Re: [R] An error in the Package JGL
Please do not multiple-post. What did the maintainer say when you asked him (see the posting guide)? On 16/07/2013 05:36, Azam Peyvand wrote: I am currently working with the package JGL. I tried to run JGL function JGL(Y,penalty=fused,...) over my data, but there is the following error which makes it stop: Error in while ((iter==0)|| (iter maxiter diff_valuetol)) missing value where TRUE/FALSE needed. Any special idea for fixing such error? [[alternative HTML version deleted]] The posting guide asked you not to send HTML. __ R-help@r-project.org mailing list 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. We don't have anything reproducible here. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list 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] Serialize data.frame to database
Hi Jeff, I think you are more right than me. I have not much experience with R-specific objects and Databases. I just know, that for languages like Java, C, etc. this process is a usual one for storing for example matrices (in case of course that I do not have to access specific elements inside of the matrix but only the matrix as a whole). Thank you for the tip with the R-sig-DB list. I switch over to this list. Best Simon On Jul 16, 2013, at 2:34 AM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: I could be wrong, but I would guess that doing what you are describing is very unusual. Most of the time the data frame is mapped to a table in the database so the rows can be searched. Storing data frames as BLOBs really seems odd. Note that there is an R-sig-db mailing list for questions of this type. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Simon Zehnder szehn...@uni-bonn.de wrote: Dear R-Users, I need a very fast and reliable database solution so I try to serialize a data.frame (to binary data) and to store this data to an SQLite database. This is what I tried to do: library(RSQLite) con - dbDriver(SQLite) db - dbConnect(con, test) dbSendQuery(db, 'CREATE TABLE frames(simID INT, data BLOB)') data.bin - serialize(iris, NULL, ascii = FALSE) dbSendQuery(db, paste(INSERT INTO frames VALUES(1, X', data.bin, '), sep = )) data.bin2 - dbGetQuery(db, SELECT DATA FROM frames WHERE simID = 1) data.bin2 data 1 58 So, only the first entry of data.bin is saved to the database. I tried to first convert the binary data to raw data: data.raw - rawToChar(data.bin) Error in rawToChar(data.bin) : embedded nul in string: 'X\n\0\0\0\002\0\003\0\001\0\002\003\0\0\0\003\023\0\0\0\005\0\0\0\016\0\0\0\x96@\024ff@\023\x99\x99\x99\x99\x99\x9a@\022\xcc\xcc\xcc\xcc\xcc\xcd@\022ff@\024\0\0\0\0\0\0@\025\x99\x99\x99\x99\x99\x9a@\022ff@\024\0\0\0\0\0\0@\021\x99\x99\x99\x99\x99\x9a@\023\x99\x99\x99\x99\x99\x9a@\025\x99\x99\x99\x99\x99\x9a@\02333@\02333@\02133@\02733@\026\xcc\xcc\xcc\xcc\xcc\xcd@\025\x99\x99\x99\x99\x99\x9a@\024ff@\026\xcc\xcc\xcc\xcc\xcc\xcd@\024ff@\025\x99\x99\x99\x99\x99\x9a@\024ff@\022ff@\024ff@\02333@\024\0\0\0\0\0\0@\024\0\0\0\0\0\0@\024\xcc\xcc\xcc\xcc\xcc\xcd@\024\xcc\xcc\xcc\xcc\xcc\xcd@\022\xcc\xcc\xcc\xcc\xcc\xcd@\02333@\025\x99\x99\x99\x99\x99\x9a@\024\xcc\xcc\xcc\xcc\xcc\xcd@\026\0\0\0\0\0\0@\023\x99\x99\x99\x99\x99\x9a@\024\0\0\0\0\0\0@\026\0\0\0\0\0\0@\023\x99\x99\x99\x99\x99\x9a@\021\x99\x99\x99\x99\x99\x9a@\024ff@\024\0\0\0\0\0\0@\022\0\0\0\0\0\0@\021\x99\x99\x99\x99\x99\x9a@\024\0\0\0\0\! 0\0 I don't know what this error should tell me. Then I tried to use the ASCII format data.ascii - serialize(iris, NULL, ascii = TRUE) data.raw - rawToChar(data.ascii) dbSendQuery(db, DELETE FROM frames) dbSendQuery(db, paste(INSERT INTO frames VALUES(1, X', data.raw, '), sep = )) Error in sqliteExecStatement(conn, statement, ...) : RS-DBI driver: (error in statement: unrecognized token: X'A This also does not work. It seems the driver does not deal that nicely with the regular INSERT query for BLOB objects in SQLite. Then I used a simpler way: dbSendQuery(db, DELETE FROM frames) dbSendQuery(db, DROP TABLE frames) dbSendQuery(db, 'CREATE TABLE frames(simID INT, data TEXT DEFAULT NULL)') dbSendQuery(db, paste(INSERT INTO frames VALUES(1, ', data.raw, '), sep = )) data.bin2 - dbGetQuery(db, SELECT data FROM frames WHERE simID = 1) Nice, that worked. Now I want to unserialize the data: unserialize(data.bin2) Error in unserialize(data.bin2) : 'connection' must be a connection unserialize(data.bin2[1, 'data']) Error in unserialize(data.bin2[1, data]) : character vectors are no longer accepted by unserialize() I feel a little stuck here, but I am very sure, that converting data.frames to binary data and storing them to a database is not that unusual. So I hope somebody has already done this and could give me the missing piece. Best Simon __ R-help@r-project.org mailing list 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
Re: [R] Problem with plot in several cases, font issue?
Thanks for the help. As indicated into the R-admin manual, it was an ubuntu install problem. But it only shows in R, as I do not use special fonts usually. Le 15/07/2013 18:17, Prof Brian Ripley a écrit : On 15/07/2013 15:59, Alice Julien-Laferrière wrote: Dear all, I am having problem on plots in R for some cases. Your machine has Cairo: Cairo-based X11 devices do not use those fonts. So it seems you have done something you have not shown us. The fix is to use the Cairo-based X11 devices. See the R-admin manual for more details. For example: plot( 1:10 ) text( 1:10, letters[1:10], cex = 1) works well but : plot(1:10) text(1:10, letters[1:10], cex = 0.9) returns : Erreur dans text.default(1:10, letters[1:10], cex = 0.9) : impossible de charger la police X11 -adobe-helvetica-%s-%s-*-*-%d-*-*-*-*-*-*-*, de face 1 et de taille 11 (sorry for the french). But it is very easy to set LANGUAGE=en to get American English messages In this message, for other cases the function may changed (it can be axis( ) for example) but it always a font problem. I encountered this issue various times (with more complicated graphics). I'm working on ubuntu 12.04 with R 3.0.1 (2013-05-16). The capabilities function returns me: jpeg png tifftcltk X11 aqua http/ftp sockets TRUE TRUE TRUE TRUE TRUEFALSE TRUE TRUE libxml fifo clediticonv NLS profmemcairo TRUE TRUE TRUE TRUE TRUEFALSE TRUE I think this may be an issue with my installation, but I could not figured out what was the missing package. I tried this on other computers. I did not see the same bug. Thanks in advance for the help, Alice __ R-help@r-project.org mailing list 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 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] Program SPACECAP help
Please, could you post the the R code and the head of your data? Are you usuing the csv template? Jose -- View this message in context: http://r.789695.n4.nabble.com/Program-SPACECAP-help-tp4670514p4671667.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] About Detrended Fluctuation Analysis
Hello~ I am just beginner in R program During my research, I should analyze my data using detrended fluctuation analysis But it is difficult to find package in R I found the package named fractal to calcuate DFA but in new version in R, that package does not work any more So...would you tell my some tools or packages to calcuated DFA? Thank you for reading this post~ -- View this message in context: http://r.789695.n4.nabble.com/About-Detrended-Fluctuation-Analysis-tp4671666.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] Ode error message
Hello,
I am creating a program with R to solve a differential equation system.
However, I get the following message I do not understand :
out - ode(y = state, times = z, func = liquide, parms = 0, atol = 0)
DLSODA- EWT(I1) is R1 .le. 0.0
In above message, I1 = 1
In above message, R1 = 0
Error in lsoda(y, times, func, parms, ...) :
illegal input detected before taking any integration steps - see written
message
or this one when I tried modifying the atoll value :
out - ode(y = state, times = z, func = liquide, parms = 0, atol = 10^-14)
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = 0, R2 = 0
DINTDY- T (=R1) illegal
In above message, R1 = 1
T not in interval TCUR - HU (= R1) to TCUR (=R2)
In above message, R1 = 0, R2 = 0
DINTDY- T (=R1) illegal
In above message, R1 = 2
T not in interval TCUR - HU (= R1) to TCUR (=R2)
In above message, R1 = 0, R2 = 0
DLSODA- Trouble in DINTDY. ITASK = I1, TOUT = R1
In above message, I1 = 1
In above message, R1 = 2
Here is my program. I also tried changing the initial values but it does not
work well.
liquide - function(z, state, parameters) {
with(as.list(c(state,parameters)),{
# rate of change
Tr - 273+90
C - CA + CB + CC + CD + CE + CI + CG + CJ + CK + CH
K32 - 6.54*10^4
K33 - 1.37*10^4
K34 - 330
K35 - 5.81*10^4
kf2 - 1.37*10^3
kf3 - 1.37*10^3
kf4 - 8.68*10^5
kf5 - 157.2
K2 - 10^1.37
K3 - 10^(-3.35)
r1 - kf4*CD - kf4/K34*CE^2
r2 - kf3*CA*CB - kf3/K33*CD
r3 - kf2*CA^2 - kf2/K32*CC
r4 - kf5*CC - kf5/K35*CE*CI^2
dCA - -r2 # dNO/dt
dCB - -r3 - r2 # dNO2/dt
dCC - r3/2 - r4 # dN2O4/dt
dCD - r2 - r1# dN2O3/dt
dCE - 2*r1 + r4# dHNO2/dt
dCI - r4 # dHNO3/dt
dCG - -r4 - r1 # dH2O/dz
dCH - (dCE + dCI)/((K2 + K3)*(CE + CI)) # dH/dz
dCJ - (CH*dCI - CI*dCH)/(K3*CH^2) # dNO3-/dz
dCK - (CH*dCE - CE*dCH)/(K2*CH^2)# dNO2-/dz
list(c(dCA, dCB, dCC, dCD, dCE, dCI, dCG, dCH, dCJ, dCK))
}) # end with(as.list ...
}
Ti - 273+90 # K
Ct - 5100 # mol/m^3
state -c(CA = 0, # mol/m^3 NO2
CB = 0, # mol/m^3 NO
CC = 0,# mol/m^3 N2O4
CD = 0, # mol/m^3 N2O3
CE = 50, # mol/m^3 HNO2
CI = 50, # mol/m^3 HNO3
CG = 5000, # mol/m^3 H2O
CH = 0, # mol/m^3 H+
CJ = 0,# mol/m^3 NO3-
CK = 0) # mol/m^3 NO2-
parameters - c(Ct = 5100)
z - seq(0, 15, by = 1) # en seconde
library(deSolve)
out - ode(y = state, times = z, func = liquide, parms = 0, atol = 10^-14)
head(out)
plot(out)
Thank you
__
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[R] MGCV: overlay fitted (marginal) curves over a plot of the original data
Dear R users, I´ve stumbled over a problem that can be easily seen from the R code below: - When I use plot.gam() on a fitted model object, I get a nice and well-looking smooth curve for all terms in the model. - However, when I use predict(model) for a given predictor, with values of all other predictors set to their means, the resulting curve doesn´t fit well at all. Is there a way to overlay the curve produced by plot.gam() over a plot of the original data? Here´s some reproducible code with mgcv version 1.7-22 on R3.0.1 (Windows 7): ## library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) b - gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat) plot(b,select=1) plot(y~x0,dat) mydata=data.frame(x0=0:1,x1=mean(dat$x1),x2=mean(dat$x2),x3=mean(dat$x3)) lines(0:1,predict(b,mydata,type=response)) ## Best wishes, Christoph -- PD Dr Christoph Scherber Georg-August University Goettingen Department of Crop Science Agroecology Grisebachstrasse 6 D-37077 Goettingen Germany phone 0049 (0)551 39 8807 fax 0049 (0)551 39 8806 http://www.gwdg.de/~cscherb1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MGCV: overlay fitted (marginal) curves over a plot of the original data
Probably you didn't want to set x0=0:1? Here is some code, to do what you want. (The CI shape is not identical to the plot(b) version as the uncertainty includes the uncertainty in the other smooths and the intercept now.) library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) b - gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat) plot(b,select=1) plot(y~x0,dat) mydata=data.frame(x0=0:200/200,x1=mean(dat$x1),x2=mean(dat$x2),x3=mean(dat$x3)) pv - predict(b,mydata,type=response,se=TRUE) lines(mydata$x0,pv$fit) lines(mydata$x0,pv$fit+2*pv$se.fit,lty=2) lines(mydata$x0,pv$fit-2*pv$se.fit,lty=2) On 16/07/13 09:52, Christoph Scherber wrote: Dear R users, I´ve stumbled over a problem that can be easily seen from the R code below: - When I use plot.gam() on a fitted model object, I get a nice and well-looking smooth curve for all terms in the model. - However, when I use predict(model) for a given predictor, with values of all other predictors set to their means, the resulting curve doesn´t fit well at all. Is there a way to overlay the curve produced by plot.gam() over a plot of the original data? Here´s some reproducible code with mgcv version 1.7-22 on R3.0.1 (Windows 7): ## library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) b - gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat) plot(b,select=1) plot(y~x0,dat) mydata=data.frame(x0=0:1,x1=mean(dat$x1),x2=mean(dat$x2),x3=mean(dat$x3)) lines(0:1,predict(b,mydata,type=response)) ## Best wishes, Christoph __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MGCV: overlay fitted (marginal) curves over a plot of the original data
Thanks, the sequence of x0 values was clearly too short. However, is there a way to overlay the (marginal) curve from plot.gam() over a plot of (x,y) values? Best wishes Christoph Am 16/07/2013 11:04, schrieb Simon Wood: Probably you didn't want to set x0=0:1? Here is some code, to do what you want. (The CI shape is not identical to the plot(b) version as the uncertainty includes the uncertainty in the other smooths and the intercept now.) library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) b - gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat) plot(b,select=1) plot(y~x0,dat) mydata=data.frame(x0=0:200/200,x1=mean(dat$x1),x2=mean(dat$x2),x3=mean(dat$x3)) pv - predict(b,mydata,type=response,se=TRUE) lines(mydata$x0,pv$fit) lines(mydata$x0,pv$fit+2*pv$se.fit,lty=2) lines(mydata$x0,pv$fit-2*pv$se.fit,lty=2) On 16/07/13 09:52, Christoph Scherber wrote: Dear R users, I´ve stumbled over a problem that can be easily seen from the R code below: - When I use plot.gam() on a fitted model object, I get a nice and well-looking smooth curve for all terms in the model. - However, when I use predict(model) for a given predictor, with values of all other predictors set to their means, the resulting curve doesn´t fit well at all. Is there a way to overlay the curve produced by plot.gam() over a plot of the original data? Here´s some reproducible code with mgcv version 1.7-22 on R3.0.1 (Windows 7): ## library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) b - gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat) plot(b,select=1) plot(y~x0,dat) mydata=data.frame(x0=0:1,x1=mean(dat$x1),x2=mean(dat$x2),x3=mean(dat$x3)) lines(0:1,predict(b,mydata,type=response)) ## Best wishes, Christoph __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] MGCV: overlay fitted (marginal) curves over a plot of the original data
Meanwhile, I found the solution myself: using plot.gam() with shift=intercept and trans=exp (for a poisson model) does the job. I can then add the original data using points() Thanks again for your help, which is greatly appreciated! Best wishes Christoph Am 16/07/2013 11:04, schrieb Simon Wood: Probably you didn't want to set x0=0:1? Here is some code, to do what you want. (The CI shape is not identical to the plot(b) version as the uncertainty includes the uncertainty in the other smooths and the intercept now.) library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) b - gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat) plot(b,select=1) plot(y~x0,dat) mydata=data.frame(x0=0:200/200,x1=mean(dat$x1),x2=mean(dat$x2),x3=mean(dat$x3)) pv - predict(b,mydata,type=response,se=TRUE) lines(mydata$x0,pv$fit) lines(mydata$x0,pv$fit+2*pv$se.fit,lty=2) lines(mydata$x0,pv$fit-2*pv$se.fit,lty=2) On 16/07/13 09:52, Christoph Scherber wrote: Dear R users, I´ve stumbled over a problem that can be easily seen from the R code below: - When I use plot.gam() on a fitted model object, I get a nice and well-looking smooth curve for all terms in the model. - However, when I use predict(model) for a given predictor, with values of all other predictors set to their means, the resulting curve doesn´t fit well at all. Is there a way to overlay the curve produced by plot.gam() over a plot of the original data? Here´s some reproducible code with mgcv version 1.7-22 on R3.0.1 (Windows 7): ## library(mgcv) set.seed(2) dat - gamSim(1,n=400,dist=normal,scale=2) b - gam(y~s(x0)+s(x1)+s(x2)+s(x3),data=dat) plot(b,select=1) plot(y~x0,dat) mydata=data.frame(x0=0:1,x1=mean(dat$x1),x2=mean(dat$x2),x3=mean(dat$x3)) lines(0:1,predict(b,mydata,type=response)) ## Best wishes, Christoph __ R-help@r-project.org mailing list 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] Question on plotting with googleVis
You can try with list options : plot(gvisBarChart(MyData, xvar=Names1, yvar=c(Values1, Values2), options=list(width=1200,height=1500))) Le 15/07/2013 20:00, Christofer Bogaso a écrit : Hello again, Let say I have following data-frame: MyData - data.frame(Names1 = paste(XXX, 1:150), Values1 = 1:150 + 10, Values2 = 1:150) Now I want to plot this data-frame with googleVis. Therefore I run following codes: library(googleVis) plot(gvisBarChart(MyData, xvar=Names1, yvar=c(Values1, Values2))) However the problem is that, hardly this plot can be read. However if I plot a fraction of my data-frame then the underlying plot is clearly visible: plot(gvisBarChart(MyData[1:15,], xvar=Names1, yvar=c(Values1, Values2))) ## This is clearly visible. I would really appreciate if someone gives me some pointer how I can clearly plot my data-frame with googleVis. I understand that there are many other plotting methods available with R like ggplot, however here I want to use googleVis because of its strength in showing the values within the plot area itself if you hover your mouse. Thanks and regards, [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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. -- Michel ARNAUD Chargé de mission auprès du DRH DGDRD-Drh - TA 174/04 Av Agropolis 34398 Montpellier cedex 5 tel : 04.67.61.75.38 fax : 04.67.61.57.87 port: 06.47.43.55.31 __ R-help@r-project.org mailing list 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] Finding parameters for residuals using GAMLSS and a lognormal dist.
Hi everyone! First of all: I am new to the forum, so please excuse my lack of knowledge on how to post a question... I am working on a project where I need to use the GAMLSS package, and the boss have asked me to try using the lognormal distribution. The regression goes as planned, but when evaluating the residuals and using the coef() function, I get multiple coefficients as theory says, but I´m not sure if they can be used as parameters. My question is: How can I model the residuals? Do I have to assume a lognormal distribution of these, or can I assume a distribution of choice? I have plotted the kernel density of the residuals and they do seem to fit a lognormal distribution, but as I am not entirely sure how to find parameters, I do not know how... I guess this is an easy question, but I just cant seem to find a solution to this. A section of the code: tmpformula = as.formula(paste(logvarnames[i], ~ , paste(logvarnames[1:i-1], collapse= +))) res = gamlss(tmpformula, family = LOGNO(), data = myall ) where logvarnames[] is a vector containing the names of columns from the dataset I use called myall. -- View this message in context: http://r.789695.n4.nabble.com/Finding-parameters-for-residuals-using-GAMLSS-and-a-lognormal-dist-tp4671674.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list 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] Masking oceans using polypath
Hi R-help I am trying to mask the ocean from an image plot I have made. Here is some example code: library(mapdata) image(x=110:155, y =-40:-10, z = outer(1:45, 1:30, +), xlab = lon, ylab = lat) outline - map(worldHires, plot=FALSE) # returns a list of x/y coords xrange - range(outline$x, na.rm=TRUE) # get bounding box yrange - range(outline$y, na.rm=TRUE) xbox - xrange + c(-2, 2) ybox - yrange + c(-2, 2) # create the grid path in the current device polypath(c(outline$x, NA, c(xbox, rev(xbox))), c(outline$y, NA, rep(ybox, each=2)), col=light blue, rule=evenodd) As you can see, the polypath is on both sides of the country outline. Any help is much appreciated. Louise [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] Serialize data.frame to database
Maybe a simple dbWriteTable( db, frames, iris ) does what you want? On Monday 15 July 2013 23:43:18 Simon Zehnder wrote: Dear R-Users, I need a very fast and reliable database solution so I try to serialize a data.frame (to binary data) and to store this data to an SQLite database. This is what I tried to do: library(RSQLite) con - dbDriver(SQLite) db - dbConnect(con, test) dbSendQuery(db, 'CREATE TABLE frames(simID INT, data BLOB)') data.bin - serialize(iris, NULL, ascii = FALSE) dbSendQuery(db, paste(INSERT INTO frames VALUES(1, X', data.bin, '), sep = )) data.bin2 - dbGetQuery(db, SELECT DATA FROM frames WHERE simID = 1) data.bin2 data 1 58 So, only the first entry of data.bin is saved to the database. I tried to first convert the binary data to raw data: data.raw - rawToChar(data.bin) Error in rawToChar(data.bin) : embedded nul in string: 'X\n\0\0\0\002\0\003\0\001\0\002\003\0\0\0\003\023\0\0\0\005\0\0\0\016\0\0\0\x96@\024ff@\023\x99\x99\x99\x99\x99\x9a@\022\xcc\xcc\xcc\xcc\xcc\xcd@\022ff@\024\0\0\0\0\0\0@\025\x99\x99\x99\x99\x99\x9a@\022ff@\024\0\0\0\0\0\0@\021\x99\x99\x99\x99\x99\x9a@\023\x99\x99\x99\x99\x99\x9a@\025\x99\x99\x99\x99\x99\x9a@\02333@\02333@\02133@\02733@\026\xcc\xcc\xcc\xcc\xcc\xcd@\025\x99\x99\x99\x99\x99\x9a@\024ff@\026\xcc\xcc\xcc\xcc\xcc\xcd@\024ff@\025\x99\x99\x99\x99\x99\x9a@\024ff@\022ff@\024ff@\02333@\024\0\0\0\0\0\0@\024\0\0\0\0\0\0@\024\xcc\xcc\xcc\xcc\xcc\xcd@\024\xcc\xcc\xcc\xcc\xcc\xcd@\022\xcc\xcc\xcc\xcc\xcc\xcd@\02333@\025\x99\x99\x99\x99\x99\x9a@\024\xcc\xcc\xcc\xcc\xcc\xcd@\026\0\0\0\0\0\0@\023\x99\x99\x99\x99\x99\x9a@\024\0\0\0\0\0\0@\026\0\0\0\0\0\0@\023\x99\x99\x99\x99\x99\x9a@\021\x99\x99\x99\x99\x99\x9a@\024ff@\024\0\0\0\0\0\0@\022\0\0\0\0\0\0@\021\x99\x99\x99\x99\x99\x9a@\024\0\0\0\! 0\! 0\0 I don't know what this error should tell me. Then I tried to use the ASCII format data.ascii - serialize(iris, NULL, ascii = TRUE) data.raw - rawToChar(data.ascii) dbSendQuery(db, DELETE FROM frames) dbSendQuery(db, paste(INSERT INTO frames VALUES(1, X', data.raw, '), sep = )) Error in sqliteExecStatement(conn, statement, ...) : RS-DBI driver: (error in statement: unrecognized token: X'A This also does not work. It seems the driver does not deal that nicely with the regular INSERT query for BLOB objects in SQLite. Then I used a simpler way: dbSendQuery(db, DELETE FROM frames) dbSendQuery(db, DROP TABLE frames) dbSendQuery(db, 'CREATE TABLE frames(simID INT, data TEXT DEFAULT NULL)') dbSendQuery(db, paste(INSERT INTO frames VALUES(1, ', data.raw, '), sep = )) data.bin2 - dbGetQuery(db, SELECT data FROM frames WHERE simID = 1) Nice, that worked. Now I want to unserialize the data: unserialize(data.bin2) Error in unserialize(data.bin2) : 'connection' must be a connection unserialize(data.bin2[1, 'data']) Error in unserialize(data.bin2[1, data]) : character vectors are no longer accepted by unserialize() I feel a little stuck here, but I am very sure, that converting data.frames to binary data and storing them to a database is not that unusual. So I hope somebody has already done this and could give me the missing piece. Best Simon __ R-help@r-project.org mailing list 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. - - - - - Der NSA keine Chance: e-mail verschluesseln! http://www.gpg4win.org/ __ R-help@r-project.org mailing list 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] Weird 'xmlEventParse' encoding issue
Hi Sascha
Your code gives the correct results on my machine (OS X),
either reading from the file directly or via readLines() and passing
the text to xmlEventParse().
The problem might be the version of the XML package or your environment
settings. And it is important to report the session information.
So you should provide the output from
sessionInfo()
Sys.getenv()
libxmlVersion()
D
On 7/15/13 4:41 AM, Sascha Wolfer wrote:
Dear list,
I have got a weird encoding problem with the xmlEventParse() function from
the 'XML' package.
I tried finding an answer on the web for several hours and a Stack Exchange
question came back without success :(
So here's the problem. I created a small XML test file, which looks like this:
?xml version=1.0 encoding=iso-8859-1?
!DOCTYPE testFile
s type=manualauch der Schulleiter steht dafür zur Verfügung. Das ist
seßhaft mit ä und ö.../s
This file is encoded with the iso-8859-1 encoding which is also defined in
its header.
I have 3 handler functions, definitions as follows:
sE2 - function (name, attrs) {
if (name == s) {
get.text - T }
}
eE2 - function (name, attrs) {
if (name == s) {
get.text - F
}
}
tS2 - function (content, ...) {
if (get.text nchar(content) 0) {
collected.text - c(collected.text, content)
}
}
I have one wrapper function around xmlEventParse(), definition as follows:
get.all.text - function (file) {
t1 - Sys.time()
read.file - paste(readLines(file, encoding = ), collapse = )
print(read.file)
assign(collected.text, c(), env = .GlobalEnv)
assign(get.text, F, env = .GlobalEnv)
xmlEventParse(read.file, asText = T, list(startElement = sE2,
endElement = eE2,
text = tS2),
error = function (...) { },
saxVersion = 1)
t2 - Sys.time()
cat(That took, round(difftime(t2,t1, units=secs), 1), seconds.\n)
cat(Result of reading is in variable 'collected.text'.\n)
collected.text
}
The output of calling get.all.text(test file) is as follows:
[1] ?xml version=\1.0\ encoding=\iso-8859-1\? !DOCTYPE testFile s
type=\manual\auch der Schulleiter steht
dafür zur Verfügung. Das ist seßhaft mit ä und ö.../s
That took 0 seconds.
