Re: [R] Finding the package providing funtion "%du%"

el stupid in public on the r-help list! F > > > > On Wed, Jun 30, 2021 at 1:03 PM Federico Calboli > wrote: > Hello All, > > I am playing with igraph (which seems to work for what I have used it). > Nevetheless: > > demo(&#x

[R] Finding the package providing funtion "%du%"

vctrs_0.3.8 generics_0.1.0 [10] ellipsis_0.3.2 tools_4.1.0 glue_1.4.2 purrr_0.3.4 compiler_4.1.0 pkgconfig_2.0.3 tidyselect_1.1.1 tibble_3.1.2 -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionary Genomics Charles Deberiotstr

[R] install_github does not work locally

5.1purrr_0.3.4 callr_3.6.0 fs_1.5.0 ps_1.6.0 curl_4.3 testthat_3.0.2 [25] memoise_2.0.0 glue_1.4.2cachem_1.0.4 compiler_4.0.4 desc_1.3.0prettyunits_1.1.1 -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionar

[R] how to feed lme() and lmer() data for a loop

building data frames on the fly, but this is cumbresome, both as code and very likely as performance, especially looping over lots of data having to generate these dummy data frames. If there is a trick I am missing I’d be grateful if anybody could set me straight. Best F -- Federico Calboli LBEG

Re: [R] keeping github packages up to date

ls. Cheers F > > On October 12, 2018 8:00:11 AM PDT, Federico Calboli > wrote: >> Hi all, >> >> more and more people (sadly) are putting stuff on github, with either >> no CRAN upload or an package. So I am stuck with using devtools and >> install

[R] keeping github packages up to date

Hi all, more and more people (sadly) are putting stuff on github, with either no CRAN upload or an package. So I am stuck with using devtools and install_github. I know how to keep stuff from CRAN updated — how do I do the same for github stuff? Cheers F -- Federico Calboli LBEG

[R] getting 21 very different colours

colourchart, but the visual differences between ’skyblue’ and ’slategrey’ elude me when plotted as dots on a plot). Cheers F -- Federico Calboli LBEG - Laboratory of Biodiversity and Evolutionary Genomics Charles Deberiotstraat 32 box 2439 3000 Leuven +32 16 32 87 67

[R] valid package repositories

that might be useful but I need to sort out. I am looking at formal claims ‘we have developed a method to do X and said method is available to the public as a R library’. If that is the claim I expect it to be true. Best F -- Federico Calboli LBEG - Laboratory of Biodiversity and

Re: [R] replicating PLINK's --genome calculations.

ed. Best F > > Cheers, > Bert > > > Bert Gunter > > "The trouble with having an open mind is that people keep coming along > and sticking things into it." > -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) > > > On Thu, Oct

[R] replicating PLINK's --genome calculations.

PLINK does, but I’d rather not reinvent the wheel so it might be worth asking: is there any package/function that would do (in R) what PLINK does with --genome? Bets wishes F -- Federico Calboli Ecological Genetics Research Unit Department of Biosciences PO Box 65 (Biocenter 3, Viikinkaari 1

Re: [R] why is 9 after 10?

ox > > > > >> -Original Message- >> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Federico >> Calboli >> Sent: February 12, 2016 10:13 AM >> To: R Help >> Subject: [R] why is 9 after 10? >> >> Hi All, >>

[R] why is 9 after 10?

incredibly silly behaviour so that my table follows a reasonable expectation that 9 comes before 10 (and so on and so forth)? BW F -- Federico Calboli Ecological Genetics Research Unit Department of Biosciences PO Box 65 (Biocenter 3, Viikinkaari 1) FIN-00014 University of Helsinki Finland

Re: [R] testing whether two character vectors contain (the same) items in the same order

work with Cayley distances. It seems to me that > distCayley() in Rankcluster does what you want. From the examples: > > x=1:5 > y=c(2,3,1,4,5) > distCayley(x,y) > 8 > > > Cheers, > Boris > > > > > > On Aug 6, 2015, at 9:51 AM, Federico

Re: [R] testing whether two character vectors contain (the same) items in the same order

> > Bert > > On Thursday, August 6, 2015, Federico Calboli > wrote: > Hi All, > > let’s assume I have a vector of letters drawn only once from the alphabet: > > x = sample(letters, 15, replace = F) > x > [1] "z" "t" "g" "l

[R] testing whether two character vectors contain (the same) items in the same order

quot;f" "n" “v" y = x[c(1:7,9:8, 10:12, 14, 15, 13)] I would now like to test how good a match y is for x. Obviously I can transform the letters in numbers and use a rank test, but I was left wondering whether this is the only solution and whether there are more appropriat

Re: [R] what constitutes a 'complete sentence'?

eal with stats, maths and computers should define what is a grammatically acceptable description, as opposed to a description. If I describe my package poorly it might not be used as much, and thus it might represent a wasted effort for *me*. Incidentally, not being able to use ‘pkgname&

Re: [R] what constitutes a 'complete sentence'?

