Re: [R] Predicted values for zero-inflated Poisson
Lee, Laura wrote Hi all- I fit a zero-inflated Poisson model to model bycatch rates using an offset term for effort. I need to apply the fitted model to a datasets of varying levels of effort to predict the associated levels of bycatch. I am seeking assistance as to the correct way to code this. --- Just use the function zeroinfl from the pscl package...fit your model...extract the estimated parameters, specify a data frame with variables for which you want to make predictions (including values for your offset), use model.matrix to convert it into the correct format and calculate your fitted values. You can also use the function predict. You can either predict the binary (pi) and count parts (mu), or the predicted values for the ZIP ((1-pi)*mu)..or better...both. For detailed examples and code see: Zero Inflated Models and Generalized Linear Mixed Models with R. (2012) Zuur, Saveliev, Ieno. http://www.highstat.com/book4.htm Alain -- Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. URL: www.springer.com/0-387-45967-7 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. http://www.springer.com/life+sci/ecology/book/978-0-387-87457-9 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer http://www.springer.com/statistics/computational/book/978-0-387-93836-3 4. Zero Inflated Models and Generalized Linear Mixed Models with R. (2012) Zuur, Saveliev, Ieno. http://www.highstat.com/book4.htm Other books: http://www.highstat.com/books.htm Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Tel: 0044 1358 788177 Email: highs...@highstat.com URL: www.highstat.com URL: www.brodgar.com Thanks in advance! Laura [[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. - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. URL: www.springer.com/0-387-45967-7 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. http://www.springer.com/life+sci/ecology/book/978-0-387-87457-9 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer http://www.springer.com/statistics/computational/book/978-0-387-93836-3 Other books: http://www.highstat.com/books.htm Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Tel: 0044 1358 788177 Email: highs...@highstat.com URL: www.highstat.com URL: www.brodgar.com -- View this message in context: http://r.789695.n4.nabble.com/Predicted-values-for-zero-inflated-Poisson-tp4635861p4635898.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] Checking for normality and homogeneity of variance
Haiyang AI wrote: Dear all, I'm a beginner of R and I need to carry out some three-way mixed ANOVAs. Following examples at http://personality-project.org/r/r.anova.html, I managed to get the ANOVA part, but I don't know how can I check data normality and homogeneity of variance in R (since they're the required assumptions of ANOVA analysis). No..normality and homogeneity of the data it is not an assumption! It is normality and homogeneity of the residuals! See also: http://www3.interscience.wiley.com/cgi-bin/fulltext/122683826/PDFSTART Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. URL: www.springer.com/0-387-45967-7 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. http://www.springer.com/life+sci/ecology/book/978-0-387-87457-9 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer http://www.springer.com/statistics/computational/book/978-0-387-93836-3 Other books: http://www.highstat.com/books.htm Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Tel: 0044 1358 788177 Email: highs...@highstat.com URL: www.highstat.com URL: www.brodgar.com -- View this message in context: http://n4.nabble.com/Checking-for-normality-and-homogeneity-of-variance-tp998821p998923.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] Paper on data exploration
R users doing data analysis may be interested in the following paper: http://methodsblog.wordpress.com/2009/11/13/first-paper-now-online/?utm_source=feedburnerutm_medium=feedutm_campaign=Feed%3A+wordpress%2Fmethodsblog+(methods.blog) All data and R code is available. Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://old.nabble.com/Paper-on-data-exploration-tp26382087p26382087.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] GLM quasipoisson error
atorso wrote: Hello, I'm having an error when trying to fit the next GLM: model-glm(response ~ CLONE_M + CLONE_F + HATCHING +(CLONE_M*CLONE_F) + (CLONE_M*HATCHING) + (CLONE_F*HATCHING) + (CLONE_M*CLONE_F*HATCHING), family=quasipoisson) anova(model, test=Chi) I guess that those variables are factors, and that you have empty combinations? Make a coplot, and see whether you have data for all combinations of the levels of your factors. Formulated differently..does it make sense, or is it possible to fit the 3-way interaction for your data? Also..you may want to use the str command to see whether response is indeed coded correctly. Alain Error in if (dispersion == 1) Inf else object$df.residual : missing value where TRUE/FALSE needed If I fit the same model by using the Poisson distribution, it works. I have not a clue about where the problem could be. Do you have any idea or suggestion I could try? Thank you in advance, Ana __ 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. - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/GLM-quasipoisson-error-tp25754404p25770491.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] how to fit time varying coefficient regression model?
R_help Help wrote: Hi - I read through dse package manual a bit. I'm not quite certain how I can use it to estimate a time varying coefficient regression model? I might pick up an inappropriate package. Any suggestion would be greatly appreciated. Thank you. Just rewrite the linear regression model into state-space equations, and apply Kalman filtering. See Chapter 16 or 17 in our Analysing Ecological Data book. There will be packages in R that can do kalman filtering and smoothing Alain rh __ 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. - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/how-to-fit-time-varying-coefficient-regression-model--tp25762040p25770615.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] Dealing with heterogeneity with varComb weights
RS27 wrote: Hi, I am trying to add multiple variance structures such as the first example below: vf1 - varComb(varIdent(form = ~1|Sex), varPower()) However my code below will not work can anybody please advise me? VFcomb-varComb(varExp(form=~depcptwithextybf),varFixed(form=~FebNAO)) VarFixed won't work if FebNAO has values equal to 0. In fact, I wouldn't use varFixed at all. A bit more info on the error message would be handy... Alain also if you have two variables with the same weights function would you write that as: VFcomb-varComb(varExp(form=~depcptwithextybf),varExp(form=~FebNAO)) thanks Rebecca - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/Dealing-with-heterogeneity-with-varComb-weights-tp25491971p25491989.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] Using anova(f1, f2) to compare lmer models yields seemingly erroneous Chisq = 0, p = 1
rapton wrote: Hello, I am using R to analyze a large multilevel data set, using lmer() to model my data, and using anova() to compare the fit of various models. When I run two models, the output of each model is generated correctly as far as I can tell (e.g. summary(f1) and summary(f2) for the multilevel model output look perfectly reasonable), and in this case (see below) predictor.1 explains vastly more variance in outcome than predictor.2 (R2 = 15% vs. 5% in OLS regression, with very large N). What I am utterly puzzled by is that when I run an anova comparing the two multilevel model fits, the Chisq comes back as 0, with p = 1. I am pretty sure that fit #1 (f1) is a much better predictor of the outcome than f2, which is reflected in the AIC, BIC , and logLik values. Why might anova be giving me this curious output? How can I fix it? I am sure I am making a dumb error somewhere, but I cannot figure out what it is. Any help or suggestions would be greatly appreciated! -Matt f1 - (lmer(outcome ~ predictor.1 + (1 | person), data=i)) f2 - (lmer(outcome ~ predictor.2 + (1 | person), data=i)) anova(f1, f2) Data: i Models: f1: outcome ~ predictor.1 + (1 | person) f2: outcome ~ predictor.2 + (1 | person) DfAIC BIClogLik Chisq Chi Df Pr(Chisq) f1 6 45443 45489 -22715 f2 25 47317 47511 -23633 0 19 1 Your models are nest nestedit doesn't make sense to do. Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/Using-anova%28f1%2C-f2%29-to-compare-lmer-models-yields-seemingly-erroneous-Chisq-%3D-0%2C-p-%3D-1-tp25297254p25333120.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] Using anova(f1, f2) to compare lmer models yields seemingly erroneous Chisq = 0, p = 1
rapton wrote: Hello, I am using R to analyze a large multilevel data set, using lmer() to model my data, and using anova() to compare the fit of various models. When I run two models, the output of each model is generated correctly as far as I can tell (e.g. summary(f1) and summary(f2) for the multilevel model output look perfectly reasonable), and in this case (see below) predictor.1 explains vastly more variance in outcome than predictor.2 (R2 = 15% vs. 5% in OLS regression, with very large N). What I am utterly puzzled by is that when I run an anova comparing the two multilevel model fits, the Chisq comes back as 0, with p = 1. I am pretty sure that fit #1 (f1) is a much better predictor of the outcome than f2, which is reflected in the AIC, BIC , and logLik values. Why might anova be giving me this curious output? How can I fix it? I am sure I am making a dumb error somewhere, but I cannot figure out what it is. Any help or suggestions would be greatly appreciated! -Matt f1 - (lmer(outcome ~ predictor.1 + (1 | person), data=i)) f2 - (lmer(outcome ~ predictor.2 + (1 | person), data=i)) anova(f1, f2) Data: i Models: f1: outcome ~ predictor.1 + (1 | person) f2: outcome ~ predictor.2 + (1 | person) DfAIC BIClogLik Chisq Chi Df Pr(Chisq) f1 6 45443 45489 -22715 f2 25 47317 47511 -23633 0 19 1 ** NOT ** nested sorrythe brain is going faster than the fingers. - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/Using-anova%28f1%2C-f2%29-to-compare-lmer-models-yields-seemingly-erroneous-Chisq-%3D-0%2C-p-%3D-1-tp25297254p25333148.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] lme, lmer, gls, and spatial autocorrelation