Result of reading is in variable 'collected.text'.
[1] auch der Schulleiter steht dafür zur
Verfügung. Das ist seßhaft mit ä und ö...
Now the REALLY weird thing (for me) is that R obviously reads in the file
correctly (first output) with 'readLines()'.
Then this output is passed to xmlEventParse. Afterwards the output is broken
and it sometimes also inserts weird breaks
were special characters occur.
Do you have any ideas how to solve this problem?
I cannot use the xmlParse() function because I need the SAX functionality of
xmlEventParse(). I also tried reading the
file with xmlEventParse() directly (with asText = F). No changes...
Thanks a lot,
Sascha W.
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Re: [R] Serialize data.frame to database
Hi Rainer, dbWriteTable is a nice function but in my case I need something that can actually save a dataframe in one row of a table. That is why I want to serialize my data.frame. Best Simon On Jul 16, 2013, at 3:05 PM, Rainer Schuermann rainer.schuerm...@gmx.net wrote: Maybe a simple dbWriteTable( db, frames, iris ) does what you want? On Monday 15 July 2013 23:43:18 Simon Zehnder wrote: Dear R-Users, I need a very fast and reliable database solution so I try to serialize a data.frame (to binary data) and to store this data to an SQLite database. This is what I tried to do: library(RSQLite) con - dbDriver(SQLite) db - dbConnect(con, test) dbSendQuery(db, 'CREATE TABLE frames(simID INT, data BLOB)') data.bin - serialize(iris, NULL, ascii = FALSE) dbSendQuery(db, paste(INSERT INTO frames VALUES(1, X', data.bin, '), sep = )) data.bin2 - dbGetQuery(db, SELECT DATA FROM frames WHERE simID = 1) data.bin2 data 1 58 So, only the first entry of data.bin is saved to the database. I tried to first convert the binary data to raw data: data.raw - rawToChar(data.bin) Error in rawToChar(data.bin) : embedded nul in string: 'X\n\0\0\0\002\0\003\0\001\0\002\003\0\0\0\003\023\0\0\0\005\0\0\0\016\0\0\0\x96@\024ff@\023\x99\x99\x99\x99\x99\x9a@\022\xcc\xcc\xcc\xcc\xcc\xcd@\022ff@\024\0\0\0\0\0\0@\025\x99\x99\x99\x99\x99\x9a@\022ff@\024\0\0\0\0\0\0@\021\x99\x99\x99\x99\x99\x9a@\023\x99\x99\x99\x99\x99\x9a@\025\x99\x99\x99\x99\x99\x9a@\02333@\02333@\02133@\02733@\026\xcc\xcc\xcc\xcc\xcc\xcd@\025\x99\x99\x99\x99\x99\x9a@\024ff@\026\xcc\xcc\xcc\xcc\xcc\xcd@\024ff@\025\x99\x99\x99\x99\x99\x9a@\024ff@\022ff@\024ff@\02333@\024\0\0\0\0\0\0@\024\0\0\0\0\0\0@\024\xcc\xcc\xcc\xcc\xcc\xcd@\024\xcc\xcc\xcc\xcc\xcc\xcd@\022\xcc\xcc\xcc\xcc\xcc\xcd@\02333@\025\x99\x99\x99\x99\x99\x9a@\024\xcc\xcc\xcc\xcc\xcc\xcd@\026\0\0\0\0\0\0@\023\x99\x99\x99\x99\x99\x9a@\024\0\0\0\0\0\0@\026\0\0\0\0\0\0@\023\x99\x99\x99\x99\x99\x9a@\021\x99\x99\x99\x99\x99\x9a@\024ff@\024\0\0\0\0\0\0@\022\0\0\0\0\0\0@\021\x99\x99\x99\x99\x99\x9a@\024\0\0\0\! 0\! 0\0 I don't know what this error should tell me. Then I tried to use the ASCII format data.ascii - serialize(iris, NULL, ascii = TRUE) data.raw - rawToChar(data.ascii) dbSendQuery(db, DELETE FROM frames) dbSendQuery(db, paste(INSERT INTO frames VALUES(1, X', data.raw, '), sep = )) Error in sqliteExecStatement(conn, statement, ...) : RS-DBI driver: (error in statement: unrecognized token: X'A This also does not work. It seems the driver does not deal that nicely with the regular INSERT query for BLOB objects in SQLite. Then I used a simpler way: dbSendQuery(db, DELETE FROM frames) dbSendQuery(db, DROP TABLE frames) dbSendQuery(db, 'CREATE TABLE frames(simID INT, data TEXT DEFAULT NULL)') dbSendQuery(db, paste(INSERT INTO frames VALUES(1, ', data.raw, '), sep = )) data.bin2 - dbGetQuery(db, SELECT data FROM frames WHERE simID = 1) Nice, that worked. Now I want to unserialize the data: unserialize(data.bin2) Error in unserialize(data.bin2) : 'connection' must be a connection unserialize(data.bin2[1, 'data']) Error in unserialize(data.bin2[1, data]) : character vectors are no longer accepted by unserialize() I feel a little stuck here, but I am very sure, that converting data.frames to binary data and storing them to a database is not that unusual. So I hope somebody has already done this and could give me the missing piece. Best Simon __ R-help@r-project.org mailing list 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. - - - - - Der NSA keine Chance: e-mail verschluesseln! http://www.gpg4win.org/ __ R-help@r-project.org mailing list 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 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] Error from running R2WinBUGS in R
Hi All:
I am getting an error (highlighted) from running R2WinBUGS in R.
To be able to replicate the situation heres the code:
.#Set working directory
setwd(H://AChaudhuri/Testing/CSVS)
matrix=NULL
csvs - paste(MVN, 1:2, .csv, sep=)
for(i in 1:length(csvs)){
matrix[[i]] - read.csv(file=csvs[i], header=T)
print(matrix[[i]])
}
So now I have read in 2 simulated datasets which look like
Y1 Y2
1 11 6
2 8 5
3 25 13
4 1 13
5 8 22
Y1 Y2
1 9 1
2 7 9
3 25 13
4 1 18
5 9 12
My next step is to run a multivariate logit normal model on these datasets
and automate this process for such simulated datasets. Heres the model
statement:
model
{
for (j in 1 : Nf)
{
p1[j, 1:2 ] ~ dmnorm(gamma[1:2 ], T[1:2 ,1:2 ])
for (i in 1:2)
{
logit(p[j,i])-p1[j,i]
Y[j,i] ~ dbin(p[j,i],n)
}}
I am trying to use the following code to run it in R
library(R2WinBUGS)
bugs.output - list()
for(i in 1:2){
Y -(matrix[i])
bugs.output[[i]] - bugs(
data=list(Y=Y, Nf=5), # change for no of sites
inits=NULL,
model.file=M-LN_model_trial.txt,
parameters.to.save = c(p,rho,sigma2),
n.chains=1, n.iter=12000, n.burnin=5000,
bugs.directory=H://AChaudhuri/winbugs14/WinBUGS14,
working.directory=NULL)}
Error in FUN(X[[1L]], ...) :
.C(..): 'type' must be real for this format
Any suggestion would be helpful.
Thanks!
[[alternative HTML version deleted]]
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[R] Setting Derived Class Slots
Dear AllI am really struggling with oo in R. Trying to set attributes of
the base class in a derived class method but the slot is only populated in
the method itself, not when I try to print out the object from the console.
Code is
library(RODBC)
#
# -
# Define a medical event class. This is abstract (VIRTUAL)
# -
#
setClass(Medical_Event,
representation(
Event_Name=character,
Capacity_Profile=numeric,
Delay_Profile=numeric,
VIRTUAL),
prototype(Event_Name=An
Event,Capacity_Profile=c(.2,.2,.2,.2,.2,0,0)))
setGeneric(getDelayProfile,function(object){standardGeneric(getDelayProfile)},simpleInheritanceOnly=T)
# --
# Now define a derived class called GP_Event
# --
setClass(GP_Event,representation(Surgery_Name=character),contains=c(Medical_Event),prototype(Surgery_Name=Unknown))
# -
# Now define a derived class called OP_Appt
# -
setClass(OP_Appt,representation(Clinic_Name=character),contains=c(Medical_Event),prototype(Clinic_Name=Unknown))
setMethod(f=getDelayProfile,signature(OP_Appt),definition=function(object)
{
OpTablesDB-odbcDriverConnect(DRIVER=Microsoft Access Driver (*.mdb,
*.accdb);
DBQ=Z:\\srp\\Development
Code\\Projects\\CancerPathwaySimulation\\Database\\CancerPathway.accdb)
strQuery-select * from op_profile
odbcQuery(OpTablesDB,strQuery)
dfQuery-odbcFetchRows(OpTablesDB)
odbcClose(OpTablesDB)
delay-dfQuery$data[[1]][1:70]
prob-dfQuery$data[[2]][1:70]
# as(object,Medical_Event)@Delay_Profile-prob
object@Delay_Profile - prob
object
}
)
if I instantiate a new instance of the derived class
*aTest-new(OPP_Appt)*and then try and populate the attribute
Delay_Profile by
*getDelayProfile(aTest) *
the object slot seems to be populated in the method because I can print it
out, viz
An object of class OP_Appt
Slot Clinic_Name:
[1] Unknown
Slot Event_Name:
[1] An Event
Slot Capacity_Profile:
[1] 0.2 0.2 0.2 0.2 0.2 0.0 0.0
*Slot Delay_Profile:
[1] 14 21 25 29 27 49 72 71 43 65 102 134 223 358 24 14 21 25
35 31 38 43 31 23 21 26 46 54 42 26
[31] 34 24 25 41 48 33 30 17 18 31 24 35 35 24 16 32 36 39
46 36 26 16 27 21 30 32 33 27 7 5
[61] 9 10 9 11 8 6 1 11 14 10*
but when the method returns and I type
*aTest*
I get
An object of class OP_Appt
Slot Clinic_Name:
[1] Unknown
Slot Event_Name:
[1] An Event
Slot Capacity_Profile:
[1] 0.2 0.2 0.2 0.2 0.2 0.0 0.0
*Slot Delay_Profile:
numeric(0)*
ie the Delay_Profile slot is empty
What haven't I done - can anybody help me please?
Many Thanks
Steve Creamer
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Re: [R] glm - change offset to avoid NA?
I did not think of something like try. I thouht that there should always be a value if I do a logistic regression but sometimes the values are far from being meaningful. So there is a cut-off. My plan was to change the cut-off. Thanks Johannes 2013/7/15 Bert Gunter gunter.ber...@gene.com I think what you want is ?try ##or ?tryCatch ## The second is more flexible but slightly more complicated. to trap the error and perhaps refit the model without interaction? Cheers, Bert On Mon, Jul 15, 2013 at 10:45 AM, Hermann Norpois hnorp...@gmail.com wrote: Hello, I use glm within a function testing for the appearence of the coexistence of (minor allels in a subset of) snps. And then I extract the Pr(|z|)-value for the interaction. Principally it works but sometimes the function stops because this value for the interaction is NA. For instance, this is the case in the following example: lz - glm(trait~rs7572685*rs10520302, data=mus, family=binomial) summary (lz) ... Coefficients: (1 not defined because of singularities) Estimate Std. Error z value Pr(|z|) (Intercept) 0.056140.16782 0.3350.738 rs7572685 0.490410.41437 1.1830.237 rs105203020.492690.43514 1.1320.258 rs7572685:rs10520302 NA NA NA NA ... I would prefer some values instead of NA (though it does not make any sense in terms of interpretation) for the sake of the smooth running of my function. How is this done? I guess I have to change the offset but I dont understand how. Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] Errors using large numbers ((i) all entries of 'x' must be nonnegative and finite and (ii) NAs introduced by coercion)
Hello,
I am fairly new to R, so please forgive me if this is a fairly easy
solution.
I am trying to perform multiple Fisher's Exact tests or Pearson's
Chi-squared contingency tests from a datamatrix in which data from each row
is data for an independent test.
My data is formatted as such:
AAA 75533 4756922556 88210 6715122129
BBB 14869 4756983220 16384 6715193955
CCC 7230 4756990859 8559 6715201780
DDD 18332 4756979757 23336 6715187003
EEE 14733 4756983356 16826 6715193513
FFF 2918 4756995171 3433 6715206906
GGG 3726 4756994363 4038 6715206301
HHH 6196 4756991893 7011 6715203328
III 7925 4756990164 9130 6715201209
JJJ 1434 4756996655 1602 6715208737
Where the 1st column is the identifier, the 2nd column = observations 1, the
3rd column = background counts 1, the 4th column = observations 2 and the
5th column = background counts 2.
I am loading my data as such:
data=read.table(My.File, header=FALSE)
And I am looping through each row to perform a test like this:
pvalues=c(pvalue)
for(i in 1:10){
+ datamatrix=matrix(c(as.integer(data[i,2:5])),nrow=2)
+ fisherresult=fisher.test(datamatrix)
+ pvalues=cbind(pvalues,fisherresult[1])
+ }
Here is the Error I am Getting:
Error in fisher.test(datamatrix) :
all entries of 'x' must be nonnegative and finite
In addition: Warning messages:
1: In matrix(c(as.integer(data[i, 2:5])), nrow = 2) :
NAs introduced by coercion
2: In matrix(c(as.integer(data[i, 2:5])), nrow = 2) :
NAs introduced by coercion
When I replace the large number in the 3rd and 5th column with smaller
numbers, the statistical calculation works fine.
Any ideas? Any help would be GREATLY appreciated!
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] glm - change offset to avoid NA?
