Re: [R] COVID-19 datasets...

On 07.05.2020 at 13:12 Deepayan Sarkar wrote: On Thu, May 7, 2020 at 4:16 PM Thomas Petzoldt wrote: On 07.05.2020 at 11:19 Deepayan Sarkar wrote: On Thu, May 7, 2020 at 12:58 AM Thomas Petzoldt wrote: Sorry if I'm joining a little bit late. I've put some related links and scripts together

Re: [R] COVID-19 datasets...

On 07.05.2020 at 11:19 Deepayan Sarkar wrote: On Thu, May 7, 2020 at 12:58 AM Thomas Petzoldt wrote: Sorry if I'm joining a little bit late. I've put some related links and scripts together a few weeks ago. Then I stopped with this, because there is so much. The data format employed by John

Re: [R] COVID-19 datasets...

Sorry if I'm joining a little bit late. I've put some related links and scripts together a few weeks ago. Then I stopped with this, because there is so much. The data format employed by John Hopkins CSSE was sort of a big surprise to me. An opposite approach was taken in Germany, that

Re: [R] Partial differential equation

On 19.12.2017 04:22, Timothy Axberg wrote: Hello, I am having troubles with heat conduction problem. Below is the given information. Should I move forward with this problem like any other 1-D PDE? Yes. You may use your favorite search engine and search for: "heat transfer" "deSolve" R or

Re: [R] Date operation Question in R

On 30.03.2017 23:34, Paul Bernal wrote: Hello everyone, Is there a way to use the function seq to generate a date sequence in this kind of format: jan-2007? format(seq(ISOdate(2017,1,1), ISOdate(2017,12,31), "months"), "%b-%Y") Also, is there a way to change the Sys.Date() format to the

Re: [R] non-linear optimisation ODE models

Hi, fitting ODE models may also be done with package FME, see: Soetaert K, Petzoldt T. Inverse modelling, sensitivity and Monte Carlo analysis in R using package FME. Journal of Statistical Software. 2010(33): 1–28. http://dx.doi.org/10.18637/jss.v033.i03 or the (interactive) poster at:

Re: [R] Differential equations

or the tutorial from L.A. http://desolve.r-forge.r-project.org/user2014/tutorial.pdf Thomas Petzoldt See also: http://desolve.r-forge.r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models Am 08.02.2017 um 16:19 schrieb peter dalgaard: It's been a while, but I think I have gott

Re: [R] Adding x and y axis labels with the function plot.sensFun (package FME)

Hi, I reproduced your example and it worked for me with "Time" and "Population size" as axis labels. Are you using the most recent version? Thomas Am 25.01.2017 um 02:32 schrieb Marine Regis: Hello, How can I add x and y axis labels for a plot that is built from the function

Re: [R] separate mixture of gamma and normal (with mixtools or ??)

ong and sticking things into it." -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip ) On Mon, Jan 23, 2017 at 2:32 PM, Thomas Petzoldt <t...@simecol.de> wrote: Dear friends, I am trying to separate bi- (and sometimes tri-) modal univariate mixtures of bio

[R] separate mixture of gamma and normal (with mixtools or ??)

mix, xlim=c(0, 25)) summary(mix) -- Thomas Petzoldt TU Dresden, Institute of Hydrobiology http://www.tu-dresden.de/Members/thomas.petzoldt __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE

Re: [R] Euler & Runge-Kutta

da and more ... and you will find many examples, papers, tutorials and books, and a special mailing list (special interest group) at: http://desolve.r-forge.r-project.org Have fun! Thomas Petzoldt Succes, Franklin - Thanks, Franklin :) Franklin Bretschneider Dept of Biology

Re: [R] PDF form Rstudio

Yes, you are right. Sweave depends on Latex too, so its no workaround in this case. Hope it helps, thpe Am 26.02.2016 um 06:54 schrieb Ulrik Stervbo: My understanding is that Sweave also depends on LaTeX to generate pdfs, so I am not sure Sweave is the solution. Just follow the advice

Re: [R] Problems with the deSolve package

NaN NaN NaN ... -- Dr. Thomas Petzoldt Technische Universitaet Dresden Faculty of Environmental Sciences Institute of Hydrobiology 01062 Dresden, Germany E-Mail: thomas.petzo...@tu-dresden.de http://tu-dresden.de/Members/thomas.petzoldt ___

Re: [R] R-help mailing list activity

Hi, from my perspective as R user and package maintainer I would consider the normalization of the r-help mailing list a good sign. r-help is still a good place for general questions, while more specific discussions moved to the r-sig-... mailing lists. Maybe a slight reduction can also be

Re: [R] deSolve package

parenthesis (that returns always zero). Thomas Petzoldt Am 10/15/2015 um 8:17 PM schrieb Andre Jackson: I have the following differential equations and return list: dCgd.dt = -kad*y[1]-kgd*y[1] # PK model equation gut d dCld.dt= kad*y[1]-rhyd-rmetd #pk model equation liver d dCgl.dt

Re: [R] fitting grid-based models

Hi, I have no example at hand, but the usual way could be indeed to calculate a time series of an adequate statistic (e.g. spatial statistic) from both, the observed and the simulated data and then to apply standard model fitting. Thomas __

Re: [R] fitting grid-based models

On 17.06.2014 10:37, Javier Rodríguez Pérez wrote: Hi Thomas, Thank you very much for your help. I will try to calculate some summary statistics and fit observed and simulated data using a time series (as your examples). With observed data, I would use two values (e.g. 0 and 10), because I do

Re: [R] Difficulty coding time-forced functions in deSolve

Hi, does the following help you? Thomas require(deSolve) SEIR - function(t, x, p) { if (t 7) xlag - x else xlag - lagvalue(t - 7) V - ifelse(xlag[3]/sum(xlag) 0.01, 0.25, 0) ## uncomment the following for printing some internal information #cat(t=, t, -- )

Re: [R] Difficulty coding time-forced functions in deSolve

at: http://desolve.r-forge.r-project.org ... or you may consider to ask the R-sig-dynamic models mailing list: https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models Hope it helps Thomas Petzoldt Dr. Thomas Petzoldt Technische Universitaet Dresden Faculty of Environmental Sciences

Re: [R] deSolve, unresolved namespace error -- solved

We have been able to reproduce the reported issue on another Linux system: Fedora 19, and the solution was quite simple: The deSolve package must always to be loaded *before* loading the shared library of the compiled model. Thomas __

Re: [R] deSolve, unresolved namespace error

On 11/6/2013 6:50 PM, Adam Clark wrote: Addendum: unloading and reloading deSolve.so does indeed fix the problem: library.dynam.unload(deSolve, libpath=paste(.libPaths()[1], //deSolve, sep=)) library.dynam(deSolve, package=deSolve, lib.loc=.libPaths()[1]) However, this is a little clunky, and

Re: [R] force pdf()

Hi, this is not a problem of R it is a problem of the pdf viewer. Solution: just use an alternative pdf viewer like gsview or (even simpler) SumatraPDF. Hope it helps Thomas P. __ R-help@r-project.org mailing list

Re: [R] ODE solver

Hi, just press ESC and the solver should stop. BTW, warnings like this are usually a sign of unrealistic parameters, problematic model equations or inappropriate tolerance settings. See also: http://cran.r-project.org/web/packages/deSolve/vignettes/deSolve.pdf#46 ThPe On 5/2/2013 10:36 AM,

Re: [R] lsoda question from deSolve package

) tin - 0.5 D- 400 V- 26.3 yini - c(Central = 0, Peripheral = 0) p- c(k=0.05, k12=0.197118, k21=0.022665, V=26.3) result - lsoda(yini, times, pkmod, p, rtol = 1e-08, atol = 1e-08) plot(result) -- Thomas Petzoldt Technische Universitaet Dresden Faculty of Environmental Sciences

Re: [R] using and event in deSolve

Hi Jannetta, as far as I can see, your implementation was almost ;-) correct, except that: init[2] - init[1] + d should be: init[2] - init[2] + d The root function with: return(init[1]-30) is correct, because this triggers an event when init[1]-30 crosses the zero line, i.e. when

Re: [R] R2OpenBUGS question with differential equations

Dear Andreas, I don't understand your question, because I can't see any fundamental difference between differential equation models and any other R function. So why not rewriting your diffeq. model in the same way like the other example? And, please use package deSolve instead of odesolve

Re: [R] stiff delay differential equations

. Thomas Petzoldt __ R-help@r-project.org 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, minimal, self-contained, reproducible code.

