Re: [R] R: Redefine default parameter values for help.start()
paul paul.domas...@gmail.com on Thu, 16 Apr 2015 18:58:12 + writes: Because of the setup of R in cygwin, help.start() requires the following parameter values: help.start(browser=cygstart,remote=R.home()) Is it possible to make these values the default? You are building R from the sources, right? Then, of course it is easily possible: Just modify your version of the R source code appropriately: It is file R/src/library/utils/R/help.start.R (And you need more changes anyway to make things work under Cygwin; but don't ask me about it: I do run R on Windows only very rarely) I do not want cygstart to be the browser except as a parameter for help.start(). __ 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] Weighted Likelihood
Hola Olivier, Muchísimas gracias por la ayuda, todo entendido. Con tan pocos datos no puedo pretender obtener lo que me imagino en mi cabeza. Me has ayudado mucho a entender como funcionaba, todo solucionado! Un abrazo, y gracias de nuevo. El 17 de abril de 2015, 9:58, Olivier Nuñez onu...@unex.es escribió: Pero, si el modelo lineal lo cubre casi todo! Tu modelo es lineal pero generalizado y estás especificando que tus datos siguen una Gamma (family=Gamma). Lo cual implica por defecto que en promedio la relación entre la variable dependiente (datos) y la independiente (num) es inversa no es precisamente lineal. Si quieres más flexibilidad puedes utilizar splines en la regresión; un ejemplo: require(splines) modelo - svyglm(formula = datos ~ ns(num,2), design = svy, family = Gamma) svyplot(formula = datos ~ num, design = svy) lines(svy$variables$num, fitted(modelo), col=red) Pero, con 10 puntos sólo ganaras inestabilidad en la predicción. -- *De: *Víctor Nalda Castellet victor.nalda.castel...@gmail.com *Para: *Olivier Nuñez onu...@unex.es *Enviados: *Jueves, 16 de Abril 2015 18:55:17 *Asunto: *Re: [R-es] Weighted Likelihood Hola Olivier, No recordaba la función fitted, muchas gracias. Lo que ocurre es que claro al utilizar glm, es un modelo lineal. Me gustaría saber si se puede ajustar mediante otro tipo de funciones como una Gamma o una normal, ¿sabes cómo? install.packages(survey) library(survey) num - c(1:10) datos - c(1.1146265, 0.9039153, 0.8374396, 0.7089485, 1.2488793, 2.5789016, 2.0976523, 0.9748834, 0.2738321, 1.1842141) pesos - c(0.7,0.7,1,1,0.02,0.01,1,0.01,0.05,0.2) df - cbind.data.frame(num, datos, pesos) svy - svydesign(datos, weights = pesos, data = df) modelo - svyglm(formula = datos ~ num, design = svy, family = Gamma) # family: binomial, gaussian, Gamma, inverse.gaussian, poisson, quasi, quasibinomial, quasipoisson svyplot(formula = datos ~ num, design = svy) lines(svy$variables$num, fitted(modelo), col=red) De verdad, muchas gracias por ayudar. El 16 de abril de 2015, 18:27, Olivier Nuñez onu...@unex.es escribió: Todo parece correcto (siempre que tus pesos son efectivamente weight sampling). El ajuste, lo puedes obtener de manera estándar con fitted(modelo) y vizualizarlo por ejemplo con svyplot(formula = datos ~ num, design = svy) lines(svy$variables$num,fitted(modelo),col=blue) -- *De: *Víctor Nalda Castellet victor.nalda.castel...@gmail.com *Para: *Olivier Nuñez onu...@unex.es *Enviados: *Jueves, 16 de Abril 2015 17:25:56 *Asunto: *Re: [R-es] Weighted Likelihood Hola Olivier, Muchas gracias por la ayuda, te he entendido perfectamente. Tengo un vector de datos y uno de pesos, por ejemplo: num - c(1:10) datos - c(1.1146265, 0.9039153, 0.8374396, 0.7089485, 1.2488793, 2.5789016, 2.0976523, 0.9748834, 0.2738321, 1.1842141) pesos - c(0.7,0.7,1,1,0.02,0.01,0.02,0.01,0.05,0.2) df - cbind.data.frame(num, datos, pesos) Ahora creo el diseño como: svy - svydesign(datos, weights = pesos, data = df) Y si hago su gráfica puedo ver que unos puntos tienen mayor peso que otros, tal y como he especificado en los pesos: svyplot(formula = datos ~ num, design = svy) Ahora quiero ajustar el modelo mediante una función Gamma, para ello: modelo - svyglm(formula = datos ~ num, design = svy, family = Gamma) # family: binomial, gaussian, Gamma, inverse.gaussian, poisson, quasi, quasibinomial, quasipoisson summary(modelo) plot(modelo) ¿Esto es correcto? ¿Cómo puedo ver el ajuste? Muchas gracias, un saludo. El 16 de abril de 2015, 11:40, Olivier Nuñez onu...@unex.es escribió: No das muchos detalles sobre porque quieres ponderar los datos, pero intuyo que es por el diseño. Si es así, la función svydesign del paquete te permite especificar bien la probabilidad de selección del dato (probs) en la muestra o de manera equivalente, o el sampling weight que puedes interpretar como la representatividad del dato en la población. Una vez especificado el diseño mediante esta función, puedes llevar cualquier análisis estandár de tus datos. Un saludo. Olivier -- *De: *Víctor Nalda Castellet victor.nalda.castel...@gmail.com *Para: *Olivier Nuñez onu...@unex.es *CC: *r-help-es r-help-es@r-project.org *Enviados: *Jueves, 16 de Abril 2015 11:25:10 *Asunto: *Re: [R-es] Weighted Likelihood Hola, He buscado por el pdf de la documentación qué función es la que me puede servir pero no encuentro ninguna. ¿Tenías alguna función especifica de ese paquete pensada? Un saludo, y muchas gracias por la ayuda. El 16 de abril de 2015, 10:45, Víctor Nalda Castellet victor.nalda.castel...@gmail.com escribió: ¡Muchas gracias Olivier! Un saludo. El 16 de abril de 2015, 10:44, Olivier Nuñez onu...@unex.es escribió: Mira el paquete survey. Un saludo. Olivier - Mensaje original - De: Víctor Nalda
Re: [R] How to calculate vif of each term of model in R?
Hi
I did not see any answer so I try.
Your question lacks some info:
Which vif - car or HH?
answers and comments in line
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
Methekar, Pushpa (GE Transportation, Non-GE)
Sent: Wednesday, April 08, 2015 10:24 AM
To: r-help@r-project.org
Subject: [R] How to calculate vif of each term of model in R?
I am beginner in R doing modelling in R, I loaded excel sheet in R, i
have chosen x elements and y elements then fitted model for linear and
second order regression. Now I have both models. I am bit confused how
to calculate vif for each term in model like
e.g model1-lm(y1~x1+x2+.x9) when I am using rms package then it's
giving me like
vif(model1)
x1 x2 x3 x4 x5 x6
x7
6.679692 1.520271 1.667125 3.618439 4.931810 2.073879
13.870630
x8 x9
220.969628 214.034135
now i want to compare each term with std vif as vif=10 and which will
satisfy this condition i want to delete that term and update model1. i
have done something like this
fun = function(model1) {
for(i in 1:length(model1)){
v=vif(model1)
ss=any(v[i]=10)
here you select only one item from vif, Why do you use any?
if(ss==1){update(model1,.~.,-v[i])}
else{print(no update)}
Why do you change i here?
i-i+1
}
return(model1)
}
if you want to get rid of all terms bigger than some threshold in once you can
use
sel - which(vif(model1)10)
and select values for update possibly by
update(model1,.~. - names(vif(model1))[sel])
or if you want to get rid one by one you can use
vmax - which.max(vif(model1))
and check if max vif value is bigger than 10.
vif(model1)[vmax]=10
If it is just update with
- names(vif(model1))[vmax])
if it is not do not update.
All of this untested.
Cheers
Petr
fun(model1)
but giving error as
Error in if (ss == 1) { : missing value where TRUE/FALSE needed.
please tell me how do i solve this problem.