On Jul 16, 2013, at 8:52 AM, Hermann Norpois wrote: I did not think of something like try. I thouht that there should always be a value if I do a logistic regression but sometimes the values are far from being meaningful. So there is a cut-off. That seems implausilbe. I think you are just seeing the effect of a random selection creating a data situation where the interaction term is aliased with the others, in which case `glm` will set the coefficient to NA. My plan was to change the cut-off. You said there was an error, but you should have said that the results were unexpected. You can create an error-condition when this occurs with the `stop` function. And then do whatever remedial work is needed. -- David. Thanks Johannes 2013/7/15 Bert Gunter gunter.ber...@gene.com I think what you want is ?try ##or ?tryCatch ## The second is more flexible but slightly more complicated. to trap the error and perhaps refit the model without interaction? Cheers, Bert On Mon, Jul 15, 2013 at 10:45 AM, Hermann Norpois hnorp...@gmail.com wrote: Hello, I use glm within a function testing for the appearence of the coexistence of (minor allels in a subset of) snps. And then I extract the Pr(|z|)-value for the interaction. Principally it works but sometimes the function stops because this value for the interaction is NA. For instance, this is the case in the following example: lz - glm(trait~rs7572685*rs10520302, data=mus, family=binomial) summary (lz) ... Coefficients: (1 not defined because of singularities) Estimate Std. Error z value Pr(|z|) (Intercept) 0.056140.16782 0.3350.738 rs7572685 0.490410.41437 1.1830.237 rs105203020.492690.43514 1.1320.258 rs7572685:rs10520302 NA NA NA NA ... I would prefer some values instead of NA (though it does not make any sense in terms of interpretation) for the sake of the smooth running of my function. How is this done? I guess I have to change the offset but I dont understand how. Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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. David Winsemius Alameda, CA, USA __ R-help@r-project.org mailing list 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] Setting Derived Class Slots
On 07/16/2013 06:36 AM, Steve Creamer wrote:
Dear AllI am really struggling with oo in R. Trying to set attributes of
the base class in a derived class method but the slot is only populated in
the method itself, not when I try to print out the object from the console.
Code is
library(RODBC)
#
# -
# Define a medical event class. This is abstract (VIRTUAL)
# -
#
setClass(Medical_Event,
representation(
Event_Name=character,
Capacity_Profile=numeric,
Delay_Profile=numeric,
VIRTUAL),
prototype(Event_Name=An
Event,Capacity_Profile=c(.2,.2,.2,.2,.2,0,0)))
setGeneric(getDelayProfile,function(object){standardGeneric(getDelayProfile)},simpleInheritanceOnly=T)
# --
# Now define a derived class called GP_Event
# --
setClass(GP_Event,representation(Surgery_Name=character),contains=c(Medical_Event),prototype(Surgery_Name=Unknown))
# -
# Now define a derived class called OP_Appt
# -
setClass(OP_Appt,representation(Clinic_Name=character),contains=c(Medical_Event),prototype(Clinic_Name=Unknown))
setMethod(f=getDelayProfile,signature(OP_Appt),definition=function(object)
{
OpTablesDB-odbcDriverConnect(DRIVER=Microsoft Access Driver (*.mdb,
*.accdb);
DBQ=Z:\\srp\\Development
Code\\Projects\\CancerPathwaySimulation\\Database\\CancerPathway.accdb)
strQuery-select * from op_profile
odbcQuery(OpTablesDB,strQuery)
dfQuery-odbcFetchRows(OpTablesDB)
odbcClose(OpTablesDB)
delay-dfQuery$data[[1]][1:70]
prob-dfQuery$data[[2]][1:70]
# as(object,Medical_Event)@Delay_Profile-prob
object@Delay_Profile - prob
object
}
)
if I instantiate a new instance of the derived class
*aTest-new(OPP_Appt)*and then try and populate the attribute
Delay_Profile by
*getDelayProfile(aTest) *
the object slot seems to be populated in the method because I can print it
out, viz
An object of class OP_Appt
Slot Clinic_Name:
[1] Unknown
Slot Event_Name:
[1] An Event
Slot Capacity_Profile:
[1] 0.2 0.2 0.2 0.2 0.2 0.0 0.0
*Slot Delay_Profile:
[1] 14 21 25 29 27 49 72 71 43 65 102 134 223 358 24 14 21 25
35 31 38 43 31 23 21 26 46 54 42 26
[31] 34 24 25 41 48 33 30 17 18 31 24 35 35 24 16 32 36 39
46 36 26 16 27 21 30 32 33 27 7 5
[61] 9 10 9 11 8 6 1 11 14 10*
but when the method returns and I type
*aTest*
I get
An object of class OP_Appt
Slot Clinic_Name:
[1] Unknown
Slot Event_Name:
[1] An Event
Slot Capacity_Profile:
[1] 0.2 0.2 0.2 0.2 0.2 0.0 0.0
*Slot Delay_Profile:
numeric(0)*
ie the Delay_Profile slot is empty
What haven't I done - can anybody help me please?
It helps to provide a more minimal example, preferably reproducible (no data
base queries needed to illustrate your problem); I'm guessing that, just as with
f = funtion(l) { l$a = 1; l }
lst = list(a=0, b=1)
one would 'update' lst with
lst = f(lst)
and not
f(lst)
you need to assign the return value to the original object
aTest - getDelayProfile(aTest)
Martin
Many Thanks
Steve Creamer
--
View this message in context:
http://r.789695.n4.nabble.com/Setting-Derived-Class-Slots-tp4671683.html
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--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
Location: Arnold Building M1 B861
Phone: (206) 667-2793
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Re: [R] Setting Derived Class Slots
Hi Steve, it seems to me, that you want to pass an object inside of getDelayProfile. In this case you must use setReplaceMethod(getDelayProfile-,) in your definition inside the virtual and of course also in the specification of OP_Appt. R does not know, that your function should give back an object, that replaces the one on which it was called. Otherwise making any modifications on the slot of the object inside the function will never arrive at the object outside of the function. They have two different environments and as soon as you modify an object inside of a function R builds a copy of it. See more about this by googling R pass-by-value. By the way: I wouldn't call this function getDelayProfile as getters and setters have usually differing a different meaning (encapsulation) in OO programming. Use rather something like fetchDelayProfile or initializeDelayProfile. It will probably make it easier for Users and Programmers to work with your program. Hope this helps Best Simon On Jul 16, 2013, at 3:36 PM, Steve Creamer stephen.crea...@nhs.net wrote: [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] Ode error message
See inline remarks.
On 16-07-2013, at 10:07, Raphaëlle Carraud raphaelle.carr...@oc-metalchem.com
wrote:
Hello,
I am creating a program with R to solve a differential equation system.
However, I get the following message I do not understand :
out - ode(y = state, times = z, func = liquide, parms = 0, atol = 0)
DLSODA- EWT(I1) is R1 .le. 0.0
In above message, I1 = 1
In above message, R1 = 0
Error in lsoda(y, times, func, parms, ...) :
illegal input detected before taking any integration steps - see written
message
or this one when I tried modifying the atoll value :
out - ode(y = state, times = z, func = liquide, parms = 0, atol = 10^-14)
DLSODA- Warning..Internal T (=R1) and H (=R2) are
such that in the machine, T + H = T on the next step
(H = step size). Solver will continue anyway.
In above message, R1 = 0, R2 = 0
DINTDY- T (=R1) illegal
In above message, R1 = 1
T not in interval TCUR - HU (= R1) to TCUR (=R2)
In above message, R1 = 0, R2 = 0
DINTDY- T (=R1) illegal
In above message, R1 = 2
T not in interval TCUR - HU (= R1) to TCUR (=R2)
In above message, R1 = 0, R2 = 0
DLSODA- Trouble in DINTDY. ITASK = I1, TOUT = R1
In above message, I1 = 1
In above message, R1 = 2
Here is my program. I also tried changing the initial values but it does not
work well.
liquide - function(z, state, parameters) {
with(as.list(c(state,parameters)),{
# rate of change
Tr - 273+90
Why are you defining Tr? It is not used anywhere
C - CA + CB + CC + CD + CE + CI + CG + CJ + CK + CH
Same thing. Not used.
K32 - 6.54*10^4
K33 - 1.37*10^4
K34 - 330
K35 - 5.81*10^4
kf2 - 1.37*10^3
kf3 - 1.37*10^3
kf4 - 8.68*10^5
kf5 - 157.2
K2 - 10^1.37
K3 - 10^(-3.35)
r1 - kf4*CD - kf4/K34*CE^2
r2 - kf3*CA*CB - kf3/K33*CD
r3 - kf2*CA^2 - kf2/K32*CC
r4 - kf5*CC - kf5/K35*CE*CI^2
dCA - -r2 # dNO/dt
dCB - -r3 - r2 # dNO2/dt
dCC - r3/2 - r4 # dN2O4/dt
dCD - r2 - r1# dN2O3/dt
dCE - 2*r1 + r4# dHNO2/dt
dCI - r4 #
dHNO3/dt
dCG - -r4 - r1 # dH2O/dz
dCH - (dCE + dCI)/((K2 + K3)*(CE + CI)) # dH/dz
dCJ - (CH*dCI - CI*dCH)/(K3*CH^2) # dNO3-/dz
You are dividing by CH, which is 0 initially. So what value does dCH then get?
dCK - (CH*dCE - CE*dCH)/(K2*CH^2)# dNO2-/dz
Same thing.
list(c(dCA, dCB, dCC, dCD, dCE, dCI, dCG, dCH, dCJ, dCK))
}) # end with(as.list ...
}
Ti - 273+90 # K
You are not using Ti.
Ct - 5100 # mol/m^3
And Ct is also not used.
state -c(CA = 0, # mol/m^3 NO2
CB = 0, # mol/m^3 NO
CC = 0,# mol/m^3 N2O4
CD = 0, # mol/m^3 N2O3
CE = 50, # mol/m^3 HNO2
CI = 50, # mol/m^3 HNO3
CG = 5000, # mol/m^3 H2O
CH = 0, # mol/m^3 H+
0!!
CJ = 0,# mol/m^3 NO3-
CK = 0) # mol/m^3 NO2-
parameters - c(Ct = 5100)
Why not parameters - c(Ct = Ct)?
z - seq(0, 15, by = 1) # en seconde
library(deSolve)
out - ode(y = state, times = z, func = liquide, parms = 0, atol = 10^-14)
head(out)
plot(out)
You will still get messages.
You should really learn to de elementary debugging.
Such as inserting
liquide(0,state,parameters)
after defining state and parameters to check and test.
Berend
Thank you
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Re: [R] Errors using large numbers ((i) all entries of 'x' must be nonnegative and finite and (ii) NAs introduced by coercion)
Well,
You could find it yourself,
as.integer(c(75533, 4756922556, 88210, 6715122129))
[1] 75533NA 88210NA
Warning message:
NAs introduced by coercion
matrix(c(75533, 4756922556, 88210, 6715122129), nrow=2)
[,1] [,2]
[1,] 75533 88210
[2,] 4756922556 6715122129
Using as.integer inputs NA as integer type has limited size.
Petr
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of jgibbons1
Sent: Tuesday, July 16, 2013 4:44 PM
To: r-help@r-project.org
Subject: [R] Errors using large numbers ((i) all entries of 'x' must be
nonnegative and finite and (ii) NAs introduced by coercion)
Hello,
I am fairly new to R, so please forgive me if this is a fairly easy
solution.
I am trying to perform multiple Fisher's Exact tests or Pearson's Chi-
squared contingency tests from a datamatrix in which data from each row
is data for an independent test.
My data is formatted as such:
AAA 75533 4756922556 88210 6715122129
BBB 14869 4756983220 16384 6715193955
CCC 7230 4756990859 8559 6715201780
DDD 18332 4756979757 23336 6715187003
EEE 14733 4756983356 16826 6715193513
FFF 2918 4756995171 3433 6715206906
GGG 3726 4756994363 4038 6715206301
HHH 6196 4756991893 7011 6715203328
III 7925 4756990164 9130 6715201209
JJJ 1434 4756996655 1602 6715208737
Where the 1st column is the identifier, the 2nd column = observations
1, the 3rd column = background counts 1, the 4th column = observations
2 and the 5th column = background counts 2.
I am loading my data as such:
data=read.table(My.File, header=FALSE)
And I am looping through each row to perform a test like this:
pvalues=c(pvalue)
for(i in 1:10){
+ datamatrix=matrix(c(as.integer(data[i,2:5])),nrow=2)
+ fisherresult=fisher.test(datamatrix)
+ pvalues=cbind(pvalues,fisherresult[1])
+ }
Here is the Error I am Getting:
Error in fisher.test(datamatrix) :
all entries of 'x' must be nonnegative and finite In addition:
Warning messages:
1: In matrix(c(as.integer(data[i, 2:5])), nrow = 2) :
NAs introduced by coercion
2: In matrix(c(as.integer(data[i, 2:5])), nrow = 2) :
NAs introduced by coercion
When I replace the large number in the 3rd and 5th column with smaller
numbers, the statistical calculation works fine.
Any ideas? Any help would be GREATLY appreciated!
