search for: kinetics

I can''t get my view to display the most recent parameters from an associated object in a view... here is a birds-eye of my app: I have two models, Ferms and Kinetics. Ferm has_many :kinetics, Kinetic belongs_to :ferm. Kinetic has the fields ferm_id, brix and temp. In my ferms/index view I have a table listing the attributes of each ferm instance. I would like to display the most recent kinetic for each ferm... My FermsController includes def index @ferms...

...ate Std. Error t-value p-value d:(Intercept) 213.435 67.094 3.1811 0.009801 ** e:(Intercept) 94.493 59.579 1.5860 0.143820 --- Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 Residual standard error: 22.03492 (10 degrees of freedom) > write(summary(mymodel), "kinetics.txt") Error in cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1), "\n"), : argument 1 (type 'list') cannot be handled by 'cat' If I try to unlist(mymodel): > write(unlist(summary(mymodel)), "kinetics.txt") I get the following contents of "ki...

...d:(Intercept) 213.435 67.094 3.1811 0.009801 ** >e:(Intercept) 94.493 59.579 1.5860 0.143820 >--- >Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 > >Residual standard error: > > 22.03492 (10 degrees of freedom) >> write(summary(mymodel), "kinetics.txt") >Error in cat(x, file = file, sep = c(rep.int(sep, ncolumns - 1), "\n"), > : > argument 1 (type 'list') cannot be handled by 'cat' > >If I try to unlist(mymodel): >> write(unlist(summary(mymodel)), "kinetics.txt") >I get the fo...

...ts and the literature cited there (e.g. Jennrich/Bright) I looked in R for functions that support the use of the matrix exponential method. Until now I used for a similar (but simpler) problem the nls package and fitted against the the parameterized solution function. But this works only for simple kinetics. The algorithms in the nls package (e.g. SSfol) work on "closed forms" of the solution function, too. My question is: Are there examples or functions in R that show the usage of the matrix exponential method or do I have to build the steps from primitive functions myself, e.g. following...

Hi, I was trying to run the example of Indomethacin kinetics from the book: ## From Pinheiro/Bates, Mixed-Effects-Models in S and S-Plus, ## Springer, Second Printing 2001, Section 6.2 library(nlme) plot(Indometh) fm1Indom.nls <- nls(conc~SSbiexp(time,A1,lrc1,A2,lrc2), data=Indometh) summary(fm1Indom.nls) plot(fm1Indom.nls,Subject~resid(.),abline=0) ## ....

Hi all, I try to assess the parameters (K1,K2) of a model that describes the adsorption of a molecule onto on adsorbent. equation: dq/dt = K1*C*(qm-q)-K2*q I know the value of 'qm' and I experimentally measure the variables 'q', 'C', and the time 't'. t C q 1 0 144.05047 0.0000000 2 565 99.71492 0.1105625 3 988 74.99426

Thanks to Dieter Menne and Spencer Graves I started to get my way through lsoda() Now I need to use it in with nls() to assess parameters I have a go with a basic example dy/dt = K1*conc I try to assess the value of K1 from a simulated data set with a K1 close to 2. Here is (I think) the best code that I've done so far even though it crashes when I call nls()

Is there any R package that implements the same capability of MatLab toolbox called SimBiology ? We are expecially interested in protein-protein interactions and network analysis. As far as I know SimBiology implements a system of ODEs reflecting the kinetic chemical reactions. We would be more interested in stochastic simulations. Thank you in advance. Maura tutti i telefonini TIM!

Hi, I'd like to know whether R is capable to assess parameters in a model describing the kinetic of a pollutant adsorption onto activated carbon. A common relation is for instance the Adam-Bohart-Thomas' one: dx/dt = K1 * (qm-x)*C - K2x where {K1,K2} are the unknown paramters and {qm,C} are known parameters Of course I get experimental data sets of measured x as a function of time.

