[R] finding roots of multivariate equation

implementing similar to a Newton-Raphson algorithm. Thanks. -- Bill Shipley North American Editor for Annals of Botany Subject Editor for Ecology Département de biologie Université de Sherbrooke Sherbrooke (Québec) J1K 2R9 Canada __ R-help

[R] installing new packages

In addition: Warning message: unable to connect to 'cran.r-project.org' on port 80. Have other people had the same problem with this version, or is it unique to my computer? Can someone suggest a solution? Thanks. Bill Shipley [[alternative HTML version deleted

[R] Duncan post-hoc tests in R?

Hello, I am looking for an R function that impliments Duncan's post-hoc test. I am aware of multcomp and its function glht but, unless I am missing something, this cannot impliment the Duncan test. Any help of pointers are welcome. Bill Shipley __ R

[R] dynamic loading error with Open Watcom object file

Win32 application I do not know what this means. Can someone help? Bill Shipley __ 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 and provide

[R] setting new working directories

directories from within Windows (please, no comments about switching to UNIX...). Thanks. Bill Shipley __ 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

[R] help with syntax of nlme call.

= na.omit) Error in nlmeCall[[i]] - NULL : subscript out of bounds Bill Shipley [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

[R] help with nlme function

variables. Could someone explain what I am doing wrong? Alternatively, is there another text besides Pinheiro Bates that explains the basic syntax of the nlme function? Thanks. Bill Shipley __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch

[R] residual df in lmer and simulation results

to calculate a lower bounds for such degrees of freedom? Thanks for any 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 [EMAIL PROTECTED

[R] using split.screen?

? Bill Shipley [[alternative HTML version deleted]] __ 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 and provide commented

[R] superimposing histograms

) - three groups of bars forming the histograms of each population (they will not overlap much, but this is a detail) - the bars from each histogram having different shadings or other visually distinguishing features. Can anyone explain how to do this? Thanks. Bill Shipley

[R] superimposing histograms con't

],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

[R] help with syntax of nlme function

=4.68)) However, there is something wrong with this syntax because I get the following error: Problem in names-: Invalid length for names attribute: structu re(.Data = list(structure(.Data = numeric(0), class Can someone explain what I am doing wrong? Bill Shipley North American

[R] using panel functions in pairs()

Question: how can one pass along different values of arguments from within a panel function such as I have described? Bill Shipley [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

[R] obtaining residuals from lmer

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

[R] error message explanation for lmer

I am getting the following error message using the lmer function for mixed models with method=Laplace: nlminb returned message false convergence (8) in: LMEopt(x=mer,value=cv) Could anyone explain what this means, and how I might overcome (or track down) the problem? Bill Shipley

[R] more documentation on lmer?

Hello. Is there any documentation on the lmer function in the lme4 package beyond what was published in the May 2005 R News (vol.5/1)? As well, has the nonlinear version of lmer appeared yet? Bill Shipley North American Editor, Annals of Botany Editor, Population and Community Biology

[R] documentation for lmer?

Hello. Besides the short paper in the May 2005 edition of R News, I have not found any documentation concerning the lmer function in the lme4 package. Does anyone know of anything more substatial? Also, does anyone know if the nonlinear equivalent of lmer exists yet? Thanks. Bill Shipley

[R] glm binomial with zero proportions

to this specific problem (i.e. regression using proportions, of which some are zero) would be welcome. Thanks. Bill Shipley [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r

[R] source of susbcript out of bounds error in nmle

nlsList to get its starting values but does not request the fixed effects (i.e. it uses the output from nlsList rather than the output from fixed(nlsList). I can't get inside the nlme function to verify this. Bill Shipley [[alternative HTML version deleted

[R] strategies to obtain convergence using nlme

the second warning mean? Thanks for any help. Bill Shipley [[alternative HTML version deleted]] __ 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

[R] coding nesting in data for nlme example of Wafer data set.

to different sites being chosen for each wafter. Thanks. Bill Shipley [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http

[R] syntax of nlme with nesting

randomly. I get the following error message: Error: subscript out of bounds. What does this mean? There are some Plante for which there is only one Groupe , some Espece for which there is only one Plante etc. Is this the source of the error? If so, how can one solve this? Bill Shipley

[R] help with a self-starting function in nonlinear least squares regression.

? 2) When a self-Starting model is called from within nlsList or nlme, is getInitial only called one (to get the values ignoring any hierarchical structure in the data) or is it called for each group? Thanks. Bill Shipley [[alternative HTML version deleted

[R] self starting function for nonlinear least squares.