--
View this message in context: http://r.789695.n4.nabble.com/Errors-
using-large-numbers-i-all-entries-of-x-must-be-nonnegative-and-finite-
and-ii-NAs-introduced-b-tp4671685.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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[R] help
Hi, i am tring to learn R own my own. From where can i download data for R (creating a subset). Right now i'm using (http://finance.yahoo.com/q/hp?s=MCD+Historical+Prices) this link for data but unable to create subset. Can someone help me using this data or help me to download different data? -- View this message in context: http://r.789695.n4.nabble.com/help-tp4671698.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help
On Tue, Jul 16, 2013 at 12:23 PM, Dia mnshd...@gmail.com wrote: Hi, i am tring to learn R own my own. From where can i download data for R (creating a subset). Right now i'm using (http://finance.yahoo.com/q/hp?s=MCD+Historical+Prices) this link for data but unable to create subset. Can someone help me using this data or help me to download different data? Use quantmod::getSymbols. library(quantmod) getSymbols(MCD) str(MCD) And read ?xts for ways to subset the MCD object. Best, -- Joshua Ulrich | about.me/joshuaulrich FOSS Trading | www.fosstrading.com __ R-help@r-project.org mailing list 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] pxR
Buenas tardes Una vez que he leído las variables, sexo, edad, estado civil y nacionalidad, ¿cómo genero un px para realizar las distintas consultas?. De momento lo único que he podido hacer con pxR es leer archivos de extensión px pero no sé escribirlos. Muchas gracias [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] Question on plotting with googleVis
The HTKIdentify (requires tcltk package) and HWIdentify (windows only) functions in the TeachingDemos package will show identifying information on a plot for the point being hovered over. Both functions are pure R code, so if they don't work for you as is you can modify the source to make whatever tweaks you may want. On Mon, Jul 15, 2013 at 12:00 PM, Christofer Bogaso bogaso.christo...@gmail.com wrote: Hello again, Let say I have following data-frame: MyData - data.frame(Names1 = paste(XXX, 1:150), Values1 = 1:150 + 10, Values2 = 1:150) Now I want to plot this data-frame with googleVis. Therefore I run following codes: library(googleVis) plot(gvisBarChart(MyData, xvar=Names1, yvar=c(Values1, Values2))) However the problem is that, hardly this plot can be read. However if I plot a fraction of my data-frame then the underlying plot is clearly visible: plot(gvisBarChart(MyData[1:15,], xvar=Names1, yvar=c(Values1, Values2))) ## This is clearly visible. I would really appreciate if someone gives me some pointer how I can clearly plot my data-frame with googleVis. I understand that there are many other plotting methods available with R like ggplot, however here I want to use googleVis because of its strength in showing the values within the plot area itself if you hover your mouse. Thanks and regards, [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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. -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] (1 - 0.7) == 0.3
HI, 2-0.7==0.3 #[1] FALSE ##May be u meant 2-0.7==1.3 #[1] TRUE Possibly R FAQ 7.31 Also, check http://rwiki.sciviews.org/doku.php?id=misc:r_accuracy all.equal(2-0.7,1.3) #[1] TRUE all.equal(1-0.7,0.3) #[1] TRUE (1-0.7)(0.3+.Machine$double.eps^0.5) #[1] TRUE p - c(0.2, 0.4, 0.6, 0.8, 1) round((1-p)*5,1)+1 #[1] 5 4 3 2 1 In your second example, p - c(0.8, 0.6, 0.4, 0.2, 0) floor((1 - p) * 5) + 1 #[1] 1 3 4 5 6 ((1-0.8)*5) +1 #[1] 2 round((1-p)*5,1)+1 #[1] 2 3 4 5 6 A.K. ...is false :( However (2 - 0.7) == 0.3 is true. Is there any way to get around this? The end goal is for this to work: p - c(0.2, 0.4, 0.6, 0.8, 1) floor((1 - p) * 5) + 1 5 4 3 1 1 whereas the correct result would have been 5 4 3 2 1. If I set p - c(0.8, 0.6, 0.4, 0.2, 0) then it works as expected. __ R-help@r-project.org mailing list 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] Errors using large numbers ((i) all entries of 'x' must be nonnegative and finite and (ii) NAs introduced by coercion)
HI,
?as.integer() #documentation
Note that current implementations of R use 32-bit integers for
integer vectors, so the range of representable integers is
restricted to about +/-2*10^9: ‘double’s can hold much larger
integers exactly.
as.numeric(c(75533, 4756922556, 88210, 6715122129))
#[1] 75533 4756922556 88210 6715122129
#or
as.double(c(75533, 4756922556, 88210, 6715122129))
#[1] 75533 4756922556 88210 6715122129
A.K.
- Original Message -
From: PIKAL Petr petr.pi...@precheza.cz
To: jgibbons1 jgibb...@hsph.harvard.edu; r-help@r-project.org
r-help@r-project.org
Cc:
Sent: Tuesday, July 16, 2013 12:54 PM
Subject: Re: [R] Errors using large numbers ((i) all entries of 'x' must be
nonnegative and finite and (ii) NAs introduced by coercion)
Well,
You could find it yourself,
as.integer(c(75533, 4756922556, 88210, 6715122129))
[1] 75533 NA 88210 NA
Warning message:
NAs introduced by coercion
matrix(c(75533, 4756922556, 88210, 6715122129), nrow=2)
[,1] [,2]
[1,] 75533 88210
[2,] 4756922556 6715122129
Using as.integer inputs NA as integer type has limited size.
Petr
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-bounces@r-
project.org] On Behalf Of jgibbons1
Sent: Tuesday, July 16, 2013 4:44 PM
To: r-help@r-project.org
Subject: [R] Errors using large numbers ((i) all entries of 'x' must be
nonnegative and finite and (ii) NAs introduced by coercion)
Hello,
I am fairly new to R, so please forgive me if this is a fairly easy
solution.
I am trying to perform multiple Fisher's Exact tests or Pearson's Chi-
squared contingency tests from a datamatrix in which data from each row
is data for an independent test.
My data is formatted as such:
AAA 75533 4756922556 88210 6715122129
BBB 14869 4756983220 16384 6715193955
CCC 7230 4756990859 8559 6715201780
DDD 18332 4756979757 23336 6715187003
EEE 14733 4756983356 16826 6715193513
FFF 2918 4756995171 3433 6715206906
GGG 3726 4756994363 4038 6715206301
HHH 6196 4756991893 7011 6715203328
III 7925 4756990164 9130 6715201209
JJJ 1434 4756996655 1602 6715208737
Where the 1st column is the identifier, the 2nd column = observations
1, the 3rd column = background counts 1, the 4th column = observations
2 and the 5th column = background counts 2.
I am loading my data as such:
data=read.table(My.File, header=FALSE)
And I am looping through each row to perform a test like this:
pvalues=c(pvalue)
for(i in 1:10){
+ datamatrix=matrix(c(as.integer(data[i,2:5])),nrow=2)
+ fisherresult=fisher.test(datamatrix)
+ pvalues=cbind(pvalues,fisherresult[1])
+ }
Here is the Error I am Getting:
Error in fisher.test(datamatrix) :
all entries of 'x' must be nonnegative and finite In addition:
Warning messages:
1: In matrix(c(as.integer(data[i, 2:5])), nrow = 2) :
NAs introduced by coercion
2: In matrix(c(as.integer(data[i, 2:5])), nrow = 2) :
NAs introduced by coercion
When I replace the large number in the 3rd and 5th column with smaller
numbers, the statistical calculation works fine.
Any ideas? Any help would be GREATLY appreciated!
--
View this message in context: http://r.789695.n4.nabble.com/Errors-
using-large-numbers-i-all-entries-of-x-must-be-nonnegative-and-finite-
and-ii-NAs-introduced-b-tp4671685.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
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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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
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] Importing data by odbcConnectExcel in 64 bit
I have probably an old question. I have R.3.0.1 installed in 64 bit windows 7. The odbcConnectExcel in RODBC library does not work. Tried odbcConnectExcel2007 still does not work. Any ideas. Thanks Melissa-sqlFetch(odbcConnectExcel2007(F:\\Cotton2012\\validation.xlsx),sqtable = Sheet3, + na.strings = NA, as.is = TRUE) Error in sqlFetch(odbcConnectExcel2007(F:\\Cotton2012\\validation.xlsx), : first argument is not an open RODBC channel In addition: Warning messages: 1: In odbcDriverConnect(con, tabQuote = c([, ]), ...) : [RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager] Data source name not found and no default driver specified 2: In odbcDriverConnect(con, tabQuote = c([, ]), ...) : ODBC connection failed Melissa-sqlFetch(odbcConnectExcel(F:\\Cotton2012\\validation.xlsx),sqtable = Sheet3, + na.strings = NA, as.is = TRUE) Error in odbcConnectExcel(F:\\Cotton2012\\validation.xlsx) : odbcConnectExcel is only usable with 32-bit Windows -- Ahmed M. Attia Research Assistant Dept. Of SoilCrop Sciences Texas AM University ahmed ahmeda...@zu.edu.eg.at...@ag.tamu.edu Cell phone: 001-979-248-5215 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] Importing data by odbcConnectExcel in 64 bit
Can't help you with the odbcConnectExcel, but I can suggest an alternative ... loadWorkbook() and readWorksheet() in the XLConnect package work on Windows 7 64-bit. library(XLConnect) wb - loadWorkbook(C:/Temp/Mydata.xlsx) dat - readWorksheet(wb, sheet=Sheet1) Jean On Tue, Jul 16, 2013 at 1:25 PM, Ahmed Attia ahmedati...@gmail.com wrote: I have probably an old question. I have R.3.0.1 installed in 64 bit windows 7. The odbcConnectExcel in RODBC library does not work. Tried odbcConnectExcel2007 still does not work. Any ideas. Thanks Melissa-sqlFetch(odbcConnectExcel2007(F:\\Cotton2012\\validation.xlsx),sqtable = Sheet3, + na.strings = NA, as.is = TRUE) Error in sqlFetch(odbcConnectExcel2007(F:\\Cotton2012\\validation.xlsx), : first argument is not an open RODBC channel In addition: Warning messages: 1: In odbcDriverConnect(con, tabQuote = c([, ]), ...) : [RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager] Data source name not found and no default driver specified 2: In odbcDriverConnect(con, tabQuote = c([, ]), ...) : ODBC connection failed Melissa-sqlFetch(odbcConnectExcel(F:\\Cotton2012\\validation.xlsx),sqtable = Sheet3, + na.strings = NA, as.is = TRUE) Error in odbcConnectExcel(F:\\Cotton2012\\validation.xlsx) : odbcConnectExcel is only usable with 32-bit Windows -- Ahmed M. Attia Research Assistant Dept. Of SoilCrop Sciences Texas AM University ahmed ahmeda...@zu.edu.eg.at...@ag.tamu.edu Cell phone: 001-979-248-5215 [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] pxR
Hola, creo que la función que buscas es write.px, que te permite guardar un objeto de tipo 'px' a un archivo. Por ejemplo: opx1 - read.px( system.file( extdata, example.px, package = pxR) ) write.px ( opx1, file = ’opx.px’) # write a copy opx2 - read.px (’opx.px’) # read the copy con el que lees un archivo px y su contenido lo guardas en otro lugar. Si tienes más dudas, puedes revisar el manual del paquete pxR, que está en http://cran.r-project.org/web/packages/pxR/pxR.pdf Recuerda que esta lista de correos es principalmente para personas que hablan en inglés, por lo que si preguntas en ese idioma, habrá más posibilidades de que te respondan. Saludos :) 2013/7/16 Belén Cillero belen.cill...@hotmail.com: Buenas tardes Una vez que he leído las variables, sexo, edad, estado civil y nacionalidad, ¿cómo genero un px para realizar las distintas consultas?. De momento lo único que he podido hacer con pxR es leer archivos de extensión px pero no sé escribirlos. Muchas gracias [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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. -- Rafael Robledo J. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to remove attributes from scale() in a matrix?
