Hi
I am working on Species Distribution Modeling in R using BIOMOD2. When
picking my algorithms to model I keep getting an error message about length
(pred)
this is the code that I'm using
library(knitr)
library(markdown)
library(rgdal)
library(raster)
library(shapefiles)
library(biomod2
This does what I needed. However, as the output is a list object, is there
any way to apply a function to such object? For example if I want to compute
the mean for the 4th subvectors, I can't simply use:
#
Y=split(X,as.numeric(gl(length(X),3,length(X
mean(Y[4])
#
as the error message
I have tried to set parameters of an effects plot with moderate success, but
I'm finding that although the plot(effect()) method uses trellis graphics (via
the lattice package), not all aspects of the plot can be controlled by standard
trellis graphics.
I am able to set any parameters that are g
Do anyone now R packages that run/test stochastic dominance
with respect to a function (SDRF) and/or stochastic efficiency
with respect to a function (SERF)?
Peter Maclean
Department of Economics
UDSM
[[alternative HTML version deleted]]
__
R-he
On Tue, Dec 10, 2013 at 6:55 PM, bakerwl wrote:
> Expected values are needed to test a null hypothesis against observed
> counts, but if total observed counts are 20 for 3 categories, then a null
> hypothesis of a random effect would use expected values = 6.67 in each of
> the 3 categories (20/3)
On Dec 10, 2013, at 8:21 PM, David Winsemius wrote:
>
> On Dec 10, 2013, at 6:55 PM, bakerwl wrote:
>
>> David,
>>
>> Thanks for your reply--I appreciate your thoughts. I will look at prop.test.
>>
>> The reason I chose fisher.test over chisq.test is that fisher.test is more
>> appropriate wh
On Dec 10, 2013, at 6:55 PM, bakerwl wrote:
> David,
>
> Thanks for your reply--I appreciate your thoughts. I will look at prop.test.
>
> The reason I chose fisher.test over chisq.test is that fisher.test is more
> appropriate when observed counts are not numerous--empty cells and cells
> with
Thanks Rolf and Andrew. I was entirely too careless and should take a
trip to the woodshed (google "David Stockman woodshed" for the
reference).
The correct answer therefore is: maybe for the residuals, for the
"right" model, of course.
But I still think the crowd on r-sig-mixed-models is the ri
On 12/11/2013 11:24 AM, Jim Lemon wrote:
...
There may be a solution using the radial.pie function, and if I find it,
I'll post it.
Hi Steve,
Here it is. Just call radial.pie twice to get the annulus, then call
radial.grid with the appropriate arguments, and then you can add
whatever radial.p
David,
Thanks for your reply--I appreciate your thoughts. I will look at prop.test.
The reason I chose fisher.test over chisq.test is that fisher.test is more
appropriate when observed counts are not numerous--empty cells and cells
with counts < 5 are less a problem.
Expected values are needed
On Dec 10, 2013, at 4:24 PM, Jim Lemon wrote:
> On 12/11/2013 10:33 AM, Hodge, Steven wrote:
>> I'm working with radial.plot in the plotrix package.
>>
>> Is there a way to show a shaded region for a specific range of values in
>> radial.lim?
>>
>> For example:
>> # test data from radial.plot{
See inline below.
On 12/11/13 11:28, Bert Gunter wrote:
This is not really an R question -- it is statistics.
In any case, you should do better posting this on the
R-Sig-Mixed-Models list, which concerns itself with matters like this.
However, I'll hazard a guess at an answer: maybe. (Vague q
On Dec 10, 2013, at 2:04 PM, bakerwl wrote:
> I seem to be able to use expected values that are decimal (e.g., 1.33) when
> using chisq.test but not when using fisher.test.
There are no expected values in the input to fisher.test.
> This happens when using an
> array/matrix as input. Fisher.te
No - it is assumed to be conditionally normal, that is, normal conditional
on the model. So you should be looking at the distributions of the
residuals rather than of the response variable, as an indicator for whether
or not the model assumptions are satisfied. Skewness in the residuals may
or m
On 12/11/2013 10:33 AM, Hodge, Steven wrote:
I'm working with radial.plot in the plotrix package.