Ben Bolker wrote: My two cents: this is a hard problem to do, period (not just in R). I would second the recommendation of the Dormann et al paper listed below; also see Zuur, Alain F., Elena N. Ieno, Neil J. Walker, Anatoly A. Saveliev, and Graham M. Smith. Mixed Effects Models and Extensions in Ecology with R. 1st ed. Springer, 2009. Thanks for the ref..:-) The last chapter in the book discusses Poisson + auto-correlation with MCMC. It shouldn't be too difficult to replace the AR-1 by some of these spatial correlation structures...I guess...I hope. - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/lme%2C-lmer%2C-gls%2C-and-spatial-autocorrelation-tp25120963p25142366.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] generalized linear models
annie Zhang wrote: Hi, Milton, Thank you for the reply. I tried, but it seems the problem is the column name of the test data is not the same as the column name of the training data. I didn't give the column name, the system seemed do. How to chang here? Annie On Fri, Aug 7, 2009 at 7:52 PM, milton ruser milton.ru...@gmail.com wrote: Hi Annie, create a new data.frame with input variables having all predictors variables on it. after give a look at ?predict best wishes milton On Fri, Aug 7, 2009 at 8:19 PM, annie Zhang annie.zhang2...@gmail.comwrote: Hi, R users, I am trying to use glm to do logistic regression. I know generally when I have two covariates, say x1 and x2, then I do fit - glm(y~x1+x2,famliy='binomial') But now my covariates form a n*p matrix, say x, so actually each column is a covariate. So I think I should do fit - glm(y~x,family='binomial') Then I need to predict new data. How should I write the newdata? I tried several thing, all failed. The x in the fit is a matrix, but is a vector for the new data. Thank you, Annie [[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.htmlhttp://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. See: ?colnames Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/generalized-linear-models-tp24873759p24885065.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] R book for economists
Thiemo Fetzer wrote: Dear Group, I am an economics student starting with PhD work in London. As preparation I would like to get to know R a little bit better. For Stata there are tons of books, however, can you recommend a book for R? I have some substantiated econometrics knowledge, so it should be more a how-to book. Best regards Thiemo --- Thiemo Fetzer, Economist http://freigeist.devmag.net http://www.devmag.net __ 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. Besides the other already mentioned econometrical references.if you are willing to read a book with life science data, then try: A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer http://www.springer.com/statistics/computational/book/978-0-387-93836-3 Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/R-book-for-economists-tp24768682p24772774.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] Compare lm() to glm(family=poisson)
Mark Na wrote: Dear R-helpers, I would like to compare the fit of two models, one of which I fit using lm() and the other using glm(family=poisson). The latter doesn't provide r-squared, so I wonder how to go about comparing these models (they have the same formula). Thanks very much, Mark Na [[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. The decision which distribution to use (Normal versus Poisson) should be an a priori choice. If you really want to compare them, then inspect the residuals of both models and see which model doesn't have any residual patterns. Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/Compare-lm%28%29-to-glm%28family%3Dpoisson%29-tp24764558p24772802.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] creating subsets within lm()
Thomas A. Groen wrote: Dear All, the lm() function has the possibility to create a subset of the possible explaining variables that you have. However, in the help there is no example how to use this subset option. I tried the following: model-lm(dependent.data$MPFD~.,data=explaining.data,subset=c(1,0,0,0,0,0,0,0,1,1,0,0)) MPFD is the dependent variable stored in the data frame dependent.data, and all 12 explaining variables are stored in the data frame explaining.data. However, this yields a model with only an intercept, and the comment Coefficients: (12 not defined because of singularities) I hope anyone would be able to give me an example how to do this correctly. Kind regards, Thomas ___ The subset option works on the rows of the data set. Not on the covariates. You would have to do something like: lm(blah blah, data=explaining.data[, pick your columns]) Alain Zuur - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/creating-subsets-within-lm%28%29-tp24735798p24735931.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] Adding picture to graph?