Re: [R] Solving a multinomial gompertz partial differential equation in r

/DifferentialEquations.html Hope it helps Thomas Petzoldt __ R-help@r-project.org 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, minimal, self

Re: [R] Defining a variable outside of optim or differential equation solver.

needs this interface. 2) the closing parenthesis ) of list is missing. 3) dvdpol vs. vdpol Hope it helps Thomas Petzoldt On 7/18/2012 3:59 AM, Tjun Kiat Teo wrote: This is applicable to either using optim or the differential equation solver or any similar solver Suppose I want to use

Re: [R] How to Read source code of function as string vector or matrix

On 7/12/2012 11:00 AM, purushothaman wrote: Hi, I need to read source code of function as a string vector or matrix. if i am using get method it return as closure type. example readcsv-function(filepath) { output-read.csv(filepath) } how to get as string vector like this

Re: [R] How to find best parameter values using deSolve n optim() ?

On 6/6/2012 3:50 PM, mhimanshu wrote: Hello Thomas, This code seems to be fine and its now working well. I read the about the FME package, but I have one doubt, as in the data set given in the paper, it showing a nice kinetics of the viral growth, so my question is what if there is a sudden

Re: [R] How to find best parameter values using deSolve n optim() ?

On 4/5/2012 6:32 PM, mhimanshu wrote: Hi Thomas, Thank you so much for your suggestion. I tried your code and it is working fine. Now when I change the values of Y in yobs I am getting so many warnings. say, yobs- data.frame( time = 0:7, Y = c(0.00, 3.40, 4.60 ,5.80, 5.80, 6.00, 6.00 ),

Re: [R] How to find best parameter values using deSolve n optim() ?

Hi Himanshu, the use of optim is described on its help page. In addition to this package FME provides additional functionality for fitting ODE models. See FME help files, package vignettes and the example below for details. Hope it helps Thomas Petzoldt

Re: [R] Logistic population growth and deSolve

= times, func = logGrowth, parms = parameters, method=euler) plot(output) Note also that you can write your problem more elegantly using vector and matrix notation. Thomas Petzoldt __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman

Re: [R] DLSODA error

Kristian, your example is rather complex and somewhat time consuming even on fast computers, so it is not easy to track your problem down to its original reason. However, what is clear to me is that this is definitely *not* not a problem of deSolve and most likely even not of optim, it is

Re: [R] precompiled ode with spline input

for such questions for getting more immediate responses. Thomas Petzoldt On 3/15/2011 1:00 PM, Daniel Kaschek wrote: I tried to use lsode with precompiled C code instead of an R function defining the derivatives. No problem so far. However, now I need to implement an ODE that contains spline

Re: [R] deSolve: Problem solving ODE including modulo-operator

-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models Hope it helps Thomas Petzoldt __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

Re: [R] non-linear fourth-order differential equations

Petzoldt -- Dr. Thomas Petzoldt Limnology and Ecological Modelling Technische Universitaet Dresden Fakulty of Forest, Geo and Hydro Sciences Institute of Hydrobiology 01062 Dresden, Germany E-Mail: thomas.petzo...@tu-dresden.de http://tu-dresden.de/Members/thomas.petzoldt

Re: [R] interpretation of stress in NMDS

for what I consider a satisfactory result may raise a few Primer-user's eyebrows. Dear Gregory, as the help file of ?isoMDS tells us: stress The final stress achieved (in percent) So 8.3 is in reality 0.083. Thomas Petzoldt __ R-help@r-project.org

