[R] xyplot squeezed together
Hi, I created the following example of a xyplot. The plot actually looks ok apart from that the x-axis is pretty squeezed/clinched. I tried aspect=fill already but I want to have all 3 sub plots next to each other. I tried loads of different scaling varieties but with no significant result... library(lattice) N - 6 d - data.frame(factor(rep(c(A1,A2,A3),each=N), levels=c(A1,A2,A3)), factor(rep(c(B1, B2, B3, B4, B5, B6, B7, B8, B9), each=N/3), levels=c(B1, B2, B3, B4, B5, B6, B7, B8, B9)), rep(c(0,1), each=N/3/2)) colnames(d) - c(ID, class, group) value - matrix(c(400,300, 320,380, 410,500, 800,670, 810,900, 560,750, 1100,1200, 1200,1300, 1300,1200)) d - cbind(d, value) xyplot(value ~ group | ID, d, groups = class, type = c(g, b), auto.key = list(lines = TRUE, columns = 3), xlab = blocked=0, released=1, ylab = value, aspect = 'xy', scales=list(x=list(at=-1:2, labels=c(,0,1, Anyone any ideas how to enlarge the x-axis? Cheers -- View this message in context: http://r.789695.n4.nabble.com/xyplot-squeezed-together-tp4156661p4156661.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.
Re: [R] Data Analysis for Gas Prices
On Sat, 3 Dec 2011 14:11:39 -0800 (PST) inferno846 robe...@uoregon.edu wrote: ... Also, could anyone help me figure out how to import a data table to R? When I try to create a .txt file from a word document and read it in R, the format of the first column always messes up. Any/all help is appreciated. For reading in data, avoid using Word, a program that is overkill for almost all purposes. Either use Notepad, or grab a simple text editor off the internet - preferably capable of block selection. Since you do not say just how the first column messes up, it is rather problematic trying suggest a solution the problem. The first line of the table and a couple data lines, the form of command you use to read in the data and the field separator in your table are all useful pieces of information. There are however a great many books about R out there and nearly all of them address at least briefly how to import data. Portland has one of the best bookstores on the planet. As a last resort you might try the command ??read.table from the R prompt. JD __ 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] frequency table?
Hello R-users, I've got a file with individuals as colums and the clusters where they occur in as rows. And I wanted a table which tells me how many times each individual occurs with another. I don't really know how such a table is called...it is not a frequency tableMy eventual goal is to make Venn-diagrams from the occurence of my individuals. So I've this: cluster ind1 ind2 ind3 etc. 10 1 2 23 01 31 1 1 And I want to go to this: ind1 ind2 ind3 ind1 0 42 ind2 4 04 ind3 2 4 1 is there a way to do this? Thank you for your help -- View this message in context: http://r.789695.n4.nabble.com/frequency-table-tp4156422p4156422.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.
Re: [R] pivot table help
Thank you very much! works perfectly! -- View this message in context: http://r.789695.n4.nabble.com/pivot-table-help-tp4155144p4156393.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.
Re: [R] density function always evaluating to zero
Sorry that was my poor copying and pasting. Here's the correct R code. The
problem does seem to be with the function I define as f.
# Model selection example in a bayesian framework
# two competiting non-nested models
# M0: y_t = alpha * x1^2 + e_t
# M1: y_t = beta * x1^4 + e_t
# where e_t ~ iidN(0,1)
#generate data
x1 - runif(100, min = -10, max = 10)
y - 2 * x1^2 + rnorm(100)
n - length(y)
k - 1
v - n - k
# want the posterior probabilities of the two models
# postprob_mj = p(y|model j true) * priorprob_mj / p(y)
# need to calculate the integral of p(y|alpha,h)p(alpha,h)
# and the integral of p(y|beta,h)p(beta,h)
# recall we chose p(alpha,h) = p(beta,h) = 1/h
# need to sample from the posterior to get an approximation of the integral
# # # # # # # # Model 0 # # # # # # #
z - x1^2
M - sum(z^2)
MI - 1/M
zy - crossprod(z,y)
alpha.ols - MI * zy
resid_m0 - y - z * alpha.ols
s2_m0 - sum(resid_m0^2)/v
# set up gibbs sampler
nrDraws - 1
h_sample_m0 - rgamma(nrDraws, v/2, v*s2_m0/2)
alpha_sample - matrix(0, nrow = nrDraws, ncol = 1)
for(i in 1:nrDraws) {
alpha_sample[i] - rnorm(1,alpha.ols,(1/h_sample_m0[i]) * MI)
}
# define posterior density for m0
f - function(alpha,h) {
e - y - alpha * x1^2
const - (2*pi)^(-n/2) / ( gamma(v/2) * (v*s2_m0/2)^(-v/2) )
kernel - h^((v-1)/2) * exp((-(h/2) * sum(e^2)) - (v*s2_m0)*h)
x - const * kernel
return(x)
}
# calculate approximation of p(y|m_0)
m0 -f(alpha_sample,h_sample_m0)
post_m0 - sum(m0) / nrDraws
--
View this message in context:
http://r.789695.n4.nabble.com/density-function-always-evaluating-to-zero-tp4155181p4156746.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.
Re: [R] problems using the thin plate spline method
Dear R users and Jeff, Sorry for not being quite explicit in my earlier message. My main problem is while my data seem to be read into R well (I manage to graph them and all), I cannot get the following line to work. tpsfit - Tps(cbind(x1, x2), y, scale.type=unscaled) and I get the following error message Error in as.matrix(x) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': Error: object 'x1' not found thanks for help minti Från: Jeff Newmiller [jdnew...@dcn.davis.ca.us] Skickat: den 3 december 2011 17:45 Till: Mintewab Bezabih; r-help@r-project.org Ämne: Re: [R] problems using the thin plate spline method I can tell that you are puzzled and confused. Unfortunately, I am not psychic, so I cannot tell what you did, and therefore cannot tell where you went astray. The solution is for you to read the posting guide mentioned at the bottom of every R-help message. Spend a little time to create a small bit of data like yours if your actual data is large (subset and dput are useful for this). Remember to include the output of sessionInfo, and so on. Many times you are likely to find the answer yourself by going through these steps, but they are essential for communication. Good luck. --- 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. Mintewab Bezabih mintewab.beza...@economics.gu.se wrote: Dear R users, I am a beginner in R trying to apply the thin plate spline method to my climate data. I used the example in R to do so, and the lines seem to run fine ( I am not getting errors) but I am not getting any output in the form of graph or anything. I got a warning message saying that 'surface extends beyond box'. Any help is much appreciated. thanks minti __ 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] problems using the thin plate spline method
Hello, On Sun, Dec 4, 2011 at 8:08 AM, Mintewab Bezabih mintewab.beza...@economics.gu.se wrote: Dear R users and Jeff, Sorry for not being quite explicit in my earlier message. And you are still not explicit. We have no idea what you've done. My main problem is while my data seem to be read into R well (I manage to graph them and all), I cannot get the following line to work. tpsfit - Tps(cbind(x1, x2), y, scale.type=unscaled) and I get the following error message Error in as.matrix(x) : error in evaluating the argument 'x' in selecting a method for function 'as.matrix': Error: object 'x1' not found I'd have to guess that there's no object x1. What does ls() tell you? str(x1)? What do your data look like? You were already given instructions on how to include sample data to construct a reproducible example. You said that graphing your data worked; how did you do so? The posting guide and the advice you were already given were both offered for a reason. The querent needs to do the work of formulating an understandable and answerable question. Sarah thanks for help minti Från: Jeff Newmiller [jdnew...@dcn.davis.ca.us] Skickat: den 3 december 2011 17:45 Till: Mintewab Bezabih; r-help@r-project.org Ämne: Re: [R] problems using the thin plate spline method I can tell that you are puzzled and confused. Unfortunately, I am not psychic, so I cannot tell what you did, and therefore cannot tell where you went astray. The solution is for you to read the posting guide mentioned at the bottom of every R-help message. Spend a little time to create a small bit of data like yours if your actual data is large (subset and dput are useful for this). Remember to include the output of sessionInfo, and so on. Many times you are likely to find the answer yourself by going through these steps, but they are essential for communication. Good luck. Sent from my phone. Please excuse my brevity. Mintewab Bezabih mintewab.beza...@economics.gu.se wrote: Dear R users, I am a beginner in R trying to apply the thin plate spline method to my climate data. I used the example in R to do so, and the lines seem to run fine ( I am not getting errors) but I am not getting any output in the form of graph or anything. I got a warning message saying that 'surface extends beyond box'. Any help is much appreciated. thanks minti -- Sarah Goslee http://www.functionaldiversity.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] density function always evaluating to zero
I didn't try out your extensive code, but here's one potentially serious
problem:
You only pass two arguments to f(), alpha and h, but within f you nonetheless
use x1 and y and several other things. This is bad practice, and dangerous:
you should pass all the necessary arguments to f(), not rely on the environment
to contain them.
After you fix that, working through your function step by step at the command
line and looking at the results of each line of code can be very educational.
Sarah
On Sun, Dec 4, 2011 at 7:47 AM, napps22 n.j.app...@gmail.com wrote:
Sorry that was my poor copying and pasting. Here's the correct R code. The
problem does seem to be with the function I define as f.
# Model selection example in a bayesian framework
# two competiting non-nested models
# M0: y_t = alpha * x1^2 + e_t
# M1: y_t = beta * x1^4 + e_t
# where e_t ~ iidN(0,1)
#generate data
x1 - runif(100, min = -10, max = 10)
y - 2 * x1^2 + rnorm(100)
n - length(y)
k - 1
v - n - k
# want the posterior probabilities of the two models
# postprob_mj = p(y|model j true) * priorprob_mj / p(y)
# need to calculate the integral of p(y|alpha,h)p(alpha,h)
# and the integral of p(y|beta,h)p(beta,h)
# recall we chose p(alpha,h) = p(beta,h) = 1/h
# need to sample from the posterior to get an approximation of the integral
# # # # # # # # Model 0 # # # # # # #
z - x1^2
M - sum(z^2)
MI - 1/M
zy - crossprod(z,y)
alpha.ols - MI * zy
resid_m0 - y - z * alpha.ols
s2_m0 - sum(resid_m0^2)/v
# set up gibbs sampler
nrDraws - 1
h_sample_m0 - rgamma(nrDraws, v/2, v*s2_m0/2)
alpha_sample - matrix(0, nrow = nrDraws, ncol = 1)
for(i in 1:nrDraws) {
alpha_sample[i] - rnorm(1,alpha.ols,(1/h_sample_m0[i]) * MI)
}
# define posterior density for m0
f - function(alpha,h) {
e - y - alpha * x1^2
const - (2*pi)^(-n/2) / ( gamma(v/2) * (v*s2_m0/2)^(-v/2) )
kernel - h^((v-1)/2) * exp((-(h/2) * sum(e^2)) - (v*s2_m0)*h)
x - const * kernel
return(x)
}
# calculate approximation of p(y|m_0)
m0 -f(alpha_sample,h_sample_m0)
post_m0 - sum(m0) / nrDraws
--
Sarah Goslee
http://www.functionaldiversity.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] xyplot squeezed together
You specified the aspect ratio, so your plots must have that ratio of width to height. It looks like you are trying to control layout by specifying aspect ratio? That, as you've discovered, is an ineffective way to do it. Instead, you should specify layout directly, using for your example layout=c(3,1,1) and deleting the aspect='xy' argument. Rereading the help for xyplot() more carefully would also be a good idea. Sarah On Sun, Dec 4, 2011 at 6:49 AM, syrvn ment...@gmx.net wrote: Hi, I created the following example of a xyplot. The plot actually looks ok apart from that the x-axis is pretty squeezed/clinched. I tried aspect=fill already but I want to have all 3 sub plots next to each other. I tried loads of different scaling varieties but with no significant result... library(lattice) N - 6 d - data.frame(factor(rep(c(A1,A2,A3),each=N), levels=c(A1,A2,A3)), factor(rep(c(B1, B2, B3, B4, B5, B6, B7, B8, B9), each=N/3), levels=c(B1, B2, B3, B4, B5, B6, B7, B8, B9)), rep(c(0,1), each=N/3/2)) colnames(d) - c(ID, class, group) value - matrix(c(400,300, 320,380, 410,500, 800,670, 810,900, 560,750, 1100,1200, 1200,1300, 1300,1200)) d - cbind(d, value) xyplot(value ~ group | ID, d, groups = class, type = c(g, b), auto.key = list(lines = TRUE, columns = 3), xlab = blocked=0, released=1, ylab = value, aspect = 'xy', scales=list(x=list(at=-1:2, labels=c(,0,1, Anyone any ideas how to enlarge the x-axis? Cheers -- Sarah Goslee http://www.functionaldiversity.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] RODBC connect to Excel (64-bit Windows 7)
Hi to all. I have a problem to connect to an Excel database using RODBC. Namely, I am using 64-bit R 2.14.0, under Windows 7 and I tried following: library(RODBC) channel - odbcConnectExcel(results.xlsx) Error in odbcConnectExcel(results.xlsx) : odbcConnectExcel is only usable with 32-bit Windows # ok this is clear why it doesn't work channel - odbcConnectExcel2007(results.xlsx) # this was one of proposals from old R help posts, but it doesn't work for me 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 After that as it suggested in R data import/export manual I installed AccessDatabaseEngine.exe. Also I used ODBC in c:\Windows\SysWOW64\odbcad32 to create data source called result. I check if it is created: odbcDataSources() dBASE Files Microsoft Access dBASE Driver (*.dbf, *.ndx, *.mdx) MS Access Database Microsoft Access Driver (*.mdb, *.accdb) Excel file Microsoft Excel Driver (*.xls, *.xlsx, *.xlsm, *.xlsb) * results* Microsoft Excel Driver (*.xls, *.xlsx, *.xlsm, *.xlsb) and tried again but it doesn't work: channel - odbcDriverConnect() Warning messages: 1: In odbcDriverConnect() : [RODBC] ERROR: state IM014, code 0, message [Microsoft][ODBC Driver Manager] The specified DSN contains an architecture mismatch between the Driver and Application 2: In odbcDriverConnect() : ODBC connection failed Could someone guide me what should I try next to fix a problem? Is this some problem with Drivers or not? Thanks in advance Andrija [[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] LaTeX output for summary.lm object - while displaying the information outside the table
This seemed to me to be basic, but I can't seem to find a solution online, so I wondered what I might be missing. I wish to include the output of an lm summary object inside an Sweave (.Rnw) document. I can either output the summary.lm as is, or use the xtable/Hmisc packages (through xtable or latex commands). Is there something like xtable that also gives the summary information which is available from outside the table? ( R2, F statistics etc...?) Thanks. Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- [[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] Programming Statistical Functions