Hi list, I am using scale() to standardize a distribution? But why does it give me attributes attached to the data? I just want a standardized matrix, that is all. library(mvtnorm) x - rmvnorm(15, mean=rep(50, 10)) x [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [1,] 51.17519 52.34341 49.63084 47.99234 51.63113 50.91391 49.36819 49.23901 51.17377 [2,] 50.57039 49.17210 48.64395 49.03940 49.65761 49.93840 49.94883 50.69044 49.57632 [3,] 50.64811 50.21503 50.13786 49.15879 48.51550 50.19444 50.23710 50.98040 51.37032 [4,] 49.22797 49.66445 49.93287 48.63681 50.49457 50.33302 52.29552 49.98424 51.04724 [5,] 49.72099 50.84510 50.60976 49.60883 53.59509 49.14728 50.23134 49.09141 49.23780 [6,] 49.49126 50.90938 49.67140 50.08951 49.79854 49.03711 50.26037 50.24975 48.26958 [7,] 51.12384 47.92778 50.60112 49.01554 49.47515 50.12756 51.65216 49.21998 49.63808 [8,] 51.45123 50.44037 50.01039 50.27511 49.97658 51.63002 50.37156 50.02685 48.95423 [9,] 51.16989 50.16200 51.17724 50.71678 50.79565 50.27128 51.05608 49.61165 47.81732 [10,] 49.54263 49.93501 49.71762 49.33378 51.44935 51.53775 50.54346 49.98333 49.59422 [11,] 51.16497 49.82914 49.08821 51.02918 49.67663 49.53498 50.26647 49.48569 50.94504 [12,] 51.16827 50.50244 49.13003 49.00155 50.26457 48.85465 49.11593 50.58031 51.14926 [13,] 48.26216 49.94866 48.62526 49.11995 50.40082 49.25359 48.57677 50.66760 49.44108 [14,] 49.82530 49.17352 50.05588 50.51265 51.04926 50.32474 49.78180 50.48349 49.92431 [15,] 50.55772 49.84691 47.95021 50.24911 49.85335 50.73062 51.48718 51.36693 50.18307 [,10] [1,] 50.13859 [2,] 51.54920 [3,] 49.23230 [4,] 50.92683 [5,] 50.97708 [6,] 50.78799 [7,] 50.53913 [8,] 49.30832 [9,] 49.43606 [10,] 49.42060 [11,] 50.21002 [12,] 51.94848 [13,] 49.41352 [14,] 52.24064 [15,] 51.19474 scale(x, center=TRUE, scale=TRUE) [,1] [,2] [,3][,4][,5] [,6][,7] [1,] 0.8890317 2.3390090 -0.040395734 -1.86089754 1.00159470 0.92533476 -0.99715965 [2,] 0.2452502 -0.9109703 -1.190404546 -0.63771097 -0.66104313 -0.21446975 -0.40514793 [3,] 0.3279747 0.1578297 0.550427419 -0.49823662 -1.62323564 0.08468695 -0.11121941 [4,] -1.1837031 -0.4064112 0.311551281 -1.10802250 0.04407804 0.24660932 1.98754311 [5,] -0.6589074 0.8035298 1.100314901 0.02749734 2.65618150 -1.13883336 -0.11709623 [6,] -0.9034419 0.8694088 0.006865424 0.58904255 -0.54231158 -1.26755243 -0.08749646 [7,] 0.8343705 -2.1861602 1.090250934 -0.66558751 -0.81476108 0.00655050 1.33157578 [8,] 1.1828615 0.3887665 0.401888014 0.80585326 -0.39231482 1.76205433 0.02587038 [9,] 0.8833860 0.1034854 1.761589113 1.32181395 0.29773018 0.17447101 0.72381232 [10,] -0.8487569 -0.1291363 0.060728488 -0.29381647 0.84844800 1.65423826 0.20113824 [11,] 0.8781560 -0.2376361 -0.672712386 1.68676651 -0.64501776 -0.68583461 -0.08127647 [12,] 0.8816611 0.4523675 -0.623990804 -0.68193230 -0.14968994 -1.48074503 -1.25436403 [13,] -2.2117715 -0.1151423 -1.212190165 -0.54361597 -0.03490809 -1.01461386 -1.80409304 [14,] -0.5478718 -0.9095198 0.454889973 1.08335795 0.51138447 0.23693367 -0.57544865 [15,] 0.2317608 -0.2194204 -1.998811911 0.77548830 -0.49613484 0.71117025 1.16336204 [,8][,9] [,10] [1,] -1.2666791 1.17934107 -0.35061189 [2,] 0.8423439 -0.28600703 1.06389274 [3,] 1.2636749 1.35963155 -1.25940610 [4,] -0.1838111 1.06327078 0.43980595 [5,] -1.4811512 -0.59653247 0.49019839 [6,] 0.2019965 -1.48467432 0.30058779 [7,] -1.2943281 -0.22935616 0.05103467 [8,] -0.1218950 -0.85664924 -1.18316969 [9,] -0.7252082 -1.89953387 -1.05507780 [10,] -0.1851315 -0.26958168 -1.07058564 [11,] -0.9082374 0.96952049 -0.27897948 [12,] 0.6823136 1.15685832 1.46428187 [13,] 0.8091562 -0.41005981 -1.07768018 [14,] 0.5416286 0.03320871 1.75724879 [15,] 1.8253278 0.27056365 0.70846058 attr(,scaled:center) [1] 50.33999 50.06102 49.66551 49.58529 50.44225 50.12196 50.34618 50.11074 49.88811 [10] 50.48823 attr(,scaled:scale) [1] 0.9394453 0.9757930 0.8581604 0.8560117 1.1869812 0.8558562 0.9807762 0.6882016 [9] 1.0901550 0.9972455 Also, attributes(x) - NULL will not work since this is matrix not vector. Thanks, Mike __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to remove attributes from scale() in a matrix?
HI, Try: x1-scale(x,center=TRUE,scale=TRUE) str(x1) # num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ... # - attr(*, scaled:center)= num [1:10] 50.2 50 49.8 49.8 50.3 ... #- attr(*, scaled:scale)= num [1:10] 1.109 0.956 0.817 0.746 1.019 ... attr(x1,scaled:center)-NULL attr(x1,scaled:scale)-NULL str(x1) #num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ... A.K. - Original Message - From: C W tmrs...@gmail.com To: r-help r-help@r-project.org Cc: Sent: Tuesday, July 16, 2013 3:59 PM Subject: [R] How to remove attributes from scale() in a matrix? Hi list, I am using scale() to standardize a distribution? But why does it give me attributes attached to the data? I just want a standardized matrix, that is all. library(mvtnorm) x - rmvnorm(15, mean=rep(50, 10)) x [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [1,] 51.17519 52.34341 49.63084 47.99234 51.63113 50.91391 49.36819 49.23901 51.17377 [2,] 50.57039 49.17210 48.64395 49.03940 49.65761 49.93840 49.94883 50.69044 49.57632 [3,] 50.64811 50.21503 50.13786 49.15879 48.51550 50.19444 50.23710 50.98040 51.37032 [4,] 49.22797 49.66445 49.93287 48.63681 50.49457 50.33302 52.29552 49.98424 51.04724 [5,] 49.72099 50.84510 50.60976 49.60883 53.59509 49.14728 50.23134 49.09141 49.23780 [6,] 49.49126 50.90938 49.67140 50.08951 49.79854 49.03711 50.26037 50.24975 48.26958 [7,] 51.12384 47.92778 50.60112 49.01554 49.47515 50.12756 51.65216 49.21998 49.63808 [8,] 51.45123 50.44037 50.01039 50.27511 49.97658 51.63002 50.37156 50.02685 48.95423 [9,] 51.16989 50.16200 51.17724 50.71678 50.79565 50.27128 51.05608 49.61165 47.81732 [10,] 49.54263 49.93501 49.71762 49.33378 51.44935 51.53775 50.54346 49.98333 49.59422 [11,] 51.16497 49.82914 49.08821 51.02918 49.67663 49.53498 50.26647 49.48569 50.94504 [12,] 51.16827 50.50244 49.13003 49.00155 50.26457 48.85465 49.11593 50.58031 51.14926 [13,] 48.26216 49.94866 48.62526 49.11995 50.40082 49.25359 48.57677 50.66760 49.44108 [14,] 49.82530 49.17352 50.05588 50.51265 51.04926 50.32474 49.78180 50.48349 49.92431 [15,] 50.55772 49.84691 47.95021 50.24911 49.85335 50.73062 51.48718 51.36693 50.18307 [,10] [1,] 50.13859 [2,] 51.54920 [3,] 49.23230 [4,] 50.92683 [5,] 50.97708 [6,] 50.78799 [7,] 50.53913 [8,] 49.30832 [9,] 49.43606 [10,] 49.42060 [11,] 50.21002 [12,] 51.94848 [13,] 49.41352 [14,] 52.24064 [15,] 51.19474 scale(x, center=TRUE, scale=TRUE) [,1] [,2] [,3] [,4] [,5] [,6] [,7] [1,] 0.8890317 2.3390090 -0.040395734 -1.86089754 1.00159470 0.92533476 -0.99715965 [2,] 0.2452502 -0.9109703 -1.190404546 -0.63771097 -0.66104313 -0.21446975 -0.40514793 [3,] 0.3279747 0.1578297 0.550427419 -0.49823662 -1.62323564 0.08468695 -0.11121941 [4,] -1.1837031 -0.4064112 0.311551281 -1.10802250 0.04407804 0.24660932 1.98754311 [5,] -0.6589074 0.8035298 1.100314901 0.02749734 2.65618150 -1.13883336 -0.11709623 [6,] -0.9034419 0.8694088 0.006865424 0.58904255 -0.54231158 -1.26755243 -0.08749646 [7,] 0.8343705 -2.1861602 1.090250934 -0.66558751 -0.81476108 0.00655050 1.33157578 [8,] 1.1828615 0.3887665 0.401888014 0.80585326 -0.39231482 1.76205433 0.02587038 [9,] 0.8833860 0.1034854 1.761589113 1.32181395 0.29773018 0.17447101 0.72381232 [10,] -0.8487569 -0.1291363 0.060728488 -0.29381647 0.84844800 1.65423826 0.20113824 [11,] 0.8781560 -0.2376361 -0.672712386 1.68676651 -0.64501776 -0.68583461 -0.08127647 [12,] 0.8816611 0.4523675 -0.623990804 -0.68193230 -0.14968994 -1.48074503 -1.25436403 [13,] -2.2117715 -0.1151423 -1.212190165 -0.54361597 -0.03490809 -1.01461386 -1.80409304 [14,] -0.5478718 -0.9095198 0.454889973 1.08335795 0.51138447 0.23693367 -0.57544865 [15,] 0.2317608 -0.2194204 -1.998811911 0.77548830 -0.49613484 0.71117025 1.16336204 [,8] [,9] [,10] [1,] -1.2666791 1.17934107 -0.35061189 [2,] 0.8423439 -0.28600703 1.06389274 [3,] 1.2636749 1.35963155 -1.25940610 [4,] -0.1838111 1.06327078 0.43980595 [5,] -1.4811512 -0.59653247 0.49019839 [6,] 0.2019965 -1.48467432 0.30058779 [7,] -1.2943281 -0.22935616 0.05103467 [8,] -0.1218950 -0.85664924 -1.18316969 [9,] -0.7252082 -1.89953387 -1.05507780 [10,] -0.1851315 -0.26958168 -1.07058564 [11,] -0.9082374 0.96952049 -0.27897948 [12,] 0.6823136 1.15685832 1.46428187 [13,] 0.8091562 -0.41005981 -1.07768018 [14,] 0.5416286 0.03320871 1.75724879 [15,] 1.8253278 0.27056365 0.70846058 attr(,scaled:center) [1] 50.33999 50.06102 49.66551 49.58529 50.44225 50.12196 50.34618 50.11074 49.88811 [10] 50.48823 attr(,scaled:scale) [1] 0.9394453 0.9757930 0.8581604 0.8560117 1.1869812 0.8558562 0.9807762 0.6882016 [9] 1.0901550 0.9972455 Also, attributes(x) - NULL will not work since this is matrix not vector. Thanks, Mike __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting
Re: [R] Importing data by odbcConnectExcel in 64 bit
Tena koe
Perhaps the help file will give you some ideas:
odbcConnectAccess, odbcConnectDbase and odbcConnectExcel are convenience
wrappers to generate connection strings for those file types. The files given
can be relative to the R working directory or absolute paths (and it seems also
relative to the user's home directory). The file name can be omitted, which
will on Rgui bring up a dialog box to search for a file.
Note: they will only work with English-language 32-bit versions of the
Microsoft drivers, which may or may not be installed in other locales, and are
not usable from 64-bit R. The 2007 versions work with the drivers which are
installed with Office 2007/2010 and give access to formats such as '*.xlsx' and
'*.accdb'. These drivers are also available separately and there is a 64-bit
version: see the package manual. (You must have the 32-bit drivers when using
32-bit R and the 64-bit drivers when using 64-bit R: otherwise there will be a
cryptic message about a driver not being found. And the 64-bit drivers cannot
be installed alongside 32-bit Microsoft Office, and vice versa.
See the package manual for some of the peculiarities of the Excel drivers.
readOnly = TRUE may allow very limited changes (to insert and update rows).
HTH
Peter Alspach
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Ahmed Attia
Sent: Wednesday, 17 July 2013 6:25 a.m.
To: r-help@r-project.org
Subject: [R] Importing data by odbcConnectExcel in 64 bit
I have probably an old question.
I have R.3.0.1 installed in 64 bit windows 7. The odbcConnectExcel in RODBC
library does not work. Tried odbcConnectExcel2007 still does not work.
Any ideas.
Thanks
Melissa-sqlFetch(odbcConnectExcel2007(F:\\Cotton2012\\validation.xlsx),sqtable
= Sheet3,
+ na.strings = NA, as.is = TRUE)
Error in sqlFetch(odbcConnectExcel2007(F:\\Cotton2012\\validation.xlsx),
:
first argument is not an open RODBC channel In addition: Warning messages:
1: In odbcDriverConnect(con, tabQuote = c([, ]), ...) :
[RODBC] ERROR: state IM002, code 0, message [Microsoft][ODBC Driver Manager]
Data source name not found and no default driver specified
2: In odbcDriverConnect(con, tabQuote = c([, ]), ...) :
ODBC connection failed
Melissa-sqlFetch(odbcConnectExcel(F:\\Cotton2012\\validation.xlsx),sqtable
= Sheet3,
+ na.strings = NA, as.is = TRUE)
Error in odbcConnectExcel(F:\\Cotton2012\\validation.xlsx) :
odbcConnectExcel is only usable with 32-bit Windows
--
Ahmed M. Attia
Research Assistant
Dept. Of SoilCrop Sciences
Texas AM University
ahmed ahmeda...@zu.edu.eg.at...@ag.tamu.edu
Cell phone: 001-979-248-5215
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and provide commented, minimal, self-contained, reproducible code.
The contents of this e-mail are confidential and may be ...{{dropped:14}}
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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] Fitting Mixture distributions
I was trying to use the normixEM in mixtools and I got this error message. And I got this error message One of the variances is going to zero; trying new starting values. Error in normalmixEM(as.matrix(temp[[gc]][, -(f + 1)])) : Too many tries! Are there any other packages for fitting mixture distributions ? Tjun Kiat Teo [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] Fitting Mixture distributions
Hello,
Try the following.
library(sos)
findFn('fitting mixture distribution')
It found several other packages.
Hope this helps,
Rui Barradas
Em 16-07-2013 21:59, Tjun Kiat Teo escreveu:
I was trying to use the normixEM in mixtools and I got this error message.
And I got this error message
One of the variances is going to zero; trying new starting values.
Error in normalmixEM(as.matrix(temp[[gc]][, -(f + 1)])) : Too many tries!
Are there any other packages for fitting mixture distributions ?