Is there a way to show a shaded region for a specific range of values in
radial.lim?
For example:
# test data from radial.plot{plotrix}
testlen<-c(sin(seq(0,1.98*pi,length=100))+2+rnorm(100)/10)
t
I'm working with radial.plot in the plotrix package.
Is there a way to show a shaded region for a specific range of values in
radial.lim?
For example:
# test data from radial.plot{plotrix}
testlen<-c(sin(seq(0,1.98*pi,length=100))+2+rnorm(100)/10)
testpos<-seq(0,1.98*pi,length=100)
# the origin
This is not really an R question -- it is statistics.
In any case, you should do better posting this on the
R-Sig-Mixed-Models list, which concerns itself with matters like this.
However, I'll hazard a guess at an answer: maybe. (Vague questions
elicit vague answers).
Cheers,
Bert
On Tue, Dec 1
Thanks, AK. That gets the job done and I learned 2 ways to do it. Much
appreciated as always.
--
View this message in context:
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Hi,
Check these links:
http://stackoverflow.com/questions/19626534/r-issue-error-in-sqliteexecstatementcon-statement-bind-data-no-such-tabl
http://r.789695.n4.nabble.com/Problem-with-SQLDF-Error-in-sqliteExecStatement-con-statement-bind-data-RS-DBI-driver-error-in-state-td4621931.html
A.K.
Hi folks,
I am using the lme package of R, and am wondering if it is assumed that
the dependent factor (what we fit for; y in many relevant texts) has to
have a normal Gaussian distribution? Is there any margins where some
skewness in the data is accepted and how within R itself one could check
di
Hi,
I have a doubt after a long time :) . I have a function which has sqldf
statements and it works fine when I call it from console but when I am
calling that function within another function, it gives me the error that
*Error in sqliteExecStatement(con, statement, bind.data) : *
* RS-DBI driver:
I seem to be able to use expected values that are decimal (e.g., 1.33) when
using chisq.test but not when using fisher.test. This happens when using an
array/matrix as input. Fisher.test returns: Error in sprintf(gettext(fmt,
domain = domain), ...) : invalid format '%d'; use format %s for character
LookupTable <- read.table(header = TRUE,
stringsAsFactors = FALSE,
text="Str IND13 IND12 IND11 IND07 IND06
1 517 529 562 562 567
2 517 529 562 562 568
3 517 529
Petr,
Thank you for you assistance. Particularly this last bit. It really
helped me understand exactly how your solution worked and why I was
confused by rapply processing rows. It was apply that could process
rows (and/or columns) of a matrix,
Anyway for anyone who wants the version of my
Dear all
I'm a beginner in R and I'm trying to get the final model after I run the
dredge function for 10 times (with a loop):
###Building the Model
Coy.glm0<-glm(pa ~ shrub + snowdep + tree + bio5 + bio6 + bio12 +
log(human+1), data=Coy.pa, family=binomial)
summary(Coy.glm0)
install.packages('
Many people do not want to download and open random attachments.
That's why I suggested dput() with part of your data.
dput(head(yourdata, 20))
is enough for many problems, though it's good to try it out.
Or use one of the datasets built into R.
Sarah
On Tue, Dec 10, 2013 at 3:23 PM, Welma Pe
Btw I am using mclust, and basically wanted to reproduce the mstep and
estep of the Mclust algorithm for new data.
Any help is appreaciated!
On 10 December 2013 21:23, Welma Pereira wrote:
> Hi,
>
> Thanks for the hint Sarah. So here is my problem again: (files train_pca
> is in train_pca and
How about this:
t2 <- table(c(10,11,12,13))
t1 <-table(c(1,1,2,4,5))
t12<-(rbind(as.data.frame(t1),as.data.frame(t2)))
xtabs(Freq~.,t12)
it works for "overlapping" tables
t2 <- table(c(10,11,12,13,1,2))
t1 <-table(c(1,1,2,4,5,11,12))
t12<-(rbind(as.data.frame(t1),as.data.frame(t2)))
xtabs(Freq~.,
Hi everyone,
you might find my question elementary but I am a beginner and unfortunately I
can't fix the problem.
