ttps://www.rforge.net/')", NOT
install.packages('PKI',,'http://www.rforge.net/'), which, for some
inscrutable reason (runaway proxying ?) fails the same way as before.
A big Kudos and Thank You to Simon Urbanek, on behalf of not-so-stable
distributions users !
Dear list,
It seems that recent changes in openssl somehow broke the installation
or update of the PKI package. This is probably specific of my setup(s)
(Debian testing, updated frequently).
Copy of a mail to Simon Urbanek (PKI maintainer), sent 5 days ago
without reply nor acknowledgement s
an help.
Sincerely yours,
Emmanuel Charpentier
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and provide commented, minimal, sel
ons (and,
on amd64, the discrepancies between Ubuntu 11.04 and Debian testing,
which are easier to explain : Debian has slightly more recent version).
I'll try to downgrade the R xml package (easier) and report results.
Again, thank you very much !
Emma
d" to 3.4.0 by the "update.packages(ask=FALSE)" I'm used to
do ...
Thank you again ! Now I can again use a multiprocessor eficiently to run
the same analyses on 18 datasets (thanks to mclapply (multicore)). A
serious win in my case...
cross-posting to r-help and r-debian-sig, but I think
that the issue is ... complicated and might not be as Debian-specific as
it seems at first view.
Sincerely,
Emmanuel Charpentier
Dear Max,
A few days ago, I started to have problems with odfWeave 0.7.17 on
es to BUGS, as you might have guessed, but the "public
health warning" that the Spiegelhalter gang put in front of the WinBUGS
manual still apply : "MCMC sampling can be dangerous". To which I add
"model checking, convergence assessment and validation might eat more
time
can Murdoch, who was able to give
a *correct* solution before I have been able to *correctly* state the
problem.
Emmanuel Charpentier
On Sat, 11 Dec 2010 22:58:10 +, Emmanuel Charpentier wrote :
[ Snip... ]
___
Dear list,
see comment at end.
On Sat, 11 Dec 2010 22:58:10 +, Emmanuel Charpentier wrote :
> Dear list,
>
> Inspired by the original Knuth tools, and for paedaogical reasons, I
> wish to produce a document presenting some source code with interspersed
> comments in the sour
Weave, in the "text" part), and spice
it with \end{verbatim} comments.. \begin{verbatim} chunks. This way, I
lose any guarantee of consistency between commented text and effective
code.
Any other idea ?
Emmanuel Charpentier
able to install these two packages on
Ubuntu Lucid (64 bits, using the g++-multilib package) and Debian
Squeeze (32 bits) and to test BRugs quickly without apparent problems.
HTH,
Emmanuel Charpentier
__
R-
censoring notation, which cannot
pass for R syntax.
The R2WinBUGS package has a write.model() function, which I shoplifted,
simplified (JAGS doesn't seem to be as picky as WinBUGS in tne numerical
notation department), extended (to take advantage of the JAGS' "data
transform" featu
(you know, the sort of ... thing ... that hit the fan when
you've been coaxed to accept Excel spreatsheet as "dats sets").
HTH,
Emmanuel Charpentier
Le lundi 10 mai 2010 à 16:06 -0400, Michael H a écrit :
> R experts,
>
> I am wor
Sorry for this late answer (I've had a seriously nonmaskable interrupt).
Since I have technical questions not related to R, I take the liberty to
follow this up by e-mail.
I might post a followup summary if another R problem arises...
Emm
gis), is
kind enough to choke on this (i. e. returning back Inf values, which
will make the regression program choke).
So please quench my thirst : what exactly is MH.Index supposed to be ?
How is it measured, estimated, guessed or divined ?
HTH,
Emmanuel Charpentier
__
903 0.5083574 0.5672021
But again, we're exploiting a shortcoming of the asin(sqrt())
transformation.
HTH,
Emmanuel Charpentier
Le vendredi 16 avril 2010 à 00:15 -0800, Kay Cichini a écrit :
> thanks thierry,
>
> i considered this transfor
hoice of epsilon, whic tends to indicate that, at small epsilon values,
the "sharp" "impossible" values dominate the evaluation of the
oefficients they are involved in.