[[alternative HTML version deleted]]
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[R] [off-topic] R Homepage
Hi there, It's a off-topic post. It seems that the R home page changed a lot. There are no plot at the right frame. Why are they removed? Will it or an alternative be back in future? Another question is about the ``What's New?'' page. The latest announcement is not archived in that page. In the last year, I always checked the latest announcement from that page. It's updated in time than http://cran.r-project.org/doc/manuals/r-release/NEWS.html Best, Jinsong __ 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] melt function chooses wrong id variable with large datasets
Yes It could be. But anyway, if you wanted to melt your frame and be sure to have norm column added to months column you shall use melt(dataset, id.vars=NULL, na.rm=TRUE) construction. Without it and considering data you sent I get head(dd.m0) norm variable value 1 45.8713463281901 januari 38.1 2 24.047250681782984 januari 32.4 3 3.7533684144746324 januari 34.5 4 38.594241119279324 januari 20.7 5 26.391897460120358 januari 21.5 6 61.746470001194638 januari 23.1 ... without this id.vars=NULL parameter. Cheers Petr PS. Keep your post to Rhelp - others may learn from it and anothers can provide you with more elaborated explanation. From: Joachim Audenaert [mailto:joachim.audena...@pcsierteelt.be] Sent: Friday, April 17, 2015 8:23 AM To: PIKAL Petr Subject: RE: [R] melt function chooses wrong id variable with large datasets Hello, I upgraded R tot version 3.1.3 and now everything in the script works perfectly. Could the troubles be due to the fact that I was running an older version? Met vriendelijke groeten - With kind regards, Joachim Audenaert onderzoeker gewasbescherming - crop protection researcher PCS | proefcentrum voor sierteelt - ornamental plant research Schaessestraat 18, 9070 Destelbergen, Belgi� T: +32 (0)9 353 94 71 | F: +32 (0)9 353 94 95 E: joachim.audena...@pcsierteelt.bemailto:joachim.audena...@pcsierteelt.be | W: www.pcsierteelt.behttp://www.pcsierteelt.be/ From:PIKAL Petr petr.pi...@precheza.czmailto:petr.pi...@precheza.cz To:Joachim Audenaert joachim.audena...@pcsierteelt.bemailto:joachim.audena...@pcsierteelt.be Cc:r-help@r-project.orgmailto:r-help@r-project.org r-help@r-project.orgmailto:r-help@r-project.org Date:16/04/2015 13:41 Subject:RE: [R] melt function chooses wrong id variable with large datasets Hi With this dataset I get dd.m0-melt(dataset, na.rm=T) Using norm as id variables head(dd.m0) norm variable value 1 45.8713463281901 januari 38.1 2 24.047250681782984 januari 32.4 3 3.7533684144746324 januari 34.5 4 38.594241119279324 januari 20.7 5 26.391897460120358 januari 21.5 6 61.746470001194638 januari 23.1 or dd.m-melt(dataset, id.vars=NULL, na.rm=T) head(dd.m) variable value 1 januari 38.1 2 januari 32.4 3 januari 34.5 4 januari 20.7 5 januari 21.5 6 januari 23.1 tail(dd.m) variable value 255 norm 4.856812959269508 256 norm 5.3982910143166514 257 norm 46.553976273304215 258 norm 17.566272518985429 259 norm 20.552451905814117 260 norm 61.894775704479279 The latter will put norm to the same column as months. Is it intended? Maybe you want dd.m1-melt(dataset[,-13], na.rm=T) No id variables; using all as measure variables head(dd.m1) variable value 1 januari 38.1 2 januari 32.4 3 januari 34.5 4 januari 20.7 5 januari 21.5 6 januari 23.1 tail(dd.m1) variable value 235 december 20.7 236 december 30.9 237 december 36.2 238 december 21.0 239 december 20.2 240 december 21.3 Cheers Petr From: Joachim Audenaert [mailto:joachim.audena...@pcsierteelt.be] Sent: Thursday, April 16, 2015 1:13 PM To: PIKAL Petr Cc: r-help@r-project.orgmailto:r-help@r-project.org Subject: RE: [R] melt function chooses wrong id variable with large datasets Hello, This is a part of my dataset: structure(list(januari = c(38.1, 32.4, 34.5, 20.7, 21.5, 23.1, 29.7, 36.6, 36.1, 20.6, 20.4, 30.1, 38.7, 41.4, 37, 36, 37, 38, 23, 26.7), februari = c(31.5, 36.2, 38.2, 26.4, 20.9, 21.5, 30.2, 33.4, 32.6, 22.2, 21.7, 30, 35.7, 32.8, 39.3, 25.5, 23, 19.9, 21.3, 20.8), maart = c(34.2, 27, 24.2, 19.9, 19.7, 21.5, 30.6, 30, 19, 19.6, 20.6, 23.6, 17.9, 17.3, 21.4, 24.1, 20.9, 30.1, 32.6, 21.3), april = c(26.3, 29.6, 30.3, 23.6, 28.4, 20.7, 24.1, 27.3, 23.2, 18.3, 24.6, 27.4, 20.4, 18.1, 25.2, 19.8, 21, 23.7, 19.6, 18.1), mei = c(23.7, 24, 17.2, 23.2, 25.2, 17.2, 16, 15.6, 13.4, 16, 16.8, 14.6, 19.4, 21, 19.5, 18.5, 13.3, 13.7, 14.3, 14.1), juni = c(17.7, 14.2, 16.6, 15.7, 13.7, 14.7, 13.1, 12.9, 15.4, 11.9, 15.2, 15.3, 16.5, 16.1, 11.7, 11.2, 11.5, 10.8, 16.1, 14.8), juli = c(15.7, 14.5, 10.8, 10.5, 13.4, 12.2, 13.2, 13, 12.4, 13.1, 9.8, 10.5, 13.4, 11, 13.1, 15, 16.7, 16.1, 18.2, 15.7), augustus = c(12.9, 12.8, 15.2, 14.5, 17.2, 14.5, 14.4, 11, 13.1, 13.6, 14.6, 12.7, 13.6, 12.7, 15.5, 17.4, 15.2, 14.2, 17.7, 19.2), september = c(15.6, 15.5, 15.9, 15.1, 16, 19.4, 21.5, 23.7, 18.7, 23.8, 18, 16.2, 18.5, 20.6, 18.3, 22.5, 26.9, 19.4, 15.9, 20.5), oktober = c(21.4, 20.8, 14, 17, 23, 26.4, 19.6, 22.7, 26.9, 14.7, 15.2, 19.8, 26.9, 20.2, 14.3, 14.8, 18.5, 21.7, 21.4, 21.8), november = c(24.7, 26.2, 29, 21.6, 17.1, 16.9, 19.1, 24.7, 25.4, 19.8, 18.2, 16.3, 17, 17.7, 15.5, 14.7, 15.8, 19.9, 20.4, 23.3), december = c(19.8, 27, 21, 33, 22.6, 28.3, 21.1, 19, 17.3, 27, 30.2, 24.8, 17.9, 17.9, 20.7, 30.9, 36.2, 21, 20.2, 21.3), norm =
Re: [R] How to calculate vif of each term of model in R?
Hi
-Original Message-
From: Methekar, Pushpa (GE Transportation, Non-GE)
[mailto:pushpa.methe...@ge.com]
Sent: Friday, April 17, 2015 1:12 PM
To: PIKAL Petr
Subject: RE: How to calculate vif of each term of model in R?
Hi Petr,
You got my problem ,the solution which u specified is little good but
with
update(model1,.~. - names(vif(model1))[vmax])
I won't be able to update my model .
Instead I have to write like
update(model1,.~. - x8)
maybe something like
fun = function(model1) {
vmax - which.max(vif(model1))
while( vif(model1)[vmax]=10) {
model1 - update(model1,.~. - names(vif(model1))[vmax]))
vmax - which.max(vif(model1))
}
return(model1)
}
I am not sure about cycle (i did not use while in R for a while).
Without some data I cannot check syntax so it is up to you.
Cheers
Petr
i.e my x which having highest vif value.
Each time for removing highest x .i have to explicitly write ..-
x8) So is there any way to avoid this?