So, I simulate this following algorithm and some values of c are NA. Therefore,
I should add these following two if-statements but I don't know how I should do
it in a for-loop.
Dear Vito, Robert and David,
thank you for your replies, although I made some step forward on my own, your
answers helped a lot and gave me more insight.
The only question I have left is why this code gives me an error (and that is
what David asked for):
m1 <- lms(BMI,age,data=adatok_fiu, cent=
Thank you,
now it works. I would never have never found the source of the problem.
I am trying
to build a data frame with results from a sensitivity analysis
for a model. I use rbind because the number of rows is
unkown and i use the timestamp as a hint for the students
that they do not analyse
I guess you will have to give us a reproducible example.
Are you still getting the same error message?
David
From: Shane Carey [mailto:careys...@gmail.com]
Sent: Tuesday, December 10, 2013 10:30 AM
To: dcarl...@tamu.edu
Cc: r-help@r-project.org
Subject: Re: [R] 3-D interpretation
Hey David,
I
it just keeps crashing on me,
It seems to crash on this line
rgl.surface(akima.li$x,akima.li$y,akima.li$z,color="green",alpha=c(0.5))
On Tue, Dec 10, 2013 at 4:32 PM, David Carlson wrote:
> I guess you will have to give us a reproducible example.
> Are you still getting the same error message
Hey David,
I set it equal to the mean. duplicate="mean"
but still no joy,
Thanks
On Tue, Dec 10, 2013 at 4:28 PM, David Carlson wrote:
> The error says you have duplicate points in dat so you need to
> set duplicate= to tell interp() how to handle them.
>
> ?interp
>
> ---
The error says you have duplicate points in dat so you need to
set duplicate= to tell interp() how to handle them.
?interp
-
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-Original Message-
From: r-help
Hi Sarah,
here is some of the data:
structure(list(X = c(9816966.951, 9816963.08, 9816947.516, 9816939.51,
9816924.005, 9816916.096, 9816901.984, 9816896.967, 9816892.928,
9816890.743, 9816886.427, 9816884.006, 9816879.185, 9816876.468,
9816871.027, 9816868.276, 9816863.404, 9816860.712, 9816855.
Hi,
On Tue, Dec 10, 2013 at 10:42 AM, Shane Carey wrote:
> Hi, I have since solved that problem,
It would be useful to post the solution, for the archives, so that
others with the same problem can benefit from your insight.
> but now R keeps crashing. I have over 20,000 points. Can R handle th
Hi,
im trying to create a 3-D interpretation of a geological fault using
the akima package. But my code fails below highlighted in red:
Does anyone have any ideas why this is.
Thanks
dat<-read.delim("D:\\fault.txt",header=T,sep=",")
library(rgl)
# data
rgl.spheres(dat$X,dat$Z , dat$Y,1,color="re
Hi, I have since solved that problem,
but now R keeps crashing. I have over 20,000 points. Can R handle that
amount?
Cheers
On Tue, Dec 10, 2013 at 3:35 PM, Shane Carey wrote:
> Hi,
>
> im trying to create a 3-D interpretation of a geological fault using
> the akima package. But my code fails
Hi Shane,
On Tue, Dec 10, 2013 at 10:35 AM, Shane Carey wrote:
> Hi,
>
> im trying to create a 3-D interpretation of a geological fault using
> the akima package. But my code fails below highlighted in red:
> Does anyone have any ideas why this is.