As Stephen pointed out, this is easy to do. The word file the OP posted has all the necessary formulae. Now you just need to learn how to convert those formulae into R functions Stephen gave you an example of how to create a function for CV. Now run with it. perhaps something like this is what you need: http://cran.r-project.org/doc/contrib/Short-refcard.pdf It is time for you to do some reading on your own. Good luck. gvjones wrote Hello, Did you find anything helpful for calculating the statistical functions in your list. I would like to also calculate these and have been looking for some code to do so. Thanks -- View this message in context: http://r.789695.n4.nabble.com/Programming-Statistical-Functions-tp2307880p4157101.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] Vectorization instead of loops problem
Hello, I am having problems vectorizing the following (i/o using a for/next/while loop): I have 2 sequences such as: x, y 1, 30 2, -40 0, 50 0, 25 1, -5 2, -10 1, 5 0, 40 etc etc The first sequence (x) takes integer numbers only: 0, 1, 2 The sequence y can be anything... I want to be able to retrieve (in a list if possible) the 3 last values of the y sequence before a value of 1 is encountered on the x sequence, i.e: On line 5 in the above dataset, x is 1 so I need to capture values: 25, 50 and -40 of the y sequence. So the outcome (if a list) should look something like: [1],[25,50,-40] [2],[-10,-5,25] # as member #7 of x sequence is 1... etc. etc. Can I do the above avoiding for/next or while loops? I am not sure I can explain it better. Any help/pointer extremely welcome. Best regards, Costas -- +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ |c|o|s|t|a|s|@|v|o|r|l|o|w|.|o|r|g| +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ [[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] Polishing my geom_bar for publication
Dear list, I am new with ggplot2 and I have spend quiet some time putting together the following code to create the attached plot. However there's still a few things that I'm having trouble with! I would be grateful if someone can tell me how to fix (1) the colour of my bars into grey scales (2) removing the y-axis (species name) on the right figure to avoid duplication, and (3) fix the width, such that both figures have the same apparence regardless of the legend. Thank you very much in advance! The code is as follow: (a-ggplot(Final2, aes(x=spp, y=CPUE, fill=season)) + geom_bar(position=position_dodge()) + geom_errorbar(aes(ymin=CPUE-cpue.se, ymax=CPUE+cpue.se), size=.3, width=.2, position=position_dodge(.9)) + xlab(Species) + scale_x_discrete(breaks=c(100,102,107,88,90,91,92,93,94,96,98,99), labels=c(WINTER,SPINYTAIL,BIGELOW'S,SKATES (NS),THORNY,SMOOTH,ABYSSAL,LITTLE,DEEPWATER,JENSEN'S,WHITE,SOFT)) + ylab(Abundance (fish/tow)) + coord_flip() + theme_bw() + opts(axis.title.x = theme_text(size = 10)) + opts(panel.grid.minor = theme_blank()) + opts(legend.position='none') ) (b-ggplot(Final2, aes(x=spp, y=WPUE, fill=season)) + geom_bar(position=position_dodge()) + geom_errorbar(aes(ymin=WPUE-wpue.se, ymax=WPUE+wpue.se), size=.3, width=.2, position=position_dodge(.9)) + xlab(NULL)+ scale_x_discrete(breaks=c(100,102,107,88,90,91,92,93,94,96,98,99), labels=c(WINTER,SPINYTAIL,BIGELOW'S,SKATES (NS),THORNY,SMOOTH,ABYSSAL,LITTLE,DEEPWATER,JENSEN'S,WHITE,SOFT))+ ylab(Biomass (Weight (kg)/tow)) + scale_fill_hue(name=Survey season, # Legend label, use darker colors breaks=c(summer, winter), labels=c(Spring, Fall)) + coord_flip() + theme_bw() + opts(axis.title.x = theme_text(size = 10)) + opts(panel.grid.minor = theme_blank())) pdf(polishing-layout2.pdf, width = 10, height = 6) grid.newpage() pushViewport(viewport(layout = grid.layout(1, 2))) vplayout - function(x, y) viewport(layout.pos.row = x, layout.pos.col = y) print(a, vp = vplayout(1, 1)) print(b, vp = vplayout(1, 2)) dev.off() Aurelie Cosandey-Godin Ph.D. student, Department of Biology Industrial Graduate Fellow, WWF-Canada Dalhousie University | Biology Dept. | 1459 Oxford Street |Halifax, NS | Canada B3H 4R2 Phone: 1-902-494-2478 | cell: 1-902-412-3404 |Fax: 1-902-494-3736 Email: god...@dal.ca | Skype: aureliegodinco | Web: wormlab.biology.dal.ca Want to learn more about sharks in Atlantic Canada? Visit ShARCC! www.atlanticsharks.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] Vectorization instead of loops problem
On 04.12.2011 16:18, Costas Vorlow wrote: Hello, I am having problems vectorizing the following (i/o using a for/next/while loop): I have 2 sequences such as: x, y 1, 30 2, -40 0, 50 0, 25 1, -5 2, -10 1, 5 0, 40 etc etc The first sequence (x) takes integer numbers only: 0, 1, 2 The sequence y can be anything... I want to be able to retrieve (in a list if possible) the 3 last values of the y sequence before a value of 1 is encountered on the x sequence, i.e: On line 5 in the above dataset, x is 1 so I need to capture values: 25, 50 and -40 of the y sequence. So the outcome (if a list) should look something like: [1],[25,50,-40] [2],[-10,-5,25] # as member #7 of x sequence is 1... etc. etc. Can I do the above avoiding for/next or while loops? I am not sure I can explain it better. Any help/pointer extremely welcome. Best regards, Costas One way is (assuming your data is in a data.frame called dat): wx - which(dat$x==1) result - lapply(wx[wx 3], function(x) dat$y[x - (1:3)]) (where lapply is a loop, implicitly). Uwe Ligges __ 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] Linear quadratic Gaussian control with Kalman filter
I need to generate Linear quadratic Gaussian control with Kalman filter in R programming. I only get matlab code. I think that R portfolio optimisation code ( quad..) is not adequate for this topic. Linear quadratic Gaussian control with Kalman filter http://en.wikipedia.org/wiki/Linear_quadratic_Gaussian_control Thanks. -- View this message in context: http://r.789695.n4.nabble.com/Linear-quadratic-Gaussian-control-with-Kalman-filter-tp4156813p4156813.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] Extract last 3 characters from numeric vector
Hi all, I have a numeric vector with 1 decimal place, and I'd like to extract the last 3 characters, including the decimal point. The vector ranges from 0 to 20. x - round(runif(100)*20, digits=1) Some of numbers have 3 characters, and some have 4. I've read up on the substr() function but that extracts characters based on exact positions. How can I extract just the last 3 characters no matter the length of the number? e.g. from 16.7 I want 6.7, from 3.5 I want 3.5 as it is. Thanks, Kang Min __ 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] problem merging data with different shapes
I have been trying to merge datasets, one of which has a long format (Adata) and one has a (different) long format (Bdata): Adata Bdata subject order bpm subject order trial agegroup gender 1 1 70.21 1 3 2 1 1 1 69.51 2 1 2 1 1 1 68.81 3 2 2 1 1 2 69.12 1 2 1 2 1 270 2 2 3 1 2 1 2 70.52 3 1 1 2 1 3 70.2... 1 3 1 3 2 1 2 1 ... ... In the end I would like to have a dataset that contains A unchanged with the additional information from B added. subject order bpm trial agegroup gender 1 1 70.2 3 2 1 1 1 69.5 3 2 1 1 1 68.8 3 2 1 ... I have tried: newdataframe - merge(Adata,Bdata, by= c(subject, order), sort = FALSE) For some reason, the trial column is not matched to the subject and order information, despite them being identified as key-variables for the merge. (The same is true for other variables, the actual dataset has more variables and trials, but this is essentially the problem.) So it results in something like: subject order bpm trial agegroup gender 1 1 70.2 3 2 1 1 1 69.5 2 2 1 1 1 68.8 1 2 1 What could be my mistake? Thank you VERY much. Miriam -- -- __ 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] Programming Statistical Functions
Hello, Did you find anything helpful for calculating the statistical functions in your list. I would like to also calculate these and have been looking for some code to do so. Thanks -- View this message in context: http://r.789695.n4.nabble.com/Programming-Statistical-Functions-tp2307880p4157012.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.
Re: [R] Extract last 3 characters from numeric vector
You can use nchar() to get the length of the string, and use that in substring: mynum - as.character(15.6) substring(mynum, nchar(mynum)-2, nchar(mynum)) [1] 5.6 On Sun, Dec 4, 2011 at 8:38 AM, Kang Min ngokang...@gmail.com wrote: Hi all, I have a numeric vector with 1 decimal place, and I'd like to extract the last 3 characters, including the decimal point. The vector ranges from 0 to 20. x - round(runif(100)*20, digits=1) Some of numbers have 3 characters, and some have 4. I've read up on the substr() function but that extracts characters based on exact positions. How can I extract just the last 3 characters no matter the length of the number? e.g. from 16.7 I want 6.7, from 3.5 I want 3.5 as it is. Thanks, Kang Min -- Sarah Goslee http://www.functionaldiversity.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] upper bound in the integrate function depends on a parameter
This is not homework, I calculate some expectations and to finish that I
must solve integral like this one..
Upper bound have some unknown parameter, but I dont know how to write it in
R.
Do I must define m like symbol, or something else, just need help with that.
I know how this work in MatLab, but in R I have problem.
Is there any solution how to solve integral like this one?
Can you help me please little more or direct me to right way, I will
appreciate your effort.
Thanks
On Sun, Dec 4, 2011 at 6:06 AM, David Winsemius dwinsem...@comcast.netwrote:
On Dec 3, 2011, at 10:23 PM, grttt nbbfg wrote:
Sorry for my English, is not my first language..
I have some trouble in terms of using integrate function in R.
fx is a function of m and x where m is supposed to be a unknown parameter.
R is not an algebraic solver (and R-help is not a homework list.).
fx=function(m,x){
+ x*2/(3*m)*(1-x/(3*m))
+ }
The problem is in upper bound, it depends on parameter m.
integrate(fx,lower=0,upper=3***m)$value
Is it possible to use the integrate function when bounds depend on a
parameter?
If it is known, yes. You could also do some investigation:
curve(x*2/(3*5)*(1-x/(3*5)), 0, 15)
How to define m to solve this integral? The result should be m.
As I said, no homework answers here.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Vectorization instead of loops problem
Thanks Uwe. What happens if these are zoo (or time series) sequences/dataframes? \ I think your solution would apply as well, no? Thanks again best wishes, Costas 2011/12/4 Uwe Ligges lig...@statistik.tu-dortmund.de On 04.12.2011 16:18, Costas Vorlow wrote: Hello, I am having problems vectorizing the following (i/o using a for/next/while loop): I have 2 sequences such as: x, y 1, 30 2, -40 0, 50 0, 25 1, -5 2, -10 1, 5 0, 40 etc etc The first sequence (x) takes integer numbers only: 0, 1, 2 The sequence y can be anything... I want to be able to retrieve (in a list if possible) the 3 last values of the y sequence before a value of 1 is encountered on the x sequence, i.e: On line 5 in the above dataset, x is 1 so I need to capture values: 25, 50 and -40 of the y sequence. So the outcome (if a list) should look something like: [1],[25,50,-40] [2],[-10,-5,25] # as member #7 of x sequence is 1... etc. etc. Can I do the above avoiding for/next or while loops? I am not sure I can explain it better. Any help/pointer extremely welcome. Best regards, Costas One way is (assuming your data is in a data.frame called dat): wx - which(dat$x==1) result - lapply(wx[wx 3], function(x) dat$y[x - (1:3)]) (where lapply is a loop, implicitly). Uwe Ligges -- +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ |c|o|s|t|a|s|@|v|o|r|l|o|w|.|o|r|g| +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ [[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] Complex multiple t tests in a data frame with several id factors
I have assayed the concentrations of various metal elements in
different anatomic regions of two strains of mice. Now, for each
element, in each region, I want to do a t test to find whether there
is any difference between the two strains.
Here is what I did (using simulated data as an example):
# create the data frame
elemconc = data.frame(expand.grid(id=1:3, geno=c('exp', 'wt'),
region=c('brain', 'spine'), elem=c('fe', 'cu', 'zn')), conc=rnorm(36, 10))
elemconc
id geno region elem conc
1 1 exp brain fe 8.497498
2 2 exp brain fe 9.280944
3 3 exp brain fe 9.726271
4 1 wt brain fe 11.556397
5 2 wt brain fe 10.992550
6 3 wt brain fe 9.711200
7 1 exp spine fe 11.168603
8 2 exp spine fe 9.331127
9 3 exp spine fe 11.048226
10 1 wt spine fe 8.480867
11 2 wt spine fe 8.887062
12 3 wt spine fe 8.329797
13 1 exp brain cu 10.242652
14 2 exp brain cu 9.865984
15 3 exp brain cu 9.163728
16 1 wt brain cu 11.099385
17 2 wt brain cu 9.364261
18 3 wt brain cu 9.718322
19 1 exp spine cu 10.720157
20 2 exp spine cu 11.505430
21 3 exp spine cu 9.499359
22 1 wt spine cu 9.855950
23 2 wt spine cu 10.120489
24 3 wt spine cu 9.526252
25 1 exp brain zn 9.736196
26 2 exp brain zn 11.938710
27 3 exp brain zn 9.668625
28 1 wt brain zn 9.961574
29 2 wt brain zn 10.461621
30 3 wt brain zn 9.873667
31 1 exp spine zn 9.708067
32 2 exp spine zn 10.109309
33 3 exp spine zn 10.973387
34 1 wt spine zn 8.406536
35 2 wt spine zn 7.797746
36 3 wt spine zn 11.127984
# use tapply to aggregate
tapply(elemconc$conc, elemconc[c('elem', 'region')], function(x) x)
region
elem brain spine
fe Numeric,6 Numeric,6
cu Numeric,6 Numeric,6
zn Numeric,6 Numeric,6
# check whether the order of data has been preserved after aggregation
x['fe', 'brain']
[[1]]
[1] 8.497498 9.280944 9.726271 11.556397 10.992550 9.711200
# create an external factor for strain grouping
tmpgeno = rep(c('exp', 'wt'), each=3)
tmpgeno
[1] exp exp exp wt wt wt
# do the t test using the grouping factor
x = tapply(elemconc$conc, elemconc[c('elem', 'region')], function(x)
t.test(x~tmpgeno) )
x
region
elem brain spine
fe List,9 List,9
cu List,9 List,9
zn List,9 List,9
I believe I have made no mistakes so far, but I wonder is there a
better way of doing this?
--
Kaiyin Zhong
--
Neuroscience Research Institute, Peking University, Beijing, P.R.China 100038
__
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] Vectorization instead of loops problem
On Sun, Dec 4, 2011 at 10:18 AM, Costas Vorlow costas.vor...@gmail.com wrote: Hello, I am having problems vectorizing the following (i/o using a for/next/while loop): I have 2 sequences such as: x, y 1, 30 2, -40 0, 50 0, 25 1, -5 2, -10 1, 5 0, 40 etc etc The first sequence (x) takes integer numbers only: 0, 1, 2 The sequence y can be anything... I want to be able to retrieve (in a list if possible) the 3 last values of the y sequence before a value of 1 is encountered on the x sequence, i.e: On line 5 in the above dataset, x is 1 so I need to capture values: 25, 50 and -40 of the y sequence. So the outcome (if a list) should look something like: [1],[25,50,-40] [2],[-10,-5,25] # as member #7 of x sequence is 1... etc. etc. Can I do the above avoiding for/next or while loops? I am not sure I can explain it better. Any help/pointer extremely welcome. Try this. embed(z, 4) places values 1,2,3,4 of vector z in the first row, values 2,3,4,5 in the second row and so on so we want the rows of embed(y, 4) for which embed(x, 4) is 1, i.e we want rows of embed(y, 4) for which embed(x, 4)[,1]==1, except the first column can be suppressed (-1). embed(y, 4)[embed(x, 4)[, 1] == 1, -1] [,1] [,2] [,3] [1,] 25 50 -40 [2,] -10 -5 25 -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.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.