Beta models (not shown) give similar results, to a lesser extend.
In short, your "sharp" data are essent
Le mercredi 07 avril 2010 à 18:03 +1000, William Venables a écrit :
[ Snip ... ]
> [ ... ] The effect is
> somewhat like that of the use of the .Data directory in S-PLUS, (a
> program not unlike R), though somewhat more manually driven.
I'm not sure
* work, be difficult and not always
succeed (numerical difficulties. Furthermore, the results of a Byesian
analysis might not be what you seek...
HTH,
Emmanuel Charpentier
Le lundi 05 avril 2010 à 11:34 +0100, Desmond Campbell a écrit :
> Dear all,
>
ic graph and that the distributions of you variables are either
from a "standard" family available in BUGS or that you are able to
express the (log-)density of the non-standard distribution you wish to
use). But, again, no p-values in sight. Would you settle for Bayes
factors between tw
Le jeudi 18 mars 2010 à 15:49 -0400, Duncan Murdoch a écrit :
> On 18/03/2010 3:10 PM, Emmanuel Charpentier wrote:
> > An old (Lisp ? C ?) quote, whose author escapes me now, was :
> >
> > "syntactic sugar causes cancer of the semicolon"
> >
> > ..
An old (Lisp ? C ?) quote, whose author escapes me now, was :
"syntactic sugar causes cancer of the semicolon"
.. but nowadays semicolons are rarely used in "real-life" R.
Emmanuel Charpentier
PS and, BTW, neither C nor Lisp have muc
ld have render myself unable to work with those
d*mn Word files for about a month, or forced me to do a maual repair
(which I hate...)).
So consider Debian as a (desirable) alternative to Ubuntu.
HTH,
Emmanuel Charpentier, DDS, MSc
em to save *serious* money or to
*seriously* streamline their current process. We all know it's possible,
but the economic|financial case still has to be done. An implementation
of such a system in a new sector (namely medical devices), using the
"Bayesian headstart" and the FDA incenti
o do with
mathematics, science or engineering|technologies, it would be smart to
at least consider this seriously.
In short, you should discuss your options (memory, X server, VNC/RDP,
Linux) with your *local* friendly help. Again, the R help list is
*definitely* *NOT* the right place for learni
Douglas Bates' description of the lmer() algorithms for
a nice, big counter-example, or consider MCMC... But coming closer to
such an organization *seems* possible : see for example biglm.
So I think that data views are a a worthy but not-so-easy possible goal
aimed at various data structure proble
Le mercredi 03 février 2010 à 09:23 -0600, Peng Yu a écrit :
> On Wed, Feb 3, 2010 at 2:12 AM, Emmanuel Charpentier
> wrote:
> > Le mercredi 03 février 2010 à 00:01 -0500, David Winsemius a écrit :
> >> On Feb 2, 2010, at 11:38 PM, Peng Yu wrote:
> >>
> >&
ucation than an R specific question.
Nonwhistanding David Winsemius' closing remark, I'd like to add
something that should be requested reading (and maybe hinted at in
lm()'s help page) :
http://www.stats.ox.ac.uk/pub/MASS3/Exegeses.pdf
(BTW, despite is age, MASS *is* r
indows "share") ?
- port gencont.exe to linux ? :-) (this might seem silly, but might be
the easiest solution if this program is (as it seems according to your
partial explanations) a simple "filter" (read data, munch them, spit
output) not using windows-specific functions or system calls).
HTH,
Emmanuel Charpentier
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and provide commented, minimal, self-contained, reproducible code.
y to use
external code (I'm thinking of the rpgsql language, which allows running
R code in a pgsql function in PostgreSQL).
HTH,
Emmanuel Charpentier
BTW, there exist a R database Special Interest Group, with a mailing
list. Lookup their archive, and ma
ocument will get produced in the foreseeable future.
Frequent R-help reading and note-taking is the second-best option...