> sentence. > > Cheers > Petr > >> -Original Message- >> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Hadley >> Wickham >> Sent: Friday, July 03, 2015 1:14 PM >> To: Federico Calboli >> Cc: R-help >> Subject

Re: [R] what constitutes a 'complete sentence'?

That exists already: last slide here — it looks like it is a know issue. BW F > On 3 Jul 2015, at 14:13, Hadley Wickham wrote: > > In that case, you need to create a minimal reproducible example and make it > publicly available. > > Hadley > > On Friday, July 3

Re: [R] what constitutes a 'complete sentence'?

it does not help. BW F > > Hadley > > On Fri, Jul 3, 2015 at 10:09 AM, Federico Calboli > wrote: >> Hi All, >> >> I am upgrading a package for CRAN, and I get this note: >> >> checking DESCRIPTION meta-information ... NOTE >> Ma

[R] what constitutes a 'complete sentence'?

coded that check? Best F -- Federico Calboli Ecological Genetics Research Unit Department of Biosciences PO Box 65 (Biocenter 3, Viikinkaari 1) FIN-00014 University of Helsinki Finland federico.calb...@helsinki.fi __ R-help@r-project.org mailing list

Re: [R] ordinary kriging: the edges of the polygons are ignored

res = autoKrige(temp~1, U, housegrid) > spplot(res$krige_output, col.regions = rev(heat.colors(100))) > # Your result is in the var1.pred-variable of res$krige_output > > You will generally get more and quicker answers to questions about spatial > data and methods from the r-sig-g

[R] ordinary kriging: the edges of the polygons are ignored

Hi All, I am trying to do some kriging of a floor, based on a number of heat sensors. My data looks like this: sensortempxy 1 1 1.25437406 390 2960 2 2 0.64384594 830 2960 3 3 1.52067733 1420 2960 4 4 1.21441928 3127 2920 5 5 1.04227694 400

[R] vcf, plink and other files in the /demo of a package

Hi All, together with colleagues we are planning to submit a 2.0 version of a package we have on CRAN. Because the package deals with high throughput genomic data we though it would be nice to have some sort of guidance for the users. This should ideally mean a 'vignette', but as the time of

Re: [R] repeating values in an index two by two

12:35, andrija djurovic wrote: > Hi. Here are two approaches: > > c(mapply(function(x,y) rep(c(x,y), 2), (1:10)[c(T,F)], (1:10)[c(F,T)])) > > c(tapply(1:10, rep(1:(10/2), each=2), rep, 2), recursive=T) > > Andrija > > > > > > On Mon, Nov 11, 2013 at 1:11 PM,

[R] repeating values in an index two by two

Hi All, I am trying to create an index that returns something like 1,2,1,2,3,4,3,4,5,6,5,6,7,8,7,8 and so on and so forth until a predetermined value (which is obviously even). I am trying very hard to avoid for loops or for loops front ends. I'd be obliged if anybody could offer a suggestion

[R] R vs octave development strategy (and success)

Hi All, if memory serves me well I recall some paper comparing the relative success in getting mainstream acceptance (as mainstream as statistics can be) of both R and Octave. I remember vaguely that the fact the development strategies (core team vs one main developer) played a major role in t

Re: [R] How many samples ACTUALLY used in regression?

>> Fort Collins, CO 80526-8818 >> >> email: ca...@usgs.gov >> tel: 970 226-9326 >> >> >> >> On Mon, Mar 18, 2013 at 8:39 AM, Marc Schwartz wrote: >> >>> >>> On Mar 18, 2013, at 7:36 AM, Federico Calboli >>> wrote: &

[R] How many samples ACTUALLY used in regression?

