l package author.
I will continue bug-fixing `ff` as time permits, although a modern C++
rewrite would be preferable, which
1) supports long vectors
2) avoids copying between Mapped Memory and R's memory
3) simplifies the package, particularly removes the "virtual windo
38 -0.1404174 -0.010338774
Std. Error 0.9042738 0.4577001 1.858138516
t value1.7991275 -0.3067890 -0.005564049
Pr(>|t|) 0.3229600 0.8104951 0.996457853
Best,
Jens
On 30.04.2019 23:03, David Winsemius wrote:
Try using do.call
—
David
Sent from my iPhone
On Apr 30, 2019, at 9:24
Hi,
`lm` won't take formula as a parameter when it is within a `sapply`; see
example below. Please, could anyone either point me to a syntax error or
confirm that this might be a bug?
Best,
Jens
[Disclaimer: This is my first post here, following advice of how to
proceed with possible
rlson"
An: "Jens Koch" , "r-help@r-project.org"
Betreff: RE: [R] discriminant analysis lda under MASS
If the textbook provides the equations, you can work through them directly. But
without knowing more, it is hard to say. You could also conta
vance,
Jens.
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Tao,
I do assume that the ff-files are still at some location and not deleted
by a finalizer. The following explains how to manipulate file locations
with ff and ffdf objects.
Kind regards
jens
library(ff)
path1 <- "c:/tmp"
path2 <- "c:/tmp2"
# create ffdf,
# us
for output shorthand
> but may not yield consistent results for input on different OS or locale
> combinations. I think "Etc/GMT-1" or "Europe/Amsterdam" will be more
> reliable depending on your typical data sources.
>
I read these dates from a database and
ut(xx)
structure(c(1142336881, 1146560988), class = c("POSIXct", "POSIXt"), tzone
= "")
Now my questions:
Shouldn't as.POSIXct() force the recommended or canonical internal
representation?
Would you regard this as a bug?
Or is the code, which created x in the
help and ur patience.
Sincerely, Jens
24 apr 2013 kl. 21:33 skrev "R. Michael Weylandt "
:
>
>
> On Apr 24, 2013, at 7:46 PM, Jens Olofsson wrote:
>
>> Ok. I apologise for not understanding. So, I have installed R-tools. It
>> changed my PATH-variable. I di
to R... So, I started RTerm (32-bit) and tried > R CMD SHLIB mango.f95
and got the same error as earlier "Error: unexpected symbol in "R CMD"".
The same goes for RTerm (64-bit). Can you pls advice me on how to proceed?
Sincerely Jens
On 24 April 2013 20:08, Duncan Murdoch w
Dear Duncan,
I know this isn't a forum for Cygwin, but for R. Pls treat me as a noob and
also remember I am on Windows. How should I use R CMD SHLIB as if I write
that at the prompt I get the error: unexpected symbol in "R CMD". I have
mango.f95 in the working directory.
//Jens
O
dition, R
stop responding when I try .Fortran("MyPBP", as.numeric(S), as.numeric(p),
as.integer(N)),
where N<-5, S<-array(0,N+1) and p<- c(0.1, 0.2, 0.5, 0.8, 0.9).
What am I doing wrong?
Any ideas, thoughts and/or comments are highly appreciated.
it is now appropriate to
claim that R has sound 64-bit integer support, for example for working
with keys or counts imported from large databases. For details
concerning approach, implementation and roadmap please check the
ANNOUNCEMENT-0.9-Details.txt file and the package h
Jonathan,
ff has a utility function file.resize() which allows to give a new filesize
in bytes using doubles.
See ?file.resize
Regards
Jens Oehlschlägel
Gesendet: Donnerstag, 27. September 2012 um 21:17 Uhr
Von: "Jonathan Greenberg"
An: r-help , r-sig-...@r-p
<- replicate(10,rnorm(10))
d <- list(d1,d2,d3,d4)
di <- c(1,2,3,4)
levelplot(x ~ y | di, data = d, layout=c(2,2))
NB! Avoiding the matrices is not an option. Some of them are obtained from raw
text files.
Thank you in advance,
-JP
Jens Peter Andersen
PhD student, MLIS
Medical L
parallel. Check the example below and see how big file creation is
immediate.