Tjun Kiat Teo
[[alternative HTML version deleted]]
__
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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-help@r-project.org mailing list
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] Fitting Mixture distributions
Hi Tjun Kiat Teo, you try to fit a Normal mixture to some data. The Normal mixture is very delicate when it comes to parameter search: If the variance gets closer and closer to zero, the log Likelihood becomes larger and larger for any values of the remaining parameters. Furthermore for the EM algorithm it is known, that it takes sometimes very long until convergence is reached. Try the following: Use as starting values for the component parameters: start.par - mean(your.data, na.rm = TRUE) + sd(your.data, na.rm = TRUE) * runif(K) For the weights just use either 1/K or the R cluster function with K clusters Here K is the number of components. Further enlarge the maximum number of iterations. What you could also try is to randomize start parameters and run an SEM (Stochastic EM). In my opinion the better method is in this case a Bayesian method: MCMC. Best Simon On Jul 16, 2013, at 10:59 PM, Tjun Kiat Teo teotj...@gmail.com wrote: I was trying to use the normixEM in mixtools and I got this error message. And I got this error message One of the variances is going to zero; trying new starting values. Error in normalmixEM(as.matrix(temp[[gc]][, -(f + 1)])) : Too many tries! Are there any other packages for fitting mixture distributions ? Tjun Kiat Teo [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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 https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to remove attributes from scale() in a matrix?
Arun, thanks for the quick response. That helps. Why does scale() give attributes? What's the point of that? I don't see apply() or any similar functions do it. Just for my curiosity. Mike On Tue, Jul 16, 2013 at 4:07 PM, arun smartpink...@yahoo.com wrote: HI, Try: x1-scale(x,center=TRUE,scale=TRUE) str(x1) # num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ... # - attr(*, scaled:center)= num [1:10] 50.2 50 49.8 49.8 50.3 ... #- attr(*, scaled:scale)= num [1:10] 1.109 0.956 0.817 0.746 1.019 ... attr(x1,scaled:center)-NULL attr(x1,scaled:scale)-NULL str(x1) #num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ... A.K. - Original Message - From: C W tmrs...@gmail.com To: r-help r-help@r-project.org Cc: Sent: Tuesday, July 16, 2013 3:59 PM Subject: [R] How to remove attributes from scale() in a matrix? Hi list, I am using scale() to standardize a distribution? But why does it give me attributes attached to the data? I just want a standardized matrix, that is all. library(mvtnorm) x - rmvnorm(15, mean=rep(50, 10)) x [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [1,] 51.17519 52.34341 49.63084 47.99234 51.63113 50.91391 49.36819 49.23901 51.17377 [2,] 50.57039 49.17210 48.64395 49.03940 49.65761 49.93840 49.94883 50.69044 49.57632 [3,] 50.64811 50.21503 50.13786 49.15879 48.51550 50.19444 50.23710 50.98040 51.37032 [4,] 49.22797 49.66445 49.93287 48.63681 50.49457 50.33302 52.29552 49.98424 51.04724 [5,] 49.72099 50.84510 50.60976 49.60883 53.59509 49.14728 50.23134 49.09141 49.23780 [6,] 49.49126 50.90938 49.67140 50.08951 49.79854 49.03711 50.26037 50.24975 48.26958 [7,] 51.12384 47.92778 50.60112 49.01554 49.47515 50.12756 51.65216 49.21998 49.63808 [8,] 51.45123 50.44037 50.01039 50.27511 49.97658 51.63002 50.37156 50.02685 48.95423 [9,] 51.16989 50.16200 51.17724 50.71678 50.79565 50.27128 51.05608 49.61165 47.81732 [10,] 49.54263 49.93501 49.71762 49.33378 51.44935 51.53775 50.54346 49.98333 49.59422 [11,] 51.16497 49.82914 49.08821 51.02918 49.67663 49.53498 50.26647 49.48569 50.94504 [12,] 51.16827 50.50244 49.13003 49.00155 50.26457 48.85465 49.11593 50.58031 51.14926 [13,] 48.26216 49.94866 48.62526 49.11995 50.40082 49.25359 48.57677 50.66760 49.44108 [14,] 49.82530 49.17352 50.05588 50.51265 51.04926 50.32474 49.78180 50.48349 49.92431 [15,] 50.55772 49.84691 47.95021 50.24911 49.85335 50.73062 51.48718 51.36693 50.18307 [,10] [1,] 50.13859 [2,] 51.54920 [3,] 49.23230 [4,] 50.92683 [5,] 50.97708 [6,] 50.78799 [7,] 50.53913 [8,] 49.30832 [9,] 49.43606 [10,] 49.42060 [11,] 50.21002 [12,] 51.94848 [13,] 49.41352 [14,] 52.24064 [15,] 51.19474 scale(x, center=TRUE, scale=TRUE) [,1] [,2] [,3][,4][,5] [,6][,7] [1,] 0.8890317 2.3390090 -0.040395734 -1.86089754 1.00159470 0.92533476 -0.99715965 [2,] 0.2452502 -0.9109703 -1.190404546 -0.63771097 -0.66104313 -0.21446975 -0.40514793 [3,] 0.3279747 0.1578297 0.550427419 -0.49823662 -1.62323564 0.08468695 -0.11121941 [4,] -1.1837031 -0.4064112 0.311551281 -1.10802250 0.04407804 0.24660932 1.98754311 [5,] -0.6589074 0.8035298 1.100314901 0.02749734 2.65618150 -1.13883336 -0.11709623 [6,] -0.9034419 0.8694088 0.006865424 0.58904255 -0.54231158 -1.26755243 -0.08749646 [7,] 0.8343705 -2.1861602 1.090250934 -0.66558751 -0.81476108 0.00655050 1.33157578 [8,] 1.1828615 0.3887665 0.401888014 0.80585326 -0.39231482 1.76205433 0.02587038 [9,] 0.8833860 0.1034854 1.761589113 1.32181395 0.29773018 0.17447101 0.72381232 [10,] -0.8487569 -0.1291363 0.060728488 -0.29381647 0.84844800 1.65423826 0.20113824 [11,] 0.8781560 -0.2376361 -0.672712386 1.68676651 -0.64501776 -0.68583461 -0.08127647 [12,] 0.8816611 0.4523675 -0.623990804 -0.68193230 -0.14968994 -1.48074503 -1.25436403 [13,] -2.2117715 -0.1151423 -1.212190165 -0.54361597 -0.03490809 -1.01461386 -1.80409304 [14,] -0.5478718 -0.9095198 0.454889973 1.08335795 0.51138447 0.23693367 -0.57544865 [15,] 0.2317608 -0.2194204 -1.998811911 0.77548830 -0.49613484 0.71117025 1.16336204 [,8][,9] [,10] [1,] -1.2666791 1.17934107 -0.35061189 [2,] 0.8423439 -0.28600703 1.06389274 [3,] 1.2636749 1.35963155 -1.25940610 [4,] -0.1838111 1.06327078 0.43980595 [5,] -1.4811512 -0.59653247 0.49019839 [6,] 0.2019965 -1.48467432 0.30058779 [7,] -1.2943281 -0.22935616 0.05103467 [8,] -0.1218950 -0.85664924 -1.18316969 [9,] -0.7252082 -1.89953387 -1.05507780 [10,] -0.1851315 -0.26958168 -1.07058564 [11,] -0.9082374 0.96952049 -0.27897948 [12,] 0.6823136 1.15685832 1.46428187 [13,] 0.8091562 -0.41005981 -1.07768018 [14,] 0.5416286 0.03320871 1.75724879 [15,] 1.8253278 0.27056365 0.70846058 attr(,scaled:center) [1] 50.33999 50.06102 49.66551 49.58529 50.44225 50.12196 50.34618 50.11074 49.88811 [10]
Re: [R] How to remove attributes from scale() in a matrix?
Hi Mike,
If you check ?scale
For ‘scale.default’, the centered, scaled matrix. The numeric
centering and scalings used (if any) are returned as attributes
‘scaled:center’ and ‘scaled:scale’
By checking the source code:
methods(scale)
getAnywhere('scale.default')
function (x, center = TRUE, scale = TRUE)
{
x - as.matrix(x)
nc - ncol(x)
if (is.logical(center)) {
if (center) {
center - colMeans(x, na.rm = TRUE)
x - sweep(x, 2L, center, check.margin = FALSE)
}
}
else if (is.numeric(center) (length(center) == nc))
x - sweep(x, 2L, center, check.margin = FALSE)
else stop(length of 'center' must equal the number of columns of 'x')
if (is.logical(scale)) {
if (scale) {
f - function(v) {
v - v[!is.na(v)]
sqrt(sum(v^2)/max(1, length(v) - 1L))
}
scale - apply(x, 2L, f)
x - sweep(x, 2L, scale, /, check.margin = FALSE)
}
}
else if (is.numeric(scale) length(scale) == nc)
x - sweep(x, 2L, scale, /, check.margin = FALSE)
else stop(length of 'scale' must equal the number of columns of 'x')
if (is.numeric(center))
attr(x, scaled:center) - center
if (is.numeric(scale))
attr(x, scaled:scale) - scale
x
}
#You can comment out the last few lines:
scale1- function (x, center = TRUE, scale = TRUE)
{
x - as.matrix(x)
nc - ncol(x)
if (is.logical(center)) {
if (center) {
center - colMeans(x, na.rm = TRUE)
x - sweep(x, 2L, center, check.margin = FALSE)
}
}
else if (is.numeric(center) (length(center) == nc))
x - sweep(x, 2L, center, check.margin = FALSE)
else stop(length of 'center' must equal the number of columns of 'x')
if (is.logical(scale)) {
if (scale) {
f - function(v) {
v - v[!is.na(v)]
sqrt(sum(v^2)/max(1, length(v) - 1L))
}
scale - apply(x, 2L, f)
x - sweep(x, 2L, scale, /, check.margin = FALSE)
}
}
else if (is.numeric(scale) length(scale) == nc)
x - sweep(x, 2L, scale, /, check.margin = FALSE)
else stop(length of 'scale' must equal the number of columns of 'x')
#if (is.numeric(center))
# attr(x, scaled:center) - center
#if (is.numeric(scale))
# attr(x, scaled:scale) - scale
x
}
x2-scale1(x,center=TRUE,scale=TRUE)
str(x2)
# num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ...
identical(x1,x2)
#[1] TRUE
A.K.
- Original Message -
From: C W tmrs...@gmail.com
To: arun smartpink...@yahoo.com
Cc: R help r-help@r-project.org
Sent: Tuesday, July 16, 2013 6:58 PM
Subject: Re: [R] How to remove attributes from scale() in a matrix?
Arun, thanks for the quick response. That helps.
Why does scale() give attributes? What's the point of that? I don't
see apply() or any similar functions do it. Just for my curiosity.
Mike
On Tue, Jul 16, 2013 at 4:07 PM, arun smartpink...@yahoo.com wrote:
HI,
Try:
x1-scale(x,center=TRUE,scale=TRUE)
str(x1)
# num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ...
# - attr(*, scaled:center)= num [1:10] 50.2 50 49.8 49.8 50.3 ...
#- attr(*, scaled:scale)= num [1:10] 1.109 0.956 0.817 0.746 1.019 ...
attr(x1,scaled:center)-NULL
attr(x1,scaled:scale)-NULL
str(x1)
#num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ...
A.K.
- Original Message -
From: C W tmrs...@gmail.com
To: r-help r-help@r-project.org
Cc:
Sent: Tuesday, July 16, 2013 3:59 PM
Subject: [R] How to remove attributes from scale() in a matrix?
Hi list,
I am using scale() to standardize a distribution? But why does it
give me attributes attached to the data? I just want a standardized
matrix, that is all.
library(mvtnorm)
x - rmvnorm(15, mean=rep(50, 10))
x
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[,8] [,9]
[1,] 51.17519 52.34341 49.63084 47.99234 51.63113 50.91391 49.36819
49.23901 51.17377
[2,] 50.57039 49.17210 48.64395 49.03940 49.65761 49.93840 49.94883
50.69044 49.57632
[3,] 50.64811 50.21503 50.13786 49.15879 48.51550 50.19444 50.23710
50.98040 51.37032
[4,] 49.22797 49.66445 49.93287 48.63681 50.49457 50.33302 52.29552
49.98424 51.04724
[5,] 49.72099 50.84510 50.60976 49.60883 53.59509 49.14728 50.23134
49.09141 49.23780
[6,] 49.49126 50.90938 49.67140 50.08951 49.79854 49.03711 50.26037
50.24975 48.26958
[7,] 51.12384 47.92778 50.60112 49.01554 49.47515 50.12756 51.65216
49.21998 49.63808
[8,] 51.45123 50.44037 50.01039 50.27511 49.97658 51.63002 50.37156
50.02685 48.95423
[9,] 51.16989 50.16200 51.17724 50.71678 50.79565 50.27128 51.05608
49.61165 47.81732
[10,] 49.54263 49.93501 49.71762 49.33378 51.44935 51.53775 50.54346
49.98333 49.59422
[11,] 51.16497 49.82914 49.08821 51.02918 49.67663 49.53498 50.26647
49.48569 50.94504
[12,]
Re: [R] How to remove attributes from scale() in a matrix?
Thanks, very clear!