Re: [R] Extract last 3 characters from numeric vector
On 04.12.2011 14:38, Kang Min wrote: Hi all, I have a numeric vector with 1 decimal place, and I'd like to extract the last 3 characters, including the decimal point. The vector ranges from 0 to 20. x- round(runif(100)*20, digits=1) formatC(round(x%%10, 1), format=f, digits=1) Uwe Ligges Some of numbers have 3 characters, and some have 4. I've read up on the substr() function but that extracts characters based on exact positions. How can I extract just the last 3 characters no matter the length of the number? e.g. from 16.7 I want 6.7, from 3.5 I want 3.5 as it is. Thanks, Kang Min __ 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] Vectorization instead of loops problem
Costas: (and thanks for giving us your name) which(x == 1) gives you the indices where x is 1 (up to floating point equality -- you did not specify whether your x values are integers or calculated as floating point, and that certainly makes a difference). You can then use simple indexing to get the y values. No loops needed. However, let's explore why your question may have been too poorly formed to get the answer you seek: 1. What if the index of the first 1 is 3 or less? -- Do you want to ignore the (less than 3) preceding values or just choose as many as you can? 2. What if, as in your example, several 1's occur in x. Do you want the 3 preceding values for all of them or just the first? 3. If the answer to 2 is all of them, what if several 1's are less than 3 indices apart -- do you want to include the overlapping sets of 3 y's -- or what? My point is that etc. etc. is simply inadequate as a coherent or useful problem description in your post. You _must_ be explicit, complete, and concise. This can be hard. Indeed, it may require considerable thought and effort. I have found -- and others have often noted here -- that going through such an exercise itself often reveals a solution. But be that as it may, the Posting Guide is actually an excellent, comprehensive discussion of how to ask good questions in forums like this. Read it. Follow it. ... and to be fair, your post below is, imho, probably above average as posts go, allowing me to focus on specific points that I thought required clarification. Quite a few posts here of late have been so muddled and incoherent that I had no clue what the OP wanted. And it's not English as a second language. I am a language ignoramus and speak only English, so I am happy to tolerate poor grammar and vocabulary from someone for whom English is only one of several languages in which they can communicate. The problem is poor thinking, not poor English. Best, Bert On Sun, Dec 4, 2011 at 7:18 AM, Costas Vorlow costas.vor...@gmail.com wrote: Hello, I am having problems vectorizing the following (i/o using a for/next/while loop): I have 2 sequences such as: x, y 1, 30 2, -40 0, 50 0, 25 1, -5 2, -10 1, 5 0, 40 etc etc The first sequence (x) takes integer numbers only: 0, 1, 2 The sequence y can be anything... I want to be able to retrieve (in a list if possible) the 3 last values of the y sequence before a value of 1 is encountered on the x sequence, i.e: On line 5 in the above dataset, x is 1 so I need to capture values: 25, 50 and -40 of the y sequence. So the outcome (if a list) should look something like: [1],[25,50,-40] [2],[-10,-5,25] # as member #7 of x sequence is 1... etc. etc. Can I do the above avoiding for/next or while loops? I am not sure I can explain it better. Any help/pointer extremely welcome. Best regards, Costas -- +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ |c|o|s|t|a|s|@|v|o|r|l|o|w|.|o|r|g| +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ [[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 __ 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] upper bound in the integrate function depends on a parameter
On Dec 4, 2011, at 9:52 AM, e eeyore wrote:
This is not homework, I calculate some expectations and to finish
that I must solve integral like this one..
Upper bound have some unknown parameter, but I dont know how to
write it in R.
You almost did write it in R. You just left the m unspecified. If
you replace m by 5 the code works.
Do I must define m like symbol, or something else, just need help
with that.
I know how this work in MatLab, but in R I have problem.
Is there any solution how to solve integral like this one?
Can you help me please little more or direct me to right way, I will
appreciate your effort.
Thanks
On Sun, Dec 4, 2011 at 6:06 AM, David Winsemius dwinsem...@comcast.net
wrote:
On Dec 3, 2011, at 10:23 PM, grttt nbbfg wrote:
Sorry for my English, is not my first language..
I have some trouble in terms of using integrate function in R.
fx is a function of m and x where m is supposed to be a unknown
parameter.
R is not an algebraic solver (and R-help is not a homework list.).
fx=function(m,x){
+ x*2/(3*m)*(1-x/(3*m))
+ }
The problem is in upper bound, it depends on parameter m.
integrate(fx,lower=0,upper=3*m)$value
Is it possible to use the integrate function when bounds depend on a
parameter?
If it is known, yes. You could also do some investigation:
curve(x*2/(3*5)*(1-x/(3*5)), 0, 15)
How to define m to solve this integral? The result should be m.
As I said, no homework answers here.
David Winsemius, MD
West Hartford, CT
[[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] Logistic Regression with genetic component
Danielle Duncan dlduncan2 at alaska.edu writes: Greetings, I have a question that I'd like to get input on. I have a classic toxicology study where I artificially fertilized and exposed embryos to a chemical and counted defects. In addition, I kept track of male-female pairs that I used to artificially fertilize and generate embryos with. I need to use logistic regression to model the response, but also check that the genetics of the pairings did or did not have an effect on the response. My data looks a bit like this: response matrix chemical concentration Genetic Matrix Present AbsentMale Female 2 152 0.13 a 1 6 121 1 a 2 21 92 2 b 3 24 89 5 b 4 0141 10 c 5 5 95 15 c 6 R code: DA-cbind(Present, Absent) glm-(DA ~ chemical concentration) If I do glm-(DA ~ chemical concentration + Male + Female, I get every possible combination, but I only want specific pairs. So, I am thinking about doing: MF-cbind(Male, Female) glm-(DA ~ chemical concentration + MF) You're on the right track. paste() is probably what you want, although you can also use interaction() to get the interactions and then droplevels() to get rid of the unobserved crosses. d - read.table(textConnection( Present Absent conc Male Female 2 152 0.13 a 1 6 121 1 a 2 21 92 2 b 3 24 89 5 b 4 0141 10 c 5 5 95 15 c 6), header=TRUE) Either of these should give you what you want: d - droplevels(transform(d,cross=interaction(Male,Female))) levels(d$cross) d - transform(d,cross=paste(Male,Female,sep=.)) levels(d$cross) You should be a little careful -- if each cross is exposed only to a single concentration, and if you treat cross as a fixed effect, you will overparameterize your model. If you treat it as a random effect, e.g. using glmer in the lme4 package: glmer(cbind(Present,Absent)~conc+(1|cross),data=d) you will effectively be fitting a model for overdispersion (see the example in ?cbpp). __ 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] Complex multiple t tests in a data frame with several id factors
The concentrations of the different metals within an animal are
correlated, so that doing as you suggest will almost certainly result
in nonsense P values. So I suggest you seek local statistical help or,
failing that, post on a statistical forum like stats.stackexchange.com
.
There are various multivariate packages -- check e.g. the ChemPhys
and Multivariate task views -- that may be pertinent, but your post
suggests that you probably need some help to use them. Ergo my
suggestion above.
Cheers,
Bert
On Sun, Dec 4, 2011 at 7:36 AM, Kaiyin Zhong kindlych...@gmail.com wrote:
I have assayed the concentrations of various metal elements in
different anatomic regions of two strains of mice. Now, for each
element, in each region, I want to do a t test to find whether there
is any difference between the two strains.
Here is what I did (using simulated data as an example):
# create the data frame
elemconc = data.frame(expand.grid(id=1:3, geno=c('exp', 'wt'),
region=c('brain', 'spine'), elem=c('fe', 'cu', 'zn')), conc=rnorm(36, 10))
elemconc
id geno region elem conc
1 1 exp brain fe 8.497498
2 2 exp brain fe 9.280944
3 3 exp brain fe 9.726271
4 1 wt brain fe 11.556397
5 2 wt brain fe 10.992550
6 3 wt brain fe 9.711200
7 1 exp spine fe 11.168603
8 2 exp spine fe 9.331127
9 3 exp spine fe 11.048226
10 1 wt spine fe 8.480867
11 2 wt spine fe 8.887062
12 3 wt spine fe 8.329797
13 1 exp brain cu 10.242652
14 2 exp brain cu 9.865984
15 3 exp brain cu 9.163728
16 1 wt brain cu 11.099385
17 2 wt brain cu 9.364261
18 3 wt brain cu 9.718322
19 1 exp spine cu 10.720157
20 2 exp spine cu 11.505430
21 3 exp spine cu 9.499359
22 1 wt spine cu 9.855950
23 2 wt spine cu 10.120489
24 3 wt spine cu 9.526252
25 1 exp brain zn 9.736196
26 2 exp brain zn 11.938710
27 3 exp brain zn 9.668625
28 1 wt brain zn 9.961574
29 2 wt brain zn 10.461621
30 3 wt brain zn 9.873667
31 1 exp spine zn 9.708067
32 2 exp spine zn 10.109309
33 3 exp spine zn 10.973387
34 1 wt spine zn 8.406536
35 2 wt spine zn 7.797746
36 3 wt spine zn 11.127984
# use tapply to aggregate
tapply(elemconc$conc, elemconc[c('elem', 'region')], function(x) x)
region
elem brain spine
fe Numeric,6 Numeric,6
cu Numeric,6 Numeric,6
zn Numeric,6 Numeric,6
# check whether the order of data has been preserved after aggregation
x['fe', 'brain']
[[1]]
[1] 8.497498 9.280944 9.726271 11.556397 10.992550 9.711200
# create an external factor for strain grouping
tmpgeno = rep(c('exp', 'wt'), each=3)
tmpgeno
[1] exp exp exp wt wt wt
# do the t test using the grouping factor
x = tapply(elemconc$conc, elemconc[c('elem', 'region')], function(x)
t.test(x~tmpgeno) )
x
region
elem brain spine
fe List,9 List,9
cu List,9 List,9
zn List,9 List,9
I believe I have made no mistakes so far, but I wonder is there a
better way of doing this?
--
Kaiyin Zhong
--
Neuroscience Research Institute, Peking University, Beijing, P.R.China 100038
__
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
__
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] upper bound in the integrate function depends on a parameter
On Sun, Dec 4, 2011 at 4:47 PM, David Winsemius dwinsem...@comcast.netwrote: You almost did write it in R. You just left the m unspecified. If you replace m by 5 the code works. Check how wolfram work with same integral, I dont need to replace anything.. http://www.wolframalpha.com/input/?i=integrate+x*2%2F%283*m%29*%281-x%2F%283*m%29%29+dx+from+x%3D0+to+3*m I need only answer is possible in R do the same work and get the same result and if is how. You dont need to try be funny.. [[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] Complex multiple t tests in a data frame with several id factors
Okay, thank you.
On Mon, Dec 5, 2011 at 12:01 AM, Bert Gunter gunter.ber...@gene.com wrote:
The concentrations of the different metals within an animal are
correlated, so that doing as you suggest will almost certainly result
in nonsense P values. So I suggest you seek local statistical help or,
failing that, post on a statistical forum like stats.stackexchange.com
.
There are various multivariate packages -- check e.g. the ChemPhys
and Multivariate task views -- that may be pertinent, but your post
suggests that you probably need some help to use them. Ergo my
suggestion above.
Cheers,
Bert
On Sun, Dec 4, 2011 at 7:36 AM, Kaiyin Zhong kindlych...@gmail.com wrote:
I have assayed the concentrations of various metal elements in
different anatomic regions of two strains of mice. Now, for each
element, in each region, I want to do a t test to find whether there
is any difference between the two strains.
Here is what I did (using simulated data as an example):
# create the data frame
elemconc = data.frame(expand.grid(id=1:3, geno=c('exp', 'wt'),
region=c('brain', 'spine'), elem=c('fe', 'cu', 'zn')), conc=rnorm(36, 10))
elemconc
id geno region elem conc
1 1 exp brain fe 8.497498
2 2 exp brain fe 9.280944
3 3 exp brain fe 9.726271
4 1 wt brain fe 11.556397
5 2 wt brain fe 10.992550
6 3 wt brain fe 9.711200
7 1 exp spine fe 11.168603
8 2 exp spine fe 9.331127
9 3 exp spine fe 11.048226
10 1 wt spine fe 8.480867
11 2 wt spine fe 8.887062
12 3 wt spine fe 8.329797
13 1 exp brain cu 10.242652
14 2 exp brain cu 9.865984
15 3 exp brain cu 9.163728
16 1 wt brain cu 11.099385
17 2 wt brain cu 9.364261
18 3 wt brain cu 9.718322
19 1 exp spine cu 10.720157
20 2 exp spine cu 11.505430
21 3 exp spine cu 9.499359
22 1 wt spine cu 9.855950
23 2 wt spine cu 10.120489
24 3 wt spine cu 9.526252
25 1 exp brain zn 9.736196
26 2 exp brain zn 11.938710
27 3 exp brain zn 9.668625
28 1 wt brain zn 9.961574
29 2 wt brain zn 10.461621
30 3 wt brain zn 9.873667
31 1 exp spine zn 9.708067
32 2 exp spine zn 10.109309
33 3 exp spine zn 10.973387
34 1 wt spine zn 8.406536
35 2 wt spine zn 7.797746
36 3 wt spine zn 11.127984
# use tapply to aggregate
tapply(elemconc$conc, elemconc[c('elem', 'region')], function(x) x)
region
elem brain spine
fe Numeric,6 Numeric,6
cu Numeric,6 Numeric,6
zn Numeric,6 Numeric,6
# check whether the order of data has been preserved after aggregation
x['fe', 'brain']
[[1]]
[1] 8.497498 9.280944 9.726271 11.556397 10.992550 9.711200
# create an external factor for strain grouping
tmpgeno = rep(c('exp', 'wt'), each=3)
tmpgeno
[1] exp exp exp wt wt wt
# do the t test using the grouping factor
x = tapply(elemconc$conc, elemconc[c('elem', 'region')], function(x)
t.test(x~tmpgeno) )
x
region
elem brain spine
fe List,9 List,9
cu List,9 List,9
zn List,9 List,9
I believe I have made no mistakes so far, but I wonder is there a
better way of doing this?