Dear All, is there a simple way that covers all regression models to extract the number of samples from a data frame/matrix actually used in a regression model? For instance I might have a data of 100 rows and 4 colums (1 response + 3 explanatory variables). If 3 samples have one or more NAs i

Re: [R] checker/chequer board pattern as a colour

; > Be careful of overusing something like this, too many patterned areas in a > plot can be more distracting and distorting than useful. thanks, but that sounds way too much hassle than it's worth BW F > > > On Mon, Jan 7, 2013 at 8:00 AM, Federico Calboli > wrote: &g

[R] checker/chequer board pattern as a colour

Hi All, is there a reasonably simple way of using a black and white chequer/checker board pattern as a colour: barplot(mydata, col = c('red', 'blue' 'checkerboard')) ? BW F -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, Lond

[R] hidden for() loop subsetting a matrix?

Hi, I am subsetting a matrix thus: test [,1] [,2] [,3] [1,]17 13 [2,]28 14 [3,]39 15 [4,]4 10 16 [5,]5 11 17 [6,]6 12 18 test[cbind(c(1,3,5), c(2,1,3))] [1] 7 3 17 This works fine, and is the equivalent of c(test[1,2], test[3,1], test

[R] rtags for VI(M)

Hi, according to the help file rtags does not support VI(M) yet. Is there any known hack to ctags to get tags for R in VI(M)? BW F -- Federico C. F. Calboli Neuroepidemiology and Ageing Research Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 75941602 Fax +44

Re: [R] closing file with close(file) *silently*

On 6 Mar 2012, at 18:01, Sarah Goslee wrote: > The help for warning offers some suggestions. none that seem to work though. F > > Sarah > > On Tue, Mar 6, 2012 at 12:53 PM, Federico Calboli > wrote: >> Hi All, >> >> I am writing a function that

[R] closing file with close(file) *silently*

Hi All, I am writing a function that reads a file in myfile = file('myfile.raw', 'rb') . . . . . close(myfile) No matter what, I get the warning Warning message: closing unused connection 3 (myfile.raw) Since the whole thing is in a function, I'd like to avoid unecessary noise for the user, a

[R] [R-pkgs] MultiPhen 0.3 is available on CRAN

Dear All, a new version of MultiPhen (0.3) is available on CRAN, and will be available to a mirror near you soon. *Please upgrade* because this release is a bug fix release. A new version, with improvements in the output and more useful error messages is basically ready, but I will wait to re

[R] Schoenfeld residuals for a null model coxph

Hi, I have a coxph model like coxph(Surv(start, stop, censor) ~ x + y, mydata) I would like to calculate the Schoenfeld residuals for the null, i.e the same model where the beta hat vector (in practical terms, the coeff vector spat out by summary()) is constrained to be all 0s --all lese stays

Re: [R] variance explained in a cox ph model

On 22 Feb 2012, at 14:01, Terry Therneau wrote: > --- begin included message --- > I have a left truncated, right censored cox model: > > coxph(Surv(start, stop, censor) ~ x + y, mydata) > > I would like to know how much of the observed variance (as a number > between 0 and 1) is explained by ea

[R] variance explained in a cox ph model

Hi All, I have a left truncated, right censored cox model: coxph(Surv(start, stop, censor) ~ x + y, mydata) I would like to know how much of the observed variance (as a number between 0 and 1) is explained by each variable. How could I do that? Adding terms sequentially and then using anova(

[R] logical subsetting, indexes and NAs

Dear All, just a quick example: > x = 1:25 > x[12] = NA > x [1] 1 2 3 4 5 6 7 8 9 10 11 NA 13 14 15 16 17 18 19 20 21 22 23 24 25 > y = x[x<10] > y [1] 1 2 3 4 5 6 7 8 9 NA Is there any way of NOT getting NA for y = x[x<10]? Similarly > y = x[x<15] > y [1] 1 2 3 4

Re: [R] cat, and printing the last separator

On 25 Jan 2012, at 11:54, Duncan Murdoch wrote: > I think the documentation for cat is a little ambiguous, but it is working as > documented if I read "If any element of sep contains a newline character," to > mean that the element consists of a newline and nothing else. I'm not sure > if that

[R] cat, and printing the last separator

Hi All, I have the following command: cat(rbind(table(gen$sex, gen$ddn2)[1,],round(table(gen$sex, gen$ddn2)[1,]/apply(table(gen$sex, gen$ddn2),2,sum) * 100)), sep = c(' (','%)\n'), file = '') 3 (20%) 17 (30%) 15 (31 i.e. it does NOT print the last separator, which is something that bugs me a