Thanks,
Pushpa
-Original Message-
From: PIKAL Petr [mailto:petr.pi...@precheza.cz]
Sent: Friday, April 17, 2015 4:16 PM
To: Methekar, Pushpa (GE Transportation, Non-GE)
Subject: RE: How to calculate vif of each term of model in R?
Comments to your first mail which are among lines and directly related
to your code.
I specifically mentioned it
answers and comments in line
If you have my first respond you can find them easier then now as they
are buried within your mail.
Cheers
Petr
-Original Message-
From: Methekar, Pushpa (GE Transportation, Non-GE)
[mailto:pushpa.methe...@ge.com]
Sent: Friday, April 17, 2015 12:10 PM
To: PIKAL Petr
Subject: RE: How to calculate vif of each term of model in R?
What comments are you talking about?
-Original Message-
From: PIKAL Petr [mailto:petr.pi...@precheza.cz]
Sent: Friday, April 17, 2015 3:38 PM
To: Methekar, Pushpa (GE Transportation, Non-GE)
Cc: r-help@r-project.org
Subject: RE: How to calculate vif of each term of model in R?
Did you follow my advice/comments?
Cheers
Petr
-Original Message-
From: Methekar, Pushpa (GE Transportation, Non-GE)
[mailto:pushpa.methe...@ge.com]
Sent: Friday, April 17, 2015 11:43 AM
To: PIKAL Petr
Subject: RE: How to calculate vif of each term of model in R?
Car package
-Original Message-
From: PIKAL Petr [mailto:petr.pi...@precheza.cz]
Sent: Friday, April 17, 2015 3:11 PM
To: Methekar, Pushpa (GE Transportation, Non-GE); r-help@r-
project.org
Subject: RE: How to calculate vif of each term of model in R?
Hi
I did not see any answer so I try.
Your question lacks some info:
Which vif - car or HH?
answers and comments in line
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
Methekar, Pushpa (GE Transportation, Non-GE)
Sent: Wednesday, April 08, 2015 10:24 AM
To: r-help@r-project.org
Subject: [R] How to calculate vif of each term of model in R?
I am beginner in R doing modelling in R, I loaded excel sheet in
R, i have chosen x elements and y elements then fitted model for
linear
and
second order regression. Now I have both models. I am bit
confused
how
to calculate vif for each term in model like
e.g model1-lm(y1~x1+x2+.x9) when I am using rms package then
it's
giving me like
vif(model1)
x1 x2 x3 x4 x5 x6
x7
6.679692 1.520271 1.667125 3.618439 4.931810 2.073879
13.870630
x8 x9
220.969628 214.034135
now i want to compare each term with std vif as vif=10 and which
will
satisfy this condition i want to delete that term and update
model1.
i
have done something like this
fun = function(model1) {
for(i in 1:length(model1)){
v=vif(model1)
ss=any(v[i]=10)
here you select only one item from vif, Why do you use any?
if(ss==1){update(model1,.~.,-v[i])}
else{print(no update)}
Why do you change i here?
i-i+1
}
return(model1)
}
if you want to get rid of all terms bigger than some threshold in
once
you can use
sel - which(vif(model1)10)
and select values for update possibly by
update(model1,.~. - names(vif(model1))[sel])
or if you want to get rid one by one you can use
vmax - which.max(vif(model1))
and check if max vif value is bigger than 10.
vif(model1)[vmax]=10
If it is just update with
- names(vif(model1))[vmax])
if it is not do not update.
All of this untested.
Cheers
Petr
fun(model1)
but giving error as
Error in if (ss == 1) { :
Re: [R] How to calculate vif of each term of model in R?
Did you follow my advice/comments?
Cheers
Petr
-Original Message-
From: Methekar, Pushpa (GE Transportation, Non-GE)
[mailto:pushpa.methe...@ge.com]
Sent: Friday, April 17, 2015 11:43 AM
To: PIKAL Petr
Subject: RE: How to calculate vif of each term of model in R?
Car package
-Original Message-
From: PIKAL Petr [mailto:petr.pi...@precheza.cz]
Sent: Friday, April 17, 2015 3:11 PM
To: Methekar, Pushpa (GE Transportation, Non-GE); r-help@r-project.org
Subject: RE: How to calculate vif of each term of model in R?
Hi
I did not see any answer so I try.
Your question lacks some info:
Which vif - car or HH?
answers and comments in line
-Original Message-
From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of
Methekar, Pushpa (GE Transportation, Non-GE)
Sent: Wednesday, April 08, 2015 10:24 AM
To: r-help@r-project.org
Subject: [R] How to calculate vif of each term of model in R?
I am beginner in R doing modelling in R, I loaded excel sheet in R, i
have chosen x elements and y elements then fitted model for linear
and
second order regression. Now I have both models. I am bit confused
how
to calculate vif for each term in model like
e.g model1-lm(y1~x1+x2+.x9) when I am using rms package then
it's
giving me like
vif(model1)
x1 x2 x3 x4 x5 x6
x7
6.679692 1.520271 1.667125 3.618439 4.931810 2.073879
13.870630
x8 x9
220.969628 214.034135
now i want to compare each term with std vif as vif=10 and which
will
satisfy this condition i want to delete that term and update model1.
i
have done something like this
fun = function(model1) {
for(i in 1:length(model1)){
v=vif(model1)
ss=any(v[i]=10)
here you select only one item from vif, Why do you use any?
if(ss==1){update(model1,.~.,-v[i])}
else{print(no update)}
Why do you change i here?
i-i+1
}
return(model1)
}
if you want to get rid of all terms bigger than some threshold in once
you can use
sel - which(vif(model1)10)
and select values for update possibly by
update(model1,.~. - names(vif(model1))[sel])
or if you want to get rid one by one you can use
vmax - which.max(vif(model1))
and check if max vif value is bigger than 10.
vif(model1)[vmax]=10
If it is just update with
- names(vif(model1))[vmax])
if it is not do not update.
All of this untested.
Cheers
Petr
fun(model1)
but giving error as
Error in if (ss == 1) { : missing value where TRUE/FALSE needed.
please tell me how do i solve this problem.
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Re: [R] Extracting xml data to data frames
Hi I will re-post using dput to recreate the xml file. I will need some time to find a small enough file that demonstrates the problem. Gavin R. -- View this message in context: http://r.789695.n4.nabble.com/Extracting-xml-data-to-data-frames-tp4705964p4705981.html Sent from the R help mailing list archive at Nabble.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.
[R-es] Integración de R y C#
Hola a todos. Se me está plantendo la posibilidad de empezar a aprender C# para hacer algunos programillas (nada grande). El tema es que el otro día en un mail de esta misma lista alguien (lo siento, no recuerdo quien) puso un link a un post en el que se hablaba de la integración entre R y C#. Por supuesto para llegar a poder hacer esto primero tengo que entender las bases de .NET y C#, pero me gustaría saber si alguno lo habéis utilizado y hasta que punto es posible ejecutar código de R en C# y que limitaciones tiene. Como primer punto me imagino que será necesario tener instalado R en el mismo ordenador que se vaya a ejecutar el programa creado en C#, pero... ¿sería posible crear una aplicación de escritorio que funcione en cualquier PC simplemente teniendo instalado R? Lo mismo estoy preguntando una tontería pero como digo apenas he visto un par de manuales pero ya me lo están preguntando en mi entorno. Muchas gracias a todo [[alternative HTML version deleted]] ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es
[R] issue with package updates
Dear R project members, I have an issue while automatically updating packages. For the packages installed in my second library, while automatically updating I get the following Permission denied” messages(details below). I suppose I know where this problem comes from: I had installed a few different versions of R. And now I have 2 library paths: .libPaths() [1] /Users/iryna/Library/R/3.1/library [2] /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library” And for some reason R just doesn’t have rights to update packages in my second library. Do you know why is that? How should I fix this issue? Here is the error message: * installing *source* package ‘mgcv’ ... ** package ‘mgcv’ successfully unpacked and MD5 sums checked mv: rename /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/00LOCK-mgcv/mgcv: Permission denied Warning in file.copy(f, instdir, TRUE) : problem copying ./NAMESPACE to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/NAMESPACE: Permission denied Warning in file(file, ifelse(append, a, w)) : cannot open file '/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/DESCRIPTION': Permission denied Error in file(file, ifelse(append, a, w)) : cannot open the connection ERROR: installing package DESCRIPTION failed for package ‘mgcv’ * removing ‘/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv’ Here are some additional information on my settings: version _ platform x86_64-apple-darwin13.4.0 arch x86_64 os darwin13.4.0 system x86_64, darwin13.4.0 status major 3 minor 1.2 year 2014 month 10 day31 svn rev66913 language R version.string R version 3.1.2 (2014-10-31) nickname Pumpkin Helmet Thanks in advance for your help, — Iryna Nikolayeva __ 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] Fast multiple match function
Hi Jeff,
Indeed the data.table package does provide a much cleaner way to achieve
the same functionality, and a lot of other functionality as bonus.