--
Kaiyin Zhong
--
Neuroscience Research Institute, Peking University, Beijing, P.R.China 100038
__
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
--
Kaiyin Zhong
--
Neuroscience Research Institute, Peking University, Beijing, P.R.China 100038
__
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] Programming Statistical Functions
On Dec 4, 2011, at 9:27 AM, gvjones wrote: Hello, Did you find anything helpful for calculating the statistical functions in your list. I would like to also calculate these and have been looking for some code to do so. A search at the site linked by the R function RSiteSearch() produces two (or more) candidate packages. Rather than naming them, I think it good exercise to do the looking and judging by yourself: http://search.r-project.org/cgi-bin/namazu.cgi?query=meteorologymax=100result=normalsort=scoreidxname=functionsidxname=Rhelp08idxname=Rhelp10idxname=Rhelp02 -- David Winsemius, MD West Hartford, CT __ 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] upper bound in the integrate function depends on a parameter
On Dec 4, 2011, at 11:04 AM, e eeyore wrote: On Sun, Dec 4, 2011 at 4:47 PM, David Winsemius dwinsem...@comcast.net wrote: You almost did write it in R. You just left the m unspecified. If you replace m by 5 the code works. Check how wolfram work with same integral, I dont need to replace anything.. http://www.wolframalpha.com/input/?i=integrate+x*2%2F%283*m%29*%281-x%2F%283*m%29%29+dx+from+x%3D0+to+3*m I need only answer is possible in R do the same work and get the same result and if is how. You dont need to try be funny.. Sometimes my sarcasm is under-interpreted, but in this case no sarcasm was intended. I told you in an earlier post that R does not do symbolic algebra. Your counter-example points to a program that does. Bottom line: R is not Mathematica. Complaining about that fact is not going to get you anywhere. There is a package which provides an interface to the open-source Yacas system if you want to pursue an R- centric approach. -- David Winsemius, MD West Hartford, CT [[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] prediction in conmode class of Nonparametric binary models
Dear R users, Is it possible to apply 'predict' to an object of class conmode? Could you please suggest me any applicable method for 'predict' for the conmode class? Thanking you, Sincerely Yours, Shyam Kumar Basnet SLU, Uppsala Sweden [[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] upper bound in the integrate function depends on a parameter
I know that is not Mhatematica, my question is only is it possible, it seams its not.. Sorry if I did not get it, I can interprete different your answer, not intentionally.. Thanks for your answer and patience. On Sun, Dec 4, 2011 at 5:15 PM, David Winsemius dwinsem...@comcast.netwrote: On Dec 4, 2011, at 11:04 AM, e eeyore wrote: On Sun, Dec 4, 2011 at 4:47 PM, David Winsemius dwinsem...@comcast.netwrote: You almost did write it in R. You just left the m unspecified. If you replace m by 5 the code works. Check how wolfram work with same integral, I dont need to replace anything.. http://www.wolframalpha.com/input/?i=integrate+x*2%2F%283*m%29*%281-x%2F%283*m%29%29+dx+from+x%3D0+to+3*m I need only answer is possible in R do the same work and get the same result and if is how. You dont need to try be funny.. Sometimes my sarcasm is under-interpreted, but in this case no sarcasm was intended. I told you in an earlier post that R does not do symbolic algebra. Your counter-example points to a program that does. Bottom line: R is not Mathematica. Complaining about that fact is not going to get you anywhere. There is a package which provides an interface to the open-source Yacas system if you want to pursue an R-centric approach. -- David Winsemius, MD West Hartford, CT [[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] How to write (complex) coercion methods or what's the reason to limit 'setAs()' the way it is limited?
Dear list, I'd like to write coercion methods for some of my Reference Classes. However, using 'setAs()' is not a real option as its argument 'def' only allows for functions depending on one single argument. In some cases, that is simply too much of a limitation for me. And I don't really see why it needs to be this way, so I guess this question is also some sort of a feature request to make 'setAs' a bit more flexible (in case anyone from the Core Team is listening ;-)) A reproducible example can be found here: http://stackoverflow.com/questions/8346654/how-to-write-coercion-methods Thanks a lot for any replies! Janko __ 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] upper bound in the integrate function depends on a parameter
Hi e eeyore,
Here is one way:
fx - function(x, m) x*2/(3*m)*(1-x/(3*m))
foo - function(m) integrate(fx, m = m, lower = 0, upper = 3*m)$value
foo(3)
# 3
foo(2)
# 2
And remember:
#install.packages('fortunes')
require(fortunes)
fortune('Yoda')
Evelyn Hall: I would like to know how (if) I can extract some of the
information
from the summary of my nlme.
Simon Blomberg: This is R. There is no if. Only how.
-- Evelyn Hall and Simon 'Yoda' Blomberg
R-help (April 2005)
HTH,
Jorge.-
On Sun, Dec 4, 2011 at 11:23 AM, e eeyore wrote:
I know that is not Mhatematica, my question is only is it possible, it
seams its not..
Sorry if I did not get it, I can interprete different your answer, not
intentionally..
Thanks for your answer and patience.
On Sun, Dec 4, 2011 at 5:15 PM, David Winsemius wrote:
On Dec 4, 2011, at 11:04 AM, e eeyore wrote:
On Sun, Dec 4, 2011 at 4:47 PM, David Winsemius wrote:
You almost did write it in R. You just left the m unspecified. If you
replace m by 5 the code works.
Check how wolfram work with same integral, I dont need to replace
anything..
http://www.wolframalpha.com/input/?i=integrate+x*2%2F%283*m%29*%281-x%2F%283*m%29%29+dx+from+x%3D0+to+3*m
I need only answer is possible in R do the same work and get the same
result and if is how.
You dont need to try be funny..
Sometimes my sarcasm is under-interpreted, but in this case no sarcasm
was
intended. I told you in an earlier post that R does not do symbolic
algebra. Your counter-example points to a program that does. Bottom
line: R
is not Mathematica. Complaining about that fact is not going to get you
anywhere. There is a package which provides an interface to the
open-source
Yacas system if you want to pursue an R-centric approach.
--
David Winsemius, MD
West Hartford, CT
[[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] problem merging data with different shapes
Please use dput() to post your example data sets. dput(Adata) dput(Bdata) **then copy and paste the results of each so that we can play around with it easily. Miriam -2 wrote I have been trying to merge datasets, one of which has a long format (Adata) and one has a (different) long format (Bdata): Adata Bdata subject order bpm subject order trial agegroup gender 1 1 70.21 1 3 2 1 1 1 69.51 2 1 2 1 1 1 68.81 3 2 2 1 1 2 69.12 1 2 1 2 1 270 2 2 3 1 2 1 2 70.52 3 1 1 2 1 3 70.2... 1 3 1 3 2 1 2 1 ... ... In the end I would like to have a dataset that contains A unchanged with the additional information from B added. subject order bpm trial agegroup gender 1 1 70.2 3 2 1 1 1 69.5 3 2 1 1 1 68.8 3 2 1 ... I have tried: newdataframe - merge(Adata,Bdata, by= c(subject, order), sort = FALSE) For some reason, the trial column is not matched to the subject and order information, despite them being identified as key-variables for the merge. (The same is true for other variables, the actual dataset has more variables and trials, but this is essentially the problem.) So it results in something like: subject order bpm trial agegroup gender 1 1 70.2 3 2 1 1 1 69.5 2 2 1 1 1 68.8 1 2 1 What could be my mistake? Thank you VERY much. Miriam -- -- __ R-help@ 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. -- View this message in context: http://r.789695.n4.nabble.com/problem-merging-data-with-different-shapes-tp4157137p4157442.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.
Re: [R] Polishing my geom_bar for publication
Sorry Dennis, Didn't realized I went off the list! I found a solution for one of my problem: removing x-axis label! with this code: ggplot(Final2, aes(x=spp, y=WPUE, fill=season)) + geom_bar(position=position_dodge()) + geom_errorbar(aes(ymin=WPUE-wpue.se, ymax=WPUE+wpue.se), size=.3,width=.2,position=position_dodge(.9)) + scale_x_discrete(, breaks=c(102,90,91,94,96), labels= rep(, 5)) + ylab(Biomass (Weight (kg)/tow)) + scale_fill_grey(name=Survey season, breaks=c(summer, winter), labels=c(Spring, Fall))+ coord_flip() + theme_bw() + opts(axis.title.x = theme_text(size = 10), panel.grid.minor = theme_blank()) However, I am still trying to figure out how to fix the width of my two plots on my final pdf. I would appreciate any help on this! Thank you. On 2011-12-04, at 12:59 PM, Aurelie Cosandey Godin wrote: Thank you Denis, I changed my code as you suggested, however the xlab didn't work I tried something else (see below my new code), but I still get my labels for my x-axis (coord_flip) in my b figure (spp 96, 94, 91, etc...). See figure below. To answer your question, I would like that both of my figure a b have the same width on the final pdf. Right now they aren't because of the legend. and (3) fix the width, such that both figures have the same appearance regardless of the legend. I'm afraid I don't understand clearly what you mean my 'same appearance'. Could you provide a reproducible example, which includes (possibly fake) data as well as code? Here's my new code: (a- ggplot(Final2, aes(x=spp, y=CPUE, fill=season)) + geom_bar(position=position_dodge()) + geom_errorbar(aes(ymin=CPUE-cpue.se, ymax=CPUE+cpue.se), size=.3,width=.2, position=position_dodge(.9)) +scale_x_discrete(Species, breaks=c(102,90,91,94,96), labels=c(SPINYTAIL,THORNY,SMOOTH,DEEPWATER,JENSEN'S)) + ylab(Abundance (fish/tow)) + coord_flip() + scale_fill_grey() + theme_bw() + opts(axis.title.x = theme_text(size = 10), panel.grid.minor = theme_blank(), legend.position='none') ) ##I added scale_x_discrete(NULL, breaks=c(102,90,91,94,96), labels= rep(NULL, 5)) thinking that this would be able to remove my x-axis label (coord_flip) but it didn't... any other ideas of how I can achieve this? (b- ggplot(Final2, aes(x=spp, y=WPUE, fill=season)) + geom_bar(position=position_dodge()) + geom_errorbar(aes(ymin=WPUE-wpue.se, ymax=WPUE+wpue.se), size=.3,width=.2,position=position_dodge(.9)) + scale_x_discrete(NULL, breaks=c(102,90,91,94,96), labels= rep(NULL, 5)) + ylab(Biomass (Weight (kg)/tow)) + scale_fill_grey(name=Survey season, breaks=c(summer, winter), labels=c(Spring, Fall))+ coord_flip() + theme_bw() + opts(axis.title.x = theme_text(size = 10), panel.grid.minor = theme_blank()) ) pdf(polishing-layout3.pdf, width = 10, height = 6) grid.newpage() pushViewport(viewport(layout = grid.layout(1, 2))) vplayout - function(x, y) viewport(layout.pos.row = x, layout.pos.col = y) print(a, vp = vplayout(1, 1)) print(b, vp = vplayout(1, 2)) dev.off() PastedGraphic-2.pdf Thank you very much! Aurelie On 2011-12-04, at 11:33 AM, Dennis Murphy wrote: Hi: On Sun, Dec 4, 2011 at 5:21 AM, Aurelie Cosandey Godin god...@dal.ca wrote: Dear list, I am new with ggplot2 and I have spend quiet some time putting together the following code to create the attached plot. However there's still a few things that I'm having trouble with! I would be grateful if someone can tell me how to fix (1) the colour of my bars into grey scales One way is to provide greyscale values to scale_fill_discrete; e.g., values = c(grey50,grey20) (2) removing the y-axis (species name) on the right figure to avoid duplication, In the second figure, insert either ylab() or if you have a labs() statement that defines several titles at once, labs(..., y = , ...) and (3) fix the width, such that both figures have the same appearance regardless of the legend. I'm afraid I don't understand clearly what you mean my 'same appearance'. Could you provide a reproducible example, which includes (possibly fake) data as well as code? Dennis Thank you very much in advance! -- You received this message because you are subscribed to the ggplot2 mailing list. Please provide a reproducible example: http://gist.github.com/270442 To post: email ggpl...@googlegroups.com To unsubscribe: email ggplot2+unsubscr...@googlegroups.com More options: http://groups.google.com/group/ggplot2 The code is as follow: (a-ggplot(Final2, aes(x=spp, y=CPUE, fill=season)) + geom_bar(position=position_dodge()) + geom_errorbar(aes(ymin=CPUE-cpue.se, ymax=CPUE+cpue.se), size=.3, width=.2, position=position_dodge(.9)) + xlab(Species) + scale_x_discrete(breaks=c(100,102,107,88,90,91,92,93,94,96,98,99), labels=c(WINTER,SPINYTAIL,BIGELOW'S,SKATES
Re: [R] Export cols to single csv files
just use indexing. without doing it all for you... df - structure(list(AA = c(0.3, 0.1, 0.6), BB = c(0.9, 0.4, 0.2), CC = c(1, 0.8, 0.6), DD = c(0.7, 0.5, 0.5)), .Names = c(AA, BB, CC, DD), class = data.frame, row.names = c(NA, -3L )) write.csv(df[,1], paste(colnames(df[1]), csv, sep=.)) Chega wrote Hi I am trying to batch export the columns of a numeric matrix to separate csv files by naming them according to the column names. So my matrix in R looks like this: AA BB CC DD etc. 1: 0.3 0.9 1.0 0.7 ... 2: 0.1 0.4 0.8 0.5 ... 3: 0.6 0.2 0.6 0.5 ... etc. Now I am looking for a way to get these files (file names in quotes): AA.csv BB.csv CC.csvetc. 1: 0.31: 0.91: 1.0 2: 0.12: 0.42: 0.8 3: 0.63: 0.23: 0.6 etc. etc. etc. As I understand this may be done using write.csv and a loop with the column names, but I have no idea how to export single columns. Thanks i.a. for help! Chega -- View this message in context: http://r.789695.n4.nabble.com/Export-cols-to-single-csv-files-tp4157484p4157537.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.