Re: [R] Desolve package: How to pass thousand of parameters to C compiled code?

of the large number of parameters you may think whether they are really parameters and not something like external forcings, for which recent versions of deSolve have separate mechanisms to deal with. See ?forcings Hope it helps Thomas Petzoldt PS: There is also a dedicated mailing list

Re: [R] finite difference scheme for 2D differential equations

/mailman/listinfo/r-sig-dynamic-models Hope it helps Thomas Petzoldt PS: You may also have a look into package ReacTran. At 26.04.2010 03:09 Subodh Acharya wrote: Hello everyone, I am trying to solve 2D differential equations using finite difference scheme in R. I have been able to work

Re: [R] How to generate Mackey-Glass time series with ddesolve package?

Hello Mike, please provide a reproducible example, so that we can see why and how ddesolve hangs. In addition you may consider using function dede from package deSolve which allows to choose between different solver methods for dealing with delay differential equations. Thomas Petzoldt Am

Re: [R] estimating the starting value within a ODE using nls and lsoda

equations too and has much more documentation. Hope it helps! Thomas Petzoldt PS: There is also a dedicated mailing list for such questions: https://stat.ethz.ch/mailman/listinfo/r-sig-dynamic-models -- Thomas Petzoldt Technische Universitaet Dresden Institut fuer Hydrobiologie 01062 Dresden

Re: [R] External signal in ODE written in C (using deSolve and approx1?)

available online: http://cran.r-project.org/web/packages/deSolve/vignettes/compiledCode.pdf See section 6. Using forcing functions. Thomas Petzoldt (co-author of deSolve) Glenn Woodart wrote: Dear list The deSolve package allows you to specify the model code in C or Fortran. Thanks to the excellent

[R] New Special Interest Group: R-SIG-DYNAMIC-MODELS

and conferences, for discussing examples and solutions or for promoting the development of new packages and tools. Please feel free to subscribe, to ask questions and to contribute! Thomas Petzoldt Woodrow Setzer Karline Soetaert __ R-help@r-project.org mailing

Re: [R] simulating a model

Dear Rafael, first of all, your simulation works, at least in a technical sense, so I don't understand what you mean with can't simulate it properly. Second, your SIR-based model is a quite different from the SIR models I know (e.g. http://en.wikipedia.org/wiki/SIR_Model). The R code,

Re: [R] object .trPaths not found

Hi, using a variable named .trPaths is a feature and a frequent nuisance of recent Tinn-R and also explained in the Tinn-R docs. Solution 1: In Tinn-R select the menu: R -- Configure -- and then Temporarily or Permanent Solution 2: Manually edit file

Re: [R] External signal in ODE written in C (using deSolve and approx1?)

hack without any warranty. Again, thank you for your brilliant work on implementing solvers for differential equations in R. Best wishes Glenn Thanks for giving feedback. Thomas Petzoldt __ R-help@r-project.org mailing list https://stat.ethz.ch

Re: [R] coupled ODE population model

formulations. The example below demonstrates a multi-species Lotka-Volterra model with an interaction matrix A. While the example is not yet your model it may serve as a starting point. If you have any further questions, please let me know. Thomas Petzoldt library(simecol

Re: [R] External signal in ODE written in C (using deSolve and approx1?)

. The best method is certainly (3) and we would be very glad to integrate such a function (or a documented example) into the deSolve or simecol package. Thomas Petzoldt -- Dr. Thomas Petzoldt Technische Universitaet Dresden Institut fuer Hydrobiologiethomas.petzo...@tu-dresden.de 01062

Re: [R] deSolve question

model formulation is correct? Please check your equations, especially parentheses and signs. Thomas Petzoldt __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

Re: [R] using lsoda() and nls() together

constrained optimization of ode systems. Hope it helps Thomas Petzoldt __ R-help@r-project.org 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

Re: [R] self organizing map advice for categorical data

://www.jstatsoft.org/v21/i05 Hope it helps Thomas Petzoldt __ R-help@r-project.org 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, minimal, self

Re: [R] extract the p value of F statistics from the lm class

Hi, what about the following: ## some test data x - 1:10 y - x + rnorm(x) ## model and summary m - lm(y~x) sm - summary(m) sm # str(sm) # sm$fstatistic ## and now: the manual case 1 - pf(sm$fstatistic[1], sm$fstatistic[2], sm$fstatistic[3]) Hope it helps, ThPe tedzzx schrieb: Dear R

Re: [R] R Style Guides?