Thanks for letting me know about it.
On Tue, 7 Apr 2015 at 15:41 Jeff Newmiller jdnew...@dcn.davis.ca.us wrote:
You might find the data.table package helpful. It uses an index sorted
with a radix sort and minimizes moving the data around in memory.
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On April 7, 2015 1:50:39 PM PDT, Keshav Dhandhania kshav...@gmail.com
wrote:
Hi all,
Thanks for the responses.
Herve's example is a good small size example of what I wanted.
y - c(16, -3, -2, 15, 15, 0, 8, 15, -2)
someCoolFunc(-2, y)
[1] 3 9
someCoolFunc(15, y)
[1] 4 5 8
The requirement is that I want someCoolFunc() to run in O(number of
matches) time, instead of O(size of y).
This is because y is big. And I don't know all the queries I want to
do up-front. And the results of some queries might change the queries
I want to do in the future.
@David: I hope the above description is more clear.
@Enrico, Herve: I want both the functionality provided by one function.
- On repeated calls, fmatch() does give O(1) performance, but it does
not give all matches.
- findMatches() gives all matches, but I need to know the entire
vector x beforehand. I don't have that luxury.
I do have something that works now, using split and fmatch (package
fastmatch). So just posting that in case anyone in the future has the
same problem.
y.unique - unique(y)
# create a map from the unique elements of y to the locations of all
occurrences of the element
y.map - split(1:length(y), match(y, y.unique))
# write a wrapper function that does a look-up on the unique list.
and then returns all matches using the map.
someCoolFunc - function(x) { y.map[[ fmatch(x, y.unique) ]] }
On Tue, 7 Apr 2015 at 13:21 Hervé Pagès hpa...@fredhutch.org wrote:
Hi Keshav,
findMatches() in the S4Vectors/IRanges packages (Bioconductor) I
think
does what you want:
library(IRanges)
y - c(16L, -3L, -2L, 15L, 15L, 0L, 8L, 15L, -2L)
x - c(unique(y), 999L)
hits - findMatches(x, y)
Then:
hits
Hits object with 9 hits and 0 metadata columns:
queryHits subjectHits
integer integer
[1] 1 1
[2] 2 2
[3] 3 3
[4] 3 9
[5] 4 4
[6] 4 5
[7] 4 8
[8] 5 6
[9] 6 7
---
queryLength: 7
subjectLength: 9
The Hits object can be turned into a list with:
as.list(hits)
[[1]]
[1] 1
[[2]]
[1] 2
[[3]]
[1] 3 9
[[4]]
[1] 4 5 8
[[5]]
[1] 6
[[6]]
[1] 7
[[7]]
integer(0)
H.
sessionInfo()
R version 3.2.0 beta (2015-04-05 r68151)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] IRanges_2.1.43 S4Vectors_0.5.22 BiocGenerics_0.13.11
loaded via a namespace (and not attached):
[1] tools_3.2.0
On 04/06/2015 01:56 PM, Keshav Dhandhania wrote:
Hi,
I know that one can find all occurrences of x in a vector v by
doing
which(x == v).
However, if I need to do this again and again, where v is remaining
the
same, then this is quite inefficient. In my particular case, I need
to do
this millions of times, and length(v) = 100 million.
Does anyone have suggestion on how to go about it?
I know of a package called fmatch that does the above for the match
function. But they don't handle multiple matches.
Thanks
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[R] Are '1st decimal' R rollouts (e.g. 3.2.0) qualitatively different?
Hi all, With the upcoming 3.2.0 upgrade, the question came up among my students, how often a regular user who is not a cutting-edge developer must upgrade their R, given that on Windows/Mac this includes the inconvenience of re-installing dozens of packages. In this context, I was wondering whether the annual '1st decimal' upgrade like 3.2.0 is qualitatively different from the interim ones like 3.1.3. In other words, whether some changes are reserved for those annual upgrades, or whether all upgrades are essentially equivalent. Thanks! Assaf -- Assaf P. Oron, Ph.D. Senior Statistician, Children's Core for Biomedical Statistics (206)884-1236, assaf.o...@seattlechildrens.org Consulting statistician, Seattle DEEDS Project http://www.duwamishdiesel.org/ Instructor, UW Certificate for Statistical Analysis with R as...@uw.edu [[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-es] Integración de R y C#
Estimado Pedro Herrero Petisco Creo que yo puse algo, no recuerdo bien pero debe ser https://rdotnet.codeplex.com/ Javier Rubén Marcuzzi El 17 de abril de 2015, 9:20, Pedro Herrero Petisco pedroherreropeti...@gmail.com escribió: Hola a todos. Se me está plantendo la posibilidad de empezar a aprender C# para hacer algunos programillas (nada grande). El tema es que el otro día en un mail de esta misma lista alguien (lo siento, no recuerdo quien) puso un link a un post en el que se hablaba de la integración entre R y C#. Por supuesto para llegar a poder hacer esto primero tengo que entender las bases de .NET y C#, pero me gustaría saber si alguno lo habéis utilizado y hasta que punto es posible ejecutar código de R en C# y que limitaciones tiene. Como primer punto me imagino que será necesario tener instalado R en el mismo ordenador que se vaya a ejecutar el programa creado en C#, pero... ¿sería posible crear una aplicación de escritorio que funcione en cualquier PC simplemente teniendo instalado R? Lo mismo estoy preguntando una tontería pero como digo apenas he visto un par de manuales pero ya me lo están preguntando en mi entorno. Muchas gracias a todo [[alternative HTML version deleted]] ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es [[alternative HTML version deleted]] ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es
Re: [R] R: Redefine default parameter values for help.start()
Martin Maechler maechler at lynne.stat.math.ethz.ch writes:
paul paul.domaskis at gmail.com
on Thu, 16 Apr 2015 18:58:12 + writes:
Because of the setup of R in cygwin, help.start() requires
the following parameter values:
help.start(browser=cygstart,remote=R.home())
Is it possible to make these values the default?
You are building R from the sources, right?
No. I haven't compiled code in a decade, but maybe I should get
back into that. It won't happen soon, though -- the situation is
that the current cygwin install can't be changed, so installing isn't
an option, at least in the immediate term. Also, expectations in
terms of time is such that getting a Windows based R would be
preferrable over compiling from scratch, though I must admit that
the latter won't happen any time soon either.
Then, of course it is easily possible: Just modify your version
of the R source code appropriately:
It is file R/src/library/utils/R/help.start.R
(And you need more changes anyway to make things work under Cygwin;
but don't ask me about it: I do run R on Windows only very rarely)
OK, so now I'm not sure I follow. By source, I normally think C. But
the file extension above is *.R. So I tried to take a look at the
file to see what kind of source it is. I can only descend down to
/usr/lib/R/library/utils/R/utils because
/usr/lib/R/library/utils/R/utils is not a directory. It is a file:
# File share/R/nspackloader.R
# Part of the R package, http://www.R-project.org
#
# Copyright (C) 1995-2012 The R Core Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
local({
info - loadingNamespaceInfo()
pkg - info$pkgname
ns - .getNamespace(as.name(pkg))
if (is.null(ns))
stop(cannot find namespace environment for , pkg, domain = NA);
dbbase - file.path(info$libname, pkg, R, pkg)
lazyLoad(dbbase, ns, filter = function(n) n != .__NAMESPACE__.)
})
I know that I have a lot to learn about R.
Anyway, for now, I am getting around the problem via the following
~/.Rprofile:
options(papersize=letter)
options(browser=cygstart)
options(help_type=html)
helpstart - function(){help.start(browser=cygstart,remote=R.home())}
require(astsa)
I do not want cygstart to be the browser except as a
parameter for help.start().