Re: [R] Vectorization instead of loops problem
Dear Bert, You are right (obviously). Apologies for any inconvenience caused. I thought my problem was simplistic with a very obvious answer which eluded me. As per your justified questions : 2: Answer is all, hence: 3. would be include overlapping set (I guess) but this does not matter for the time being. I didn't give it too much thought admittedly... If I got 1 2 right I could have modified the code for point 3 (if answer in 2 != all'), so I did not consider it when I was formulating my query. However, I can see now why this is confusing. Anyways, thanks again for the pointers. BTW, is there a good quick read/guide on vectorization in R that one could recommend? That would minimize my queries at least in the list. :-) Apologies again and best regards, Costas On 4 December 2011 17:45, Bert Gunter gunter.ber...@gene.com wrote: Costas: (and thanks for giving us your name) which(x == 1) gives you the indices where x is 1 (up to floating point equality -- you did not specify whether your x values are integers or calculated as floating point, and that certainly makes a difference). You can then use simple indexing to get the y values. No loops needed. However, let's explore why your question may have been too poorly formed to get the answer you seek: 1. What if the index of the first 1 is 3 or less? -- Do you want to ignore the (less than 3) preceding values or just choose as many as you can? 2. What if, as in your example, several 1's occur in x. Do you want the 3 preceding values for all of them or just the first? 3. If the answer to 2 is all of them, what if several 1's are less than 3 indices apart -- do you want to include the overlapping sets of 3 y's -- or what? My point is that etc. etc. is simply inadequate as a coherent or useful problem description in your post. You _must_ be explicit, complete, and concise. This can be hard. Indeed, it may require considerable thought and effort. I have found -- and others have often noted here -- that going through such an exercise itself often reveals a solution. But be that as it may, the Posting Guide is actually an excellent, comprehensive discussion of how to ask good questions in forums like this. Read it. Follow it. ... and to be fair, your post below is, imho, probably above average as posts go, allowing me to focus on specific points that I thought required clarification. Quite a few posts here of late have been so muddled and incoherent that I had no clue what the OP wanted. And it's not English as a second language. I am a language ignoramus and speak only English, so I am happy to tolerate poor grammar and vocabulary from someone for whom English is only one of several languages in which they can communicate. The problem is poor thinking, not poor English. Best, Bert On Sun, Dec 4, 2011 at 7:18 AM, Costas Vorlow costas.vor...@gmail.com wrote: Hello, I am having problems vectorizing the following (i/o using a for/next/while loop): I have 2 sequences such as: x, y 1, 30 2, -40 0, 50 0, 25 1, -5 2, -10 1, 5 0, 40 etc etc The first sequence (x) takes integer numbers only: 0, 1, 2 The sequence y can be anything... I want to be able to retrieve (in a list if possible) the 3 last values of the y sequence before a value of 1 is encountered on the x sequence, i.e: On line 5 in the above dataset, x is 1 so I need to capture values: 25, 50 and -40 of the y sequence. So the outcome (if a list) should look something like: [1],[25,50,-40] [2],[-10,-5,25] # as member #7 of x sequence is 1... etc. etc. Can I do the above avoiding for/next or while loops? I am not sure I can explain it better. Any help/pointer extremely welcome. Best regards, Costas -- +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ |c|o|s|t|a|s|@|v|o|r|l|o|w|.|o|r|g| +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ [[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 -- +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ |c|o|s|t|a|s|@|v|o|r|l|o|w|.|o|r|g| +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ [[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] equating approximate values
Hello List, I am having trouble finding the command for my problem. I have two arrays x and y. now i would like to compare the values of x and y and then get the index of x which is exactly or approximately equal(+/- some value ) to the values in y. x - runif(100,min=0,max=5) y - runif(10,min=0,max=5) the threshold value(+/-) value can vary. for this example lets take it to be .5 I know the regular method of doing this by writing different if and for loops. But i have very big dataframe the computation time is very high for this method. can anyone please tell me if there any functions to do this. thank you for your help. -- View this message in context: http://r.789695.n4.nabble.com/equating-approximate-values-tp4157551p4157551.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] similarity matrix
Hello R-users, I've got a file with individuals as colums and the clusters where they occur in as rows. And I wanted a similarity matrix which tells me how many times each individual occurs with another. My eventual goal is to make Venn-diagrams from the occurence of my individuals. So I've this: cluster ind1 ind2 ind3 etc. 10 1 2 23 01 31 1 1 And I want to go to this: ind1 ind2 ind3 ind1 0 42 ind2 4 04 ind3 2 4 1 is there a way to do this? Thank you for your help -- View this message in context: http://r.789695.n4.nabble.com/similarity-matrix-tp4157576p4157576.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.
Re: [R] RODBC connect to Excel (64-bit Windows 7)
Do you need to use RODBC specifically? I've been using XLConnect quite a lot recently and have been quite pleased with it. Michael On Dec 4, 2011, at 9:40 AM, andrija djurovic djandr...@gmail.com wrote: Hi to all. I have a problem to connect to an Excel database using RODBC. Namely, I am using 64-bit R 2.14.0, under Windows 7 and I tried following: library(RODBC) channel - odbcConnectExcel(results.xlsx) Error in odbcConnectExcel(results.xlsx) : odbcConnectExcel is only usable with 32-bit Windows # ok this is clear why it doesn't work channel - odbcConnectExcel2007(results.xlsx) # this was one of proposals from old R help posts, but it doesn't work for me 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 After that as it suggested in R data import/export manual I installed AccessDatabaseEngine.exe. Also I used ODBC in c:\Windows\SysWOW64\odbcad32 to create data source called result. I check if it is created: odbcDataSources() dBASE Files Microsoft Access dBASE Driver (*.dbf, *.ndx, *.mdx) MS Access Database Microsoft Access Driver (*.mdb, *.accdb) Excel file Microsoft Excel Driver (*.xls, *.xlsx, *.xlsm, *.xlsb) * results* Microsoft Excel Driver (*.xls, *.xlsx, *.xlsm, *.xlsb) and tried again but it doesn't work: channel - odbcDriverConnect() Warning messages: 1: In odbcDriverConnect() : [RODBC] ERROR: state IM014, code 0, message [Microsoft][ODBC Driver Manager] The specified DSN contains an architecture mismatch between the Driver and Application 2: In odbcDriverConnect() : ODBC connection failed Could someone guide me what should I try next to fix a problem? Is this some problem with Drivers or not? Thanks in advance Andrija [[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] RODBC connect to Excel (64-bit Windows 7)
Hi. Not specifically, but I used it before with 32-bit R under Windows XP and it worked just fine so i though to keep using it.Anyway I will lookt at XLConnect. Thank you for suggestion. Andrija On Sun, Dec 4, 2011 at 7:41 PM, R. Michael Weylandt michael.weyla...@gmail.com michael.weyla...@gmail.com wrote: Do you need to use RODBC specifically? I've been using XLConnect quite a lot recently and have been quite pleased with it. Michael On Dec 4, 2011, at 9:40 AM, andrija djurovic djandr...@gmail.com wrote: Hi to all. I have a problem to connect to an Excel database using RODBC. Namely, I am using 64-bit R 2.14.0, under Windows 7 and I tried following: library(RODBC) channel - odbcConnectExcel(results.xlsx) Error in odbcConnectExcel(results.xlsx) : odbcConnectExcel is only usable with 32-bit Windows # ok this is clear why it doesn't work channel - odbcConnectExcel2007(results.xlsx) # this was one of proposals from old R help posts, but it doesn't work for me 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 After that as it suggested in R data import/export manual I installed AccessDatabaseEngine.exe. Also I used ODBC in c:\Windows\SysWOW64\odbcad32 to create data source called result. I check if it is created: odbcDataSources() dBASE Files Microsoft Access dBASE Driver (*.dbf, *.ndx, *.mdx) MS Access Database Microsoft Access Driver (*.mdb, *.accdb) Excel file Microsoft Excel Driver (*.xls, *.xlsx, *.xlsm, *.xlsb) * results* Microsoft Excel Driver (*.xls, *.xlsx, *.xlsm, *.xlsb) and tried again but it doesn't work: channel - odbcDriverConnect() Warning messages: 1: In odbcDriverConnect() : [RODBC] ERROR: state IM014, code 0, message [Microsoft][ODBC Driver Manager] The specified DSN contains an architecture mismatch between the Driver and Application 2: In odbcDriverConnect() : ODBC connection failed Could someone guide me what should I try next to fix a problem? Is this some problem with Drivers or not? Thanks in advance Andrija [[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] equating approximate values
Hi. Maybe this can help you (you can try additionally to incorporate
threshold):
set.seed(1)
x-rnorm(10,10,1)
values - sample(1:10,10) #values that we are looking for
mat - matrix(c(x,values),ncol=2)
closest-function(x,values)#function is an example from The R book
(Crawley)
+ {
+ x[which(abs(x-values)==min(abs(x-values)))]
+ }
apply(mat[,2,drop=FALSE],1,function(y) closest(mat[,1],y))
[1] 10.183643 9.164371 9.164371 9.164371 9.164371 9.164371 9.164371
9.164371
[9] 9.164371 9.164371
On Sun, Dec 4, 2011 at 7:00 PM, vamshi999 vamshi...@gmail.com wrote:
Hello List,
I am having trouble finding the command for my problem.
I have two arrays x and y. now i would like to compare the values of x and
y
and then get the index of x which is exactly or approximately equal(+/-
some
value ) to the values in y.
x - runif(100,min=0,max=5)
y - runif(10,min=0,max=5)
the threshold value(+/-) value can vary. for this example lets take it to
be
.5
I know the regular method of doing this by writing different if and for
loops. But i have very big dataframe the computation time is very high for
this method. can anyone please tell me if there any functions to do this.
thank you for your help.
--
View this message in context:
http://r.789695.n4.nabble.com/equating-approximate-values-tp4157551p4157551.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.
[[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] similarity matrix
I apologize to the list and you if I am mis-understanding something, but... As an example: ind2 occurs with ind1 only in cluster#3, so why does it get a value of 4 in your similarity matrix? Also, if this isn't a recognized similarity algorithm, perhaps you should at the very least put quotes around similarity. Again, sorry if I am confused here. set wrote Hello R-users, I've got a file with individuals as colums and the clusters where they occur in as rows. And I wanted a similarity matrix which tells me how many times each individual occurs with another. My eventual goal is to make Venn-diagrams from the occurence of my individuals. So I've this: cluster ind1 ind2 ind3 etc. 10 1 2 23 01 31 1 1 And I want to go to this: ind1 ind2 ind3 ind1 0 42 ind2 4 04 ind3 2 4 1 is there a way to do this? Thank you for your help -- View this message in context: http://r.789695.n4.nabble.com/similarity-matrix-tp4157576p4157840.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.
Re: [R] Vectorization instead of loops problem
Inline below On Sun, Dec 4, 2011 at 10:29 AM, Costas Vorlow costas.vor...@gmail.com wrote: Dear Bert, You are right (obviously). Apologies for any inconvenience caused. I thought my problem was simplistic with a very obvious answer which eluded me. As per your justified questions : 2: Answer is all, hence: 3. would be include overlapping set (I guess) but this does not matter for the time being. I didn't give it too much thought admittedly... If I got 1 2 right I could have modified the code for point 3 (if answer in 2 != all'), so I did not consider it when I was formulating my query. However, I can see now why this is confusing. Anyways, thanks again for the pointers. BTW, is there a good quick read/guide on vectorization in R that one could recommend? That would minimize my queries at least in the list. :-) Vectorization is a central paradigm in R, so practically all books on the S language discuss this. The R language definition manual that ships with R is pretty comprehensive, but VR's MASS or S Programming Books, Patrick Burns's website tutorials (he has several well suited for beginners), John Chambers's Programming with R , etc. are just a few among many. It is impossible for me to be more specific than that. -- Bert Apologies again and best regards, Costas On 4 December 2011 17:45, Bert Gunter gunter.ber...@gene.com wrote: Costas: (and thanks for giving us your name) which(x == 1) gives you the indices where x is 1 (up to floating point equality -- you did not specify whether your x values are integers or calculated as floating point, and that certainly makes a difference). You can then use simple indexing to get the y values. No loops needed. However, let's explore why your question may have been too poorly formed to get the answer you seek: 1. What if the index of the first 1 is 3 or less? -- Do you want to ignore the (less than 3) preceding values or just choose as many as you can? 2. What if, as in your example, several 1's occur in x. Do you want the 3 preceding values for all of them or just the first? 3. If the answer to 2 is all of them, what if several 1's are less than 3 indices apart -- do you want to include the overlapping sets of 3 y's -- or what? My point is that etc. etc. is simply inadequate as a coherent or useful problem description in your post. You _must_ be explicit, complete, and concise. This can be hard. Indeed, it may require considerable thought and effort. I have found -- and others have often noted here -- that going through such an exercise itself often reveals a solution. But be that as it may, the Posting Guide is actually an excellent, comprehensive discussion of how to ask good questions in forums like this. Read it. Follow it. ... and to be fair, your post below is, imho, probably above average as posts go, allowing me to focus on specific points that I thought required clarification. Quite a few posts here of late have been so muddled and incoherent that I had no clue what the OP wanted. And it's not English as a second language. I am a language ignoramus and speak only English, so I am happy to tolerate poor grammar and vocabulary from someone for whom English is only one of several languages in which they can communicate. The problem is poor thinking, not poor English. Best, Bert On Sun, Dec 4, 2011 at 7:18 AM, Costas Vorlow costas.vor...@gmail.com wrote: Hello, I am having problems vectorizing the following (i/o using a for/next/while loop): I have 2 sequences such as: x, y 1, 30 2, -40 0, 50 0, 25 1, -5 2, -10 1, 5 0, 40 etc etc The first sequence (x) takes integer numbers only: 0, 1, 2 The sequence y can be anything... I want to be able to retrieve (in a list if possible) the 3 last values of the y sequence before a value of 1 is encountered on the x sequence, i.e: On line 5 in the above dataset, x is 1 so I need to capture values: 25, 50 and -40 of the y sequence. So the outcome (if a list) should look something like: [1],[25,50,-40] [2],[-10,-5,25] # as member #7 of x sequence is 1... etc. etc. Can I do the above avoiding for/next or while loops? I am not sure I can explain it better. Any help/pointer extremely welcome. Best regards, Costas -- +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ |c|o|s|t|a|s|@|v|o|r|l|o|w|.|o|r|g| +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ [[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:
[R] Group several variables and apply a function to the group
Dear R-experts, I am struggling with the following problem, and I am looking for advice from more experienced R-users: I have a data frame with 2 identifying variables (comn and mi), and an output variable (x). comn is a variable for a company and mi is a variable for a month. comn-c(abc, abc, abc, abc, abc, abc, xyz, xyz,xyz, xyz) mi- c(1, 1,1, 2, 2, 2, 1, 1, 3, 3) x- c(-0.0031, 0.0009, -0.007, 0.1929,0.0087, 0.099,-0.089, 0.005, -0.0078, 0.67 ) df- data.frame(comn=comn, mi=mi, x=x) For each company, within a particular month, I would like to compute the standard deviation of x: for example, for abc, I would like to compute the sd of x for month1 (when mi=1) and for month2 (when mi=2). In other languages (Stata for instance), I would create a grouping variable (group comnn and mi) and then, apply the sd function for each group. However, I don't find an elegant way to do the same in R: I was thinking about the following: I could subset my data frame by mi and create one file per month, and then make a loop and in each file, use a by operator for each comn. I am sure it would work, but I feel that it would be like killing an ant with a tank. I was wondering if anyone knew a more straightforward way to implement that kind of operation? Thanks a lot, Best, Aurelien [[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] Group several variables and apply a function to the group
Like this? library(plyr) ddply(df,.(comn,mi),summarise,stDEV=sd(x)) Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx From: Aurélien PHILIPPOT aurelien.philip...@gmail.com To: R-help@r-project.org Sent: Sunday, December 4, 2011 12:32 PM Subject: [R] Group several variables and apply a function to the group Dear R-experts, I am struggling with the following problem, and I am looking for advice from more experienced R-users: I have a data frame with 2 identifying variables (comn and mi), and an output variable (x). comn is a variable for a company and mi is a variable for a month. comn-c(abc, abc, abc, abc, abc, abc, xyz, xyz,xyz, xyz) mi- c(1, 1,1, 2, 2, 2, 1, 1, 3, 3) x- c(-0.0031, 0.0009, -0.007, 0.1929,0.0087, 0.099,-0.089, 0.005, -0.0078, 0.67 ) df- data.frame(comn=comn, mi=mi, x=x) For each company, within a particular month, I would like to compute the standard deviation of x: for example, for abc, I would like to compute the sd of x for month1 (when mi=1) and for month2 (when mi=2). In other languages (Stata for instance), I would create a grouping variable (group comnn and mi) and then, apply the sd function for each group. However, I don't find an elegant way to do the same in R: I was thinking about the following: I could subset my data frame by mi and create one file per month, and then make a loop and in each file, use a by operator for each comn. I am sure it would work, but I feel that it would be like killing an ant with a tank. I was wondering if anyone knew a more straightforward way to implement that kind of operation? Thanks a lot, Best, Aurelien [[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] Group several variables and apply a function to the group
exactly like that! thanks a lot. Aurelien 2011/12/4 Felipe Carrillo mazatlanmex...@yahoo.com Like this? library(plyr) ddply(df,.(comn,mi),summarise,stDEV=sd(x)) Felipe D. Carrillo Supervisory Fishery Biologist Department of the Interior US Fish Wildlife Service California, USA http://www.fws.gov/redbluff/rbdd_jsmp.aspx *From:* Aurélien PHILIPPOT aurelien.philip...@gmail.com *To:* R-help@r-project.org *Sent:* Sunday, December 4, 2011 12:32 PM *Subject:* [R] Group several variables and apply a function to the group Dear R-experts, I am struggling with the following problem, and I am looking for advice from more experienced R-users: I have a data frame with 2 identifying variables (comn and mi), and an output variable (x). comn is a variable for a company and mi is a variable for a month. comn-c(abc, abc, abc, abc, abc, abc, xyz, xyz,xyz, xyz) mi- c(1, 1,1, 2, 2, 2, 1, 1, 3, 3) x- c(-0.0031, 0.0009, -0.007, 0.1929,0.0087, 0.099,-0.089, 0.005, -0.0078, 0.67 ) df- data.frame(comn=comn, mi=mi, x=x) For each company, within a particular month, I would like to compute the standard deviation of x: for example, for abc, I would like to compute the sd of x for month1 (when mi=1) and for month2 (when mi=2). In other languages (Stata for instance), I would create a grouping variable (group comnn and mi) and then, apply the sd function for each group. However, I don't find an elegant way to do the same in R: I was thinking about the following: I could subset my data frame by mi and create one file per month, and then make a loop and in each file, use a by operator for each comn. I am sure it would work, but I feel that it would be like killing an ant with a tank. I was wondering if anyone knew a more straightforward way to implement that kind of operation? Thanks a lot, Best, Aurelien [[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] Group several variables and apply a function to the group
Aurélien PHILIPPOT wrote Dear R-experts, I am struggling with the following problem, and I am looking for advice from more experienced R-users: I have a data frame with 2 identifying variables (comn and mi), and an output variable (x). comn is a variable for a company and mi is a variable for a month. comn-c(abc, abc, abc, abc, abc, abc, xyz, xyz,xyz, xyz) mi- c(1, 1,1, 2, 2, 2, 1, 1, 3, 3) x- c(-0.0031, 0.0009, -0.007, 0.1929,0.0087, 0.099,-0.089, 0.005, -0.0078, 0.67 ) df- data.frame(comn=comn, mi=mi, x=x) For each company, within a particular month, I would like to compute the standard deviation of x: for example, for abc, I would like to compute the sd of x for month1 (when mi=1) and for month2 (when mi=2). In other languages (Stata for instance), I would create a grouping variable (group comnn and mi) and then, apply the sd function for each group. However, I don't find an elegant way to do the same in R: I was thinking about the following: I could subset my data frame by mi and create one file per month, and then make a loop and in each file, use a by operator for each comn. I am sure it would work, but I feel that it would be like killing an ant with a tank. I was wondering if anyone knew a more straightforward way to implement that kind of operation? Thanks a lot, Best, Aurelien [[alternative HTML version deleted]] __ R-help@ 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. One way would be to use the aggregate function. # Your Data ... # Note: I have removed the quotes off the output variable x comn-c(abc, abc, abc, abc, abc, abc, xyz, xyz,xyz, xyz) mi- c(1, 1,1, 2, 2, 2, 1, 1, 3, 3) x- c(-0.0031, 0.0009, -0.007, 0.1929,0.0087, 0.099,-0.089, 0.005, -0.0078, 0.67) df- data.frame(comn=comn, mi=mi, x=x) # Aggregate Function aggregate(df$x, by=list(df$comn,df$mi),FUN=sd) HTH Pete -- View this message in context: http://r.789695.n4.nabble.com/Group-several-variables-and-apply-a-function-to-the-group-tp4158017p4158090.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.
