
> > and delete the material from any system and destroy any copies.
> >
> > We make every effort to keep our network free from viruses. However, it
> is your
> > responsibility to ensure that this e-mail and any attachments are free
> of viruses as
> > we can take no responsibility for any computer virus which might be
> transferred by
> > way of this e-mail.
> >
> >
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> >
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> > PLEASE do read 

Re: [ESS] why a release from time to time would be nice

[Sparapani, Rodney via ESS-help]

Hi Gang:

Resurrecting this old thread from 09/2021�

For the last few years, the lack of an ESS release has been decried.
And, deservedly so.  Now, I�m happy to report that we intend to
create a new release roughly by XMAS.  The reason that I am
telling all of you this: we are very interested in hearing what
issues that you are experiencing.  As you all know, Emacs has
evolved rapidly recently from v26 to 29: a more rapid release
schedule than we have been used to.  Speaking for myself,
there have been Emacs changes that have impacted ESS
features that I use frequently.  So, I�m assuming that others
have seen the same and, potentially, have nice workarounds.
If you check github, then you will see that we have not really
started.  But, hopefully, that should change over the next month.
Thanks

--
Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
Vice President, Wisconsin Chapter of the American Statistical Association
Institute for Health and Equity, Division of Biostatistics
Medical College of Wisconsin, Milwaukee Campus

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Re: [ESS] run R code upon starting each ESS session

[Dirk Eddelbuettel via ESS-help]

On 3 October 2023 at 18:52, Manuel Teodoro via ESS-help wrote:
| Is there a way to run R code upon starting each ESS session?
| 
| Something like Rprofile but I'd like to make it more dependent to emacs.
| 
| What I want is to have a few options settings in my R sessions by default.
| Since I use it in different computers but my Emacs configuration is shared
| among all of them, I would prefer to keep this also within my emacs config.
| 
| It can be either calling an R script, specifying the path to Rprofile
| directly to ESS or passing a string of R code to run at startup.
| 
| Any ideas are appreciated

Cool question. My immediate thought (weighted by the fact that I cannot write
elisp code ;-) ) was to test for that in the _the standard R startup files_.
A quick check of what `Sys.getenv()` returns inside Emacs reveals the
`INSIDE_EMACS` env var so now I just added

if (interactive() && nzchar(Sys.getenv("INSIDE_EMACS")))  {
cat("Hello Emacs user.\n")
}

to the bottom of .Rprofile and indeed:

  [... other stuff including the fortunes::fortune call output ...] 

  Hello Emacs user.
  > setwd('/home/edd/')
  > 

but not when I start R on the terminal.  That could be start for you.

Dirk

-- 
dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org

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[ESS] run R code upon starting each ESS session

[Manuel Teodoro via ESS-help]

Is there a way to run R code upon starting each ESS session?

Something like Rprofile but I'd like to make it more dependent to emacs.

What I want is to have a few options settings in my R sessions by default.
Since I use it in different computers but my Emacs configuration is shared
among all of them, I would prefer to keep this also within my emacs config.

It can be either calling an R script, specifying the path to Rprofile
directly to ESS or passing a string of R code to run at startup.

Any ideas are appreciated

Manuel

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Re: [R] Question about R software and output

[Michael Dewey]

Dear Charity

Since your organisation is a member of King's Health Partners you might 
like to ask colleagues in KCL for local support.


Michael

On 02/10/2023 08:48, Ferguson Charity (CEMINFERGUSON) wrote:

To whom it may concern,



My understanding is that the R software is downloaded from a CRAN network and 
data is imported into it using Microsoft Excel for example. Could I please just 
double check whether any data or results from the output is held on external 
servers or is it just held on local files on the computer?



Many thanks,



Charity


*

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--
Michael

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Re: [R] Question about R software and output

[avi.e.gross]

Charity,

As some of the answers I have seen show, your question is not clear.

You need to be clear on what you mean about R software and other concepts
before an answer makes sense.

The Base version of R may come on your computer already but likely has been
installed from some external source, or updated and the CRAN mirrors are one
such installation. As far as I know, it downloads the main R software as
well as packages considered important as part of that distribution and from
then on, you can disconnect your computer from any network and it will work
fine for any programs that operate only locally. 

Of course any program you run that wishes to access external resources can
do so. In particular, it is quite common for you at the prompt, or within an
R program, to ask for a package stored externally to be placed within your
computer but once done, it remains there until and unless you want to get a
newer version or something.

There are packages that include data within themselves and may well be some
that dynamically go out and get info from somewhere but I know of no simple
way to find out other than reading the source code or seeing what happens if
you disconnect from the internet.