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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.
[R] R: Idea behind .First() vs. ~/.Rprofile
I'm ramping up on R, and reading http://stuff.mit.edu/afs/sipb/project/r- project/lib/R/library/base/html/Startup.html. I'm probably wrong about this, but ~/.Rprofile seems to serve the same purpose as a .First() function. Why do both exist, and what considerations go into a decision to choose one over the other for startup 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.
[R] vi[m] editing of past commands in R command line
I've been told that my messages are being rejected because it is being posted via nabble in HTML format. I was advised to re-send this directly to r-help@r-project.org. My apologies if you get this twice. When I use bash + readline and ~/.inputrc contains editing-mode vi, I can press v to switch to from the command line editing to a full vi session editing of a command. This doesn't seem to happen in R. Is there a configuration setting/file that I can set to get this behaviour? Furthermore, when using bash, the fc command allows me to edit the history of commands, and when I exit the editor, all the remaining (and likely modified) commands are submitted to the bash shell as if I typed them at the prompt. Is there a way to get similar functionality in R? __ 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] Need online version of R help pages
Hi Paul a quick search popped up these: http://astrostatistics.psu.edu/datasets/R/html/index.html http://finzi.psych.upenn.edu/ http://r.789695.n4.nabble.com/Online-R-documentation-td1009656.html Are they what you are looking for? Collin. On Thu, Apr 16, 2015 at 5:02 PM, paul paul.domas...@gmail.com wrote: The help for the cygwin port of R is buggy and hides random lines of text. Consquently, I've been relying on Google, but it is often not clear how directly relevant the info is for the specific command that I'm using. For example, reshape is complicated, and has more than 1 version. Is there an online version of the help pages? I tried looking for html versions of the help pages by ferruting through the R.home() subtree. Haven't found them so far. There are package pages in subdirectories package/html/00Index.html, but they just contain links to html files that don't reside in my R.home() subtree. There are also subdirectories package/help, but they contain pages that I don't recognize (*.rds, *.rdb, *.rdx). Getting desparate here, and realizing how the web is not in any way a substituted for locally available help pages that you can be confident is right for your installation. __ 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] Need online version of R help pages
On Fri, Apr 17, 2015 at 3:22 PM, Collin Lynch cfly...@ncsu.edu wrote: Hi Paul a quick search popped up these: http://astrostatistics.psu.edu/datasets/R/html/index.html http://finzi.psych.upenn.edu/ http://r.789695.n4.nabble.com/Online-R-documentation-td1009656.html Are they what you are looking for? Collin. I was looking for a site where I could simply punch in the command and get the man page without navigating searching. But I found a way around my problem with the help in Cygwin's R port. In ~/.Rprofile, I have: options(browser=cygstart) options(help_type=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.
[R] project.org help mailing list the same as ethz.ch mailing list?
The page http://www.r-project.org/mail.html says that the mailing list is r-help_AT_R-project.org (with @ in place of _AT_), but the gmane page http://gmane.org/list-address.php?group=gmane.comp.lang.r.general has the mailing list as r-help_AT_stat.math.ethz.ch. Are these different mailing lists? __ 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] R: Idea behind .First() vs. ~/.Rprofile
Hi, On Thursday, April 16, 2015, paul paul.domas...@gmail.com wrote: I'm ramping up on R, and reading http://stuff.mit.edu/afs/sipb/project/r- project/lib/R/library/base/html/Startup.html. I'm probably wrong about this, but ~/.Rprofile seems to serve the same purpose as a .First() function. Why do both exist, and what considerations go into a decision to choose one over the other for startup code? It's the timing and where the info comes from, as that document explains in great detail. .Rprofile is read on start-up unless R is specifically told to skip it. .First() is sourced after it's loaded, and thus must be loaded from somewhere such as an existing .RData file or a package. ~/.Rprofile is thus most convenient for things you want to have happen in every R session, while .First() is useful for specific sessions loaded from saved objects, or for constructing packages. Though on linux, I use a local .Rprofile if I need per-session options, because I often don't have a saved .RData file. Sarah -- Sarah Goslee http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org [[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] R: Redefine default parameter values for help.start()
Martin Maechler maechler at lynne.stat.math.ethz.ch writes:
paul paul.domaskis at gmail.com
on Thu, 16 Apr 2015 18:58:12 + writes:
Because of the setup of R in cygwin, help.start() requires
the following parameter values:
help.start(browser=cygstart,remote=R.home())
Is it possible to make these values the default?
You are building R from the sources, right?
No. I haven't compiled code in a decade, but maybe I should get
back into that. It won't happen soon, though -- the situation is
that the current cygwin install can't be changed, so installing isn't
an option, at least in the immediate term. Also, expectations in
terms of time is such that getting a Windows based R would be
preferrable over compiling from scratch, though I must admit that
the latter won't happen any time soon either.
Then, of course it is easily possible: Just modify your version
of the R source code appropriately:
It is file R/src/library/utils/R/help.start.R
(And you need more changes anyway to make things work under Cygwin;
but don't ask me about it: I do run R on Windows only very rarely)
OK, so now I'm not sure I follow. By source, I normally think C. But
the file extension above is *.R. So I tried to take a look at the
file to see what kind of source it is. I can only descend down to
/usr/lib/R/library/utils/R/utils because
/usr/lib/R/library/utils/R/utils is not a directory. It is a file:
# File share/R/nspackloader.R
# Part of the R package, http://www.R-project.org
#
# Copyright (C) 1995-2012 The R Core Team
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# A copy of the GNU General Public License is available at
# http://www.r-project.org/Licenses/
local({
info - loadingNamespaceInfo()
pkg - info$pkgname
ns - .getNamespace(as.name(pkg))
if (is.null(ns))
stop(cannot find namespace environment for , pkg, domain = NA);
dbbase - file.path(info$libname, pkg, R, pkg)
lazyLoad(dbbase, ns, filter = function(n) n != .__NAMESPACE__.)
})
I know that I have a lot to learn about R.
Anyway, for now, I am getting around the problem via the following
~/.Rprofile:
options(papersize=letter)
options(browser=cygstart)
options(help_type=html)
helpstart - function(){help.start(browser=cygstart,remote=R.home())}
require(astsa)
I do not want cygstart to be the browser except as a
parameter for help.start().
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and provide commented, minimal, self-contained, reproducible code.
[R] Need online version of R help pages
The help for the cygwin port of R is buggy and hides random lines of text. Consquently, I've been relying on Google, but it is often not clear how directly relevant the info is for the specific command that I'm using. For example, reshape is complicated, and has more than 1 version. Is there an online version of the help pages? I tried looking for html versions of the help pages by ferruting through the R.home() subtree. Haven't found them so far. There are package pages in subdirectories package/html/00Index.html, but they just contain links to html files that don't reside in my R.home() subtree. There are also subdirectories package/help, but they contain pages that I don't recognize (*.rds, *.rdb, *.rdx). Getting desparate here, and realizing how the web is not in any way a substituted for locally available help pages that you can be confident is right for your installation. __ 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] project.org help mailing list the same as ethz.ch mailing list?
On Friday, April 17, 2015, Paul Domaskis paul.domas...@gmail.com wrote: The page http://www.r-project.org/mail.html says that the mailing list is r-help_AT_R-project.org (with @ in place of _AT_), but the gmane page http://gmane.org/list-address.php?group=gmane.comp.lang.r.general has the mailing list as r-help_AT_stat.math.ethz.ch. Are these different mailing lists? They are the same. r-help@r-project.org is the preferred address, but the mailserver is run out of stat.ethz.ch. Sarah Useful info __ R-help@r-project.org javascript:; 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 http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org [[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] R: Idea behind .First() vs. ~/.Rprofile
Sarah Goslee sarah.goslee at gmail.com writes: |On Thursday, April 16, 2015, paul paul.domaskis at gmail.com |wrote: | I'm ramping up on R, and reading | http://stuff.mit.edu/afs/sipb/project/r- | project/lib/R/library/base/html/Startup.html. I'm probably wrong | about this, but ~/.Rprofile seems to serve the same purpose as a | .First() function. Why do both exist, and what considerations go | into a decision to choose one over the other for startup code? | | It's the timing and where the info comes from, as that document | explains in great detail. | | .Rprofile is read on start-up unless R is specifically told to skip | it. | | .First() is sourced after it's loaded, and thus must be loaded from | somewhere such as an existing .RData file or a package. | | ~/.Rprofile is thus most convenient for things you want to have | happen in every R session, while .First() is useful for specific | sessions loaded from saved objects, or for constructing packages. | Though on linux, I use a local .Rprofile if I need per-session | options, because I often don't have a saved .RData file. Thanks, Sarah. Yes, the documentation has a great deal of detail, but I needed was your explanation in the final paragraph of your response. __ 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] project.org help mailing list the same as ethz.ch mailing list?