Rainer M Krug-6 wrote: Hi while teaching R, the question came up if it would be possible to add a picture (saved on the HDD) to a graph (generated by plot()), which we could not answer. It might easily kill a clean graph, but: is there a way of doing this, even one should not do it? On a similar line of thought: is it possibe to define own symbols so that they can be used in the plot function with pch=? Rainer -- Rainer M. Krug, Centre of Excellence for Invasion Biology, Stellenbosch University, South Africa __ 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. See our Beginner's Guide to R for an example; a time series of the date the penguins lay eggs is plotted, and a jpg with penguins is used as background. The code is on the book's website at: www.highstat.com(follow the link to the R book). It was quite a challenge to do this...not because of the R code (we used Murrel, 2006)...but because of figuring out the optimal the size of the jpg. R didn't like to use the original 5Mb jpg file. So..I had to reduce it size. Alain Zuur - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/Adding-picture-to-graph--tp24714724p24736042.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] Moving Average on Defined Intervals
Hadassa Brunschwig-2 wrote:
Hi all
I have been looking (in the help archives) for a function
which does a moving average. Nothing new, I know.
But I am looking for a function which is very flexible:
The user should be able to input a vector of breaks
which define the bins (and not just the number of observations in a bin).
The function would then calculate which observations fall into this bin
and calculate, say, an average.
Another parameter should be the overlap (probably only when
the breaks of the bins are equidistant).
I am sure I am not the first one to think about this problem.
Thanks for any hints.
Hadassa
--
Hadassa Brunschwig
PhD Student
Department of Statistics
The Hebrew University of Jerusalem
http://www.stat.huji.ac.il
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I think you have to program that yourself...can't be difficultwill only
take 30 minutes. Something like:
MyFunction - function(Y,MyBin){
#Create a new vector of the same length as Y that defines the groupings
#Something like: 1 1 1 1 2 2 2 2 2 2 2 2 3 3 3 3 3 4 4 4 4 4 5 5 5 6 6 6 6
6
# This is a bit of rep magic, and conditional statements.
#Apply sapply on Y using this new vector
}
Instead of this, you can also make a loop, bit it is a bit more old
fashioned.
Easy-peasy
Alain
-
Dr. Alain F. Zuur
First author of:
1. Analysing Ecological Data (2007).
Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p.
2. Mixed effects models and extensions in ecology with R. (2009).
Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer.
3. A Beginner's Guide to R (2009).
Zuur, AF, Ieno, EN, Meesters, EHWG. Springer
Statistical consultancy, courses, data analysis and software
Highland Statistics Ltd.