To come back to R-vs-S+ topic : unless I'm mistaken, R seems to be
currently the dominant version of the S language, and most published S
material will nowadays (implicitly) b
Le dimanche 08 novembre 2009 à 19:05 -0600, Frank E Harrell Jr a écrit :
> Emmanuel Charpentier wrote:
> > Le dimanche 08 novembre 2009 à 17:07 -0200, Iuri Gavronski a écrit :
> >> Hi,
> >>
> >> I would like to fit Logit models for ordered data, such as thos
x27;ve been unable to use it
recently (numerical exceptions).
> By the way, my dependent variable is ordinal and my independent
> variables are ratio/intervalar.
Numeric ? Then maybe some recoding/transformation is in order ... in
which case Design/rms might or might not be us
is a factor, so you get an estimate for
each treatment level except the first, to be interpreted as difference
of means with the first level.
I fell in that trap myself a few times, and took the habit to give evels
to my fctors tht cannot be interpreted as numbers (such as f<-paste("F&quo
distribution with only very few possible values, at most as many value
as the sample. Exercise : derive the distribution of median(x)...).
To convince yourself, look at the histogram of the bootstrap
distribution of median(x). Contrast with the bootstrap distribution of
mean(x). Meditate. Conclude.
hat...).
>
> Not so: they are clearly stated in ?contrMat.
Oops.. I oversaw that.
With my apologies,
Emmanuel Charpentier
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PLE
e a good complement to
somewhat incomplete help pages : what in h*ll are valid arguments to
mcp() beyond "Tukey" ??? Curently, you'll have to dig in the source to
learn that...).
HTH
Emmanuel Charpentier
_
tation and the r-help list archives didn't turn up
anything relevant. This error survived restarting OOo, restarting R,
restarting its enclosing Emacs session and even rebooting the damn
hardware...
Any idea ?
find any help on how to do that.
>
> Could you help me and tell me what to do? Or tell me where to find help on
> this topic?
?anova? Check the "test" argument ...:-)
Emmanuel Charpentier
__
ile (reusable...).
HTH,
Emmanuel Charpentier
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and provide commented,
w that you tell it, you got me a nice
idea for a workaround ... :-)
> So, back to your question, the relevant code for captions is in
> odfWeave:::withCaptionXML (odfInsertPlot uses this to write the xml).
> You can try that and I might be able to look at it in the next few
Le mardi 30 juin 2009 à 14:51 -0400, Max a écrit :
> I just put a new version on cran...
Now, *that's* support !!! bug report at 17:31, acknowledgement at 20:12,
(probable) bug fix at 20:51. Bravo, bravissimo, Max !
Try that, SAS support !
erely,
Emmanuel Charpentier
Annex : log of compilation with fig=true, results=xml.
> odfWeave("Test1Src.odt", "Test1.odt")
Copying Test1Src.odt
Setting wd to /tmp/RtmpenMTgz/odfWeave3023572231
Unzipping ODF file using unzip -o Test1Src
or" package
seems also quite interesting.
Another (smarter(?)) alternative is to ask yourself *why* you need Z and
p. Z is just a computing device allowing you to use a known density. And
the real meaning of p and its usefulness has been discussed, disputed
and fought over at exceedingl
art is fast forgotten, if not totally lost. If you
insist, I might try to unearth my copy of Winer's handbook (ca. 1959)
and look up specific questions.
HTH,
Emmanuel Charpentier
__
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ataset)
independent linear equations with nrow(dataset) unknowns (the beta[i]),
whose solution is trivially beta[i]=log(x[i]/n[i])-log(sum(x)/sum(n),
except when n[i]=0 in which case your equation has no solution.
Could you try to re-express your problem ?
Em
p with your *real* problem...
Emmanuel Charpentier
> And we are left with
> nothing: no result file was produced since the calculations were
> interrumpted!
> Consequently, I am looking for a way to accelerate calculation
mu)-1.7037 -0.82997 0.072275 0.78520 1.72834
> > log(shape) -2.5152 -0.32448 0.254698 0.58772 0.70678
> >
> >
> > # NEED P-VALUES HERE #
>
> Perhaps:
>
> dt(summary( modl2 )@coef3[ , 3], 1)
???
