similar to: syntax of nlme with nesting

Hello. I am having a problem setting up a self-starting function for use in nonlinear regression (and eventually in the mixed model version). The function is a non-rectangular hyperbola - called "NRhyperbola" - which is used for fitting leaf photosynthetic rate to light intensity. It has one independent variable (Irr) and four parameters (theta, Am, alpha and Rd). I have created this

A few days ago I posted a question to this discussion group concerning to origin of an error message < subscript out of bounds > while using the nonlinear mixed model (nlme) function in R with a self-starting function. Thanks for those who responded. This posting is to explain what (I think) it causing the error. Pinheiro & Bates (2000, pages 342-347) describe how to construct a

I am having difficulty understanding the syntax of the nlme() function for nonlinear mixed models. The data frame is called Marouane.chlorophyll. The model involves a dependent variable (Absorb) and an independent variable (Ch.surf), which are both numeric variables in the data frame. The data are hierarchically grouped as Espece, Plante nested within Espece, and Feuille nested within Plante

Hello. I am working on an analysis involving the nonlinear mixed model function (nlme) in R. The data consist of measures of carbon fixation by leaves as a function of light intensity and the parametric function (standard in this area because it has a biological interpretation) is a non-rectangular hyperbola. I cannot get the nonlinear mixed model (nlme) function to converge cleanly. I am

Hello. Following pages 342-347 of Pinheiro & Bates, I am trying to write a self-starting nonlinear function (a non-rectagular hyperbola) to be used in nonlinear least squares regression (and eventually for a mixed model). When I use the getInitial function for my self-starting function I get the following error message: > getInitial(photo~NRhyperbola(Irr,theta,Am,alpha,Rd),dat) Error

Following on my posting of this morning, concerning a problem that I am having constructing a self-starting function for use with nls (and eventually with nlsList and nlme), the following is the self-starting function called NRhyperbola: > NRhyperbola function (Irr,theta,Am,alpha,Rd) { # Am is the maximum gross photosynthetic rate # Rd is the dark resiration rate (positive value) #

Hi, I am new to R, and as a first exercise, I decided to try to implement an XIRR function using the secant method. I did a quick search and saw another posting that used the Bisection method but wanted to see if it was possible using the secant method. I would input a Cash Flow and Date vector as well as an initial guess. I hardcoded today's initial date so I could do checks in Excel.

I am trying to understand the proper way to encode the nesting structure for data in the context of nlme, in the specific case of individuals nested within species for which each individual is unique. I have searched through Pinheiro & Bates and also past postings, but without success. Take the Wafer data set which has 2 levels: Wafer (8 values) and Site nested within Wafer (10 values for

The irr package seems to install correctly: > install.packages("irr") trying URL 'http://cran.us.r-project.org/src/contrib/irr_0.61.tar.gz' Content type 'application/x-tar' length 13848 bytes opened URL ================================================== downloaded 13Kb * Installing *source* package 'irr' ... ** R ** data ** help >>>

Dear all, in the package its the print() method does not seem to correctly work in all circumstances: > selectMethod(print, "its") Method Definition: function (x, ...) { print(x@.Data <mailto:x@.Data> , ...) } <environment: namespace:its> Signatures: x target "its" defined "its" > fundPME.lst[[1]]$irr An object of

Dear R-Users, I have been using R for about 1 week and recently learned about the Aggregate function, and from reading online it seems like it is comparable to a SQL group by to perform summary functions. I am looking to do a summary function, such as SUM/MIN, but instead of these basic functions, I would like to calculate the IRR. Assuming I have a data set DS01: FirstName LastName

hi: could someone please point me to a function that allows me to solve general non-linear functions? > irr.in <- function(r, c1, c2, c3 ) { return(c1+c2/(1+r) + c3/(1+r)^2); } > solve.nonlinear( irr.in, -100, 60, 70 ); 0.189 If someone has written an irr function, this would be helpful, too---though not difficult to write, either. thanks for any pointers. Regards, /iaw

I am trying to replace a spreadsheet model of a project justification with an R script. I can't seem to track down R functions to calculate Internal Rate of Return and NPV? Am I missing something? NPV doesn't seem so difficult to calculate (at least for a regular series) but I am struggling to identify how to solve for IRR in R. It would be sufficient if it worked for a regular

The report on R_help about problems loading package irr (in a UTF-8 locale, it seemed) prompted me to look a little deeper. There are quite a few packages with Latin-1 chars in their .R files, and a couple in UTF-8. Apart from non-ASCII chars in comments, this is a problem as the code concerned cannot be represented in some locales R runs in (for example Japanese on Windows). It happens

Hello dear R help group. I encountered this old thread (http://tinyurl.com/dklgsk) containing the a similar question to the one I have, but left without an answer. I am and hoping one of you might help. A simplified situation: I have a factorial design (with 2^3 experiment combinations), for 167 subjects, each one has answered the same question twice (out of a bunch of "types" of

Dear R-colleagues, I am quite a newbie to R fighting my stupidity to solve a probably quite simple problem of generating artificial data with defined features. I am conducting a study of inter-observer-agreement in child-bronchoscopy. One of the most important measures is Kappa according to Fleiss, which is very comfortable available in R through the irr-package. Unfortunately medical doctors

I actually have several questions revolving around the generation of wireframe plots. The most pressing is that which is described by the subject line. I am trying to produce a figure with x, y, and z labels, but only tick marks on the x, and y axes. I have supplied sample code below substituting the volcano data set for my own such that you may run the code and see the results.

Hello. I am trying to fit a nonlinear mixed model involving 3 parameters. I have successfully made a self-starting function. getInitial() correctly outputs the initial estimates. I can also use the nlsList with this function to get the separate nonlinear fits by group. However, I get an error message when using the nlme function. Here is the relevent code:

Hi All, I am using fleiss kappa for inter rater agreement. Are there any know issues with Fleiss kappa calculation in R? Even when I supply mock data with total agreement among the raters I do not get a kappa value of 1. instead I am getting negative values. I am using the irr package version 0.70 Any help is much appreciated. Thanks and Regards M [[alternative HTML version deleted]]

Hi, all There are 62 samples in my data and I tested 3 times for each one, then I want to use ICC(intraclass correlation) from irr package to test the consistency among the tests. *combatexpdata_p[1:62] is the first text results and combatexpdata_p[63:124] * is the second one and *combatexpdata_p[125:186]* is the third. Here is the result: