search for: kinetic

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 @ferm...

I have dose response data analyzed with the package 'drc'. 'summary(mymodel)' prints my kinetic parameters. I want that text in an ASCII text file. I want to get exactly what I would get if I copied and pasted from the terminal window. I've read the documentation on data export to text files here: https://cran.r-project.org/doc/manuals/r-release/R-data.html#Export-to-text-files write(...

?sink On May 18, 2018 9:47:25 AM PDT, Ed Siefker <ebs15242 at gmail.com> wrote: >I have dose response data analyzed with the package 'drc'. >'summary(mymodel)' prints my kinetic parameters. I want >that text in an ASCII text file. I want to get exactly what I >would get if I copied and pasted from the terminal window. > >I've read the documentation on data export to text files here: >https://cran.r-project.org/doc/manuals/r-release/R-data.html#Export-t...

I try to fit reaction kinetic data to a given hypothetical model consisting of 3 ODEs. After some reading in Bates/Watts 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 an...

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

...deS$file) # writes an R script file to "getwd()" In spite of the name, this vignette includes an example entirely in R. By comparing it with your code, I see that you do NOT provide a connection between y, parms, K1, C0, m, V, K2 and q. Something like the following might work: kinetic.model<-function(t,y,parms){ dq.dt = parms['K1']*y['C0'] - (parms['K1']*y['m']/y['V']+ parms['K2'])*y['q'] list(dq.dt) } This may not be correct, but I hope the changes will help you see how to make it work. Bon Chance....

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! [[alternative HTML version deleted]]

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....

Hi, I try to minimize the sum of the sum of sce. The following program has been created but it only takes in consideration the last kinetic and not the first ones. I think that I have forget a subscrib but I don't know where. so if you can help me, it will be great.... I have try an other program where y and x are directly calculate in sce function but the time of running was to long. Thanks in advance, Anne...

...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 pathways or to estimate concentrations or kinetic parameters. If no convenient method to import RDF/OWL exists, I would be happy to take the lead in creating a light-weight R package based on rjava and OpenRDF Sesame Rio that could query RDF/OWL data and turn the results into data frames. Thanks! Take care Oliver -- Oliver Ruebe...

...vcyrQ5sycnIhmJablDfXsc9tshaGIVyNIei7.e7"] works ok. What am I doing wrong if the keys are the same and explicite string works while variable doesn''t? Can you explain me that and write how to solve that problem? Thanks in advance, greetz -- K.O.N.L.I.N. konlin@post.pl Kinetic Organism Normally for Logical Infiltration and Nullification, "Day after day, love turns grey Like the skin of a dying man"

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 release. I fit this equation to 100 different datasets (by linear regression, after logarithmic transformation) and then I plot n vs k. What I g...

...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)...

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...

...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 gives correct answers for the size of the pool of quantity of substrat...

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 impl...

...template matching" T1 quantification via multiple flip-angle acquistions (inversion recovery coming soon!) Conversion to gadolinium contrast agent concentration Parametric models for the arterial input function (AIF), both literature-based (Tofts-Kermode and Fritz-Hansen) and data-adaptive. Kinetic parameter estimation using a variety of compartmental models (e.g., Kety, extended Kety, etc.) Estimation via nonlinear regression (Levenburg-Marquardt optimization) or Bayesian methods (MCMC) Semi-parametric methods via Bayesian P-splines (MCMC) A detailed vignette has been included as a "...