1) dt() is the density. didn't you mean pt() ?
2
for assessing the model fit and obtaining case diagnostics.
Thank you very much ! I think that this package was expected ...
Emmanuel Charpentier
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aluation rules, and it turns out that lme()
doesn't evaluate extra arguments like subset in the parent environment",
but this does not tell me why a "..." argument is *not* found. Different
frame of evaluation ?
May some kind soul point
Le mardi 02 juin 2009 à 16:32 +, ms.com a écrit :
> Dear all
> i got a problem in monthly mean temperature. here i am attaching the data set
> as well as the plot i got with the following command
> plot(month,type='n')
> plot(month,X1999)
>
> this command gave the plot where the month names a
t touch a Windows
computer for years...
HTH,
Emmanuel Charpentier
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an
lower=c(-Inf,0,0),
+ upper=c(Inf,1,1)))
utilisateur système écoulé
0.004 0.000 0.004
>
> D2.bound
$par
c1 c2 c3
2.0995442 0.2192566 0.000
# The optimizer bangs is pretty little head on the c3 wall.
way to
express your objective function, not an independent parameter).
Of course, if it's homework, get lost !
Emmanuel Charpentier
> Is "optim" in the stats package the right function to use?
last
two months.
Time for a FAQ entry ? (It does not seem to exist : I checked...)
Emmanuel Charpentier
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PLEASE do read the posting
"bar"
> bar("Foo1.RData")
[1] "filename" "Foo" # Note : by default, ls() list the function's
# environment, not the global one... **> no "bar" here...
[1] 0.8030422 0.6326055 0.8188481 0.6161665 0.5
entry. Epidata entry
> is much more professional.
Irony squared ?
This *must* go in the fortunes file !
Emmanuel Charpentier
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PLE
,drop=TRUE]})
AAT<-lmer(y~S+A+(1|SAH),data=AT,REML=TRUE)
> :confused:
Enlightened ?
Emmanuel Charpentier
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PLEASE do read the posting guide http://www.R-pr
a) import data in an SQL database, and b) prepare
some routines to dump SQL tables / R dataframes in Excel tor returning
back to the original data author...
HTH
Emmanuel Charpentier
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Seconded !
Emmanuel Charpentier
Le lundi 02 mars 2009 à 21:06 -0700, Greg Snow a écrit :
> > -Original Message-
> > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
> > project.org] On Behalf Of Prof Brian Ripley
>
Answering to myself (for future archive users' sake), more to come
(soon) :
Le jeudi 23 avril 2009 à 00:31 +0200, Emmanuel Charpentier a écrit :
> Dear list,
>
> I'd like to use multiple imputations to try and save a somewhat badly
> mangled dataset (lousy data collec
Danke sehr, herr Professor ! This one escaped me (notably because it's a
trifle far from my current interests...).
Emmanuel Charpentier
Le samedi 25 avril 2009 à 08:25 -0500, Frank E Harrell Jr a écrit :
> Emmanuel Charpentier wrote:
> >
:
coxph(Surv(min(x,,na.rm=TRUE),
!is.na(x),type="left")~) to do this on-the-fly).
Another possible idea is to split your (supposedly x) variable in two :
observed (logical), and value (observed value if observed, if not) and include these two data in your model. You probably
will
lines(final.weight~birth.vec, type="p", data=my.data) ;
lines(center~time, lty=1) ;
lines(lb~time, lty=3) ;
lines(ub~time, lty=3)
})
Adding your empirical centiles to this graph might help...
NB : on your example data set, there is a big gap between the earliest
point
mix) runs perfectly (and fast !).
=
I might be particularly stupid and misunderstanding manual and the
"textbook" examples of one or two packages, but five !
Visual/manual/graphical examination of my dataset does no
e.html in the graph
> "Four circles surrounding illusion").