Robert Biddle schrieb: Hi: I am looking for style guides for larger R programs, and would like suggestions of web pages or documents to look at. I am particularly interested in guidelines for how to structure programs, and such issues as managing scope, passing data around, data hiding, and so

Re: [R] ttest in R

1Rnwb schrieb: Thanks for the help, but ANOVA will give me a single pvalue, then how i can make sure which group is showing the significant differences. Hi, ANOVA is fine and please have a look on ?TukeyHSD and don't forget to consult your statistics textbook about post-hoc testing. If you

Re: [R] ttest in R

1Rnwb wrote: since the estimation is not done pairwise so i cannot use pairwise.t.test, how do i apply tukeyHSD Note correct capitalization: TukeyHSD and follow the examples on the help page: ?TukeyHSD You may also contact a statistics textbook. In addition I send you some links off list.

Re: [R] Problems in Recommending R

probably not the point. (And I know that there are graphics experts with a masters in psychology between us.) So, why not a new Homepage Graphics Competition 2009? There is still some time until useR!2009 in Rennes: http://www2.agrocampus-ouest.fr/math/useR-2009/ Thomas Petzoldt PS to all

Re: [R] 1-Pearson's R Distance

Rodrigo Aluizio wrote: Hi again List, Well this time I?m writing for a friend (really J). He needs to create a distance matrix based on an abundance matrix using the 1-Pearson?s R index. Well I told him to look at the proxy package, but there is only Pearson Index. He needs it to perform a

Re: [R] LaTeX and R-scripts/-results

Oliver Bandel wrote: Hello, at some places I read about good interaction of LaTeX and R. Can you give me a starting point, where I can find information about it? Are there special LaTeX-packages for the support, or does R have packages for support of LaTeX? Or will an external Code-Generator

Re: [R] Count days of current year

Felipe Carrillo wrote: Hi: Is there a function that counts the number of days of any given or current year based on the date? See ?Date and ?strptime and try the following: y - as.numeric(format(as.Date(2008-11-25), %Y)) as.numeric(format(as.Date(paste(y, 12, 31, sep=-)), %j)) HTH Thomas

Re: [R] Rendering Dendrograms

Hi Mark, similar questions were at least two times during the last weeks, see http://tolstoy.newcastle.edu.au/R/e5/help/08/11/6722.html http://tolstoy.newcastle.edu.au/R/e5/help/08/11/6736.html or http://tolstoy.newcastle.edu.au/R/e5/help/08/11/7790.html or search the archives yourself:

Re: [R] lsoda warning too much accuracy requested

in the respective state equation. Thomas P. Thomas Petzoldt wrote: Hi Colleen, this error was not uncommon and is usually a sign of a numerically problematic or wrongly implemented model. Please use package deSolve, the successor of odesolve, that is more robust and has also a bunch

Re: [R] lsoda warning too much accuracy requested

(on R 2.8.0, Windows) and it runs without problems. Thomas Petzoldt BTW: your system worked also with odesolve, so my question: which versions (R, odesolve) and operating system are you using? Colleen Carlson wrote: Dear list - Does anyone have any ideas / comments about why I am

Re: [R] Fitting a sine wave using solver

Ben Zuckerberg schrieb: Greetings, I have several sets of oscillation data and would like to estimate the parameters of a sine function to each set (and hopefully automate this). A colleague provided an excel sheet that uses solver to minimize the RSS after fitting the sine function to each

Re: [R] skeleton for package containing C code?

