search for: shipley

...ct to this topic and have searched through the documentation but cannot find a clear explanation for doing this. Can someone point me to the proper documentation for creating and using different working directories from within Windows (please, no comments about switching to UNIX...). Thanks. Bill Shipley

...ys out the advantages and disadvantages of using different types 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/ [[alt...

...asts are the same between two models, they ARE comparable, 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/ [[alternat...

..._mean. More generally, Z=f(X_mean, Y_mean). The standard error of Z will be a function of the standard errors of the means of X and Y. I want to calculate this se of Z. Can someone direct me to a reference (text book or other) that gives the solution to this *general* problem? Thanks. Bill Shipley [[alternative HTML version deleted]]

...problems with convergence. When 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.factor(species.type),data=group.means, + strip=function(...) + strip.default(...,style=1,factor.levels=c("Conifers","Trees","Herbs","Mo nocots"))) As a default, this produces the bars in a pale blue and the strip in orange-yellow. 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/ [[alt...

...me statisticians recommend instead that significance be judged 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/ [[alternat...

...+ abs(Rd) if(sum(xy[,"x"]<50)>3)alpha<-coef(lm(y~x,data=xy,subset=x<50))[2] if(sum(xy[,"x"]<50)<=3)alpha<-0.07 value<-c(theta,Am,alpha,Rd) names(value)<-mCall[c("theta","Am","alpha","Rd")] value } Bill Shipley Bill.Shipley@USherbrooke.ca <http://callisto.si.usherb.ca:8080/bshipley/> http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]]

...a tradeoff between precision and bias. Are there rules of thumb 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/ [[alt...

...odel in which I can specify a binomial distribution. I can’t find 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/ [[alt...

...distribution of a continuous variable (y) in each of two groups 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/ [[alt...

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/ [[alte...

...load.file(url, destfile, method, 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/ [[alte...

...the error source for the repeated measures over time. Can 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/ [[alternat...

...n gives out cryptic error messages. I have tried playing with the 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/ [[alt...

...nsform the data to achieve homogeneity of variance, but this would 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/ [[alt...

...s that spans the entire range. par(new=T) - to keep on the same graph hist(x[sel2],main=Null,xlab=NULL,ylab=NULL,axes=F) -superimposes the second histogram par(new=T) - to keep on the same graph hist(x[sel3],main=Null,xlab=NULL,ylab=NULL,axes=F) -superimposes the third histogram 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/ [[alte...

...ssion smoother, and I have been considering cubic spline smoothers. However, I do not know if this can be done given that the error variance would increase over time. Does anyone know what the effect of a non-constant error variance has on the estimates of the 1st derivative and its se? Bill Shipley Departement de biologie Universite de Sherbrooke Sherbrooke (Quebec) CANADA J1K 2R9 Bill.Shipley at USherbrooke.ca http://callisto.si.usherb.ca:8080/bshipley/ -.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.-.- r-help mailing list -- Read http://www.ci.tuwien.ac.at/~hor...

...iple comparisons changes the model-wise error rate, but even if I did all 15 comparisons of the 6 groups, the Bonferroni correction to a 5% alpha is 0.003, yet the Bonferroni correction gives conservative rejection levels. How can such a result occur? Any clues would be helpful. Thanks. 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/ [[alternat...

...(Ln.nar-log(0.0011))|STUDY.CODE),na.action=na. omit) I get back an error saying that I have zero degrees of freedom. Clearly, the syntax of the command is wrong but I can’t figure out why. The data set (meta.analysis) is not defined as a groupedData object. Any help is 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/ [[alternat...