Sarah Goslee sarah.goslee at gmail.com writes: On Friday, April 17, 2015, Paul Domaskis paul.domaskis at gmail.com wrote: The page http://www.r-project.org/mail.html says that the mailing list is r-help_AT_R-project.org (with at in place of _AT_), but the gmane page http://gmane.org/list-address.php?group=gmane.comp.lang.r.general has the mailing list as r-help_AT_stat.math.ethz.ch. Are these different mailing lists? They are the same. r-help at r-project.org is the preferred address, but the mailserver is run out of stat.ethz.ch. Thanks again, Sarah. Imagine my shock when that suspicion dawned on me. I expected to be banned for life for duplicate posts. __ 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] Handling NA values in a if statement
On Apr 17, 2015, at 5:23 PM, Luigi Marongiu marongiu.lu...@gmail.com wrote:
Dear all,
I have a vector with a certain range of values including infinity and
NA. I would like to remove the values that are outside a given range
(lower level = ll and upper level = ul) but I am getting the error due
to the NA values (missing value where TRUE/FALSE needed). I then
included the !is.na() but now the resulting error is all NA, as in the
example.
In addition, here I have implemented a for loop to scan all the
elements of the vector, but I should be able to use the sapply();
however I don't know how to send the ll and ul arguments to sapply().
Could you please help?
best regards
Luigi
EXAMPLE
x - c(-Inf, Inf,NA,5.9,6.08,5281391136138.75,
4.35,4.79,
9474097322.96,3.64,16.42,-12211.11,4.37,
-1097.79,4.78,
3.71,32.59,4.01,35.36,3.17,1.61,
-3678.28,2.9,4.67,
4.1,348410866.78,5.35,4.3101519459837E+016,
1467030866.75,
1.10376094956278E+018,32.55,1.17,5339028670388.94,
34.14,
33205967009.57,4.42,1.76,7.08,-8428.84,
-113491.08,17.81)
ll - 1
ul - 45
clipper - function(x, ll, ul) {
for(i in 1:length(x)) {
if(x[i] ll) {
x[i] - NA
} else if(x[i] ul) {
x[i] - NA
} else {
x[i] - x[i]
}
}
return(x)
}
(X-clipper(x, ll, ul))
missing value where TRUE/FALSE needed
clipper - function(x, ll, ul) {
for(i in 1:length(x)) {
if(!is.na(x[i]) ll) {
x[i] - NA
} else if(!is.na(x[i]) ul) {
x[i] - NA
} else {
x[i] - x[i]
}
}
return(x)
}
(X-clipper(x, ll, ul))
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA
[28] NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Hi,
Something along the lines of:
subset(x, is.finite(x) (x ll) (x ul))
[1] 5.90 6.08 4.35 4.79 3.64 16.42 4.37 4.78 3.71 32.59 4.01
[12] 35.36 3.17 1.61 2.90 4.67 4.10 5.35 32.55 1.17 34.14 4.42
[23] 1.76 7.08 17.81
or:
x[is.finite(x) (x ll) (x ul)]
[1] 5.90 6.08 4.35 4.79 3.64 16.42 4.37 4.78 3.71 32.59 4.01
[12] 35.36 3.17 1.61 2.90 4.67 4.10 5.35 32.55 1.17 34.14 4.42
[23] 1.76 7.08 17.81
See ?subset and ?is.finite:
is.finite(x)
[1] FALSE FALSE FALSE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[12] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[23] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[34] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
Regards,
Marc Schwartz
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[R] Smart detection of wrap width?
I suspect that the answer is no, but just in case, is there a way to have R detect the window width and wrap accordingly? I don't want to set an option every time I dock a window or shrink it. In my ideal paradise, R would not only format output according to window width, but it would also me to specify a virtual window width. So if I specify a virtual window width of 200 characters, and the actual window width is 100, then the output has a carriage return at the 200 character mark but I only see the 1st 100 characters of each line of text (the rest being truncated from view). And of course, the user would be able to specify when the virtual width mirrors the actual window width. I know that this is dreaming in technicolour (which is not that fantastical these days), but I would be pleasantly surprised if there was a way to simply have the output wrap according to the actual window width. __ 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] Handling NA values in a if statement
Dear all,
I have a vector with a certain range of values including infinity and
NA. I would like to remove the values that are outside a given range
(lower level = ll and upper level = ul) but I am getting the error due
to the NA values (missing value where TRUE/FALSE needed). I then
included the !is.na() but now the resulting error is all NA, as in the
example.
In addition, here I have implemented a for loop to scan all the
elements of the vector, but I should be able to use the sapply();
however I don't know how to send the ll and ul arguments to sapply().
Could you please help?
best regards
Luigi
EXAMPLE
x - c(-Inf, Inf,NA,5.9,6.08,5281391136138.75,
4.35,4.79,
9474097322.96,3.64,16.42,-12211.11,4.37,
-1097.79,4.78,
3.71,32.59,4.01,35.36,3.17,1.61,
-3678.28,2.9,4.67,
4.1,348410866.78,5.35,4.3101519459837E+016,
1467030866.75,
1.10376094956278E+018,32.55,1.17,5339028670388.94,
34.14,
33205967009.57,4.42,1.76,7.08,-8428.84,
-113491.08,17.81)
ll - 1
ul - 45
clipper - function(x, ll, ul) {
for(i in 1:length(x)) {
if(x[i] ll) {
x[i] - NA
} else if(x[i] ul) {
x[i] - NA
} else {
x[i] - x[i]
}
}
return(x)
}
(X-clipper(x, ll, ul))
missing value where TRUE/FALSE needed
clipper - function(x, ll, ul) {
for(i in 1:length(x)) {
if(!is.na(x[i]) ll) {
x[i] - NA
} else if(!is.na(x[i]) ul) {
x[i] - NA
} else {
x[i] - x[i]
}
}
return(x)
}
(X-clipper(x, ll, ul))
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
NA NA NA NA NA
[28] NA NA NA NA NA NA NA NA NA NA NA NA NA NA
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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.
Re: [R] Smart detection of wrap width?
A lot of this depends on what context you are running R in, e.g., Windows
console, Mac console, or command line in a unix-alike. Or within ESS in
emacs. Those are different interfaces supported by, to some extent,
different people, and are based on the underlying capabilities provided by
the operating system.
Have you yet encountered
options()$width
?
For example,
options(width=100)
will cause wrapping at 100, at least for certain kinds of output.
In an xterm shell running in an X windows context, I frequently use
setwid - function ()
{
if (!interactive())
return(invisible(NULL))
scon - pipe(stty -a)
stty - scan(scon, what = , sep = ;, quiet = T)
close(scon)
cstr - stty[grep(columns, stty)]
options(width = as.numeric(gsub([^0-9], , cstr, ignore.case = T)))
paste(width =, options()$width, \n)
}
A function I wrote that resets the width option to match the window
widths, and therefore adjusts the wrapping after I resize a windwo.
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 4/17/15, 3:52 PM, paul paul.domas...@gmail.com wrote:
I suspect that the answer is no, but just in case, is there a way to
have R detect the window width and wrap accordingly? I don't want to
set an option every time I dock a window or shrink it.
In my ideal paradise, R would not only format output according to
window width, but it would also me to specify a virtual window width.
So if I specify a virtual window width of 200 characters, and the
actual window width is 100, then the output has a carriage return at
the 200 character mark but I only see the 1st 100 characters of each
line of text (the rest being truncated from view). And of course, the
user would be able to specify when the virtual width mirrors the
actual window width.
I know that this is dreaming in technicolour (which is not that
fantastical these days), but I would be pleasantly surprised if there
was a way to simply have the output wrap according to the actual
window width.
__
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.
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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.
[R] Programming R to avoid loops
I have two large data frames with the following structure:
df1
id date test1.result
1 a 2009-08-28 1
2 a 2009-09-16 1
3 b 2008-08-06 0
4 c 2012-02-02 1
5 c 2010-08-03 1
6 c 2012-08-02 0
df2
id date test2.result
1 a 2011-02-03 1
2 b 2011-09-27 0
3 b 2011-09-01 1
4 c 2009-07-16 0
5 c 2009-04-15 0
6 c 2010-08-10 1
I need to match items in df2 to those in df1 with specific matching criteria. I
have written a looped matching algorithm that works, but it is very slow with
my large datasets. I am requesting help on making a version of this code that
is faster and “vectorized so to speak.
My algorithm is currently something like this code. It works but is damn slow.
findTestPairs - function(test1, id1, date1, test2, id2, date2, predays=-30,
lagdays=30){
# Function to find, within subjects, two tests that occur with a timeframe
#
# test1 = the reference test result for which matching second tests are sought
# test2 = the second test result
# date1 = the date of test1
# date2 = the date of test2
# id1 = unique identifier for subject undergoing test 1
# id2 = unique identifier for subject undergoing test 2
# predays = maximum number of days prior to test1 date that test2 date might
occur
# lagdays = maximum number of days after test1 date that test2 date might
occur
result - data.frame(matrix(ncol=5, nrow=length(test1)))
colnames(result) - c('id','test1','date','test2count',’test2lag.result')
result$id- id1
result$test1 - test1
result$date - date1
for(i in 1:length(test1)){
l - 0# Counter of test2 results that matches test1 within lag interval
m - NA # Indicator of positive test2 within lag interval
for(j in 1:length(test2)){
if(id1[i] == id2[j]){ # STEP1: Match IDs
interval - date2[j] - date1[i]
intmatch - ifelse(interval = predays interval = lagdays, 1, 0)
if(intmatch == 1){# STEP2: Does test2 fall within lag
interval?
l - l+1# If test2 within lag interval, count
it
if(test2[j] == 1) { # STEP3: Is test 2 positive?
m - 1# If test2 is positive, set indicator
to 1
} else {
m - 0
}
}
}
}
result$test2count[i] - l
result$test2lag.result[i] - m
}
return(result)
}
I would appreciate help on building a faster matching algorithm. I am pretty
certain that R functions can be used to do this but I do not have a good grasp
of how to make it work.
Brant Inman
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] assign variables to function output
I don't disagree with the other answers, but I'd like to talk about what I
see as a more underlying issue.
Generally speaking, functions return the value of the last expression
within them.
myfun - function(x) {
z - sqrt(x)
2
}
Then
y - myfun(7)
assigns 2 to y because 2 was the last expression in the function.
myfun - function(z) {
cat('inside myfun\n')
y - z-7
x - 2*z
sqrt(z)
}
y - myfun(c(1,4,9))
assigns c(1,2,3) to y because sqrt(z) was the last expression. x and y are
lost and gone forever.
Note that return() was not used, and does not need to be used.
Thus, if you want to return something that includes some of the variables
introduced inside the function, you gather them into a suitable structure
and make that the last expression in the function.
myfun - function(z) {
y - z-7
x - 2*z
list(x=x, y=y, rtz=sqrt(z))
}
Then y - myfun(4) returns a list with three elements whose values are -3,
8, and 2.
Again no use of return(). There are cases where return() is useful, but it
is not needed in simple cases like these.
(and I can't imagine what's awkward about using return(value), but that's
another question)
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 4/15/15, 3:17 PM, merm pione...@student.unimelb.edu.au wrote:
Hi!
So I'm trying as the header suggests to assign the value(s) output by a
function to a variable, say 'y'
Problem is from what I gather any variables introduced within the function
are contained and the only output I can get is return(value) which is
awkward to work with. Any suggestions?
Cheers!
--
View this message in context:
http://r.789695.n4.nabble.com/assign-variables-to-function-output-tp470592
0.html
Sent from the R help mailing list archive at Nabble.com.
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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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] lag1.plot {astsa} vs. lag.plot {stats}
I'm following http://www.stat.pitt.edu/stoffer/tsa3/R_toot.htm to ramp up on both time series and R. About 40% of the way down, the tutorial uses lag1.plot from astsa and lag.plot from stats. The positioning of the dots look different between the two. Nothing jumps out at me from the help pages that explains why they would be different. Can anyone confirm this difference, and hopefully suggest explanations? __ 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] lag1.plot {astsa} vs. lag.plot {stats}
Not certain which plot you are looking at, but my guess is the answer is contained somewhere here: http://www.stat.pitt.edu/stoffer/tsa3/Rissues.htm in particular perhaps issues 4-5. -Roy M. On Apr 17, 2015, at 7:30 PM, Paul Domaskis paul.domas...@gmail.com wrote: I'm following http://www.stat.pitt.edu/stoffer/tsa3/R_toot.htm to ramp up on both time series and R. About 40% of the way down, the tutorial uses lag1.plot from astsa and lag.plot from stats. The positioning of the dots look different between the two. Nothing jumps out at me from the help pages that explains why they would be different. Can anyone confirm this difference, and hopefully suggest explanations? __ 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. ** The contents of this message do not reflect any position of the U.S. Government or NOAA. ** Roy Mendelssohn Supervisory Operations Research Analyst NOAA/NMFS Environmental Research Division Southwest Fisheries Science Center ***Note new address and phone*** 110 Shaffer Road Santa Cruz, CA 95060 Phone: (831)-420-3666 Fax: (831) 420-3980 e-mail: roy.mendelss...@noaa.gov www: http://www.pfeg.noaa.gov/ Old age and treachery will overcome youth and skill. From those who have been given much, much will be expected the arc of the moral universe is long, but it bends toward justice -MLK Jr. __ 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] Smart detection of wrap width?
Yes, I found the width option in the help pages, but I was wondering
if there was automatic setting of the wrapping according to the
current window width.
Your function works exactly as I wished. I'll probably get smarter
with time (I hope) but would it be reasonably good practice to stick
this into ~/.Rprofile? I don't suppose there is a way to have it
automatically invoked when the window size/positition changes? (It's
still priceless even without automatic triggering).
On Fri, Apr 17, 2015 at 7:20 PM, MacQueen, Don macque...@llnl.gov
wrote:
A lot of this depends on what context you are running R in, e.g.,
Windows console, Mac console, or command line in a unix-alike. Or
within ESS in emacs. Those are different interfaces supported by, to
some extent, different people, and are based on the underlying
capabilities provided by the operating system.
Have you yet encountered
options()$width
?
For example,
options(width=100)
will cause wrapping at 100, at least for certain kinds of output.
In an xterm shell running in an X windows context, I frequently use
setwid - function ()
{
if (!interactive())
return(invisible(NULL))
scon - pipe(stty -a)
stty - scan(scon, what = , sep = ;, quiet = T)
close(scon)
cstr - stty[grep(columns, stty)]
options(width = as.numeric(gsub([^0-9], , cstr, ignore.case = T)))
paste(width =, options()$width, \n)
}
A function I wrote that resets the width option to match the window
widths, and therefore adjusts the wrapping after I resize a windwo.