Re: [R] Group several variables and apply a function to the group
?aggregate should do it aggregate(df$x,list(df$comn, df$mi), sd) There are other ways of course Using the reshape2 package library(reshape2) x1 - melt(df, id=c(comn, mi)) dcast(x1, comn + mi ~ variable, sd) --- On Sun, 12/4/11, Aurélien PHILIPPOT aurelien.philip...@gmail.com wrote: From: Aurélien PHILIPPOT aurelien.philip...@gmail.com Subject: [R] Group several variables and apply a function to the group To: R-help@r-project.org Received: Sunday, December 4, 2011, 3:32 PM Dear R-experts, I am struggling with the following problem, and I am looking for advice from more experienced R-users: I have a data frame with 2 identifying variables (comn and mi), and an output variable (x). comn is a variable for a company and mi is a variable for a month. comn-c(abc, abc, abc, abc, abc, abc, xyz, xyz,xyz, xyz) mi- c(1, 1,1, 2, 2, 2, 1, 1, 3, 3) x- c(-0.0031, 0.0009, -0.007, 0.1929,0.0087, 0.099,-0.089, 0.005, -0.0078, 0.67 ) df- data.frame(comn=comn, mi=mi, x=x) For each company, within a particular month, I would like to compute the standard deviation of x: for example, for abc, I would like to compute the sd of x for month1 (when mi=1) and for month2 (when mi=2). In other languages (Stata for instance), I would create a grouping variable (group comnn and mi) and then, apply the sd function for each group. However, I don't find an elegant way to do the same in R: I was thinking about the following: I could subset my data frame by mi and create one file per month, and then make a loop and in each file, use a by operator for each comn. I am sure it would work, but I feel that it would be like killing an ant with a tank. I was wondering if anyone knew a more straightforward way to implement that kind of operation? Thanks a lot, Best, Aurelien [[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.
[R] trouble with installXLSXsupport()
Dear R People: I'm using gdata and read.xls for a couple of projects. When I load gdata, it says to run installXLSXsupport() When I do that, I get a not responding error. I tried it with verbose=TRUE, but nothing appears. Has anyone else run into this, please? This is on Windows 7, 64 bit, compiled from source. Thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@gmail.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] a weird question about gdata:::
Dear R People:
If I put in:
findPerl
Error: object 'findPerl' not found
But if I use:
gdata:::findPerl
function (perl, verbose = FALSE)
{
errorMsg - perl executable not found. Use perl= argument to
specify the correct path.
if (missing(perl)) {
perl = perl
}
perl = Sys.which(perl)
if (perl == || perl == perl)
stop(errorMsg)
if (.Platform$OS == windows) {
if (length(grep(rtools, tolower(perl))) 0) {
perl.ftype - shell(ftype perl, intern = TRUE)
if (length(grep(^perl=, perl.ftype)) 0) {
perl - sub(^perl=\([^\]*)\.*, \\1, perl.ftype)
}
}
}
if (verbose)
cat(Using perl at, perl, \n)
perl
}
environment: namespace:gdata
Why does one work but not the other, please?
Thanks,
Erin
--
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: erinm.hodg...@gmail.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.
Re: [R] Estimation of AR(1) Model with Markov Switching
I did not quite get what the problem was from your description ...
However, I did search on CRAN and found at least two packages that can fit
markov switching ar models so that may be an easier way to go.
Hth, Ingmar
On Thu, Dec 1, 2011 at 5:58 PM, napps22 n.j.app...@gmail.com wrote:
Dear R users,
I have been trying to obtain the MLE of the following model
state 0: y_t = 2 + 0.5 * y_{t-1} + e_t
state 1: y_t = 0.5 + 0.9 * y_{t-1} + e_t
where e_t ~ iidN(0,1)
transition probability between states is 0.2
I've generated some fake data and tried to estimate the parameters using
the
constrOptim() function but I can't get sensible answers using it. I've
tried
using nlminb and maxLik but they haven't helped. Any tips on how I could
possibly rewrite my likelihood in a better way to improve my results would
be welcome.
Given below is my R code
# markov switching regime model
# generate data for a AR(1) markov switching model with the following pars
# state 0: y_t = 2 + 0.5 * y_{t-1} + e_t
# state 1: y_t = 0.5 + 0.9 * y_{t-1} + e_t
# where e_t ~ N(0,1)
# transition probabilities p_s0_s1 = p_s1_s0 = 0.20
# generate realisations of the state
gamma_s0 - qnorm(0.8)
gamma_s1 - qnorm(0.2)
gamma - rep(0,100)
state - rep(0,100)
# choose initial state at t=0 to be state 0
gamma[1] - gamma_s0
state[1] - 0
for(i in 2:100) {
if(rnorm(1) gamma[i-1]) {
gamma[i] - gamma_s0
state[i] - 0
}
else {
gamma[i] - gamma_s1
state[i] - 1
}
}
# generate observations
# choose y_0 = 0
# recall state at t=1 was set to 0
y1 - 2 + 0.5 * 0 + rnorm(1)
y - rep(0,100)
y[1] - y1
for(i in 2:100) {
if(state[i]==0) {
y[i] - 2 + 0.5 * y[i-1] + rnorm(1)
}
else {
y[i] - 0.5 + 0.9 * y[i-1] + rnorm(1)
}
}
# convert into time series object
y - ts(y, start = 1, freq = 1)
# construct negative conditional likelihood function
neg.logl - function(theta, data) {
# construct parameters
beta_s0 - theta[1:2]
beta_s1 - theta[3:4]
sigma2 - exp(theta[5])
gamma0 - theta[6]
gamma1 - theta[7]
# construct probabilities
#probit specification
p_s0_s0 - pnorm(gamma_s0)
p_s0_s1 - pnorm(gamma_s1)
p_s1_s0 - 1-pnorm(gamma_s0)
p_s1_s1 - 1-pnorm(gamma_s1)
# create data matrix
X - cbind(1,y)
# assume erogodicity of the markov chain
# use unconditional probabilities
p0_s0 - (1 - p_s1_s1) / (2 -p_s0_s0 -p_s1_s1)
p0_s1 - 1-p0_s0
# create variables
p_s0_t_1 - rep(0, nrow(X))
p_s1_t_1 - rep(0, nrow(X))
p_s0_t - rep(0, nrow(X))
p_s1_t - rep(0, nrow(X))
f_s0 - rep(0,nrow(X)-1)
f_s1 - rep(0,nrow(X)-1)
f - rep(0,nrow(X)-1)
logf - rep(0, nrow(X)-1)
p_s0_t[1] - p0_s0
p_s1_t[1] - p0_s1
# initiate hamilton filter
for(i in 2:nrow(X)) {
# calculate prior probabilities using the TPT
# TPT for this example gives us
# p_si_t_1 = p_si_t_1_si * p_si_t + p_si_t_1_sj * p_si_t
# where p_si_t_1 is the prob state_t = i given information @ time t-1
# p_si_t_1_sj is the prob state_t = i given state_t_1 = j, and all info @
time t-1
# p_si_t is the prob state_t = i given information @ time t
# in this simple example p_si_t_1_sj = p_si_sj
p_s0_t_1[i] - (p_s0_s0 * p_s0_t[i-1]) + (p_s0_s1 * p_s1_t[i-1])
p_s1_t_1[i] - (p_s1_s0 * p_s0_t[i-1]) + (p_s1_s1 * p_s1_t[i-1])
# calculate density function for observation i
# f_si is density conditional on state = i
# f is the density
f_s0[i] - dnorm(y[i]-X[i-1,]%*%beta_s0, sd = sqrt(sigma2))
f_s1[i] - dnorm(y[i]-X[i-1,]%*%beta_s1, sd = sqrt(sigma2))
f[i] - (f_s0[i] * p_s0_t_1[i]) + (f_s1[i] * p_s1_t_1[i])
# calculate filtered/posterior probabilities using bayes rule
# p_si_t is the prob that state = i given information @ time t
p_s0_t[i] - (f_s0[i] * p_s0_t_1[i]) / f[i]
p_s1_t[i] - (f_s1[i] * p_s1_t_1[i]) / f[i]
logf[i] - log(f[i])
}
logl -sum(logf)
return(-logl)
}
# restrict intercept in state model 0 to be greater than intercept in state
model 1
# thus matrix of restrictions R is [1 0 -1 0 0 0 0]
R - matrix(c(1,0,-1,0,0,0,0), nrow = 1)
# pick start values for the 7 unknown parameters
start_val - matrix(runif(7), nrow = 7)
# ensures starting values are in the feasible set
start_val[1,] - start_val[3,] + 0.1
# estimate pars
results -constrOptim(start_val,neg.logl,grad = NULL, ui = R, ci = 0)
Regards,
N
--
View this message in context:
http://r.789695.n4.nabble.com/Estimation-of-AR-1-Model-with-Markov-Switching-tp4129417p4129417.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.
[[alternative HTML version deleted]]
Re: [R] a weird question about gdata:::
??namespace
?getAnywhere
?::
See also: http://www.stat.uiowa.edu/~luke/R/namespaces/morenames.pdf
Bottom line: namespaces provide a mechanism to hide certain
variables within a package. Special measures as documented above are
required to view them
-- Bert
On Sun, Dec 4, 2011 at 1:19 PM, Erin Hodgess erinm.hodg...@gmail.com wrote:
Dear R People:
If I put in:
findPerl
Error: object 'findPerl' not found
But if I use:
gdata:::findPerl
function (perl, verbose = FALSE)
{
errorMsg - perl executable not found. Use perl= argument to
specify the correct path.
if (missing(perl)) {
perl = perl
}
perl = Sys.which(perl)
if (perl == || perl == perl)
stop(errorMsg)
if (.Platform$OS == windows) {
if (length(grep(rtools, tolower(perl))) 0) {
perl.ftype - shell(ftype perl, intern = TRUE)
if (length(grep(^perl=, perl.ftype)) 0) {
perl - sub(^perl=\([^\]*)\.*, \\1, perl.ftype)
}
}
}
if (verbose)
cat(Using perl at, perl, \n)
perl
}
environment: namespace:gdata
Why does one work but not the other, please?
Thanks,
Erin
--
Erin Hodgess
Associate Professor
Department of Computer and Mathematical Sciences
University of Houston - Downtown
mailto: erinm.hodg...@gmail.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.