Jens Oehlschlägel
> library(ff)
> library(snowfall)
> ncpus <- 2
> n <- 1e8
> system.time(
+ x <- ff(vmode="double", length=n, filename="c:/Temp/x.ff&quo
ck the
'Limitations' sections at the help page and the numerics involving "long
double" in C. If the conclusion is that this should be better done in
Base R - I happly donate the code and drop this package. If we have to
go with an external package for 64bit
= NULL)
However, as seen in the image, this results in a messy looking bathymetry,
with erros. Any suggestions on what went wrong or other packages or
functions I could try to would be greatly appreciated?
I played around with the krig.image function in the "fields" package, but
didn
und in the package help manual.
The package is available as of now via
http://cran.r-project.org/web/packages/orddom/index.html
Your comments and suggestions are appreciated; please send your email to
jens.rogmann _AT_ uni-hamburg.de
Thank you,
Kind regards
Jens J. Rogmann
---
ff files are still in the same location.
And yes, each column of a ffdf dataframe is stored as a separate ff file.
Jens Oehlschlägel
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now because it leads to too
complex code. Let us know if you urgently need this and why.
Feedback, ideas and contributions appreciated. To those who offered code during
the last months: please forgive us that integrating and documenting was not
possible with this release.
Jens &
!
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+
Dipl.Biol. Jens Oldeland
Biodiversity of Plants
Biocentre Klein Flottbek and Botanical Garden
University of Hamburg
Ohnhorststr. 18
22609 Hamburg,
Germany
Tel:0049-(0)40-42816-407
Fax:0049-(0)40-42816-543
Mail: oldel...@botanik.uni-hamburg.de
oldel...@gmx.de (for
No...but it works!
I do not know why I did not find it...
Many thanks!
Hi David, thanks to you as well.
Greg Snow schrieb:
> Did you try gray.colors(3)?
>
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PLEASE do re
Hi,
sorry for beeing unprecise. I am looking for a legend that has the same
colors as the barplot. For a coloured version I would simply use the
same fill=rainbow() option as used in creating the barplot. However,
this does not work when there are gray values, because there are not
defined in the
2,legend=rownames(mat),fill=gray(0.1:0.3)) # this gray does
not work
could anyone help me out, please?
Thank you!
Jens
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hich means that two references to an
ff object will share the data and SOME features (like the 'length') while OTHER
features (like 'dim') are copied on modify (see 'vt' for an powerful
application of this concept). You might want to
multiple processes writing simultaneously to the same ff
datafile.
(it is your responsibility to avoid conflicts and to make sure you do not
suffer problems with delayed cache refreshs as can happen on network drives)
HTH
Jens Oehlschlägel
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multiple processes writing simultaneously to the same ff
datafile.
(it is your responsibility to avoid conflicts and to make sure you do not
suffer problems with delayed cache refreshs as can happen on network drives)
HTH
Jens Oehlschlägel
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e 'biglm'
- and it is your responsibility to extract those chunks from ff, a database or
whatever other source.
HTH
Jens Oehlschlägel
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PLEASE do read the postin
me know if you write a fast read.fwf.ffdf - we would be happy to
include it into the ff package.
Jens
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for assigning formulas to arrays use an array of list
nr form.arr[[31,5]]y ~ 1 + 2
Jens Oehlschlägel
-Ursprüngliche Nachricht-
Von: McLovin
Gesendet: Jul 6, 2010 9:13:49 AM
An: r-help@r-project.org
Betreff: [R] Assign Formulas to Arrays or Matrices?
>
>Hi,
>
>I am very
olean, short integers etc.).
Jens Oehlschlägel
-Ursprüngliche Nachricht-
Von: john
Gesendet: Jun 16, 2010 12:20:17 PM
An: r-help@r-project.org
Betreff: [R] memory management in R
>
>
>I have volunteered to give a short talk on "memory management in R"
> to my lo
,] # returns a subset of data
Do read and understand the help concerning filename location and implications
for finalizers and permanency.
Cheers
Jens Oehlschlägel
-Ursprüngliche Nachricht-
Von: Joris Meys
Gesendet: Jun 8, 2010 1:11:20 PM
An: dhanush
Betreff: Re: [R] how to read CSV file in
. An ff archive
consists of two files, a zip file which stores the data (and to which you can
add) and a standard .RData file which stores the meta-data using standard
save().
HTH
Jens
-Ursprüngliche Nachricht-
Von: Jannis
Gesendet: May 25, 2010 8:22:26 PM
An: r-help@r-project.org
Betreff
, you might consider using the 32bit
win version of R and ff on a 64bit win machine: while 32bit R itself has
limited memory access, ff can handle larger objects faster because it benefits
from *all* RAM via filesystem-caching.