__
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] Need online version of R help pages
On 16/04/2015 5:02 PM, paul wrote: The help for the cygwin port of R is buggy and hides random lines of text. You've already been told not to use the Cygwin port. It's buggy in the help pages, and probably in many other respects as well. It doesn't pass the R self-tests. Don't use it. Duncan Murdoch Consquently, I've been relying on Google, but it is often not clear how directly relevant the info is for the specific command that I'm using. For example, reshape is complicated, and has more than 1 version. Is there an online version of the help pages? I tried looking for html versions of the help pages by ferruting through the R.home() subtree. Haven't found them so far. There are package pages in subdirectories package/html/00Index.html, but they just contain links to html files that don't reside in my R.home() subtree. There are also subdirectories package/help, but they contain pages that I don't recognize (*.rds, *.rdb, *.rdx). Getting desparate here, and realizing how the web is not in any way a substituted for locally available help pages that you can be confident is right for your installation. __ 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] Need online version of R help pages
With all due respect, Duncan, I can't find the message advising against using the Cygwin port. I did find a message about the mishandling of line endings, and I've asked on the cygwin forum (as advised). As I mentioned, I'm in an environment where updates are not possible, and I'm clarifying now that this means installations are even more impossible, at least not without extensive adminstrative delay. Basically, this is what I have to work with. If anyone can suggest good ideas for the challenges as-is, that would be much appreciated. However, given your posts, I fully understand if the answer is no. On the other hand, simply demanding a solution consisting of a course of action which is impossible at present...well, it's just impossible. Having said that, I'll just say that I've managed to exort the powers that be to install a Windows based version of R, but I have to work with what I currently have for at least a week. I should also mention that I've submitted an update to the mailing list on a workaround for the R help problem on cygwin. It might not have propagated to recipients yet. I appreciate the further info on the extent of the bugginess of the cygwin port. On Fri, Apr 17, 2015 at 9:04 PM, Duncan Murdoch murdoch.dun...@gmail.com wrote: On 16/04/2015 5:02 PM, paul wrote: The help for the cygwin port of R is buggy and hides random lines of text. You've already been told not to use the Cygwin port. It's buggy in the help pages, and probably in many other respects as well. It doesn't pass the R self-tests. Don't use it. Consquently, I've been relying on Google, but it is often not clear how directly relevant the info is for the specific command that I'm using. For example, reshape is complicated, and has more than 1 version. Is there an online version of the help pages? I tried looking for html versions of the help pages by ferruting through the R.home() subtree. Haven't found them so far. There are package pages in subdirectories package/html/00Index.html, but they just contain links to html files that don't reside in my R.home() subtree. There are also subdirectories package/help, but they contain pages that I don't recognize (*.rds, *.rdb, *.rdx). Getting desparate here, and realizing how the web is not in any way a substituted for locally available help pages that you can be confident is right for your installation. __ 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] issue with package updates
Hi Iryna, The two paths seem to be a user path (one beneath your home directory) and a system path (one in another branch of the directory tree). You usually have to have superuser privileges to write files in the second. In most *NIX systems you use su to become root (the superuser), and if you can do this, then perform the update. Jim On Fri, Apr 17, 2015 at 7:25 PM, Iryna Nikolayeva iryna.v.nikolay...@gmail.com wrote: Dear R project members, I have an issue while automatically updating packages. For the packages installed in my second library, while automatically updating I get the following Permission denied” messages(details below). I suppose I know where this problem comes from: I had installed a few different versions of R. And now I have 2 library paths: .libPaths() [1] /Users/iryna/Library/R/3.1/library [2] /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library” And for some reason R just doesn’t have rights to update packages in my second library. Do you know why is that? How should I fix this issue? Here is the error message: * installing *source* package ‘mgcv’ ... ** package ‘mgcv’ successfully unpacked and MD5 sums checked mv: rename /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/00LOCK-mgcv/mgcv: Permission denied Warning in file.copy(f, instdir, TRUE) : problem copying ./NAMESPACE to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/NAMESPACE: Permission denied Warning in file(file, ifelse(append, a, w)) : cannot open file '/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/DESCRIPTION': Permission denied Error in file(file, ifelse(append, a, w)) : cannot open the connection ERROR: installing package DESCRIPTION failed for package ‘mgcv’ * removing ‘/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv’ Here are some additional information on my settings: version _ platform x86_64-apple-darwin13.4.0 arch x86_64 os darwin13.4.0 system x86_64, darwin13.4.0 status major 3 minor 1.2 year 2014 month 10 day31 svn rev66913 language R version.string R version 3.1.2 (2014-10-31) nickname Pumpkin Helmet Thanks in advance for your help, — Iryna Nikolayeva __ 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] Are '1st decimal' R rollouts (e.g. 3.2.0) qualitatively different?
On 17/04/2015 11:50 AM, Assaf P. Oron wrote: Hi all, With the upcoming 3.2.0 upgrade, the question came up among my students, how often a regular user who is not a cutting-edge developer must upgrade their R, given that on Windows/Mac this includes the inconvenience of re-installing dozens of packages. In this context, I was wondering whether the annual '1st decimal' upgrade like 3.2.0 is qualitatively different from the interim ones like 3.1.3. In other words, whether some changes are reserved for those annual upgrades, or whether all upgrades are essentially equivalent. In an x.y.z upgrade, our policy is that a change to z should not break any well-behaved code, but a change to y or x might do so. In the case of 3.2.0, I don't know of anything that is broken relative to 3.1.3, but there are probably a few obscure things. Changes to z are almost always a good idea to adopt. They shouldn't break anything that isn't taking advantage of bugs, but should fix bugs. So I would say regular users should *always* adopt changes where z becomes a value greater than 0. The question of z=0 is harder. There are likely to be changes in x.y.0 which are not as well tested as those in other versions. However, R is an open source project. You aren't paying anything for using it. The reason it works so well is because so many people use it, and report bugs. If you choose not to use a z=0 version, you are essentially stealing the effort of the rest of the community who contribute to testing and development. You are also making the z=1 version worse, by not reporting bugs in the z=0 version. In the particular case of 3.2.0, there are not a lot of new changes, so probably not a lot of new bugs, and you may well be better off from a reliability point of view using it instead of 3.1.3. This isn't always true, so you should pay attention to the news about changes in the new version, and make your decision based on your own circumstances. Duncan Murdoch __ 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] issue with package updates
See below. On 18/04/15 12:04, Jim Lemon wrote: Hi Iryna, The two paths seem to be a user path (one beneath your home directory) and a system path (one in another branch of the directory tree). You usually have to have superuser privileges to write files in the second. In most *NIX systems you use su to become root (the superuser), and if you can do this, then perform the update. Jim: (1) The OP seems to be using a Mac OSX system (which has Unix underlying a great deal of gloppedy obfuscating point-and-click crap). (2) My reading of the help for install.packages() leads me to believe that by default the requested package should be installed into the *first* entry of .libPaths(), whence no superuser privileges should be required. It is mysterious to me why the system seems to be intent on using the *second* entry of .libPaths() so that superuser privileges *are* required. (3) Since this is Mac OSX stuff, the OP might get better mileage by posting on R-Sig-Mac. cheers, Rolf Jim On Fri, Apr 17, 2015 at 7:25 PM, Iryna Nikolayeva iryna.v.nikolay...@gmail.com wrote: Dear R project members, I have an issue while automatically updating packages. For the packages installed in my second library, while automatically updating I get the following Permission denied” messages(details below). I suppose I know where this problem comes from: I had installed a few different versions of R. And now I have 2 library paths: .libPaths() [1] /Users/iryna/Library/R/3.1/library [2] /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library” And for some reason R just doesn’t have rights to update packages in my second library. Do you know why is that? How should I fix this issue? Here is the error message: * installing *source* package ‘mgcv’ ... ** package ‘mgcv’ successfully unpacked and MD5 sums checked mv: rename /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/00LOCK-mgcv/mgcv: Permission denied Warning in file.copy(f, instdir, TRUE) : problem copying ./NAMESPACE to /opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/NAMESPACE: Permission denied Warning in file(file, ifelse(append, a, w)) : cannot open file '/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv/DESCRIPTION': Permission denied Error in file(file, ifelse(append, a, w)) : cannot open the connection ERROR: installing package DESCRIPTION failed for package ‘mgcv’ * removing ‘/opt/local/Library/Frameworks/R.framework/Versions/3.1/Resources/library/mgcv’ Here are some additional information on my settings: version _ platform x86_64-apple-darwin13.4.0 arch x86_64 os darwin13.4.0 system x86_64, darwin13.4.0 status major 3 minor 1.2 year 2014 month 10 day31 svn rev66913 language R version.string R version 3.1.2 (2014-10-31) nickname Pumpkin Helmet Thanks in advance for your help, — Iryna Nikolayeva -- Rolf Turner Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 Home phone: +64-9-480-4619 __ 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.