On Tue, Jul 16, 2013 at 7:08 PM, arun smartpink...@yahoo.com wrote:
Hi Mike,
If you check ?scale
For ‘scale.default’, the centered, scaled matrix. The numeric
centering and scalings used (if any) are returned as attributes
‘scaled:center’ and ‘scaled:scale’
By checking the source code:
methods(scale)
getAnywhere('scale.default')
function (x, center = TRUE, scale = TRUE)
{
x - as.matrix(x)
nc - ncol(x)
if (is.logical(center)) {
if (center) {
center - colMeans(x, na.rm = TRUE)
x - sweep(x, 2L, center, check.margin = FALSE)
}
}
else if (is.numeric(center) (length(center) == nc))
x - sweep(x, 2L, center, check.margin = FALSE)
else stop(length of 'center' must equal the number of columns of 'x')
if (is.logical(scale)) {
if (scale) {
f - function(v) {
v - v[!is.na(v)]
sqrt(sum(v^2)/max(1, length(v) - 1L))
}
scale - apply(x, 2L, f)
x - sweep(x, 2L, scale, /, check.margin = FALSE)
}
}
else if (is.numeric(scale) length(scale) == nc)
x - sweep(x, 2L, scale, /, check.margin = FALSE)
else stop(length of 'scale' must equal the number of columns of 'x')
if (is.numeric(center))
attr(x, scaled:center) - center
if (is.numeric(scale))
attr(x, scaled:scale) - scale
x
}
#You can comment out the last few lines:
scale1- function (x, center = TRUE, scale = TRUE)
{
x - as.matrix(x)
nc - ncol(x)
if (is.logical(center)) {
if (center) {
center - colMeans(x, na.rm = TRUE)
x - sweep(x, 2L, center, check.margin = FALSE)
}
}
else if (is.numeric(center) (length(center) == nc))
x - sweep(x, 2L, center, check.margin = FALSE)
else stop(length of 'center' must equal the number of columns of 'x')
if (is.logical(scale)) {
if (scale) {
f - function(v) {
v - v[!is.na(v)]
sqrt(sum(v^2)/max(1, length(v) - 1L))
}
scale - apply(x, 2L, f)
x - sweep(x, 2L, scale, /, check.margin = FALSE)
}
}
else if (is.numeric(scale) length(scale) == nc)
x - sweep(x, 2L, scale, /, check.margin = FALSE)
else stop(length of 'scale' must equal the number of columns of 'x')
#if (is.numeric(center))
#attr(x, scaled:center) - center
#if (is.numeric(scale))
#attr(x, scaled:scale) - scale
x
}
x2-scale1(x,center=TRUE,scale=TRUE)
str(x2)
# num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ...
identical(x1,x2)
#[1] TRUE
A.K.
- Original Message -
From: C W tmrs...@gmail.com
To: arun smartpink...@yahoo.com
Cc: R help r-help@r-project.org
Sent: Tuesday, July 16, 2013 6:58 PM
Subject: Re: [R] How to remove attributes from scale() in a matrix?
Arun, thanks for the quick response. That helps.
Why does scale() give attributes? What's the point of that? I don't
see apply() or any similar functions do it. Just for my curiosity.
Mike
On Tue, Jul 16, 2013 at 4:07 PM, arun smartpink...@yahoo.com wrote:
HI,
Try:
x1-scale(x,center=TRUE,scale=TRUE)
str(x1)
# num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ...
# - attr(*, scaled:center)= num [1:10] 50.2 50 49.8 49.8 50.3 ...
#- attr(*, scaled:scale)= num [1:10] 1.109 0.956 0.817 0.746 1.019 ...
attr(x1,scaled:center)-NULL
attr(x1,scaled:scale)-NULL
str(x1)
#num [1:15, 1:10] -0.2371 -0.5606 -0.8242 1.5985 -0.0164 ...
A.K.
- Original Message -
From: C W tmrs...@gmail.com
To: r-help r-help@r-project.org
Cc:
Sent: Tuesday, July 16, 2013 3:59 PM
Subject: [R] How to remove attributes from scale() in a matrix?
Hi list,
I am using scale() to standardize a distribution? But why does it
give me attributes attached to the data? I just want a standardized
matrix, that is all.
library(mvtnorm)
x - rmvnorm(15, mean=rep(50, 10))
x
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[,8] [,9]
[1,] 51.17519 52.34341 49.63084 47.99234 51.63113 50.91391 49.36819
49.23901 51.17377
[2,] 50.57039 49.17210 48.64395 49.03940 49.65761 49.93840 49.94883
50.69044 49.57632
[3,] 50.64811 50.21503 50.13786 49.15879 48.51550 50.19444 50.23710
50.98040 51.37032
[4,] 49.22797 49.66445 49.93287 48.63681 50.49457 50.33302 52.29552
49.98424 51.04724
[5,] 49.72099 50.84510 50.60976 49.60883 53.59509 49.14728 50.23134
49.09141 49.23780
[6,] 49.49126 50.90938 49.67140 50.08951 49.79854 49.03711 50.26037
50.24975 48.26958
[7,] 51.12384 47.92778 50.60112 49.01554 49.47515 50.12756 51.65216
49.21998 49.63808
[8,] 51.45123 50.44037 50.01039 50.27511 49.97658 51.63002 50.37156
50.02685 48.95423
[9,] 51.16989 50.16200 51.17724 50.71678 50.79565 50.27128 51.05608
49.61165 47.81732
[10,] 49.54263
Re: [R] Announcing TIBCO Enterprise Runtime for R
Hi Michael Thanks for your questions. Posting them here is fine, or you can also post them on the TERR Community site: https://www.tibcommunity.com/community/products/analytics/terr. Initial answers below--feel free to ask follow ups: 1. Do you have concrete benchmarks of what sorts of operations are faster? In particular, are you, like Revolution, licensing MKL? Yes we have benchmarks, and yes we license MKL. It's challenging to come up with comprehensive, meaningful benchmarks, and so we are looking to the community for benchmarks they'd like to see. Feel free to post anything you are interested in on the community site, or email me directly. - Generally we will be much faster for pure R language operations (e.g., for loops), since we have written a new, R-compatible interpreter from the ground up. The performance ratio will tend to improve with larger data sets, since we have implemented highly efficient memory management. - Since we license MKL (and distribute it in the free Developer's Edition), we will have all the related matrix-operation speed advantages. - For more detailed info and some benchmarks, see the presentation that Michael Sannella (the chief architect for TERR) gave at useR 2013. It's now available on slideshare: http://www.slideshare.net/loubajukyorgan/sannella-use-r2013terrmemorymanagement 2. Your white-paper boasts of superior memory management; can you give more details? Are we now reference counting, or abandoning copy-on-write to play better with fork(), or running concurrently? In turn, does this mean the C-API is not kept as is and any package with compiled code isn't usable? See Michael's presentation Memory Management in TERR, referenced above for full details. In particular, yes, full reference counting has been implemented. Our goal is to have packages with compiled code work as-is, without modification. To do this, since the internals of our engine are different, we need to emulate the APIs for these packages to work. We have done this for many APIs and packages so far. See the Community site for a list of packages known to run successfully. 3. You speak of being more robust: is this at a language level (i.e.,something simpler to use than try()/tryCatch()) or an implementation level? If the latter, what non-robustnesses are being addressed? Primarily, the greater robustness comes from the improvements to memory management. Beyond that, we do extensive automated testing (using the deep array of tests we have built up over the years for S+ development) to ensure reliability, and we have done some work at the language level (around improvements to signal handling, throwing and catching errors, etc.). If you'd like more info the last point, email me directly and I can get you in touch with Michael. 4. What are y'all's plans for supporting TERR as 'regular R' evolves? Will it track or will things diverge over time? Our intent is to keep up with current R as closely as possible. In talking to our customers, we have heard loud and clear that they love the idea of an enterprise R engine, but they don't want to be locked into a proprietary flavor of R. 5. Known (and not intended to change) differences? Very minor items. Full list on the Community Site. 6. Is the whole R-level API exposed or only a selected subset? I'm thinking in particular of (1) things like .colMeans() which seem rather tied to the implementation; (2) graphics devices; (3) the promise mechanism and copy-on-write semantics? As mentioned in #2 above, we are implementing the R APIs over time. For a full list of what we have and haven't yet implemented, check out the community site, and feel free to leave comments about what you'd like us to prioritize next. Regards, and thanks again for your interest. Lou -Original Message- From: R. Michael Weylandt [mailto:michael.weyla...@gmail.com] Sent: Thursday, July 11, 2013 1:59 PM To: Louis Bajuk-Yorgan Cc: r-help Subject: Re: [R] Announcing TIBCO Enterprise Runtime for R Hi Louis, I apologize in advance if this isn't the right forum; feel free to direct me elsewhere. Can you say a bit more about what exactly constitute the advantages of TERR over R as most readers of this list know it? Some random points of interest to me: 1. Do you have concrete benchmarks of what sorts of operations are faster? In particular, are you, like Revolution, licensing MKL? 2. Your white-paper boasts of superior memory management; can you give more details? Are we now reference counting, or abandoning copy-on-write to play better with fork(), or running concurrently? In turn, does this mean the C-API is not kept as is and any package with compiled code isn't usable? 3. You speak of being more robust: is this at a language level (i.e.,something simpler to use than try()/tryCatch()) or an implementation level? If the latter, what non-robustnesses are being addressed? 4. What are y'all's plans for
[R] interfacing with website
Hello,
I have a question about interfacing with the Atlas of Living Australia
website: http://biocache.ala.org.au/#tab_simpleSearch
The following code works and I am able to download species observations.
The problem I am having is that I would like additional fields of data. If
I manually download records for a species from ALA then you can choose to
download all records (detailed). I cannot figure out how to automate this.
I specifically need the field Locality. If done correctly this
information would be present in the rawResponse data that is returned from
ALA.
Any help with this problem would be greatly appreciated.
Thanks,
Daisy
species-Vinca minor
nRecords=FALSE
library(RCurl)
library(rjson)
sp - strsplit(as.character(species), )[[1]]
h - basicHeaderGatherer()
BaseALA_Data_URL - biocache.ala.org.au
Referer -
DataStr - paste0(/ws/webportal/occurrences?q=,sp[1],+,sp[2])
message(Querying number of records...)
rawResponse - getURL(paste0(BaseALA_Data_URL,DataStr), headerfunction =
h$update)
ResponseCode - as.integer(h$value()[status])
if(ResponseCode == 200) {
jsres - fromJSON(rawResponse)
} else {
message(No proper response.)
return(invisible())
}
nrecords - jsres$totalRecords
if(nRecords)return(nrecords)
message(Downloading , nrecords, records.)
# Download all
DataStr - paste0(DataStr, pageSize=, nrecords)
rawResponse - getURL(paste0(BaseALA_Data_URL,DataStr), headerfunction =
h$update)
if(ResponseCode == 200) {
jsres - fromJSON(rawResponse)
} else {
message(No proper response.)
return(invisible())
}
totalRecords - jsres$totalRecords
res - lapply(jsres$occurrences,
function(x)c(nameSci=x$raw_scientificName,
latitude=x$decimalLatitude,
longitude=x$decimalLongitude))
res - as.data.frame(do.call(rbind, res))
res$longitude - as.numeric(as.character(res$longitude))
res$latitude - as.numeric(as.character(res$latitude))
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] writing multiple lines to a file
HI, May be this helps: printer1- file(out1.txt,w) write(sprintf(This is line %d.\n,1),printer1,append=TRUE) write(This is line 2,printer1,append=TRUE) close(printer1) #or printer1- file(out1.txt,w) writeLines(This is line,con=printer1,sep=\n) writeLines(This is line 2,con=printer1) close(printer1) A.K. Hello, I am trying to wrote multiple lines to a file, but I only seem to be able to write the last line. printer = file(out.txt) write(sprintf(This is line %d.\n,1),printer,append=T) write(This is line 2.,printer,append=T) close(printer) How can I fix this? I would like to be able to do this in a for-loop with hundreds of elements. __ R-help@r-project.org mailing list 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] (no subject)
hi I need to use boxplot for two subsets at the same page thank you in advance Sent from Windows Mail [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] ERROR: missing value where TRUE/FALSE needed
Hello, I have a problem... I tried using a function and I get the error: ERROR: missing value where TRUE/FALSE needed Here is my code: a-mctp(Ecoli~Fecha, data=Datos, type = Tukey, alternative = two.sided, asy.method = mult.t, plot.simci = TRUE)summary(a) Ecoli, Fecha and Datos are well defined. I don't know what is the problem... THANKS [[alternative HTML version deleted]] __ R-help@r-project.org mailing list 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] Masking oceans using polypath
Hi There are a couple of problems: 1. Your 'outline' is much bigger than it needs to be. For example, the following produces just Australia ... outline - map(worldHires, regions=Australia, exact=TRUE, plot=FALSE) # returns a list of x/y coords 2. The outline you get still has NA values in it (the coastline of Australia in this database is a series of distinct lines; I don't know why that is). Fortunately, you can stitch Australia back together again like this ... subset - !is.na(outline$x) polypath(c(outline$x[subset], NA, c(xbox, rev(xbox))), c(outline$y[subset], NA, rep(ybox, each=2)), col=light blue, rule=evenodd) With those two changes, I get a much better result. You may want to fiddle a bit more to add Tasmania and bits of PNG and Indonesia back in the picture OR you could replace these problems with a different approach and use a more sophisticated map outline via a shapefile (see the 'sp' package and the 'maptools' package and possibly the R-sig-geo mailing list). Hope that helps. Paul On 07/16/13 23:17, Louise Wilson wrote: library(mapdata) image(x=110:155, y =-40:-10, z = outer(1:45, 1:30, +), xlab = lon, ylab = lat) outline - map(worldHires, plot=FALSE) # returns a list of x/y coords xrange - range(outline$x, na.rm=TRUE) # get bounding box yrange - range(outline$y, na.rm=TRUE) xbox - xrange + c(-2, 2) ybox - yrange + c(-2, 2) # create the grid path in the current device polypath(c(outline$x, NA, c(xbox, rev(xbox))), c(outline$y, NA, rep(ybox, each=2)), col=light blue, rule=evenodd) -- Dr Paul Murrell Department of Statistics The University of Auckland Private Bag 92019 Auckland New Zealand 64 9 3737599 x85392 p...@stat.auckland.ac.nz http://www.stat.auckland.ac.nz/~paul/ __ R-help@r-project.org mailing list 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.