...3,2.69897,2.6127839,1.9777236,1.3222193,1.4149733,0.7781513,1.322219) x_c<-c(0,3,6,10,12,14,16,18,20,24,26,28,30,34) y_c<-c(5.5185139,5.1461280,4.3617278,3.771513,3.20412,3.0413927,2.7781513,2. 5682017,2.255272,1.7823917,1.447158,1.3222193,1.2787536,0.69897) #number of kinetics nb=3 #complete data set x<-c(x_a,x_b,x_c) y<-c(y_a,y_b,y_c) #cumulative length long<-c(0,15,30,44) coeff<-matrix(nrow=1,ncol=(nb*2)+2) #function to minimise sce<-function(param){ return(sum(sum((yy-(param[i+nb]-(xx/param[i]...

Hello, Is there a convenient way to import RDF/OWL data into R? I'm interested in importing BioPAX/SBPAX data into R to make them available for a wider audience. One exciting application would be to use pathway data to explain differential microarray measurements by identifying upstream nodes that are likely involved in causing the differences. This could also be used to validate

Hi all, My app is going to count sth based on poll id in the url. The url looks like: http://address.com?id=dwNKiItvcyrQ5sycnIhmJablDfXsc9tshaGIVyNIei7.e7&some_other_parameters In a controller, I''ve created a hash where the keys are the ids: @codes = { ''dwNKiItvcyrQ5sycnIhmJablDfXsc9tshaGIVyNIei7.e7'' => {:partner_id => 0,

Dear list members, this is not an R question and forgive me for using the list for irrelevant questions, but this is the only place I know where I can find some good statisticians and I need an expert opinion. There is this power law kinetic model of the form: M=kt^n where t is the time, M is the fraction of drug released, k is the rate constant and n is an exponent related to the mechanism of

...use if I pass in a metabolite label generated from a loop (e.g. metaboliteNames[i]) it's taken verbatim in "quote()," so I get "metaboliteNames[i]^-stoich[i, j]" instead of "met1^2." My goal is to make a package of functions for modeling and simulation of chemical kinetics and I want to make sure that they are open-source and freely available to all researchers, so any advice on how to proceed would be greatly appreciated! Erin -- Erin Rachael Shellman The University of Michigan Bioinformatics PhD Candidate http://www.erinshellman.com shellman at umich.edu (937) 3...

Dear R Gang, I'm interested in using R and the nls package for fitting kinetic models. I'm having some difficulty getting a model specified for nls though. The math for the model that I want to fit is dg(t)/dt = K1 f(t) - k2 g(t) where g(t) and f(t) are measured data at a sequence of times t. K1 and k2 are the parameters of the model. If I solve this, the solution is g(t) = K1

...like to receive R code to analyze the data no matter which variables I collect. I do value your time, so you will get my everlasting thanks. Note that I will be out of the office from 1:15pm to 1:25pm today. This information should be valuable to many. I. Ben Fuld Technical University of Plant Kinetics Slapout, Alabama LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}

I'm just getting to grips with using ode function and have used the examples and vignettes to produce a small model of a one-pool, michaelis-menten, enzyme kinetic reaction. The rate of flux of substrate into pool A is constant (fluxoa) however the rate of flux out of pool A is controlled by the HMM equation (v = Vmax/ ( 1 + (Km / Concentration A )) ). This function works fine and

Hi all, I have this microarray large microarray data set (ALL) from which I would like to subset or extract a set of data based on a factor ($mol.biol). I looked up some example of subsetting in, picked up two commands and tried both but I got error messages as follows > testset <- subset(ALL, ALL$mol.biol %in% c("BCR/ABL","ALL1/AF4")) >> Error in

...evaluated at v, and t, t1 and t2 are the variance function coefficients. The covariate can also be the fitted response. The idea that the residual variance has an additive component and a component proportional to the observed or fitted response is found in analytical chemistry [2, 3], pharmacokinetics [4], and has recently also been introduced to chemical degradation kinetics [5, 6]. As discussed in a recent monograph on mixed effects models [7, p. 55] and in a manuscript dedicated to the comparison of different variants of this error model [4], there are two principal possibilities to imple...

dcemri 0.10 has been released on CRAN "dcemri" is (to the best of my knowledge) the first public-domain software package for the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI) and diffusion-weighted MRI (DW-MRI or DWI). Data import and export is availble for ANALYZE or NIfTI data formats (sorry, no DICOM). Images are stored in neurological format regardless of the