6 Laverock road
UK - AB41 6FN Newburgh
Email: highs...@highstat.com
URL: www.highstat.com
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Re: [R] local regression using loess
cindy Guo wrote: Hi, All, I have a dataset with binary response ( 0 and 1) and some numerical covariates. I know I can use logistic regression to fit the data. But I want to consider more locally. So I am wondering how can I fit the data with 'loess' function in R? And what will be the response: 0/1 or the probability in either group like in logistic regression? Thank you, Cindy [[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. Why don't you fit a GAM with a logistic link function and binomial distirbution? Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/local-regression-using-loess-tp24689834p24696908.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] Multiple graphs
Data Analytics Corp. wrote: Hi, I wrote a simple master function, run(), that has inside six qplot functions. The goal is to type run() and have all six graphs appear as separate windows so that I can copy them into PowerPoint for a client. When I type run(), only the last graph appears, the first five apparently being overwritten. How do I get all six in separate windows, ready for copying? By the way, is the a way to create a PowerPoint deck directly in R the way you can in S-Plus? Thanks, Walt -- Walter R. Paczkowski, Ph.D. Data Analytics Corp. 44 Hamilton Lane Plainsboro, NJ 08536 (V) 609-936-8999 (F) 609-936-3733 dataanalyt...@earthlink.net www.dataanalyticscorp.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. There is an example in our A Beginner's Guide to R that exports the graphs automatically to jpg files (from a loop inside a function)...which you could then import into powerpoint. But as you can see from the other post, it can even be done automatically. Alain - Dr. Alain F. Zuur First author of: 1. Analysing Ecological Data (2007). Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p. 2. Mixed effects models and extensions in ecology with R. (2009). Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer. 3. A Beginner's Guide to R (2009). Zuur, AF, Ieno, EN, Meesters, EHWG. Springer Statistical consultancy, courses, data analysis and software Highland Statistics Ltd. 6 Laverock road UK - AB41 6FN Newburgh Email: highs...@highstat.com URL: www.highstat.com -- View this message in context: http://www.nabble.com/Multiple-graphs-tp24690227p24697026.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] Zinb for Non-interger data
JPS2009 wrote: Sorry bit of a Newbie question, and I promise I have searched the forum already, but I'm getting a bit desperate! I have over-dispersed, zero inflated data, with variance greater than the mean, suggesting Zero-Inflated Negative Binomial - which I attempted in R with the pscl package suggested on http://www.ats.ucla.edu/stat/R/dae/zinbreg.htm However my data is non-integer with some pesky decimals (i.e. 33.12) and zinb / pscl doesn't like that - not surprising as zinb is for count data, normally whole integers etc. Does anyone know of a different zinb package that will allow non-integers or and equivalent test/ model to zinb for non-integer data? Or should I try something else like a quasi-Poisson GLM? Apologies for the Newbie question! Any help much appreciated! Thanks! Is it really non-integer...or is it a density (in which case you could use NB + offset)? The quasi-Poisson will not help you with the zero inflation. I'm afraid you will have to do some hard programming by combining the 0-1 binomial part with a continuous distribution on the second part of the data..and I guess the easiest is to do this in MCMC. Perhaps the Gamma distribution can be used? You would have to adjust all likelihood equations as Gamma doesn't allow for zeros. But perhaps another continuous distribution is more appropriate...depends on your data. Alain Zuur -- View this message in context: http://www.nabble.com/Zinb-for-Non-interger-data-tp24550044p24568326.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] Re gression for loop test HELP! URGENT!
Rbeginner wrote:
Hi everyone!
I'm new to R, and I've sent this message as a non-member, but since it's
pretty urgent, I'm sending it again now I'm on the mailing list (Thanks
Daniel for your suggestion nevertheless).
I have calculated a regression in the form of M ~ D + O + S, and I would
like to take this regression and test it with other samples, 5 sets of M,
D,
O, and S at a time(I actually have 2000 sets, so it's probably not
efficient
to make each a separate set and then index). Since I'll need to test the
regression for 400 groups, I thought a for loop might be necessary. I've
put
everything into a data frame already. Can anyone tell me how to write the
code? I'm especially not sure about how to do the for loop.
And then how would I calculate the error of how well the test samples fit
the original regression?
This is for my internship, so it's very urgent.
One option (out of the many):
for (i in 1:2000) {
M - lm(M ~ D + O + S, subset = blah blah, data = YourData)
print(summary(M))
}
The blah blah select your rows of data for iteration i.
See also:
A Beginner's Guide to R (2009). Zuur, Ieno, Meesters.
for something very similar. You can dump everything in a text file, or
just extract the required info from the summary function (like R^2 etc).
Alain
Dr. Alain F. Zuur
First author of:
1. Analysing Ecological Data (2007).
Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p.
2. Mixed effects models and extensions in ecology with R. (2009).
Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer.
3. A Beginner's Guide to R (2009).
Zuur, AF, Ieno, EN, Meesters, EHWG. Springer
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Re: [R] Re gression function lm() not giving proper results
Read the warning message! It has converted your variables into factors. Figure out why...and you will have solved the problem. Alain Zuur moumita wrote: * * Hi , Can anyone help me please with this problem?* * *CASE-I* all_raw_data_NAomitted is my data frame.It has columns with names i1 ,i2, i3,i4 , till i15.It has 291 rows actually ,couldnt show here. The data frame looks like this:-- i1 i2 i3 i4 i5 i6 i7 i8 i9 i10 i11 i12 i13 i14 i15 22 2 2 2 2 2 2 2 2 2 1 2 2 3 2 32 2 2 2 3 2 2 3 3 3 2 3 333 42 2 2 2 2 2 2 1 1 1 2 1 222 62 2 1 2 1 1 2 2 1 1 1 1 22 2 83 2 2 2 3 3 3 2 3 2 3 2 332 92 2 2 2 2 2 3 3 3 2 3 3 32 2 10 1 1 1 1 1 1 1 1 1 1 1 1 11 1 12 2 2 2 3 2 2 2 1 3 2 1 2 23 3 While doing regression i1 being the dependent variable and i2 as the predictor the outputs produced are not correct.The o/ps are as shown below:--- *all_raw_data_NAomitted$i1-as.vector(as.matrix(all_raw_data_NAomitted$i1)) all_raw_data_NAomitted$i2-as.vector(as.matrix(all_raw_data_NAomitted$i2)) * * * *fit-lrm(i1 ~ i2 + NULL,all_raw_data_NAomitted)* source(regression.R) [1] Printing regression value. Call: lm(formula = i1 ~ i2, data = all_raw_data_NAomitted) Residuals: Min 1Q Median 3Q Max -1.46154 -0.19277 -0.03529 -0.03529 1.96471 *Coefficients:* *Estimate Std. Error t value Pr(|t|)* *(Intercept) 1.192770.05302 22.50 2e-16 *i22 0.842520.06469 13.03 2e-16 *i23 1.527230.11021 13.86 2e-16 *i24 2.268770.14409 15.74 2e-16 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Residual standard error: 0.4831 on 287 degrees of freedom Multiple R-squared: 0.5815, Adjusted R-squared: 0.5771 F-statistic: 132.9 on 3 and 287 DF, p-value: 2.2e-16 Error in main() : In addition: Warning messages: 1: In model.matrix.default(mt, mf, contrasts) : variable 'i1' converted to a factor 2: In model.matrix.default(mt, mf, contrasts) : variable 'i2' converted to a factor *The results produced are incorrect and do not match with SPSS results ,you can find it out having a look at the coefficients sections of the result.my variables were i1 and i2.* *CASE-II* Whereas if I do this the results produced are correct:-- d1-c(1,2,3,NA,6,7,8) d2-c(2,3,4,3,1,2,2) d3-c(2,1,2,1,2,1,3) d4-c(5,6,2,1,1,2,2) d-data.frame(d1,d2,d3,d4) d d1 d2 d3 d4 1 1 2 2 5 2 2 3 1 6 3 3 4 2 2 4 NA 3 1 1 5 6 1 2 1 6 7 2 1 2 7 8 2 3 2 fit-lm(d1 ~ d2+d3+d4) summary(fit) Call: lm(formula = d1 ~ d2 + d3 + d4) Residuals: 1 2 3 5 6 7 -1.7865 0.9698 -1.2250 -1.4802 1.2761 2.2459 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) 9.1912 5.1807 1.7740.218 d2 -0.7570 1.2208 -0.6200.598 d30.0151 1.7474 0.0090.994 d4 -0.9842 0.6772 -1.4530.283 Residual standard error: 2.692 on 2 degrees of freedom (1 observation deleted due to missingness) Multiple R-squared: 0.6507, Adjusted R-squared: 0.1267 F-statistic: 1.242 on 3 and 2 DF, p-value: 0.4751 In case (I) if I make the individual columns as vectors also ,I do not get correct results.what could be the cause of the incorrect results produced. -- Thanks Moumita [[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. -- View this message in context: http://www.nabble.com/Regression-function-lm%28%29-not-giving-proper-results-tp24569513p24569838.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.