(NRhyperbola,initial=NRhyperbolaInit) Bill Shipley [[alternative HTML version deleted]] __ 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

[R] making self-starting function for nls

)] value } Bill Shipley [EMAIL PROTECTED] http://callisto.si.usherb.ca:8080/bshipley/ http://callisto.si.usherb.ca:8080/bshipley/ [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman

[R] function for maximum entropy distributions

. If anyone is interested in this function, or is willing to test it, I will send it to them. Bill Shipley North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA [EMAIL PROTECTED] http://callisto.si.usherb.ca:8080

[R] 1st derivatives using gam.

? Bill Shipley [[alternative HTML version deleted]] __ 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] planned means and loess?

smoothing splines via loess. Is there any way to adapt a test of planned means (say, Dunnett's test) to this problem? If not, can anyone suggest how this problem can be tackled via loess? Any suggestions are gratefully welcomed. Bill Shipley [[alternative HTML version deleted

[R] problem with intervals in mixed model

components? Any help is appreciated. Bill Shipley [[alternative HTML version deleted]] __ 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

[R] anova with gam?

,.) fit1-fam(y~s(x),.) anova(fit2,fit1,test=F) Thanks. Bill Shipley [[alternative HTML version deleted]] __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http

[R] constraining initial slope in smoother.spline

Hello. I want to fit a smoother spline (or an equivalent local regression method) to a series of data in which the initial value of the 1st derivative (slope) is constrained to a specific value. Is it possible to do this? If so, how? Bill Shipley [[alternative HTML version

[R] shrinkage estimates in lme

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 [EMAIL PROTECTED] http

[R] testing equality of variances across groups in lme?

)) This allows the residual variances to increase with the independent variable. However, I have no expectation of how the variances might change, only that they might be different across groups. Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de

[R] variance of combinations of means - off topic

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

[R] cubic spline smoother with heterogeneous variance.

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

[R] inferential test for smoother df?

. If this is not an acceptable strategy, what would people recommend beyond using the built in cross-validation criterion? Thanks for any leads. Bill Shipley Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA [EMAIL PROTECTED] http://callisto.si.usherb.ca:8080

[R] question about df in linear mixed model function lme

for the interaction term (Y:Z) also based on the total number of observations? Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA [EMAIL PROTECTED] http://callisto.si.usherb.ca:8080

[R] (off topic) article on advantages/disadvantages of types of SS?

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

[R] lme function with marginal terms for ANOVA?

, if “fit” is a lme object, and I specify anova(fit,type=”marginal”), so I get the type III sum of squares? Thanks Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA [EMAIL

[R] controlling colour in Trellis histogram

, 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 [EMAIL PROTECTED] http://callisto.si.usherb.ca

[R] histograms with more than one variable

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 [EMAIL PROTECTED] http://callisto.si.usherb.ca:8080/bshipley/ http://callisto.si.usherb.ca:8080

[R] specifying a function in nls

,alpha=0.006,LCP=45)) and I get the error message: Error in lhs - rhs : non-numeric argument to binary operator What am I doing wrong? Thanks. Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke

[R] specifying a complex function in nls

(I[yes])) apply(cbind(a,b),1,min) } This is a non-rectangular hyperbola (a) Bill Shipley Subject Matter Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA [EMAIL PROTECTED] http

[R] error message in mle function

to provide confidence intervals for the fixed and random effects because: of an error in the variance-covariance structure. The error says that the intervals are non-positive definitive. Bill Shipley [[alternative HTML version deleted

[R] nls function

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

[R] controlling nls errors

adjust the starting value and retry. To do this I have to be able to test if the function has converged within the loop. I need something like an “if.error(fit)” function that will return true if there has been an error. Does such a thing exist? Bill Shipley Associate Editor, Ecology North

[R] specifying partial nesting in lme

3 1986 5.5 ... 2 1 1985 3.3 2 2 1986 4.1 ... Can someone explain how to specify this in the random part of the model specification in the lme function of R? If I were to ignore the year effect, I would specify: lme(mass~age, random=age|ind) Bill Shipley

[R] typeIII SS for lme?

… 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 [EMAIL

[R] using pdMAT in the lme function?

(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

[R] interpreting output of lme

slopes between groups). Does this make sense? If not, how should one explain the differences in the significance of the fixed terms in these two nested models? Bill Shipley Associate Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke

[R] help with lme()

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

[R] constrained nonlinear optimisation in R?

of the form: SUM(T_i*p_i)=k_i for given values of T_i and k_i (these are constraints on expectations). Can this be done in R? Bill Shipley Associate Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1

[R] setting up complicated ANOVA in R

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

[R] explaining curious result of aov

, 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

[R] summary of explaining curious results of aov

constitutes “moderate”! Bill Shipley Associate Editor, Ecology North American Editor, Annals of Botany Département de biologie, Université de Sherbrooke, Sherbrooke (Québec) J1K 2R1 CANADA [EMAIL PROTECTED] http://callisto.si.usherb.ca:8080/bshipley/ http://callisto.si.usherb.ca:8080/bshipley