--
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
__
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] Group several variables and apply a function to the group
... with() is useful here: e.g. in base R, simply tapply() or ave() with with() with(df,ave(x, comn,mi, FUN = sd)) -- Bert On Sun, Dec 4, 2011 at 1:07 PM, John Kane jrkrid...@yahoo.ca wrote: ?aggregate should do it aggregate(df$x,list(df$comn, df$mi), sd) There are other ways of course Using the reshape2 package library(reshape2) x1 - melt(df, id=c(comn, mi)) dcast(x1, comn + mi ~ variable, sd) --- On Sun, 12/4/11, Aurélien PHILIPPOT aurelien.philip...@gmail.com wrote: From: Aurélien PHILIPPOT aurelien.philip...@gmail.com Subject: [R] Group several variables and apply a function to the group To: R-help@r-project.org Received: Sunday, December 4, 2011, 3:32 PM Dear R-experts, I am struggling with the following problem, and I am looking for advice from more experienced R-users: I have a data frame with 2 identifying variables (comn and mi), and an output variable (x). comn is a variable for a company and mi is a variable for a month. comn-c(abc, abc, abc, abc, abc, abc, xyz, xyz,xyz, xyz) mi- c(1, 1,1, 2, 2, 2, 1, 1, 3, 3) x- c(-0.0031, 0.0009, -0.007, 0.1929,0.0087, 0.099,-0.089, 0.005, -0.0078, 0.67 ) df- data.frame(comn=comn, mi=mi, x=x) For each company, within a particular month, I would like to compute the standard deviation of x: for example, for abc, I would like to compute the sd of x for month1 (when mi=1) and for month2 (when mi=2). In other languages (Stata for instance), I would create a grouping variable (group comnn and mi) and then, apply the sd function for each group. However, I don't find an elegant way to do the same in R: I was thinking about the following: I could subset my data frame by mi and create one file per month, and then make a loop and in each file, use a by operator for each comn. I am sure it would work, but I feel that it would be like killing an ant with a tank. I was wondering if anyone knew a more straightforward way to implement that kind of operation? Thanks a lot, Best, Aurelien [[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. -- 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 __ 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] RODBC sqlSave / append problem (windows XP, R 2.13.2)
Dear All,
Using RODBC I have read in a (429 x 11) dataframe from Access, and would
like to append two columns of transformed data (429 x 2) to the original
table (thereby making it a 429 x 13 table). I would ideally like this to
be the same name etc as the original table in Access.
I have used the following command:
R
sqlSave(con,as.data.frame(SA_data),tablename=Const_mats_8301_t1,rownam
es=T,fast=T, append=T)
And get the error:
Error in odbcUpdate(channel, query, mydata, coldata[m, ], test = test, :
missing columns in 'data'
Thanks in advance,
mj
Visit our website at http://www.ubs.com
This message contains confidential information and is in...{{dropped:26}}
__
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] equating approximate values
Not sure what to make of the fact that your x, y are of different
lengths: if you mean to check all possible pairings, this is probably
what you need:
which(outer(x, y, -) threshold, arr.ind = TRUE)
Michael
On Sun, Dec 4, 2011 at 2:24 PM, andrija djurovic djandr...@gmail.com wrote:
Hi. Maybe this can help you (you can try additionally to incorporate
threshold):
set.seed(1)
x-rnorm(10,10,1)
values - sample(1:10,10) #values that we are looking for
mat - matrix(c(x,values),ncol=2)
closest-function(x,values) #function is an example from The R book
(Crawley)
+ {
+ x[which(abs(x-values)==min(abs(x-values)))]
+ }
apply(mat[,2,drop=FALSE],1,function(y) closest(mat[,1],y))
[1] 10.183643 9.164371 9.164371 9.164371 9.164371 9.164371 9.164371
9.164371
[9] 9.164371 9.164371
On Sun, Dec 4, 2011 at 7:00 PM, vamshi999 vamshi...@gmail.com wrote:
Hello List,
I am having trouble finding the command for my problem.
I have two arrays x and y. now i would like to compare the values of x and
y
and then get the index of x which is exactly or approximately equal(+/-
some
value ) to the values in y.
x - runif(100,min=0,max=5)
y - runif(10,min=0,max=5)
the threshold value(+/-) value can vary. for this example lets take it to
be
.5
I know the regular method of doing this by writing different if and for
loops. But i have very big dataframe the computation time is very high for
this method. can anyone please tell me if there any functions to do this.
thank you for your help.
--
View this message in context:
http://r.789695.n4.nabble.com/equating-approximate-values-tp4157551p4157551.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.
[[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] equating approximate values
My apologies: you need an abs() call as well:
which(abs(outer(x, y, -)) threshold, arr.ind = TRUE)
Michael
On Sun, Dec 4, 2011 at 6:25 PM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
Not sure what to make of the fact that your x, y are of different
lengths: if you mean to check all possible pairings, this is probably
what you need:
which(outer(x, y, -) threshold, arr.ind = TRUE)
Michael
On Sun, Dec 4, 2011 at 2:24 PM, andrija djurovic djandr...@gmail.com wrote:
Hi. Maybe this can help you (you can try additionally to incorporate
threshold):
set.seed(1)
x-rnorm(10,10,1)
values - sample(1:10,10) #values that we are looking for
mat - matrix(c(x,values),ncol=2)
closest-function(x,values) #function is an example from The R book
(Crawley)
+ {
+ x[which(abs(x-values)==min(abs(x-values)))]
+ }
apply(mat[,2,drop=FALSE],1,function(y) closest(mat[,1],y))
[1] 10.183643 9.164371 9.164371 9.164371 9.164371 9.164371 9.164371
9.164371
[9] 9.164371 9.164371
On Sun, Dec 4, 2011 at 7:00 PM, vamshi999 vamshi...@gmail.com wrote:
Hello List,
I am having trouble finding the command for my problem.
I have two arrays x and y. now i would like to compare the values of x and
y
and then get the index of x which is exactly or approximately equal(+/-
some
value ) to the values in y.
x - runif(100,min=0,max=5)
y - runif(10,min=0,max=5)
the threshold value(+/-) value can vary. for this example lets take it to
be
.5
I know the regular method of doing this by writing different if and for
loops. But i have very big dataframe the computation time is very high for
this method. can anyone please tell me if there any functions to do this.
thank you for your help.
--
View this message in context:
http://r.789695.n4.nabble.com/equating-approximate-values-tp4157551p4157551.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.
[[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] a weird question about gdata:::
See end of message.
On 05/12/11 10:19, Erin Hodgess wrote:
Dear R People:
If I put in:
findPerl
Error: object 'findPerl' not found
But if I use:
gdata:::findPerl
function (perl, verbose = FALSE)
{
errorMsg- perl executable not found. Use perl= argument to
specify the correct path.
if (missing(perl)) {
perl = perl
}
perl = Sys.which(perl)
if (perl == || perl == perl)
stop(errorMsg)
if (.Platform$OS == windows) {
if (length(grep(rtools, tolower(perl))) 0) {
perl.ftype- shell(ftype perl, intern = TRUE)
if (length(grep(^perl=, perl.ftype)) 0) {
perl- sub(^perl=\([^\]*)\.*, \\1, perl.ftype)
}
}
}
if (verbose)
cat(Using perl at, perl, \n)
perl
}
environment: namespace:gdata
Why does one work but not the other, please?
Because findPerl is ``not exported'' from the gdata namespace.
Uhhh, what does that mean? I have a vague idea, but I'm not sufficiently
confident/competent to elaborate. You'll just have to read up on
namespaces.
I'm *sure* namespaces are really a Good Thing, but they sure do add to the
mysteries of R usage.
Has Pat Burns written anything by way of explaining namespace to bunnies
like me?
cheers,
Rolf
__
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] a weird question about gdata:::
On Sun, Dec 4, 2011 at 6:57 PM, Rolf Turner rolf.tur...@xtra.co.nz wrote:
See end of message.
On 05/12/11 10:19, Erin Hodgess wrote:
Dear R People:
If I put in:
findPerl
Error: object 'findPerl' not found
But if I use:
gdata:::findPerl
function (perl, verbose = FALSE)
{
errorMsg- perl executable not found. Use perl= argument to
specify the correct path.
if (missing(perl)) {
perl = perl
}
perl = Sys.which(perl)
if (perl == || perl == perl)
stop(errorMsg)
if (.Platform$OS == windows) {
if (length(grep(rtools, tolower(perl))) 0) {
perl.ftype- shell(ftype perl, intern = TRUE)
if (length(grep(^perl=, perl.ftype)) 0) {
perl- sub(^perl=\([^\]*)\.*, \\1, perl.ftype)
}
}
}
if (verbose)
cat(Using perl at, perl, \n)
perl
}
environment: namespace:gdata
Why does one work but not the other, please?
Because findPerl is ``not exported'' from the gdata namespace.
Uhhh, what does that mean? I have a vague idea, but I'm not sufficiently
confident/competent to elaborate. You'll just have to read up on
namespaces.
I'm *sure* namespaces are really a Good Thing, but they sure do add to the
mysteries of R usage.
The idea is to divide objects into those that are there for the user
to access (exported objects) and those that are internal objects that
only the package itself uses (everything else). findPerl is there
only so that read.xls and other routines that depend on perl scripts
can use it internally to find perl. It was not intended that users
access it so its better hidden from view.
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.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.
Re: [R] a weird question about gdata:::
I prefer to think of namespaces as preventing clashes with similarly-named
functions in the main workspace or in other packages that might serve a
different need.
Given that purpose, I don't think I would have confined that particular
function behind the namespace, because any other use of that name is likely to
duplicate the functionality of that particular function, and any improvements
to it probably ought to be incorporated into that particular function just as
much as any other implementation would deserve improvement.
---
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.
Gabor Grothendieck ggrothendi...@gmail.com wrote:
On Sun, Dec 4, 2011 at 6:57 PM, Rolf Turner rolf.tur...@xtra.co.nz
wrote:
See end of message.
On 05/12/11 10:19, Erin Hodgess wrote:
Dear R People:
If I put in:
findPerl
Error: object 'findPerl' not found
But if I use:
gdata:::findPerl
function (perl, verbose = FALSE)
{
errorMsg- perl executable not found. Use perl= argument to
specify the correct path.
if (missing(perl)) {
perl = perl
}
perl = Sys.which(perl)
if (perl == || perl == perl)
stop(errorMsg)
if (.Platform$OS == windows) {
if (length(grep(rtools, tolower(perl))) 0) {
perl.ftype- shell(ftype perl, intern = TRUE)
if (length(grep(^perl=, perl.ftype)) 0) {
perl- sub(^perl=\([^\]*)\.*, \\1,
perl.ftype)
}
}
}
if (verbose)
cat(Using perl at, perl, \n)
perl
}
environment: namespace:gdata
Why does one work but not the other, please?
Because findPerl is ``not exported'' from the gdata namespace.
Uhhh, what does that mean? I have a vague idea, but I'm not
sufficiently
confident/competent to elaborate. You'll just have to read up on
namespaces.
I'm *sure* namespaces are really a Good Thing, but they sure do add
to the
mysteries of R usage.
The idea is to divide objects into those that are there for the user
to access (exported objects) and those that are internal objects that
only the package itself uses (everything else). findPerl is there
only so that read.xls and other routines that depend on perl scripts
can use it internally to find perl. It was not intended that users
access it so its better hidden from view.
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.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-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] convert table to a string in matrix
Hello everybody! I need help in collecting the information about Russian elections. There is a table at the web-site http://www.moscow_city.vybory.izbirkom.ru/region/region/moscow_city?action=showroot=774003008tvd=477400389537vrn=100100028713299region=77global=truesub_region=77prver=0pronetvd=nullvibid=477400389537type=242 the problem is how to convert this table to a string in order to add it to the table with 25 columns. ReadHTMLTable doesn't work because I need only bold digits and it takes both normal and bold digits and stick them together. What can be done? Thanks! Philipp [[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] upper bound in the integrate function depends on a parameter
Jorge I Velez jorgeivanvelez at gmail.com writes:
And remember:
#install.packages('fortunes')
require(fortunes)
fortune('Yoda')
Evelyn Hall: I would like to know how (if) I can extract some of the
information
from the summary of my nlme.
Simon Blomberg: This is R. There is no if. Only how.
-- Evelyn Hall and Simon 'Yoda' Blomberg
R-help (April 2005)
Yes, although if you really wanted to compute (symbolic) indefinite integrals,
it would be awfully hard. R is Turing-complete so of course you could do
it ... but ...
Ben Bolker
__
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] Save debugging session info and resume from the middle?
Hi all,
In debugging, I've met the following problem:
myfunction = function (x, y)
{
for (i in 1:length(x)}
{
Part_A;
#save the debugging session here?
Part_B;
}
}
All these parts are of very heavy computations and often can take hours to
finish.
How do I debug them efficiently?
I am thinking of to save a snapshot of the debugging session (everything
including the stack trace, etc.) in between Part_A and Part_B,
and then when I want to focus on Part_B only, I can replace the code
Part_A by LoadDebugSession...so that I don't have recompute Part_A
again and again...
Is ths possible to do?
Can stack traces be saved and then recovered?
Thanks
Thanks a lot!
[[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] equating approximate values
this is exactly what i wanted. How to i select only the minimum value from this?. thank you My apologies: you need an abs() call as well: which(abs(outer(x, y, -)) threshold, arr.ind = TRUE) Michael -- View this message in context: http://r.789695.n4.nabble.com/equating-approximate-values-tp4157551p4158691.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] Rggobi pdf output
Good day everyone. I have a question concerning *ggobi* and
*rggobi*package. I am using R version 2.13.2 and Ubuntu 11.04. I am
new to ggobi
and I'm reading the book *Interactive and Dynamic Graphics for Data Analysis
*. The book was published 2007.
My question is: how can I export a graph for *rggobi* to pdf to include it
in latex. For example: I have lots of variables in ggobi and I need to
export the ggplot like scatterplot of any two variables or parallel
cordinates graph to a pdf. So far I've read that the authors suggests to
solve it like this:
library(DescribeDisplay)
d - dd_load(fig.R)
plot(d)
or
p - ggplot(d)
print(p)
which produces nice graphics which you can use with pdf() function. But
neither the *DescribeDisplay* package, nor *ggplot* are available in
2.13.2.
I browsed the web for solution, but I found only that
ggobi_display_save_picture() could be useful for image graphs but not for
pdf. I also tried save display description (tools-save display
description) and then plotting it with qplot() or plot(). But all I get is
a blank screen while ggobi_display_save_picture() gives a good picture.
There is probably a much easier solution since R is changing and becoming
more convenient to use.