>
> Does anybody has a nice solution, ideally with a possible solution in R?
Plot on a torus. Should be trivial in R once you've found the torus
feeder for your printer... :-)
Dear Ben,
Le samedi 18 avril 2009 à 23:37 +, Ben Bolker a écrit :
> Emmanuel Charpentier bacbuc.dyndns.org> writes:
>
> >
> > I forgot to add that yes, I've done my homework, and that it seems to me
> > that answers pointing to zero-inflated Poisson
d) ears...
Of course, I could also bootstrap the damn thing and study the
distribution of my contrasts. I'd still been hard pressed to formally
test hypotheses on factors...
Any ideas ?
Emmanuel Charpentier
Le samedi 18 avril 2009 à 19:28 +0200, Emmanuel C
with unobserved "0"
values ?
Sincerely,
Emmanuel Charpentier
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that
will pass a medical journal's reviewer unquestioned), you can always use
SAS' proc mixed. But I wouldn't swear this answer is "exact", or even
sensible, as far as I can judge...
Pr Bates seems to answer readily any (sensible) questions on the ME
mailing list, where you
es being
the "residual degrees of freedom" of the model) or by the F value, which
will fluctuate as a Fisher F statistic with 1 and n_res dof, which
happens (but that's not happenstance...) to be the *square* of a t with
n_dof.
May I suggest consulting a textbook *before* flunking A
sn't need any intermediary step, thus
allowing for automatisation. Be aware, however, that the embedded EPS
images are not editable in-place by OpenOffice nor, as far as I know, by
MS Word. But my point was to *avoid* post-production as much as humanly
possible (I tend to be inhumanly lazy...).
language.
I don't know zilch about it ...
HTH
Emmanuel Charpentier
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and provi
Le vendredi 03 avril 2009 à 20:01 -0400, Murray Cooper a écrit :
> For science yes. For pleasure I'll still take a pint instead of 570ml!
Yes, but do you realize that you'll have to pee in fl. oz ? Aie ...
Emmanue
ies with
meaningless conversion factors...
Emmanuel Charpentier
who has served his time with
pounds per cubic feet, furlongs
per fortnight, BTU and other
reauire(MASS) ; ?predict.lda should enlighten you. Glancing at V&R4
might be a bit more illuminating...
HTH
Emmanuel Charpentier
Le vendredi 03 avril 2009 à 22:29 +0200, Pavel Kúr a écrit :
> Hello!
>
> I need some help with the linear
nction that returns a matrix of the direction of the vectors between points
> (angles 0-360°)?
>
> testdata <- matrix(1:8, nrow=4, ncol=2,
> dimnames=list(c("A","B","C","D"), c("x"
understand that Douglas Bates has already way too much work and not
too much time on his hands, and I doubt he might be coaxed to work in
this direction right now...
A suggestion : you might forward your question to the "r-mixed-models"
SIG mailing list with some profit...
rix_0.999375-21
[5] nlme_3.1-90
>
On Tue, 17 Mar 2009 06:53:20 +, Emmanuel Charpentier wrote :
> Dear list,
>
> "+" (and "-") being defined for difftime class, I expected mean() to
> return something sensible. This is only half-true :
>
>> mean(
")
[ ... doesn't return anything relevant ]
NB : this isn't done for the hell of it. I intended to replace some
missing dates, with something computed from other dates and mean time
intervals).
Any thoughs ?
Emmanuel Charpentier
__
Le dimanche 08 mars 2009 à 13:22 -0500, Dirk Eddelbuettel a écrit :
> On 8 March 2009 at 13:27, Duncan Murdoch wrote:
> | But we don't even have that data, since CRAN is distributed across lots
> | of mirrors.
>
> On 8 March 2009 at 19:01, Emmanuel Charpentier wrote:
> | A
use(s). Data may or may not become available
with more or less of an effort, but I can't see the point.
Emmanuel Charpentier
Le dimanche 08 mars 2009 à 16:08 +, Barry Rowlingson a écrit :
> > I think the situation is worse than messy. If a cli
hink "fortunes"...), to vital need tthink lme4 if/when a consensus on
denominator DFs can be reached :-)...). What can you infer in good faith
from such a mess ?