Re: [R] barplot ignoring col parameter

1:24] 2 108 0 0 0 1 3 0 0 0 ... - attr(*, "dimnames")=List of 2 ..$ : NULL ..$ : chr [1:24] "A" "B" "C" "D" ... Basically, using the 'x' object as you created the code works, and I can have a workaround. I fail to see why it would no

[R] barplot ignoring col parameter

Hi All, I'm having a problem with barplot: mydata [1,] 2 108 0 0 0 1 3 0 0 0 0 0 7 18 3 4 8 20 26 20 19 7 1 1 mycol = c(rep('yellow', 2), rep('white', 3), rep('orange',2), rep('white', 5), rep('orange',3), rep('red',9)) barplot(mydata, col = mycol) gives me an uniformly yell

[R] fitting some form of linear model with bimodal distribution of dependent variable

Hi All, I have a parameter that is bimodal, and I want to get some sort of linear model done with it results = some.linear.function(bimodal.param ~ factor1 + some other stuff, mydata) I want to see if factor 1 matters (it has 3 levels, of of which can be taken as baseline), i.e: summary(resu

Re: [R] strsplit and forward slash '/'

sure that your first column contains strings and not factors? > What does str(my.data) tell you? > > Does > strsplit(as.character(my.data[1,1]), "/") > work? yes! Thanks Federico > > If you used read.table() to get your data in, you might want the > as.is=TRUE o

Re: [R] strsplit and forward slash '/'

On 3 Aug 2011, at 17:41, Duncan Murdoch wrote: > > It looks as though your my.data[1,1] value is a factor, not a character value. > > strsplit(as.character(my.data[1,1]), "/") Thanks Duncan, this solved it. Best Federico > > would work, or you could avoid getting factors in the first plac

[R] strsplit and forward slash '/'

Hi All, is there a way of using strsplit with a forward slash '/' as the splitting point? For data such as: 1 T/TC/C 16/33 2 T/TC/C 33/36 3 T/TC/C 16/34 4 T/TC/C 16/31 5 C/CC/C 28/29 6 T/TC/C 16/34 strsplit(my.data[1,1], "/") # and an

Re: [R] RES: applying function to multiple columns of a matrix

b > [1] 3 6 9 12 >> mapply(x=rng.a, y=rng.b, function(x,y) sum(dta[,c(x:y)])) > [1] 30 75 120 165 >> > > Cheers, > Filipe > > -Mensagem original- > De: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Em > nome de Federico Calboli

[R] applying function to multiple columns of a matrix

Hi, I want to apply a function to a matrix, taking the columns 3 by 3. I could use a for loop: for(i in 1:3){ # here I assume my data matrix has 9 columns j = i*3 set = my.data[,c(j-2,j-1,j)] my.function(set) } which looks cumbersome and possibly slow. I was hoping there is some function in th

Re: [R] Making a new package: licence

On 8 Jul 2011, at 16:12, Barry Rowlingson wrote: > On Fri, Jul 8, 2011 at 4:07 PM, Federico Calboli > wrote: >> On 8 Jul 2011, at 15:56, Spencer Graves wrote: >>>> Ok, thanks for that. I though that, since R in under GPL-v2, I can only >>>> release my c

Re: [R] Making a new package: licence

On 8 Jul 2011, at 15:56, Spencer Graves wrote: >> Ok, thanks for that. I though that, since R in under GPL-v2, I can only >> release my code under GPL-v2 because the code is written in R and probably >> qualifies as a derivative work. > > Did you include someone else's GPL-vx code (possibly

Re: [R] Making a new package: licence

On 8 Jul 2011, at 12:06, Duncan Murdoch wrote: > On 11-07-08 6:20 AM, Federico Calboli wrote: >> HI All, >> >> I have written and succesfully uploaded a new package. The licence it is >> under is 'GPL' --no version. My assumption is, since all the code is wr

[R] Making a new package: licence

HI All, I have written and succesfully uploaded a new package. The licence it is under is 'GPL' --no version. My assumption is, since all the code is written in R the licence R used for R would affect the code (hence my "GPL" stands for "whatever version of the GPL R is under") I am happy with

Re: [R] Surv(): Stop time must be > start time, NA created

topic > (http://www.jstatsoft.org/v38). > > I hope it helps. > > Best, > Dimitris > > > On 6/3/2011 12:17 PM, Federico Calboli wrote: >> I am writing to get a better handle on a warning I am getting from a coxph >> analysis I am doing. >> >> I

[R] Surv(): Stop time must be > start time, NA created

I am writing to get a better handle on a warning I am getting from a coxph analysis I am doing. I am analysing age of onset of dementia *after* the onset of parkinson disease. My data looks like: age.park age.dem age.death censor x1 x2 x3 x4 1 76 8788 0 16 33 E3

[R] where are my pspline knots?

