Following Ben Bolker's methodology (described here
https://rpubs.com/bbolker/3423) I incorporated non-trivial fixed effects in
NLMER for a four-parameter logistic. I placed a reproducible example here:
https://rpubs.com/ramirob/648103
To summarize the question, if we have a dataset with
My basic question is, how do I specify random effects in gamm4 properly?
Reproducible example:
library(gamm4)
library(ggplot2)
residualNoise <- 20
blockNoise<- 10
nBlocks <- 3
n<-100
df <- data.frame(x=rep(1:n,nBlocks),y=rep(0.01*(1:n)^2,nBlocks))
df$block <- rep(1:nBlocks,each=n)
blockNoise <-
Hello,
I am developing some packages. Package1 requires Package2, both of which I
developed:
Right now Package2 is installed properly here:
/myHome/libraries/Package2
Package1 needs Package2. Package1 refers to Package2 both in the Roxygen
@import field for one of the functions, and also
ust found out about the vdiffr package and was going to explore it, not sure
about the speed.
Any suggestions appreciated.
Thank you,
<https://west.exch023.serverdata.net/owa/?ae=Item=New=IPM.Note=MTQuMy4zMTkuMixlbi1VUyw2LEhUTUwsMCww=_1525698150389_875737489#>
Ramiro
Ramiro Barrantes Ph.D.
Hello,
I was relying on withTimeout (from R.utils) to help me stop nlme when it
“hangs”. However, recently this stopped working. I am pasting a reproducible
example below: withTimeout should stop nlme after 10 seconds but in this
example it does not. I tried this both on a linux (64 bit,
graphics grDevices utils datasets methods base
>
Thank you,
Ramiro
Ramiro Barrantes Ph.D.
Precision Bioassay, Inc.
431 Pine St., Suite 110
Burlington, VT 05401
802 865 0155
802 861 2365 FAX
www.precisionbioassay.com
Thank you so much!! This is very helpful.
On 02/01/2017 02:46 PM, Ramiro Barrantes wrote:
> Hello,
>
> I have a function that applies to an S4 object which contains a slot called
> @analysis:
>
> function calculation(myObject) {
> tmp <- myObjects@analysis
>
to invoke my external constructor function, hence making this test focus
exclusively on the function that I am trying to test. Is it possible to do
this in R?
On 2/1/17, 6:57 PM, "David Winsemius" <dwinsem...@comcast.net> wrote:
>
>> On Feb 1, 2017, at 11:46 AM
Hello,
I have a function that applies to an S4 object which contains a slot called
@analysis:
function calculation(myObject) {
tmp <- myObjects@analysis
result <- ...operations on analysis...
return result
}
I am writing a unit test for this function. So I was hoping to create a mock
Hello,
I have the following reproducible knitr document:
\documentclass{article}
\usepackage[sc]{mathpazo}
\usepackage[T1]{fontenc}
\usepackage{geometry}
\begin{document}
test,dev=png,echo=FALSE=
library(lattice)
xyplot(1:2~1:2)
@
\end{document}
but knitr is giving me an error:
Quitting
Hello,
I am trying to do something that I am able to do with the by function within
data.frame but can't figure out how to achieve with data.table.
Consider
dt-data.table(name=c(rep(a,5),rep(b,6)),var1=0:10,var2=20:30,var3=40:50)
myFunction - function(x) { mean(x) }
I am aware that I can do
.
From: Charles C. Berry [ccbe...@ucsd.edu]
Sent: Monday, February 23, 2015 10:20 PM
To: Ramiro Barrantes
Cc: Rolf Turner; r-help@r-project.org
Subject: Re: Not finding superclass in library
On Mon, 23 Feb 2015, Ramiro Barrantes wrote:
Thank you for pointing this out. I had no idea about
through the code in an ESS R session it works fine.
Thanks in advance,
Ramiro
From: Rolf Turner [r.tur...@auckland.ac.nz]
Sent: Monday, February 23, 2015 3:41 PM
To: Ramiro Barrantes; r-help@r-project.org
Subject: Re: [R] Not finding superclass in library
Hello,
I have a library that I created that defines a parent class, assayObject.
I created other classes that inherit from it, say assayObjectDemo. Each one of
those classes I wanted to make in its own directory separate from where the
assayObject is defined (there are reasons for that).
But
: Martin Maechler [maech...@stat.math.ethz.ch]
Sent: Wednesday, December 03, 2014 3:26 AM
To: Bert Gunter
Cc: Ramiro Barrantes; r-help@r-project.org
Subject: Re: [R] How to have NLME return when convergence not reached
Bert Gunter gunter.ber...@gene.com
on Tue, 2 Dec 2014 14:03:44 -0800 writes
Hello,
I am trying to fit many hundreds of simulated datasets using NLME (it's all in
a big loop in R). Some don't seem to converge. I am working on addressing the
issues by perhaps adjusting my simulation, or tweaking iteration steps in nlme,
etc. However, when it doesn't converge, NLME
Great suggestion!! Will give that a try.
From: William Dunlap [wdun...@tibco.com]
Sent: Tuesday, December 02, 2014 4:49 PM
To: Ramiro Barrantes
Cc: r-help@r-project.org
Subject: Re: [R] How to have NLME return when convergence not reached
You could try using
!