Emmanuel Charpentier
__
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ero, the associated null hypothesis isn't nonsensical and the test of
this null isn't worthless.
End of the loosely related methodological rant ====
In any case, my point is : hypothesis testing is *not* the alpha and
omega of biostatistics, and other methods of describi
On Mon, 08 Sep 2008 01:45:51 +0200, Peter Dalgaard wrote :
> Emmanuel Charpentier wrote:
>> Dear list,
>>
[ Snip ... ]
> This looks reasonably sane, I think. The last loop could be d[] <-
> lapply(d, conv1, from, to), but I think that is cosmetic. You can&#
}
else if (is.character(v)) return(condconv(v,from,to))
else return(v)
}
for(i in names(d)) d[,i]<-conv1(d[,i],from,to)
return(d)
}
Any advice for enhancement is welcome...
Sincerely yours,
Emmanuel Charpentier
_
d enough to have first-hand knowledge of this
history.
I was born, but not weaned, when McCarthy unleashed Lisp on an unsuspecting
world ...
I learned that ca. 1978-9, while discovering VLisp.
While I can't really help you (I still think that processing "..." at C level
is eit
enlightening...
Emmanuel Charpentier
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Le dimanche 17 août 2008 à 09:36 +, Dieter Menne a écrit :
[ Snip .. ]
> Trellis graphics are a bit like hash functions: you can be close to the
> target, but get a far-off result.
Nice candidate for a fortune() entry ...
Emmanuel Charp
e (and not attached):
[1] grid_2.7.1 tools_2.7.1
Hoping this might help,
Emmanuel Charpentier
PS : don't try to answer to my subscribed address (charpent (at) bacbuc
(dot) dyndns (dot) org), which is the apparent source of this message :
bacbuc (dot) dyndns (dot) org is down and will quit
e (and not attached):
[1] grid_2.7.1 tools_2.7.1
Hoping this might help,
Emmanuel Charpentier
PS : don't try to answer to my subscribed address (charpent (at) bacbuc
(dot) dyndns (dot) org), which is the apparent source of this message :
bacbuc (dot) dyndns (dot) org is down and will quit
This one should (I am tempted to write "must") make its way to fortune
()...
Thankyouthankyouthankyou ...
Emmanuel Charpentier
On Mon, 14 Jul 2008 14:58:13 -0600, Greg Snow wrote :
> For those people who feel the need for a p-value to test
m
in SQL and read in R only the relevant part(s). There also are some
contributed packages that might help in special situations : biglm, birch.
HTH,
Emmanuel Charpentier
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https://
ncy works, the
loss of an USB key with my current work on this and some
non-unsignificant sickness...
Emmanuel Charpentier
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PLEASE do re
does the variables change ?!?
'Cause you build your new data frame from vectors with no name
(casesCNST$case is a vector with no name). to keep the original names,
you should subset the original data frame, with casesCNST[,c(1,6)] or
casesCNST[,c("case","expected")
arting
from the Debian sources ; a cursory check lets me think that these
builds are correct. Let me know if you want them (no guarantees : caveat
emptor).
I plan to check them extensively and propose them to the SIG-Debian
mailing list, but this will
extensively.
HTH,
Emmanuel Charpentier
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and provid
ns ? You should be a bit more descriptive...
> res<-dbSendQuery(con,'select * from sjlc_ld')
require(MindeReaderAlpha).
H ... Isn't the "breakage" just a loooong wait with no answer ? Or
maybe a timeout ?
In which case I'd try to put a semicolon (&quo
annel,query), ...)
...
}
If you already use a DBMS with some connection to R (via RODBC or
otherwise), use that. If not, sqlite is a very lightweight library that
enables you to use a (very considerable) subset of SQL92 to manipulate
your data.
I understand that some people of this list have under
of the process of understanding the problem.
Which was probably the point of this (probable) homework...
Emmanuel Charpentier
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