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...of SS in the context of unbalanced data in ANOVA, regression and ANCOVA, especially including the use of different types of contrasts and the meaning of the hypotheses that are tested in such cases. Thanks for any leads. Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca <http://callisto.si.usherb.ca:8080/bshipley/> http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

...know). However there are three estimators already built-in the fracdiff package (GPH, Sperio, MLE) I was wondering if there is someone who had used an estimation introduced by P.M. Robinson (related paper: "Log-Periodogram regression of time series with long range dependence", 1995, The Annals of Statistics, Vol. 23, p. 1048 - 1072) The estimator is similar to GPH and Sperio based on the periodogram. Thank you in advance, Fotis -- fp [[alternative HTML version deleted]]

...this happens the function stops and prints an error message, thus preventing the loop from continuing. Is there some what of detecting the convergence problem while preventing the nls function from stopping when this happens, so that the loop can continue? Bill Shipley North American Editor, Annals of Botany Département de biologie Université de Sherbrooke Sherbrooke (Québec) J1K 2R1 Canada (819) 821-8000, poste 62079 (819) 821-8049 FAX http://pages.usherbrooke.ca/jshipley/recherche/ [[alternative HTML version deleted]]

...s: 1. Remeber the rule of thumb for a Cox model of 20 events per variable (not n=20). Many microarray studies will have very marginal sample size. 2. If you are looking at many genes then a completely different strategy is required. There is a large and growing literature; I like Newton et al, Annals of Applied Statistictis, 2007, 85-106 as an intro; but expect to read much more. Terry Therneau -------- begin included message --------- I want to test the expression of a subset of genes for correlation with patient survival. I found out that the coxph function is appropriate for doing th...

...nd the appropriate package in R. I have looked at glmmML, but it doesn’t seem to allow any mixed structure beyond a simple 2-level one. Can anyone point me to the appropriate package, so that I don’t have to go to SAS? Thanks. Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca <http://callisto.si.usherb.ca:8080/bshipley/> http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

...on the same graph as histograms. I suppose one could call this a 2-d histogram? Can this be done in R? Here is a typical data.set: y group 1.2 1 3.3 1 2.4 2 5.7 1 0.2 2 etc. Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca <http://callisto.si.usherb.ca:8080/bshipley/> http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

Hello. I cannot find out how to extract the residuals from a mixed model using the lmer function. Can someone help? Bill Shipley North American Editor, Annals of Botany Editor, "Population and Community Biology" series, Springer Publishing Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

...I know Emmanuel Candes has Matlab routines to do this but I was wondering if someone had ported those to R. Thanks, T ---Reference--- @article{candes2007dantzig, title={{The Dantzig selector: statistical estimation when p is much larger than n}}, author={Candes, E. and Tao, T.}, journal={Annals of Statistics}, volume={35}, number={6}, pages={2313--2351}, year={2007}, publisher={Hayward, Calif.[etc] Institute of Mathematical Statistics [etc]} }

Wherever I look up the following reference the name of the author is spelled Mauchly contrary to the naming of the R function. Mauchly, J.W., Significance test for sphericity of a normal $n$-variate distribution, Annals of mathematical statistics, 11(1940), p. 204-209. Is this a typo on the original article (which R Core has corrected) or is it a typo in the function name ? Best regards, Tobias

...ious case for using the bootstrap. A paper by Mallows, the exact reference escapes me, establishes the conditions under which asymtotics of the marginal distribution imply a well behaved limit. Perhaps a better discussion of the issues can be found and a pair of papers by Bickel and Freedman, see Annals Of Statistics Vol 9, Number 6. HTH Phineas Campbell >>> Vadim Ogranovich <vograno at evafunds.com> 05/06/05 1:36 AM >>> Hi, This is more of a general stat question. I am looking for a easily computable measure of a distance between two empirical distributions. Say I...

...mode = "wb") : cannot open URL `http://cran.r-project.org/bin/windows/contrib/2.0/Matrix_0.95-5.zip' In addition: Warning message: cannot open: HTTP status was `404 Not Found' Can someone please explain what I am doing wrong? Bill Shipley North American Editor, Annals of Botany Editor, "Population and Community Biology" series, Springer Publishing Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

...Rao, C. R., 1997. Statistic and True. Putting chance to work. World Scientific Publishing. Cox, D. R., 1969. Some Sampling Problems in Technology. New Developments in Survey Sampling, pg. 506--527 John Wiley, New York. Vardi, Y., 1982. Nonparametric estimation in the presence of length bias The Annals of Statistics, vol. 10, num. 2 , pg. 616--620. Gill, Richard D. and Vardi, Yehuda and Wellner, Jon A., 1988. Large sample theory of empirical distributions in biased sampling models. The Annals of Statistics, vol. 16, num. 3, pg. 1069--1112. and all the references there in. In this case, and fo...

...an these be somehow combined to include a split-plot & repeated-measures design? If not, can I perhaps use a mixed-model analysis with random subjects nested within the whole-plot? Any suggestions or leads are appreciated. Bill Shipley Associate Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca <http://callisto.si.usherb.ca:8080/bshipley/> http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

...ckage as 'qDiptab' (but at greater accuracy). n=63 is not tabled but n=50 and 100 are. In the table for n=100 the value given for 90% is 0.0471 so where does the 0.474 come from? Any help appreciated! Kylie. [1] Hartigan JA & Hartigan PM. "The Dip Test of Unimodality", The Annals of Statistics, v13(1):70-84, 1985.

...he control parameters but this does not always help. Is there another non-linear regression function in R that I might try (other than regression smoothers, which won’t give the parameter estimates of the specified function)? Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca <http://callisto.si.usherb.ca:8080/bshipley/> http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

...but are NOT comparable if the types of contrasts are changes? Or rather, does it simply mean that one should use t or F tests for the fixed effects, and restrict the likelihood ratio tests to the random effects only if using REML? Bill Shipley Associate Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca <http://callisto.si.usherb.ca:8080/bshipley/> http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

...ld give me the mean of Ln(Y) at each time (i.e. the mode of Y when back-transformed) and the derivative of Ln(Y) with time (i.e. d(Ln(Y))/dt = dY/YDt), not dY/dt. Can anyone suggest the best strategy for solving this problem? Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca <http://callisto.si.usherb.ca:8080/bshipley/> http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

...ged using the non-marginal terms in the ANOVA. However, given that type III SS is also demanded by some… is there a function (equivalent to drop1 for lm) to obtain type III sums of squares for mixed models using the lme function? Bill Shipley Associate Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca <http://callisto.si.usherb.ca:8080/bshipley/> http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

...) give the same output since they correspond to Type I and III sums of squares in the SAS terminology. At least, this is the case with normal (i.e. not mixed) linear models. However, he finds very different results of these two types of ANOVA tables. Why? Bill Shipley North American Editor, Annals of Botany Département de biologie Université de Sherbrooke Sherbrooke (Québec) J1K 2R1 Canada (819) 821-8000, poste 62079 (819) 821-8049 FAX <http://pages.usherbrooke.ca/jshipley/recherche/> http://pages.usherbrooke.ca/jshipley/recherche/ [[alternative HTML version deleted]]

...to help determine when it is better to use the OLS slope estimates and when to use the mixed model (lme) shrinkage estimates? I have 35 groups but the numbers per group vary from over 50 to as low as 4. Thanks for any help. Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA Bill.Shipley@USherbrooke.ca <http://callisto.si.usherb.ca:8080/bshipley/> http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]