From: Bert Gunter [gunter.ber...@gene.com]
Sent: Tuesday, December 02, 2014 4:30 PM
To: Ramiro Barrantes
Cc: r-help@r-project.org
Subject: Re: [R] How to have NLME return when convergence not reached
?try
Or
?tryCatch
Bert
Sent from my iPhone -- please excuse typos
Hello,
I have stored R objects as hexadecimals in a mysql database, I then usually
transform them to binary and then save it into a file. E.g.
hex - getBlob #gets blob from database as hexadecimal
binary - transformToBinary(hex) #moves from hex to binary
I would usually save them into
rawConnection did it!!
Thank you very much!!!
From: Prof Brian Ripley [rip...@stats.ox.ac.uk]
Sent: Wednesday, July 30, 2014 4:14 PM
To: Ramiro Barrantes; r-help@r-project.org
Subject: Re: [R] binary to R object
What type actually is 'binary' here? We
Hello,
Sorry if this is repeated somewhere, I imagine it must be a common issue but I
can't find an answer!
I have a data.frame with two responses, example (response variables to x are y1
and y2):
df-data.frame(x=1:10,y1=1:10,y2=11:20)
I would like to see it on the same plot with different
Hello,
I am working on a web system (php) that uses R in the backend, and we need some
basic fast encryption/decryption for the underlying mysql database that can be
used by both R AND php. It does not need to be top-of-the-line, but just
provide some basic level of fast
...@gmail.com] on behalf of Suzen,
Mehmet [msu...@gmail.com]
Sent: Wednesday, January 09, 2013 3:38 PM
To: Ramiro Barrantes
Cc: r-help@r-project.org
Subject: Re: [R] R encrypt/decrypt
On 9 January 2013 18:59, Ramiro Barrantes ram...@precisionbioassay.com wrote:
I am working on a web system (php) that uses
]
Sent: Friday, August 31, 2012 12:33 PM
To: Bert Gunter
Cc: David Winsemius; r-help@r-project.org; Ramiro Barrantes
Subject: Re: [R] Class that wraps Data Frame
I guess there are two issues with data.frame. It comes with more than
you probably want to support (e.g., list and matrix- like subsetter
Hello,
I have again a good practices/programming theory question regarding
data.frames.
One of the fundamental objects that I use is the data frame with a particular
set of columns that I would fill or get information from, and an entire system
would revolve around getting information from or
Hello,
I come from using different programming languages (C++, Mathematica, Perl) but
have been using R extensively for several months. I see the data frame as a
key piece of the language and wanted to inquire people's experience regarding
its use.
Say you have a data frame D
D -
process' memory use would grow but
not as much as to hit against memory limits.
Thanks again to Drew, William and Liviu for the suggestions.
Ramiro
From: Drew Tyre [aty...@unl.edu]
Sent: Tuesday, April 10, 2012 11:17 AM
To: William Dunlap
Cc: Ramiro Barrantes; r
any other suggestions or clues.
Ramiro
From: William Dunlap [wdun...@tibco.com]
Sent: Thursday, April 05, 2012 9:21 PM
To: Drew Tyre; Ramiro Barrantes
Cc: r-help@r-project.org
Subject: RE: [R] reclaiming lost memory in R
-Original Message-
From: r
Dear list,
I am trying to reclaim what I think is lost memory in R, I have been using
gc(), rm() and also using Rprof to figure out where all the memory is going but
I might be missing something.
I have the following situation
basic loop which calls memoryHogFunction:
for i in (1:N) {
Hello,
I am using CentOS Linux 6.0, R 2.14.1 and nlme 3.1-103
I am trying to fit some models using nlme, and what was happening was that it
would get to some datasets and just stall, the memory usage would grow and
grow and eventually crash.
I looked carefully into one of the datasets and ran
_ ___
From: Prof Brian Ripley [rip...@stats.ox.ac.uk]
Sent: Sunday, April 01, 2012 4:04 PM
To: Ramiro Barrantes
Cc: r-help@r-project.org
Subject: Re: [R] R process taking over memory
You haven't even told us your OS (see the posting guide).
But the usual way is to get
Hello,
I have a general question on the possibility of how to catch and stop a
function when it uses too much memory.
The problem is that some datasets, when applied to nlme (a relatively older
version), cause the nlme function to just hang forever and start taking over
memory (this afternoon
Hello,
I have a program that consists of a loop fitting a function over many models.
Sometimes the fitting on a particular model takes minutes to converge. Is
there a way that I can limit the amount of time that R spends on a given model:
say if my line is:
fittingFunction( func,
the
Lundholm article: http://journal.r-project.org/current.html
From: Michael Friendly [frien...@yorku.ca]
Sent: Monday, January 16, 2012 8:45 PM
To: Ramiro Barrantes
Cc: r-help@r-project.org
Subject: Re: Using Sweave to generate multiple documents
On 1/16
Hello,
I tried looking for a Sweave-specific list but didn't find one, nor did I find
an answer via google, so will send this question to the general R list. Please
feel free to point me in the right direction.
I am using Sweave and would like to have a single .Rnw document that generates
1)
Hello,
I am trying to convert BY to a data frame, consider the following example:
exampleDF-data.frame(a=c(1,2),b=c(10,20),name=c(first,second))
exampleBY-by(exampleDF,with(exampleDF,paste(a,b,sep=_)),
function(x) {
data.frame(
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