Your mention of EXCEL also needs clarification. EXCEL has absolutely nothing
to do with R. It is an unrelated product and you do not need to have it
installed to run R and vice versa. That does not mean your program cannot
interact with EXCEL or the files it makes, just that it is not part of base
R. R does allow importing data (locally or not) in lots of formats including
some that EXCEL can save data in. But generally, internal to R there are
storage methods such as the data.frame that hold data and manipulate it and
a typical R program may read in some data from files like .CSV that can be
saved from EXCEL or many other sources or with the proper packages, you can
read directly from more native EXCEL formats such as XLSX files. And, you
can write out results in many ways using packages that include those
formats.

Once data has been received, I know of no way in R that tags it with the
source of the data as being internal or external. Often the fact that
something is external is well hidden as many R packages have ways to access
external data as if it were local.

Perhaps you can explain more clearly what your concerns are. But note R is
not atypical among computer languages and many others might share the same
issues that concern you. 

Avi

-Original Message-
From: R-help  On Behalf Of Ferguson Charity
(CEMINFERGUSON)
Sent: Monday, October 2, 2023 3:49 AM
To: r-help@r-project.org
Subject: [R] Question about R software and output

To whom it may concern,



My understanding is that the R software is downloaded from a CRAN network
and data is imported into it using Microsoft Excel for example. Could I
please just double check whether any data or results from the output is held
on external servers or is it just held on local files on the computer?



Many thanks,



Charity



*

The information contained in this message and or attachments is intended
only for the
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and/or 
privileged material. Unless otherwise specified, the opinions expressed
herein do not
necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or
any of its subsidiaries. The information contained in this e-mail may be
subject to 
public disclosure under the Freedom of Information Act 2000. Unless the
information 
is legally exempt from disclosure, the confidentiality of this e-mail and
any replies
cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any
action in 
reliance upon, this information by persons or entities other than the
intended
recipient is prohibited. If you received this in error, please contact the
sender
and delete the material from any system and destroy any copies.

We make every effort to keep our network free from viruses. However, it is
your
responsibility to ensure that this e-mail and any attachments are free of
viruses as
we can take no responsibility for any computer virus which might be
transferred by 
way of this e-mail.


*

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Re: [R] Question about R software and output

[Ebert,Timothy Aaron]

I would answer "local files only," but with sufficient motive it is possible 
for some people to abuse a system. Base R does not download any of your data. 
The packages that I know about do not download data. You can add a layer of 
protection by only downloading directly from the source rather than through 
some third party. If you are skilled, you should be able to read through the 
source code to check for statements that would write your data to an external 
source.

Another viewpoint: R is an approved software for the University of Florida. The 
University is very aware of regulations and risks associated with personally 
identifiable information. Downloading to an external location would be a 
security risk that the University would not allow. That said, the university 
provides students and employees  an approved link for downloading the software. 
It is designed to help people avoid third party sites and associated risks.

If this is an issue with personally identifiable information, then you should 
check with your employer if R is an approved software.


-Original Message-
From: R-help  On Behalf Of Ferguson Charity 
(CEMINFERGUSON)
Sent: Monday, October 2, 2023 3:49 AM
To: r-help@r-project.org
Subject: [R] Question about R software and output

[External Email]

To whom it may concern,



My understanding is that the R software is downloaded from a CRAN network and 
data is imported into it using Microsoft Excel for example. Could I please just 
double check whether any data or results from the output is held on external 
servers or is it just held on local files on the computer?



Many thanks,



Charity


*

The information contained in this message and or attachments is intended only 
for the person or entity to which it is addressed and may contain confidential 
and/or privileged material. Unless otherwise specified, the opinions expressed 
herein do not necessarily represent those of Guy's and St Thomas' NHS 
Foundation Trust or any of its subsidiaries. The information contained in this 
e-mail may be subject to public disclosure under the Freedom of Information Act 
2000. Unless the information is legally exempt from disclosure, the 
confidentiality of this e-mail and any replies cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any 
action in reliance upon, this information by persons or entities other than the 
intended recipient is prohibited. If you received this in error, please contact 
the sender and delete the material from any system and destroy any copies.

We make every effort to keep our network free from viruses. However, it is your 
responsibility to ensure that this e-mail and any attachments are free of 
viruses as we can take no responsibility for any computer virus which might be 
transferred by way of this e-mail.

*

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Re: [R] Question about R software and output

[Bert Gunter]

I am pretty sure you'll get more replies than mine, so just consider this
as part of the story.

Your understanding is confused/flawed.

