Displaying 20 results from an estimated 700 matches similar to: "Has anyone used SIAR package add on?"
2006 Dec 20
2
RuleFit & quantreg: partial dependence plots; showing an effect
Dear List,
I would greatly appreciate help on the following matter:
The RuleFit program of Professor Friedman uses partial dependence plots
to explore the effect of an explanatory variable on the response
variable, after accounting for the average effects of the other
variables. The plot method [plot(summary(rq(y ~ x1 + x2,
t=seq(.1,.9,.05))))] of Professor Koenker's quantreg program
2007 Jan 09
1
contingency table analysis; generalized linear model
Dear List,
I would appreciate help on the following matter:
I am aware that higher dimensional contingency tables can be analysed using either log-linear models or as a poisson regression using a generalized linear model:
log-linear:
loglm(~Age+Site, data=xtabs(~Age+Site, data=SSites.Rev, drop.unused.levels=T))
GLM:
glm.table <- as.data.frame(xtabs(~Age+Site, data=SSites.Rev,
2006 Oct 06
1
sparklines in lattice
Dear R-help,
Has anyone implemented sparklines in the strips of a lattice plot? What I have in mind is, say, highlighting that part of a time series that one is examining in more detail in a set of lattice plots.
Regads,.
Mark Difford.
PS: (Andreas Loffler has implemented a simple but functional version for
TeX/LaTeX:
http://www.tug.org/tex-archive/help/Catalogue/entries/sparklines.html)
2011 Nov 10
1
Errors in SIAR
Help!
model1 <- siarmcmcdirichletv4(data, source, tef, concdep=0, 500000, 50000)
Error in matrix(1, ncol = (numsources + numiso) * numgroups, nrow =
(siardata$iterations - :
invalid 'ncol' value (too large or NA)
In addition: Warning message:
In Ops.ordered((numsources + numiso), numgroups) :
'*' is not meaningful for ordered factors
Previous message, but more
2011 Aug 04
2
Graphical option to update.packages in development version (build of the 2011-07-31 r56569) for Windows not working properly
Dear R-core/development-team,
The problem noted in the subject-line has been a problem in the last three
development versions of R for Windows that I have downloaded and tested, the
most recent of them being a version I downloaded this morning.
Update.packages() using the graphical option, i.e. called as
update.packages(ask='graphics', checkBuilt=TRUE)
does not work as it should, but
2006 Oct 13
1
Fw: nested linear model; with common intercept
Dear R-help,
I posted this on 4 Oct but got no response (I wasn't even told to go away and do some more background reading ;) ). I am reposting it in the, perhaps, vain hope that someone with knowledge of the subject will reply, if only to point me in a different direction to which I am now facing.
Earlier Posting:---
I am sorry if this is more of a stats question than an R-question, but I
2006 Oct 04
1
nested design; intercept
Dear R-help,
I am sorry if this is more of a stats question than an R-question, but I have found it difficult to get a clear answer by other means.
Q. Would it be "wrong" to specify a nested model and retain a common intercept, e.g.
lm(NH4 ~ Site/TideCode + 1)
I am aware (?) that my Site-coefficients are now calculated relative to my reference Site (treatment.contrasts), *but* that
2011 May 25
1
Multinomial Logistical Model
On May 24, 2011; 11:06pm Belle wrote:
> Does anyone know how to run Multinomial logistical Model in R in order to
> get predicted probability?
Yes. I could stop there but you shouldn't. The author of the package
provides plenty of examples (and two good vignettes) showing you how to do
this. Suggest you do some work in that area. Look especially at how model
formulas are
2006 May 17
1
Fix for augPred/gsummary problem (nlme library)
Dear R-users,
I am a newbie to this site and a relative new-comer to S/R, so please tread lightly, for you tread...
There have been several posting relating to problems with augPred() from the nlme library. Here is a "fix" for one of these problems which may lie at the root of others.
In my case the problem with augPred() lay in gsummary(), which augPred() uses, causing it to fail.
2012 Nov 14
0
SIAR: problem> session aborted
I'm absolutely not brilliant with R yet and working with package SIAR.
1) SIAR reads the first column of a table.txt as "int" instead of "num". Who
can help?
2) I therefore made tables with a data.frame() > that seems to work. But at
the end of the loading proces of the SIARmodel, I get a warning screen with
"Session Aborted". Everything crashes and I can start
2012 Apr 15
3
Problems loading siar package
Hello,
I recently bought a new Macbook Pro and installed R via a disk image from an
older computer - it seems to work fine. I then installed the package "siar",
tried to load it via the library command and received the following messages
(note the "mvtnorm" package did not appear to load correctly):
trying URL
2013 Oct 31
0
SIAR problem with model running
Hi there,
I am trying to run an MCMC on stable isotope data from certain organisms to
determine their dietary habits in the package SIAR.
I have prepared my data according to Inger, R., Jackson, A., Parnell, A.,
Bearhop, S. : SIAR V4 (Stable Isotope Analysis in R) an Ecologist's Guide
(also better known as 'SIAR for dummies'), which is as follows:
- consumer data table (columns
2012 Jul 04
2
problem loading siar
Hi,
I have a problem while loading the "siar" program in R.
When I am loading siar, system does not load convexhull. On the screen I
have seen such writings.
The following object(s) are masked from ‘package:spatstat’:
convexhull
How can I load the convexhull, how can I unmask from this package? I will
be appreciated if you give advice about this.
Best
Sukran
2010 Sep 07
1
problems with siar package
Hi, my name is Julio, I'm trying to run a script, specifically with the siar
package on R (I have attached the script) but the program collapses on
during the run. The error message says:
*** caught segfault ***
address 0xb31941cc, cause 'memory not mapped'
Traceback:
1: .C("siarmcmcv4", as.integer(numdata), as.integer(numsources),
as.integer(numiso),
2012 Oct 18
0
siar error
Hello,
I am trying to run the demoscript for the package "siar". However, using
the example script and example data supplied I cannot get 1) the model to
run unless I specify iterations =500 and burnin = 500 and 2) if the model
does work without crashing R then the function "siarhistograms" does not
work . Can anyone point out where I am going wrong?
>model1 <-
2011 Nov 10
3
Error in matrix, not ordered vectors or numerical value, and SIAR.
Help!
model1 <- siarmcmcdirichletv4(data, source, tef, concdep=0, 500000, 50000)
Error in matrix(1, ncol = (numsources + numiso) * numgroups, nrow =
(siardata$iterations - :
invalid 'ncol' value (too large or NA)
In addition: Warning message:
In Ops.ordered((numsources + numiso), numgroups) :
'*' is not meaningful for ordered factors
Previous message, but more problems:
2012 Sep 09
1
PCA legend outside of PCA plot
Hi All,
I have been trying to get to plot my PCA legend outside of the PCA plot,
but success still alludes me.
Can you guys please advise how I can achieve this. I used locater() to
obtain coordinates for below the Comp.1 axis. Using these coordinates the
legend disappears.
Below is the code for the PCA and legend.
Thanks in advance for the help.
Regards
Tinus
r.cols <-
2011 Dec 10
3
PCA on high dimentional data
Hi:
I have a large dataset mydata, of 1000 rows and 1000 columns. The rows
have gene names and columns have condition names (cond1, cond2, cond3,
etc).
mydata<- read.table(file="c:/file1.mtx", header=TRUE, sep="")
I applied PCA as follows:
data_after_pca<- prcomp(mydata, retx=TRUE, center=TRUE, scale.=TRUE);
Now i get 1000 PCs and i choose first three PCs and make a
2012 Sep 11
4
Maintaining specific order when using aggregate or change order on axis
Hi All,
I'm using the following code to produce some stacked bar graphs.
*setwd("C:\\Users\\Tinus\\Documents\\NMMU\\R\\Seamounts")*
*SChla <- read.csv("SM_Chla_data.csv")*
*
*
*#Extract mean values from data file*
*
*
*Coral <- SChla[185:223,] #Reduce SChla to Coral only*
*coral <- with(Coral , aggregate(cbind(Pico, Nano, Micro),
list(Depth),FUN=mean))*
How to use PC1 of PCA and dim1 of MCA as a predictor in logistic regression model for data reduction
2011 Aug 17
4
How to use PC1 of PCA and dim1 of MCA as a predictor in logistic regression model for data reduction
Hi all,
I'm trying to do model reduction for logistic regression. I have 13
predictor (4 continuous variables and 9 binary variables). Using subject
matter knowledge, I selected 4 important variables. Regarding the rest 9
variables, I tried to perform data reduction by principal component
analysis (PCA). However, 8 of 9 variables were binary and only one
continuous. I transformed the data by