Rainer M Krug wrote: Hi I looked in the writing R extensions and also into package.skeleton, but could not find anything: I am looking for a skeleton or simple example on how to create a package which contains C++ code. I only want to implement one function, so nothing complicated. The idea

Re: [R] Cluster Graph

Jared Chapman schrieb: I am an uber nubie with r but I have a question that I hope someone can help me with. I have a data set with 1200+ data points that I want to put into a cluster graph. the problem is that when the cluster graph is generated there are too many data points to view the

Re: [R] Changing the position of the origin

Plantky wrote: Hi all, Can anyone tell me how I can make 0,0 start at the top left hand corner of a graph, instead of the typical lower left hand corner? I've tried to plot with axes=F and then putting on the axes later, but I want the points to correspond to the axes. Thanks, Kang Min Does

Re: [R] Arms Race

dennis campos wrote: hey can anybody help me? i have to simulate the richardson Arms race model on R.. for my simulation class... Hi Dennis, this list is not intended for solving your homework, however, the following may help you to go one step ahead. You should have a look into the help

Re: [R] Agent-based social simulation and R

almost the same as ABMs in other areas. See http://simecol.r-forge.r-project.org for the package, examples, pdf's, and in particular the useR!2008 slides. Thomas Petzoldt Tom Backer Johnsen wrote: Do anyone know anything about the use of R for agent-based social simulation? It should be possible

Re: [R] plot.hclust with lots of objects

and provide commented, minimal, self-contained, reproducible code. -- Thomas Petzoldt Technische Universitaet Dresden Institut fuer Hydrobiologie[EMAIL PROTECTED] 01062 Dresden http://tu-dresden.de/hydrobiologie/ GERMANY __ R-help@r

Re: [R] lines, ecdf and colors

eric lee wrote: Hi. I'm trying to plot two ecdf's on the same graph using two different colors. I can plot using the same color, but it doesn't work when I change colors? Any suggestions? Thanks in advance for your help. x - c(0.80, 0.83, 1.89, 1.04, 1.45, 1.38, 1.91, 1.64, 0.73, 1.46) y -

Re: [R] getting the p-value from lm as a list object

eric lee wrote: Hi, I'm trying to get the p-value from the 'lm' regression function as a list object. For example, I can get r^2 from the following code by entering summary(fm)$r.squared. Is there a way to get the p-value? If not, is there a function where I can enter the f-value and degrees

Re: [R] Help needed with Waterfall plot

Philip Twumasi-Ankrah schrieb: Hi friends, I need suggestions/directions on how to producing a waterfall plot for present extend of change in tumour size for a set of respondents in a study. Example of use of waterfall plot is in the following slides presented at ASCO 2007 by Axel Grothey. Link

[R] pretty formatting of lists

Hello, is there already a function in any R package which does source code formatting of deparsed lists? Let's create the following list: x - list(a = round(rnorm(3), 2), b = round(rnorm(3), 2)) xx -c(aa = round(rnorm(30)), f = function(a) a + b, list(x, x)) Now, I want deparse it

Re: [R] pretty formatting of lists

own solution. Thomas P. On Sun, Mar 16, 2008 at 8:47 AM, Thomas Petzoldt [EMAIL PROTECTED] wrote: Hello, is there already a function in any R package which does source code formatting of deparsed lists? Let's create the following list: x - list(a = round(rnorm(3), 2), b

Re: [R] pdf() device uses fonts to represent points - data alteration?

of transparency and opaqueness are not yet the way to increase the trust of point-and-click users to R. Maybe this is a topic for r-devel? Thomas -- Thomas Petzoldt Technische Universitaet Dresden Institut fuer Hydrobiologie 01062 Dresden GERMANY http://tu-dresden.de/Members/thomas.petzoldt

Re: [R] pdf() device uses fonts to represent points - data alteration?

. While I had some problems with a former version, it worked now out of the box and was able to do both, algebra (plotmath) and geometry (circles) ;-) in high quality. Let's see if there is any other drawback. Thomas P. jiho wrote: On 2007-November-01 , at 20:18 , Thomas Petzoldt wrote: I