Jens
-
Von: "Hunsicker, Lawrence"
G
rs, you might want to write the results rather to
an integer ff matrix because this saves disk space and improves caching.
HTH
Jens Oehlschlägel
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rs, you might want to write the results rather to
an integer ff matrix because this saves disk space and improves caching.
HTH
Jens Oehlschlägel
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PLEA
Ramon,
for me this works
> setwd("d:/tmp")
> ffd <- as.ffdf(d, col_args=list(pattern = paste(getwd(), "/fftmp", sep = "")))
> filename(ffd)
$x
[1] "d:/tmp/fftmp35c34861.ff"
$y
[1] "d:/tmp/fftmp5be946bb.ff"
$z
[1] "d:/tmp/fftmp26
sure how to fill in the start=c() for more than 2
groups.
Thanks
Jens
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Try to close the file on the first nfs client before reopening it on the second
nfs client. NFS has something called "close-to-open cache consistency".
This means that two clients which have the same nfs file open, cannot rely on
seeing the updates from the respective other client. If one clients
t hyperthreading with 8 parallel processes (snowfall,
sockets) gives about 5x the performance of a single process, but already 7
processes with HT perform worse than 4 processes without HT. Conclusion: if a
machine is dedicated to R for RAM-critical applications, try switching
hyperthreading
igData[select,]
3) keep your logical in a ff logical or ff boolean and then do chunked looping
over both - the ff with the subscripts and the ffdf - and in each chunk convert
the logical selection to integers, see 2)
HTH
Jens Oehlschlägel
P.S. you might want to try the newer version on
I don't see how I can get any hook into the dispatch mechanism, my methods are
always bypassed if the classes of e1 and e2 differ (simple example below).
Best wishes for 2010
Jens Oehlschlägel
> ca <- function(x){
+ x <- as.integer(x)
+ oldClass(x) <- "a"
ended way to get my methods reliably dispatched?
Jens Oehlschlägel
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can be configured when compiling your OS.
Please test and let us know your experience.
Regards
Jens Oehlschlägel
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have ffsave()
which will store a mixture of normal and ff objects
*and* all ff-files into a ffarchive, i.e. two files
.RData and .ffData
from which you can restore all or a selection of
ff objects / files using the ffload() command.
Regards
Jens Oehlschlägel
___
#An example of this is in read.table.ffdf
#which reads a csv file in chunks and extends the
#number of rows in the ffdf
Jens Oehlschlägel
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Preisknaller: GMX DSL Flatrate für nur 16,99 Euro/mtl.!
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___
me on disk and in fs-cache.
The code below should give an idea of how to do pairwise stats on columns where
each pair fits easily into RAM. In the real world, you would not create the
data but import it using read.csv.ffdf (expect that reading your file takes
longer than reading/writing the ff
be written row by row from your
program) and link the file into R as a single ff_matrix.
Since ffdf in ff is new, I give a mini-tutorial below.
Let me know how that works for you.
Kind regards
Jens Oehlschlägel
library(ff)
# Create example csv
fnam <- "/tmp/example.csv&qu
ge dataset just by sending ff's small metadata from
master to slaves (e.g. with snowfall)
ff is hosted on r-forge now and you find some presentations on ff at
http://ff.r-forge.r-project.org/
Hope you find this useful. We appreciate any feedback.
t;- numeric(n)
>
> and then see how fast it works.
>
> On Sun, Nov 8, 2009 at 2:11 PM, Jens Malmros wrote:
>> Hello,
>>
>> I have written a simple Metropolis-Hastings MCMC algorithm for a
>> binomial parameter:
>>
>> MHastings = function(n,p0,d){
&g
Hello,
I have written a simple Metropolis-Hastings MCMC algorithm for a
binomial parameter:
MHastings = function(n,p0,d){
theta = c()
theta[1] = p0
t =1
while(t<=n){
phi = log(theta[t]/(1-theta[t]))
phisim = phi + rnorm(1,0,d)
Gene,
You might want to look at function read.csv.ffdf from package ff which can read
large csv-files into a ffdf object. That's kind of data.frame which is stored
on disk resp. in the file-system-cache. Once you subscript part of it, you get
a regular data.frame.
Jens Oehlsch
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Hi,
Does anyone know where the following package is available:
Holleczek B, Gondos A, Brenner H.