This is a plain-text email list, so no highligh
David Winsemius comcast.net> writes:
> So what happens if you try this:
>
> mapply(assign, kkk$vars, kkk$vals, MoreArgs = list(envir = .GlobalEnv)
>
Yes, it works in certain situations, as well as the equivalent code:
kkk <- data.frame(vars=c("var1", "var2", "var3"),
Hi,
It's unlikely that anyone will be able to see your problem without a
reproducible example.
http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
Are you using the mclust package? That would be the first thing we need to know.
Then, have you worked through the
andrewH wrote:
However, my suspicion is that there are some funky characters, either
control characters or characters with some non-standard encoding, somewhere
in this 14 gig file. Moreover, I am concerned that these characters may
cause me trouble down the road even if I use a different approa
Hi,
Try:
library(reshape2)
m1 <- melt(LookupTable,id.vars="Str")
m2 <- m1
res <- merge(MainDataFrame,m1,by.x=c("Str","index"),by.y=c("Str","variable"))
res[order(res$Str),c(3:6,1:2,7)]
#or
library(plyr)
colnames(m2)[-1] <- c("index","index_num")
m2$index <- as.character(m2$index)
join(MainDataF
try this:
> sensitivity=rbind(sensitivity,data.frame(mtype=2,cdate=as.POSIXct(Sys.time(),
> origin="1970-01-01")))
> sensitivity
mtype cdate
1 1 2013-12-10 09:35:53
2 2 2013-12-10 09:37:02
The 'c' function is coercing to numeric. If you want to 'rbind' rows
to a datafram
Hello world,
I am stuck somehow...
I am trying to add a timestamp to a sensitivity matrix:
#this code works:
sensitivity=data.frame(mtype=1,cdate=2)
sensitivity=rbind(sensitivity,c(mtype=2,cdate=2))
# this code does not work - no idea why
sensitivity=data.frame(mtype=1,cdate=as.POSIXct(Sys.ti
>I want to plot on the same diagram, curves from two different populations,
>that have different "n".
>
>How can I do this?
Use lines() as well as plot()
S
***
This email and any attachments are confidential. Any use...{{dropped:8
Hi,
I am trying to use mclust to cluster some data (train_pca_10), I get the
clusters, but when I try to use the model to predict new data (test1) I get
this error
mClust2 <- Mclust(train_pca_10,G=2)
pred<-predict.Mclust(mClust2,test1)
Error in if (warn) warning(WARNING) : argument is of lengt
Thank you very much, Rich, for the fast and very helpful reply! It helped
me to reach my goal.
Regards -- Gerrit
PS: I extended your solution to a version that allows slightly finer
control over the components of the boxplots, in particular if one wants to
combine it with, e.g., panel.stripp
In that case you need correct those cases inside the function. Everything else
stays same.
Something like
fff <- function(x) {
tb<-table(x)
if(max(tb)==min(tb)) res <- "None" else res <- names(which.max(table(x)))
}
Regards
Petr
From: Walter Anderson [mailto:wandrso...@gmail.com]
Sent: Monday,
On Tue, Dec 10, 2013 at 10:06 AM, Jeff Newmiller
wrote:
> It is bad netiquette to hijack an existing thread for a new topic. Please
> start a new email thread when changing topics.
>
> If your data really consists of what you show, then read.csv won't behave
> that way. I suggest that you open t
It is bad netiquette to hijack an existing thread for a new topic. Please start
a new email thread when changing topics.
If your data really consists of what you show, then read.csv won't behave that
way. I suggest that you open the file in a text editor and look for odd
characters. They may be
Why does R interpret a column of numbers in a csv file as a factor when
using read.csv() and how can I prevent that. The data looks like
9928
3502
146
404
1831
686
249
I tried kick=read.csv("kick.csv",stringsAsFactors =FALSE)
as well as
kick=read.csv("kick.csv")
Thanks
On Mon, Dec 2, 2013 at 5
You don't need to wrap 1:12 in c().
Since matrices are just folded vectors, you can convert vector X to a matrix
Xm:
Xm <- matrix( X, nrow=3 )
and access columns to get your your sub-vectors:
Xm[,1]
Xm[,2]
and so on.
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