Hi All, I am trying to figure out how to get the position of the knots in a pspline used in a cox model. my.model = coxph(Surv(agein, ageout, status) ~ pspline(x), mydata) # x being continuous How do I find out where the knot of the spline are? I would like to know to figure out how many case

[R] rounding issues

Hi All, I'm running the now almost-to-be upgraded R 2.11.1 on a Intel Mac, and on a Ubuntu machine, but the problem I see is the same. I noticed the following behaviour: 407585.91 * 0.8 [1] 326068.7 -- the right asnwer is 326068.728 round(407585.91 * 0.8, 2) [1] 326068.7 -- same issue 407585.

Re: [R] coxph and remaing events

On 15 Jun 2010, at 18:34, Federico Calboli wrote: > I'm running a cox ph model on a dataset with a number of variables. Each > variable has a different number of missing data, so that coxph() drops the > individuals who are missing data at one or more variables. Because of th

[R] coxph and remaing events

Hi everyone, I'm running a cox ph model on a dataset with a number of variables. Each variable has a different number of missing data, so that coxph() drops the individuals who are missing data at one or more variables. Because of this dropping (totally fine btw) I want to know how many events

[R] coxph and completely missing strata/subsetting

Hi everyone, I'm doing some coxph() analyses with a large and complex dataset. The data was collected in different centers, so I am using strata(centers) to stratify the analysis. My main issue is, not all centers collected all the variables, so for a model such as: coxph(Surv(days, cancer)

Re: [R] multhist,labels and percentages

some users), does not seem worth it. > I think you have a lot of options to plot what you want. Your suggestion for the axis is excellent, thank you very much. F > > -tgs > > > On Fri, May 14, 2010 at 11:51 AM, Federico Calboli > wrote: > On 14 May 2010, at

Re: [R] multhist,labels and percentages

(0,1)) I'm using multhist(). The above would not work for me. F > > If your question were clearer, I might be able to help in more specific ways. > > -tgs > > On Fri, May 14, 2010 at 10:19 AM, Federico Calboli > wrote: > Hi All, > > I am in the annoying

[R] multhist,labels and percentages

Hi All, I am in the annoying position of having to present some data to someone who seems to be somewhat less than numerate. I need to label the y-axes of a multhist with the y-axis labeled not as counts but as percentage of a population. Plotting the standard histogram is in a way fine, all I

[R] renaming factors *efficiently*

Hi All, I have a data frame where a couple of columns are factors, with long and complex names. Everything works ok --in R, but I need to export the data so it can be used on a dumber program (one with a three letters name starting with S...). I know that those complex factor names are causing

Re: [R] R, NIH and FDA

On 13 Nov 2009, at 12:25, Barry Rowlingson wrote: "Working with" is different to "Working for". Assuming they want to work with you then they want you for your abilities and skills, and if those skills are with R then you go ahead and use R. You don't employ a bricklayer to build a wall and then

[R] R, NIH and FDA

Dear All, I will soon be working with NIH and possibly FDA. Will I be able to use R or will I be forced to use SAS? Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Health Imperial College, St. Mary's Campus Norfolk Place, London W2 1PG Tel +44 (0)20 759416

Re: [R] when vectorising does not work: silent function fail?

enough to justify any more work than a measly script. Cheers, Fede -thomas On Tue, Nov 10, 2009 at 10:04 AM, Federico Calboli wrote: Dear All, I'm using apply to do some genetic association analysis along a chromosome, with many thousands markers. For each marker the anal

[R] when vectorising does not work: silent function fail?