1. R can be downloaded from hundreds/thousands of software repositories,
not just CRAN.

2. R can read/upload data in hundreds of different formats, not just
Excel's. R makes no use of Excel to read external files (I wasn't clear
what you meant here).

3. As Ben said, it is certainly possible that some R packages -- optional
add-ons extending R capabilities ---  communicate with and store data or
results on external servers. R,  itself, can run locally and can store
results either locally or externally. Like most software, it can also be
integrated as part of the infrastructure on a server for web applications.

If you have a specific question not addressed by these various replies, ask
it. You will most likely get a useful reply.

Cheers,
Bert

On Tue, Oct 3, 2023 at 7:17 AM Ferguson Charity (CEMINFERGUSON) <
charity.eminfergu...@gstt.nhs.uk> wrote:

> To whom it may concern,
>
>
>
> My understanding is that the R software is downloaded from a CRAN network
> and data is imported into it using Microsoft Excel for example. Could I
> please just double check whether any data or results from the output is
> held on external servers or is it just held on local files on the computer?
>
>
>
> Many thanks,
>
>
>
> Charity
>
>
>
> *
>
> The information contained in this message and or attachments is intended
> only for the
> person or entity to which it is addressed and may contain confidential
> and/or
> privileged material. Unless otherwise specified, the opinions expressed
> herein do not
> necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or
> any of its subsidiaries. The information contained in this e-mail may be
> subject to
> public disclosure under the Freedom of Information Act 2000. Unless the
> information
> is legally exempt from disclosure, the confidentiality of this e-mail and
> any replies
> cannot be guaranteed.
>
> Any review, retransmission,dissemination or other use of, or taking of any
> action in
> reliance upon, this information by persons or entities other than the
> intended
> recipient is prohibited. If you received this in error, please contact the
> sender
> and delete the material from any system and destroy any copies.
>
> We make every effort to keep our network free from viruses. However, it is
> your
> responsibility to ensure that this e-mail and any attachments are free of
> viruses as
> we can take no responsibility for any computer virus which might be
> transferred by
> way of this e-mail.
>
>
> *
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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Re: [R] Question about R software and output

[Ivan Krylov]

В Mon, 2 Oct 2023 07:48:36 +
"Ferguson Charity (CEMINFERGUSON)" 
пишет:

> My understanding is that the R software is downloaded from a CRAN
> network

This is mostly true. (There are other ways of installing R, but it is
most frequently downloaded from a CRAN mirror.)

> and data is imported into it using Microsoft Excel for example.

This is not exactly the case.

It is possible to prepare data using Microsoft Excel and store it in
the Microsoft Excel format, but the actual import process is performed
either using base R functions (e.g. read.csv(), which is built into R),
or using third-party packages running inside R (e.g. "openxlsx", which
is available on CRAN) that implement the functions necessary to
transform Excel format into R data structures.

It is also possible to prepare data using other software, or type it
manually into R, or store it only in R's native data format (using
the saveRDS() or save() functions).

> Could I please just double check whether any data or results from the
> output is held on external servers or is it just held on local files
> on the computer?

As long as you're running R on your own computer, it should keep the
data locally. The words of a J. Random Hacker from the Internet don't
carry much weight with government agencies (as they shouldn't), but the
source code of R is open to audits. Additionally, there are some
guidance documents at .

Note that this only covers R itself and not any third-party software
packages that you could be using together with R. (You could also be
connecting to an RStudio server or running an instance of webR in your
web browser, in which case your data is subject to the privacy policy
of the server administrators.) For example, the "googleCloudRunner"
package available on CRAN is designed for the purpose of running code
on Google infrastructure and will send the data there if asked to.

CRAN packages are required never to do anything that might be regarded
as antisocial ,
but a dedicated attacker may be able to slip something past the
reviewers anyway.

Since your e-mail address contains nhs.uk, the
 website could help you find the
information you need.

-- 
Best regards,
Ivan

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Re: [R] Question about R software and output

[Ben Bolker]

   It's conceivable that functions in a contributed package would 
communicate/transmit or receive data from a remote server, but base R 
does nothing like that (unless you explicitly ask it to).


  cheers
   Ben Bolker

On 2023-10-02 3:48 a.m., Ferguson Charity (CEMINFERGUSON) wrote:

To whom it may concern,



My understanding is that the R software is downloaded from a CRAN network and 
data is imported into it using Microsoft Excel for example. Could I please just 
double check whether any data or results from the output is held on external 
servers or is it just held on local files on the computer?