I i'm also including the code of the example i'm doing
f.std.data-function(x) {
return((x-mean(x,na.rm=T))/sd(x,na.rm=T))
}
# Read data, and standardize before running SOM
d.music-read.csv(music-sub.csv,row.names=1)
d.music.std-cbind(d.music[,c(1,2)],apply(d.music[,-c(1,2)],2,f.std.data))
# Load libraries
library(rggobi)
library(som)
# Run SOM
music.som-som(d.music.std[,-c(1:2)],6,6,neigh=bubble,rlen=100)
music.som-som(d.music.std[,-c(1:2)],6,6,neigh=bubble,rlen=1000)
# Set up data for ggobi - data needs to have any labels in the first few columns
f.ggobi.som-function(x,x.som) {
xmx-jitter(x.som$visual$x,factor=2)
xmy-jitter(x.som$visual$y,factor=2)
ncols-ncol(x)
x.ggobi-cbind(x,xmx,xmy)
dimnames(x.ggobi)[[2]][ncols+1]-Map 1
dimnames(x.ggobi)[[2]][ncols+2]-Map 2
x.grid-cbind(x.som$code,x.som$code.sum[,1:2])
dimnames(x.grid)[[2]]-dimnames(x.ggobi)[[2]]
x.clust-rbind(x.ggobi,x.grid)
}
f.ggobi.som.net-function(x.som) {
x.net-NULL
for (i in 1:x.som$xdim) {
for (j in 1:x.som$ydim) {
if (jx.som$ydim)
x.net-rbind(x.net,c((i-1)*x.som$xdim+j,(i-1)*x.som$xdim+j+1))
if (ix.som$xdim) x.net-rbind(x.net,c((i-1)*x.som$xdim+j,i*x.som$xdim+j))
}
}
return(x.net)
}
d.music.som-f.ggobi.som(d.music.std[,-c(1,2)],music.som)
d.music.som-list(Songs=factor(c(as.character(row.names(d.music)),rep(0,36))),
Artist=factor(c(as.character(d.music[,1]),rep(0,36))),
Type=factor(c(as.character(d.music[,2]),rep(0,36))),
LVar=d.music.som[,1],LAve=d.music.som[,2],LMax=d.music.som[,3],
LFEner=d.music.som[,4],LFreq=d.music.som[,5],Map.1=d.music.som[,6],
Map.2=d.music.som[,7])
gg-ggobi(d.music.som)
g-gg[1]
#load edges
d.music.som.net-f.ggobi.som.net(music.som)
edges(g) - d.music.som.net + 62
# Color points according to type of music, and som net
gcolor- rep(8,98)
gcolor[d.music.som$Type==Rock]-6
gcolor[d.music.som$Type==Classical]-4
gcolor[d.music.som$Type==New wave]-1
glyph_color(g)-gcolor
[[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] [rggobi] ggplot like pdf output
Good day everyone. I have a question concerning *ggobi* and
*rggobi*package. I am using R version 2.13.2 and Ubuntu 11.04. I am
new to ggobi
and I'm reading the book *Interactive and Dynamic Graphics for Data Analysis
*. The book was published 2007.
My question is: how can I export a graph for *rggobi* to pdf to include it
in latex. For example: I have lots of variables in ggobi and I need to
export the ggplot like scatterplot of any two variables or parallel
cordinates graph to a pdf. So far I've read that the authors suggests to
solve it like this:
library(DescribeDisplay)
d - dd_load(fig.R)
plot(d)
or
p - ggplot(d)
print(p)
which produces nice graphics which you can use with pdf() function. But
neither the *DescribeDisplay* package, nor *ggplot* are available in
2.13.2.
I browsed the web for solution, but I found only that
ggobi_display_save_picture() could be useful for image graphs but not for
pdf. I also tried save display description (tools-save display
description) and then plotting it with qplot() or plot(). But all I get is
a blank screen while ggobi_display_save_picture() gives a good picture.
There is probably a much easier solution since R is changing and becoming
more convenient to use.
I i'm also including the code of the example i'm doing
f.std.data-function(x) {
return((x-mean(x,na.rm=T))/sd(x,na.rm=T))
}
# Read data, and standardize before running SOM
d.music-read.csv(music-sub.csv,row.names=1)
d.music.std-cbind(d.music[,c(1,2)],apply(d.music[,-c(1,2)],2,f.std.data))
# Load libraries
library(rggobi)
library(som)
# Run SOM
music.som-som(d.music.std[,-c(1:2)],6,6,neigh=bubble,rlen=100)
music.som-som(d.music.std[,-c(1:2)],6,6,neigh=bubble,rlen=1000)
# Set up data for ggobi - data needs to have any labels in the first few columns
f.ggobi.som-function(x,x.som) {
xmx-jitter(x.som$visual$x,factor=2)
xmy-jitter(x.som$visual$y,factor=2)
ncols-ncol(x)
x.ggobi-cbind(x,xmx,xmy)
dimnames(x.ggobi)[[2]][ncols+1]-Map 1
dimnames(x.ggobi)[[2]][ncols+2]-Map 2
x.grid-cbind(x.som$code,x.som$code.sum[,1:2])
dimnames(x.grid)[[2]]-dimnames(x.ggobi)[[2]]
x.clust-rbind(x.ggobi,x.grid)
}
f.ggobi.som.net-function(x.som) {
x.net-NULL
for (i in 1:x.som$xdim) {
for (j in 1:x.som$ydim) {
if (jx.som$ydim)
x.net-rbind(x.net,c((i-1)*x.som$xdim+j,(i-1)*x.som$xdim+j+1))
if (ix.som$xdim) x.net-rbind(x.net,c((i-1)*x.som$xdim+j,i*x.som$xdim+j))
}
}
return(x.net)
}
d.music.som-f.ggobi.som(d.music.std[,-c(1,2)],music.som)
d.music.som-list(Songs=factor(c(as.character(row.names(d.music)),rep(0,36))),
Artist=factor(c(as.character(d.music[,1]),rep(0,36))),
Type=factor(c(as.character(d.music[,2]),rep(0,36))),
LVar=d.music.som[,1],LAve=d.music.som[,2],LMax=d.music.som[,3],
LFEner=d.music.som[,4],LFreq=d.music.som[,5],Map.1=d.music.som[,6],
Map.2=d.music.som[,7])
gg-ggobi(d.music.som)
g-gg[1]
#load edges
d.music.som.net-f.ggobi.som.net(music.som)
edges(g) - d.music.som.net + 62
# Color points according to type of music, and som net
gcolor- rep(8,98)
gcolor[d.music.som$Type==Rock]-6
gcolor[d.music.som$Type==Classical]-4
gcolor[d.music.som$Type==New wave]-1
glyph_color(g)-gcolor
[[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] Prediction from censReg?
Just posting again here... -- View this message in context: http://r.789695.n4.nabble.com/Prediction-from-censReg-tp4155855p4158844.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] Persp3d freezes when run from within Python
G'day everyone, I've been trying to get an interactive OpenGL plot to work from within Python 2.6 using Rpy2 and the persp3d function. The problem is that the plot seems to freeze upon activation. All interactivity is lost even though it works fine when run from within the R console (version 2.11.1). Is this a known issue? Any ideas as to what might be causing this, or possibly how to fix it? cheers, wchips -- View this message in context: http://r.789695.n4.nabble.com/Persp3d-freezes-when-run-from-within-Python-tp4158940p4158940.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.
Re: [R] a weird question about gdata:::
On Sun, Dec 4, 2011 at 8:07 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: I prefer to think of namespaces as preventing clashes with similarly-named functions in the main workspace or in other packages that might serve a different need. Given that purpose, I don't think I would have confined that particular function behind the namespace, because any other use of that name is likely to duplicate the functionality of that particular function, and any improvements to it probably ought to be incorporated into that particular function just as much as any other implementation would deserve improvement. The idea of hiding the the internals is that they can then be changed with reasonable likelihood that it won't affect users. Only those who attempted to circumvent the barriers put in place would be affected. For example, suppose that read.xls and the related Excel routines were to be changed so that internally they use C instead of perl. In that case findPerl would not serve any purpose in the package and the current design would allow it to be dropped. On the other hand, if the purpose of the package were specifically to interface to perl then it would make sense to export it. -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.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.
Re: [R] Extract last 3 characters from numeric vector
Thanks Sarah, but I discovered that numbers like 3.0 only have 1 character, so I had a range of character lengths from 1 to 4 (e.g. 17.0 has 2 characters, 3.4 has 3 and 12.4 has 4). Uwe's method worked well. Thanks again. Kang Min On Dec 4, 11:42 pm, Uwe Ligges lig...@statistik.tu-dortmund.de wrote: On 04.12.2011 14:38, Kang Min wrote: Hi all, I have a numeric vector with 1 decimal place, and I'd like to extract the last 3 characters, including the decimal point. The vector ranges from 0 to 20. x- round(runif(100)*20, digits=1) formatC(round(x%%10, 1), format=f, digits=1) Uwe Ligges Some of numbers have 3 characters, and some have 4. I've read up on the substr() function but that extracts characters based on exact positions. How can I extract just the last 3 characters no matter the length of the number? e.g. from 16.7 I want 6.7, from 3.5 I want 3.5 as it is. Thanks, Kang Min __ r-h...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ r-h...@r-project.org mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guidehttp://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] similarity matrix
I'm sorry, I made a mistake in my example. you're right. I don't really know how a similarity alogrithm worksbut I'm willing to try that...are there any good examples available? Thank you -- View this message in context: http://r.789695.n4.nabble.com/similarity-matrix-tp4157576p4159547.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] Toggle cASE
Hello R-help list, I am looking for way to toggle the case of the characters like a flip-flop; that is from ''Hello'' to hELLO or vice versa. I know that there are a number of functions like casefold, tolower, toupper, etc. but these functions change the case in an uniform way. Thanks in advance, Antonio Rivero Ostoic Antonio Rivero Ostoic PhD Student, Department of Leadership and Strategy From 1 Jul until 31 Dec 2011 Tel. +61 3 8344 4300 Fax +61 3 9347 6618 Email j...@sdu.dk Addr. The University of Melbourne, Victoria 3010 Australia - UNIVERSITY OF SOUTHERN DENMARK Sdr. Stationsvej 28 · DK-4200 Slagelse · Denmark · Tel. +45 6550 1000 · www.sdu.dk [[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] about interpretation of anova results...
quantreg package is used.
*fit1 results are*
Call:
rq(formula = op ~ inp1 + inp2 + inp3 + inp4 + inp5 + inp6 + inp7 +
inp8 + inp9, tau = 0.15, data = wbc)
Coefficients:
(Intercept) inp1 inp2 inp3 inp4
inp5
-0.191528450 0.005276347 0.021414032 0.016034803 0.007510343
0.005276347
inp6 inp7 inp8 inp9
0.058708544 0.005224906 0.006804871 -0.003931540
Degrees of freedom: 673 total; 663 residual
*fit2 results are*
Call:
rq(formula = op ~ inp1 + inp2 + inp3 + inp4 + inp5 + inp6 + inp7 +
inp8 + inp9, tau = 0.3, data = wbc)
Coefficients:
(Intercept) inp1 inp2 inp3 inp4
-1.11e-01 5.776765e-19 4.635734e-18 1.874715e-18 2.099872e-18
inp5 inp6 inp7 inp8 inp9
-4.942052e-19 1.11e-01 2.205289e-18 4.138435e-18 9.300642e-19
Degrees of freedom: 673 total; 663 residual
anova(fit1,fit2);
Quantile Regression Analysis of Deviance Table
Model: op ~ inp1 + inp2 + inp3 + inp4 + inp5 + inp6 + inp7 + inp8 + inp9
Joint Test of Equality of Slopes: tau in { 0.15 0.3 }
Df Resid Df F value Pr(F)
1 9 1337 0.5256 0.8568
Warning messages:
1: In summary.rq(x, se = nid, covariance = TRUE) : 93 non-positive fis
2: In summary.rq(x, se = nid, covariance = TRUE) : 138 non-positive fis
how to interpret the above results??
what is the use of anova function??
will it give the best among fit1 fit2..
--
View this message in context:
http://r.789695.n4.nabble.com/about-interpretation-of-anova-results-tp4159510p4159510.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 error while using anova function
fit1-rq(formula=op~inp1+inp2+inp3+inp4+inp5+inp6+inp7+inp8+inp9,tau=0.15,data=wbc) fit2-rq(formula=op~inp1+inp2+inp3+inp4+inp5+inp6+inp7+inp8+inp9,tau=0.5,data=wbc) fit3-rq(formula=op~inp1+inp2+inp3+inp4+inp5+inp6+inp7+inp8+inp9,tau=0.15,data=wbc) fit4-rq(formula=op~inp1+inp2+inp3+inp4+inp5+inp6+inp7+inp8+inp9,tau=0.15,data=wbc) fit5-rq(formula=op~inp1+inp2+inp3+inp4+inp5+inp6+inp7+inp8+inp9,tau=0.15,data=wbc) *output of tau=0.15*fit1 Call: rq(formula = op ~ inp1 + inp2 + inp3 + inp4 + inp5 + inp6 + inp7 + inp8 + inp9, tau = 0.15, data = wbc) Coefficients: (Intercept) inp1 inp2 inp3 inp4 inp5 -0.191528450 0.005276347 0.021414032 0.016034803 0.007510343 0.005276347 inp6 inp7 inp8 inp9 0.058708544 0.005224906 0.006804871 -0.003931540 Degrees of freedom: 673 total; 663 residual *output of tau=0.3*fit2 Call: rq(formula = op ~ inp1 + inp2 + inp3 + inp4 + inp5 + inp6 + inp7 + inp8 + inp9, tau = 0.3, data = wbc) Coefficients: (Intercept) inp1 inp2 inp3 inp4 -1.11e-01 5.776765e-19 4.635734e-18 1.874715e-18 2.099872e-18 inp5 inp6 inp7 inp8 inp9 -4.942052e-19 1.11e-01 2.205289e-18 4.138435e-18 9.300642e-19 Degrees of freedom: 673 total; 663 residual *output of tau=0.5*fit3 Call: rq(formula = op ~ inp1 + inp2 + inp3 + inp4 + inp5 + inp6 + inp7 + inp8 + inp9, tau = 0.5, data = wbc) Coefficients: (Intercept) inp1 inp2 inp3 inp4 -1.40e-01 5.810236e-17 4.00e-02 1.087160e-16 4.297771e-18 inp5 inp6 inp7 inp8 inp9 8.045868e-17 8.00e-02 6.841101e-17 2.00e-02 7.560947e-17 Degrees of freedom: 673 total; 663 residual *output of tau=0.65* Call: rq(formula = op ~ inp1 + inp2 + inp3 + inp4 + inp5 + inp6 + inp7 + inp8 + inp9, tau = 0.65, data = wbc) Coefficients: (Intercept) inp1 inp2 inp3 inp4 inp5 -0.193593706 0.005012804 0.044208182 0.008994346 0.006214294 0.007622629 inp6 inp7 inp8 inp9 0.064595895 0.006214294 0.028904532 0.001775512 Degrees of freedom: 673 total; 663 residual *output of tau=0.9:* fit5 Call: rq(formula = op ~ inp1 + inp2 + inp3 + inp4 + inp5 + inp6 + inp7 + inp8 + inp9, tau = 0.9, data = wbc) Coefficients: (Intercept) inp1 inp2 inp3 inp4 inp5 -0.249006688 0.040430238 0.010854846 0.031021326 0.013558943 0.024867111 inp6 inp7 inp8 inp9 0.050441784 0.024867111 0.027018345 0.001079872 Degrees of freedom: 673 total; 663 residual b so fit1 fit2,fit3,fit4,fit5 are the 5 quantiles of the wbc dataset.but why i am encoutering the following error while using anova* *anova(fit1,fit2,fit3,fit4,fit5); Error in solve.default(D %*% W %*% t(D), D %*% coef) : system is computationally singular: reciprocal condition number = 5.58091e-19 In addition: Warning messages: 1: In summary.rq(x, se = nid, covariance = TRUE) : 93 non-positive fis 2: In summary.rq(x, se = nid, covariance = TRUE) : 138 non-positive fis 3: In summary.rq(x, se = nid, covariance = TRUE) : 206 non-positive fis 4: In summary.rq(x, se = nid, covariance = TRUE) : 53 non-positive fis 5: In summary.rq(x, se = nid, covariance = TRUE) : 30 non-positive fis* -- View this message in context: http://r.789695.n4.nabble.com/about-error-while-using-anova-function-tp4159463p4159463.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] local minima/ maxima
__ 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.