Dear All, I'm using apply to do some genetic association analysis along a chromosome, with many thousands markers. For each marker the analysis is the same, so I was planning to use apply(chrom, 2, somefunction) In the specific case I do: my.results = apply(chr, 2, function(x){anova(lrm( cps

Re: [R] vglm(), t values and p values

On 4 Nov 2009, at 18:40, Gavin Simpson wrote: Additionally, while extracting the t value is a piece of cake with polr(), the p-value I get a nowhere close to a null distribution. Yes - I see that polr() also doesn't produce p-values in the output from summary. You can use it to get "a" p-va

Re: [R] vglm(), t values and p values

On 4 Nov 2009, at 18:11, Gavin Simpson wrote: Is there a particular reason for choosing a VGLM here? My reading of your post suggests the response is an univariate, ordered factor and VGLMs are especially for multivariate responses. In which case, can you not use polr() in package MASS that co

[R] vglm(), t values and p values

Hi All, I'm fitting an proportional odds model using vglm() from VGAM. My response variable is the severity of diseases, going from 0 to 5 (the severity is actually an ordered factor). The independent variables are: 1 genetic marker, time of medical observation, age, sex. What I *need* is a

Re: [R] fitted.values less than observed values

e. Best, Federico -- David On Aug 4, 2009, at 12:51 PM, Federico Calboli wrote: Actually, I tried doing data2 = unique(data) mod = lm(y ~ x1 + ... + xn, data2) fitted(mod) and I still get les fitted values than observations. Federico On 4 Aug 2009, at 12:18, Federico Calboli wrote: Hi Al

Re: [R] fitted.values less than observed values

with explicit attention to the numbers involved? Even better would be small *reproducible* example. I'll have to cook that up, the data is more or less confidential. Not very much but enough no to go on google ;) F -- David On Aug 4, 2009, at 12:51 PM, Federico Calboli wrote: Ac

Re: [R] fitted.values less than observed values

Actually, I tried doing data2 = unique(data) mod = lm(y ~ x1 + ... + xn, data2) fitted(mod) and I still get les fitted values than observations. Federico On 4 Aug 2009, at 12:18, Federico Calboli wrote: Hi All, I have some data where the dependent variable is a score, low (1:3) or high (8

[R] fitted.values less than observed values

Hi All, I have some data where the dependent variable is a score, low (1:3) or high (8:9), and the independent variables are 21 genotypic markers. I'm fitting a logistic regression on the whole dataset after transforming the score to 0/1 and normal linear regression on the high and low su

Re: [R] tiff() woes

I checked on the affected computer and both tiff and cairo capabiliies return FALSE. How that is I would not know, it's a bog standard R installation on windows XP. The 2.9.0 Windows install does not have TIFF capability. Try png() or something else. I don't know about that, but R is definit

Re: [R] tiff() woes

On 17 Jun 2009, at 18:15, Dirk Eddelbuettel wrote: On Wed, Jun 17, 2009 at 05:29:26PM +0100, Federico Calboli wrote: Hello all, a friend has a problem with tiff() which I was unable to help about. I searched the error messages to no avail. When he tries: tiff(filename

[R] tiff() woes

Hello all, a friend has a problem with tiff() which I was unable to help about. I searched the error messages to no avail. When he tries: tiff(filename = "FedeWhyDoesntThisBloodyWork.tif", width = 5, height = 5, units = "cm", bg = "white", res = 1200) Error in tiff(filename = "FedeWhyDoesnt

[R] problem with svyglm()

Hello, I'm trying to use the function svyglm in the library survey. I create a data survey object: data_svy<- svydesign(id=~PSU, strata=~sample_domain, weights=~sample_weight, data=data, nest=TRUE) and I try to use svyglm() with little success: R<-svyglm(data_svy[,4]~(data_svy[,iCol]==listMo

[R] liknage analysis

Dear All, is there a package in R that implements parametric and non parametric genetic linkage analysis (with both case/control or quantitative phenos)? I tried using Merlin, which could not deal with pedigrees the size I have, and SimWalk2 does not look like the answer either --for insta

[R] Plink bed files

Hi All, does anyone know how to import binary .bed files generated by Plink (http://pngu.mgh.harvard.edu/~purcell/plink/ ) into R? the Plink FAQ explains how to conver other types of files, not the .bed. Cheers, Federico -- Federico C. F. Calboli Department of Epidemiology and Public Healt

Re: [R] [R-sig-ME] lme nesting/interaction advice

On 12 May 2008, at 17:09, Douglas Bates wrote: I'm entering this discussion late so I may be discussing issues that have already been addressed. As I understand it, Federico, you began by describing a model for data in which two factors have a fixed set of levels and one factor has an extensibl