PeriodR - an R package to calculate long term survival estimates using period
analysis.
Methods of Information in Medicine 2009; 48: 123-128.
Thanks
Jens Oehlschlägel
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GRATIS für alle GMX
") - here the LESS specific class "POSIXt" is
in the first position and would win in class-dispatch over the MORE specific
class "POSIXct". Why?
Jens Oehlschlägel
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GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!
_
get -> 1 4 4 1
1 4 4 0 <- how do I get -> 1 4 4 1
1 4 4 0 <- how do I keep -> 1 4 4 0
1 4 4 0 <- how do I keep -> 1 4 4 0
1 4 4 0
1 4 4 0
1 4 4 0
Thanks a lot for any help
Jens
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1 3 12 1
1 3 13 2
1 3 14 3
1 3 15 4
1 4 12 1
1 4 11 2
1 4 10 3
1 4 9 4
1 4 11 5
Any idea how to solve this problem? I tried but did not succeed :-(
Best Jens Bölte
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PLEASE
Hello,
I have written a function in order to analyse gaze paths. It works with the test data but when I try to apply the function to a data frame that stores "the real data" in columns I receive the error message that the
" In if (pp > 1) { :
condition has length > 1 only the first element wi
question separately.
Your kind help will be highly appreciated!
Jens
--
+
Dipl.Biol. Jens Oldeland
University of Hamburg
Biocentre Klein Flottbek and Botanical Garden
Ohnhorststr. 18
22609 Hamburg,
Germany
Tel:0049-(0)40-42816-407
Fax:0049-
mples) from an eye-tracking
experiment. I receive the data in this format and need to eliminate unwanted
samples.
Thanks Jens Bölte
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as one of the subexpressions in a braced list of expressions.
"
So my recommendation is
1) use R's assignment operator with two spaces around (or assign()) and don't
obscure assignments by using C's assignment operator (or other languages
equality operator)
2) do not assi
ct on
the response series Y,
Z[t] measures the long-term effect of either
(1) two policies by a step dummy or
(2) various policies with a continuous variable.
I appreciate any kind of help!
Thanks in advance!
Jens
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Dear help list,
I think I found a bug a the R Random Forest. Hopefully, you are able to
reproduce it.
I use R version 2.7.2 and RF version 4.5-27.
This is a minimal code to describe the problem:
library(randomForest)
tries <- 20
dimension <- 20
n <- 200
outlyingness <- rep(NaN,tries)
for (o_numbe
which' and 'xor' are made S3 generic, 'xor.default' is implemented
much faster than in base R (this should go into base R).
The package has automated regression-tests and is hopefully useful for better
handling large datasets, together with packages 'rindex&#
sit our presentation
August 5th at JSM "High-Performance Processing of Large Data Sets via Memory
Mapping: A Case Study in R And C++" or the official package presentation at
UseR!2008 in Dortmund scheduled for August 13th.
The ff authors
Daniel Adler <[EMAIL PROTECTED]>
Chr
never implemented one of those. :(
I would be very grateful for any help!
thank you
Jens
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? i have looked in several packages
(vegan, labdsv etc.) because I am working with species by site tables,
but without success. perhaps I looked for the wrong terms (rank matrix etc.)
thank you for your help
regards,
Jens
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Uni
ving forgotten an 8 year old wish!
Jens Oehlschlaegel
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at/html/import.asc.html
this allows to import your raster files and use it for calculations.
are you sure about your floating point data? or are there only "some"
digits after the "." ?
hope this helped?
best,
Jens
--
>
manually for the "empty" columns.
Any possible Ideas?
> A250[1:5,1:4]
AAPU ACTO ACRA ADBA
A1100 0 0.0 0 0
A20100 0 0.1 0 0
A20200 0 0.0 0 0
A400 0 1.0 0 0
A4100 0 0.0 0 0
I also didn´t find anything useful in "An Introduction to R&
Dear R-Users,
I was wondering if there is a way to test the significance of the
clarkevans statistic in spatstat package?
I did not find any related function or the related values to calculate
it by hand.
does someone has any ideas?
thank you,
Jens
GS 84 S33 ? would be nice
thank you
JEns
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), get))
[,1] [,2]
[1,]11
[2,]22
[3,]33
[4,]41
Warning message:
In cbind(1:4, 1:3) :
number of rows of result is not a multiple of vector length (arg 2)
Best regards
Jens Oehlschlägel
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