Re: [R] Padding in lattice plots
On Friday 15 July 2005 17:00, Deepayan Sarkar wrote: On 7/15/05, Federico Gherardini [EMAIL PROTECTED] wrote: On Friday 15 July 2005 14:42, you wrote: Hi all, I've used the split argument to print four lattice plots on a single page. The problem now is that I need to reduce the amount of white space between the plots. I've read other mails in this list about the new trellis parameters layout.heights and layout.widhts but I haven't been able to use them properly. I've tried to input values between 0 and 1 as the padding value (both left and right and top and bottom) but nothing changed. It seems I can only increase the padding by using values 1. Any ideas? Thanks in advance for your help Federico Gherardini It seems like I've found an answer myself you have to use negative values to decrease the padding. I thought it was something like the cex parameter which acts like a multiplier I thought so too. but this is not the case. Could you post what you used? There are several different padding parameters you need to set to 0, did you change them all? Deepayan Hi Deepayan This is what I used I don't know if I did everything the proper way but at least I got the result I was seeking! :) trellis.par.set(list(layout.heights = list(top.padding = -1))) trellis.par.set(list(layout.heights = list(bottom.padding = -1, axis.xlab.padding = 1, xlab = -1.2))) trellis.par.set(list(layout.widths = list(left.padding = -1))) trellis.par.set(list(layout.widths = list(right.padding = -1, ylab.axis.padding = -0.5))) Do these settings make any sense? Federico __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Padding in lattice plots
Hi all, I've used the split argument to print four lattice plots on a single page. The problem now is that I need to reduce the amount of white space between the plots. I've read other mails in this list about the new trellis parameters layout.heights and layout.widhts but I haven't been able to use them properly. I've tried to input values between 0 and 1 as the padding value (both left and right and top and bottom) but nothing changed. It seems I can only increase the padding by using values 1. Any ideas? Thanks in advance for your help Federico Gherardini __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Padding in lattice plots
On Friday 15 July 2005 14:42, you wrote: Hi all, I've used the split argument to print four lattice plots on a single page. The problem now is that I need to reduce the amount of white space between the plots. I've read other mails in this list about the new trellis parameters layout.heights and layout.widhts but I haven't been able to use them properly. I've tried to input values between 0 and 1 as the padding value (both left and right and top and bottom) but nothing changed. It seems I can only increase the padding by using values 1. Any ideas? Thanks in advance for your help Federico Gherardini It seems like I've found an answer myself you have to use negative values to decrease the padding. I thought it was something like the cex parameter which acts like a multiplier but this is not the case. Thanks anyway Federico __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Negative intercept in glm poisson model
Dear list, I'm trying to fit a glm model using family=poisson(link = identity). The problem is that the glm function fits a model with a negative intercept, which sounds like a nonsense to me, being the response a Poisson variable. From a previous discussion on this list I've understood that the glm function uses IRLS for the fitting without any constraint so it is possible for it to end up in a region of values which are not admissible given the model, and in fact sometimes it fails asking for valid starting values. In this case I expected it to fail asking to supply starting values, and instead it fits the model just nice with this negative intercept. What am I missing? Thanks, Cheers Federico __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Negative intercept in glm poisson model
On Tuesday 01 March 2005 14:31, Douglas Bates wrote: Not really. The negative intercept is on the scale of the linear predictor. The expected response, which is the exponential of the linear predictor, is always positive. Thank you very much for the quick response. Actually I used link = linear, so I suppose that the response is on the same scale of the linear predictor, isn't it? Cheers, Federico __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Exact poisson confidence intervals
Thanks everybody for their answers! Cheers, fede __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Exact poisson confidence intervals
Hi all, Is there any R function to compute exact confidence limits for a Poisson distribution with a given Lambda? Thanks in advance Federico __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Error using glm with poisson family and identity link
Thanks very much to everybody for your replies and comments! Cheers, Federico __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Error using glm with poisson family and identity link
Hi all I'm trying to use the function glm from the MASS package to do the following fit. fit - glm(FP ~ rand, data = tab, family = poisson(link = identity), subset = rand = 1) (FP is = 0) but I get the following error Error: no valid set of coefficients has been found:please supply starting values In addition: Warning message: NaNs produced in: log(x) in contrast if I fit a model without intercept fit - glm(FP ~ rand - 1, data = tab, family = poisson(link = identity), subset = rand = 1) everything goes fine. Now my guess is that the points naturally have a negative intercept so the error is produced because I'm using the poisson distribution for the y and negative values are of course not admitted. Am I right? Also if this is the cause, shouldn't the function always try to do the best fit given the parameters? I mean shouldn't it fit a model with intercept 0 anyway and report it as a bad fit? Thanks Federico __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Poisson regression
Dear all, First of all sorry if this is a dumb question... I'm trying to fit a linear model between the logarithm of two numerical variables (log(y) ~ log(x)). A log-log plot shows that the variance of log(y) is decreasing with the mean of log(x), in other words the points are quite dispersed for low values of log(x) and approach a straight line as log(x) increases. I have tried the following glm model fit - glm(y ~ log(x), data = tab, family = poisson) The residuals seem very good but I have a doubt: I have used y and not log(y) in the model formula because, as far as I understand, the poisson regression assumes a logarithmic transformation of the response. Is this correct? I mean is it correct to watch a y ~ log(x) poisson regression line on a log(y) ~ log(x) xyplot or I am confusing the two things? Thank you very much Federico __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Combining columns of different length
Hi all, Simple and direct question Is it possible to add a shorter column to a data frame or matrix in such a way that the missing values are replaced with NAs? For example suppose I have 3 2 4 2 5 8 and I want to add a column 3 3 to get... 3 2 3 4 2 3 5 8 NA Thanks Federico __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Testing for normality of residuals in a regression model
Prof Brian Ripley wrote: However, stats 901 or some such tells you that if the distributions have even slightly longer tails than the normal you can get much better estimates than OLS, and this happens even before a test of normality rejects on a sample size of thousands. Robustness of efficiency is much more important than robustness of distribution, and I believe robustness concepts should be in stats 101. (I was teaching them yesterday in the third lecture of a basic course, albeit a graduate course.) This is a very interesting discussion. So you are basically saying that it's better to use robust regression methods, without having to worry too much about the distribution of residuals, instead of using standard methods and doing a lot of tests to check for normality? Did I get your point? Cheers, Federico __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Testing for normality of residuals in a regression model
Hi all, Is it possible to have a test value for assessing the normality of residuals from a linear regression model, instead of simply relying on qqplots? I've tried to use fitdistr to try and fit the residuals with a normal distribution, but fitdsitr only returns the parameters of the distribution and the standard errors, not the p-value. Am I missing something? Cheers, Federico __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Testing for normality of residuals in a regression model
Thank you very much for your suggestions! The residuals come from a gls model, because I had to correct for heteroscedasticity using a weighted regression... can I simply apply one of these tests (like shapiro.test) to the standardized residuals from my gls model? Cheers, Federico __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Testing for normality of residuals in a regression model
Berton Gunter wrote: Quite right, John! I have 2 additional questions: 1) Why test for normality of residuals? Suppose you reject -- then what? (residual plots may give information on skewness, multi-modality, data anomalies that can affect the data analysis). Because I want to know if my model satisfies the basic assumptions of regression theory... in other words I want to know if I can trust my model. Cheers, Federico 2) Why test for normality? Is it EVER useful? Suppose you reject -- then what? (I am tempted to add a 3rd question -- why test at all? -- but that is perhaps too iconoclastic and certainly off topic. Let the hounds remain leashed for now.) Cheers, -- Bert Gunter Genentech Non-Clinical Statistics South San Francisco, CA __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Testing for normality of residuals in a regression model
Berton Gunter wrote: Exactly! My point is that normality tests are useless for this purpose for reasons that are beyond what I can take up here. Thanks for your suggestions, I undesrtand that! Could you possibly give me some (not too complicated!) links so that I can investigate this matter further? Cheers, Federico Hints: Balanced designs are robust to non-normality; independence (especially clustering of subjects due to systematic effects), not normality is usually the biggest real statistical problem; hypothesis tests will always reject when samples are large -- so what!; trust refers to prediction validity which has to do with study design and the validity/representativeness of the current data to future. I know that all the stats 101 tests say to test for normality, but they're full of baloney! Of course, this is free advice -- so caveat emptor! Cheers, Bert __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Fw: [R] Another big data size problem
On Wed, 28 Jul 2004 09:53:08 +0200 Uwe Ligges [EMAIL PROTECTED] wrote: If your data is numeric, you will need roughly 1220 * 2 * 8 / 1024 / 1024 ~~ 200 MB just to store one copy in memory. If you need more than two copies, your machine with its 512MB will start to use swap space . Hence either use a machine with more memory, or don't use all the data at once in memory, e.g. by making use of a database. Uwe Ligges Well I'd be happy if it used swap space instead of locking itself up! By the way I don't think that the problem is entirely related to memory consumption. I have written a little function that reads the data row by row and does a print each time, to monitor its functioning. Everything starts to crwal to an horrible slowness long before my memory is exhausted... i.e.: after about 100 lines. It seems like R has problems managing very large objects per se? By the way I'll try to upgrade to 1.9 and see what happens... Ernesto Jardim wrote: Hi, It looks like you're running linux !? if so it will be quite easy to create a table in MySQL, upload all the data into the database and access the data with RMySQL (it's _very_ fast). Probably there will be some operations that you can do on MySQL instead of eating memory in R. Regards EJ I'll give that a try. Thanks everybody for their time fede __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Another big data size problem
On Wed, 28 Jul 2004 13:28:20 +0100 Ernesto Jardim [EMAIL PROTECTED] wrote: Hi, When you're writing a table to MySQL you have to be carefull if the table is created by RMySQL. The fields definition may not be the most adequate and there will be no indexes in your table, which makes the queries _very_ slow. So, if I understood correctly, if you want to use SQL you'll have to upload the table in SQL, directly from MySQL without using R at all, and then use RMySQL to read the elements in R? Uwe Ligges [EMAIL PROTECTED] wrote: Note that it is better to initialize the object to full size before inserting -- rather than using rbind() and friends which is indeed slow since it need to re-allocate much memory for each step. Do you mean something like this? tab - matrix(rep(0, 1227 * 2), 1227, 2, byrow = TRUE) for(i in 0:num.lines) tab[i + 1,] - scan(mytab, nlines = 1, what=PS, skip = i) The above doesn't get very far either... it seems that, once it has created the table, it becomes so slow that it's unusable. I'll have to try this with more RAM by the way. Cheers, fede __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
Re: [R] Another big data size problem
Thanks for your suggestions, On Wed, 28 Jul 2004 17:04:57 +0200 Henrik Bengtsson [EMAIL PROTECTED] wrote: Anyway, I think you also should read the help for scan(). What do you want with argument 'what=PS'? PS is not a valid data type; 'what' does not specify a name of field/column to be read. From the scan help page... what: the type of 'what' gives the type of data to be read. It seems to me that I had read somewhere (maybe on the mailing list archives), that 'what' was supposed to be a sort of example of the kind of data you had to read... so I put a character string because I wanted the data to be read as character because I had a column of factors. I know this is not a great way to do it (better have a matrix made up of nubers only, instead of having to subsequently convert columns of character strings to number) but I wanted to do a quick test without having to rearrange my file. Cheers, fede __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] Another big data size problem
Hi all, I'm trying to read a 1220 * 2 table in R but I'm having lot of problems. Basically what it happens is that R.bin starts eating all my memory until it gets about 90%. At that point it locks itself in a uninterruptible sleep status (at least that's what top says) where it just sits there barely using the cpu at all but keeping its tons of memory. I've tried with read.table and scan but none of them did the trick. I've also tried some orrible hack like reading one line a time and gradually combining everything in a matrix using rbind... nope! It seems I can read up to 500 lines in a *decent* time but nothing more. The machine is a 3 GHz P4 with HT and 512 MB RAM running R-1.8.1. Will I have to write a little a C program myself to handle this thing or am I missing something? Thanks in advance for your help, fede __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