Many thanks,



Charity


*

The information contained in this message and or attachments is intended only 
for the
person or entity to which it is addressed and may contain confidential and/or
privileged material. Unless otherwise specified, the opinions expressed herein 
do not
necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or
any of its subsidiaries. The information contained in this e-mail may be 
subject to
public disclosure under the Freedom of Information Act 2000. Unless the 
information
is legally exempt from disclosure, the confidentiality of this e-mail and any 
replies
cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any 
action in
reliance upon, this information by persons or entities other than the intended
recipient is prohibited. If you received this in error, please contact the 
sender
and delete the material from any system and destroy any copies.

We make every effort to keep our network free from viruses. However, it is your
responsibility to ensure that this e-mail and any attachments are free of 
viruses as
we can take no responsibility for any computer virus which might be transferred 
by
way of this e-mail.

*

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[R] Question about R software and output

[Ferguson Charity (CEMINFERGUSON)]

To whom it may concern,



My understanding is that the R software is downloaded from a CRAN network and 
data is imported into it using Microsoft Excel for example. Could I please just 
double check whether any data or results from the output is held on external 
servers or is it just held on local files on the computer?



Many thanks,



Charity


*

The information contained in this message and or attachments is intended only 
for the
person or entity to which it is addressed and may contain confidential and/or 
privileged material. Unless otherwise specified, the opinions expressed herein 
do not
necessarily represent those of Guy's and St Thomas' NHS Foundation Trust or
any of its subsidiaries. The information contained in this e-mail may be 
subject to 
public disclosure under the Freedom of Information Act 2000. Unless the 
information 
is legally exempt from disclosure, the confidentiality of this e-mail and any 
replies
cannot be guaranteed.

Any review, retransmission,dissemination or other use of, or taking of any 
action in 
reliance upon, this information by persons or entities other than the intended
recipient is prohibited. If you received this in error, please contact the 
sender
and delete the material from any system and destroy any copies.

We make every effort to keep our network free from viruses. However, it is your
responsibility to ensure that this e-mail and any attachments are free of 
viruses as
we can take no responsibility for any computer virus which might be transferred 
by 
way of this e-mail.

*

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[R] [R-pkgs] maptools, rgdal, rgeos and rgrass7 retiring Monday, October 16

[Roger Bivand]

The legacy R spatial infrastructure packages maptools, rgdal and rgeos will be 
archived by CRAN on Monday, October 16, 2023; rgrass7 has  already been 
replaced by rgrass and will be archived with the retiring packages. 

The choice of date matches the previously announced archiving during October 
2023, and the specific date matches the release schedule of Bioconductor 3.18 
(some Bioconductor packages depend on retiring packages).

sp_2.1-0 was published October 2, 2023, dropping all dependencies on the 
retiring packages. sp will continue to be available and maintained, but not 
developed further. Users of sp classes may continue to make use of them, but 
will have to use sf or terra to read, write or manipulate objects with coercion 
(for a guide to coercion, see 
https://cran.r-project.org/web/packages/rgrass/vignettes/coerce.html).

Information about the evolution project may be found in reports and resources 
at https://r-spatial.github.io/evolution/; a recent blog by Jakub Nowosad may 
also be useful as an overview of what has been going on: 
https://geocompx.org/post/2023/rgdal-retirement/. For more detail, see 
https://r-spatial.github.io/evolution/ogh23_bivand.html and a video recording 
of this presentation https://av.tib.eu/media/63141 (August 28).

All directly affected package maintainers have been alerted to the impending 
changes, some in December 2022, most others in March-April 2023. Many have 
already updated their packages on CRAN - thank you for your understanding! The 
remainder received github issue comments and email reminders in the last ten 
days, and will receive final notices to update by October 9. 

On R-universe, builds of packages archived on CRAN are dropped automatically 
(https://github.com/r-universe-org/help/issues/286). Read-only github mirrors 
of archived packages will remain available in principle while github exists 
(https://github.com/r-hub/rhub/issues/568), for example 
https://github.com/cran/rgdal. Other binary builds (Debian, Fedora, Ubuntu) 
have been alerted; support at Anaconda has been alerted.

On CRAN, the retired packages will continue to be available as source packages 
on https://cran.r-project.org/src/contrib/Archive. maptools, rgdal and rgeos 
also retain their R-forge repositories, which may be used to retrieve functions 
for adding to other packages.

A snapshot of Windows and macOS binary packages may be found on 
https://github.com/r-spatial/evolution/tree/main/backstore.

Please raise questions by replying to this post, or as issues on 
https://github.com/r-spatial/evolution.

--
Roger Bivand
Emeritus Professor
Norwegian School of Economics
Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway
roger.biv...@nhh.no
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