Re: [R] [R-sig-ME] lme nesting/interaction advice

On 12 May 2008, at 14:37, Doran, Harold wrote: I haven't followed this thread carefully, so apologies if I'm too off base. But, in response to Rolf's questions/issues. First, SAS cannot handle models with crossed random effects (at least well at all). SAS is horribly incapable of handling eve

Re: [R] [R-sig-ME] lme nesting/interaction advice

On 12 May 2008, at 12:21, Nick Isaac wrote: I *think* the syntax for the model Federico wants is this: lmer(y~selection*males+ (selection|month) + (males|month)) I'll try and check against some back of the envelope calculations -- as I said, the model is, per se, nothing really new, and my

Re: [R] lme nesting/interaction advice

On 12 May 2008, at 11:16, Andrew Robinson wrote: Well. I have documentation relevant to nlme that goes back about 10 years. I don't know when it was first added to S-plus, but I assume that it was about then. Now, do you think that if the thing that you want to do was really bog standard, that

Re: [R] [R-sig-ME] lme nesting/interaction advice

On 12 May 2008, at 10:05, Ken Beath wrote: There is only one random effect, so where does the crossing come from ? The fixed effects vary across blocks, but they are fixed so are just covariates. For this type of data the usual model in lme4 is y~fixed1+fixed2+1|group and for lme split into

Re: [R] lme nesting/interaction advice

On 12 May 2008, at 01:05, Andrew Robinson wrote: On Mon, May 12, 2008 at 10:34:40AM +1200, Rolf Turner wrote: On 12/05/2008, at 9:45 AM, Andrew Robinson wrote: On Sun, May 11, 2008 at 07:52:50PM +0100, Federico Calboli wrote: The main point of my question is, having a 3 way anova (or

Re: [R] lme nesting/interaction advice

On 11 May 2008, at 23:34, Rolf Turner wrote: It doesn't seem to me to be a complaint as such. It is a request for insight. I too would like some insight as to what on earth is going on. And why do you say Federico shows no evidence of having searched the archiv

Re: [R] lme nesting/interaction advice

On 12 May 2008, at 09:29, Dieter Menne wrote: Federico: First, mixed models are different from "standard 101 Anova", and quite a lot of the nesting stuff I used to ponder about 30 year ago when I started teaching this is no longer relevant and works implicitely when you code the parameter

Re: [R] lme nesting/interaction advice

On 11 May 2008, at 22:45, Andrew Robinson wrote: lme(y ~ selection * males, random = ~1|replica/selection/males, mydata) forgive me, but I seem to see nesting in the random statement. That is what happens when we separate factors with a '/'; they are nested. We would expect that stateme

Re: [R] lme nesting/interaction advice

e I have sorted how to specify such trivial model I'll face the horror of the nesting, in any case I attach a toy dataset I created especially to test how to specify the correct model (silly me). Best, Federico Calboli [1] So much bog standard that the Zar, IV ed, gives a nice table of

Re: [R] lme nesting/interaction advice

Note that random can be a list: "a one-sided formula of the form ~x1+...+xn, or a pdMat object with a formula (i.e. a non-NULL value for formula(object)), or a list of such formulas or pdMat objects. " If you can translate that into *informative* English I'd be grateful. I have the Pinheiro a

[R] lme nesting/interaction advice

Hi everyone, I am confused on how to specify some nesting and interaction terma with lme(). I have a dataset where some flies where selected for accessory gland size, made to mate in presence/absence of another male and the level of some protein measured. Now the complex stuff. The selection

[R] predicting memory usage

Hi All, is there a way of predicting memory usage? I need to build an array of 86000 by 2500 numbers (or I might create a list of 2 by 2500 arrays 43000 long). How much memory should I expect to use/need? Cheers, Fede -- Federico C. F. Calboli Department of Epidemiology and Public Health I

[R] writing summary() to a text file

Hi All, I would like to output the results of a function into a text file, legible as a such. The function produces a summary quite like: summary(lm(x ~ y + w * z)) [for instance] and I am not clear how to save this summary into a text file 'automagically', because I need to be able to do i

[R] errorbar il lattice plot

colour) } else { segments(x, up, x, dn, lwd = lwd, lty = 1, col = colour) segments(wid.lf, up, wid.rt, up, lwd = lwd, lty = 1, col = colour) segments(wid.lf, dn, wid.rt, dn, lwd = lwd, lty = 1, col = colour) } invisible(data.frame(x, up, dn)) } } )