from:"hiemstra"

utkarshsinghal wrote:

Hi All,

I have recently *re*-installed R-2.9.1 in my Linux machine. 

Hi,

Did you use the package manager of you linux distro, or did you compile 
from source.

cheers,
Paul
Since then, 
I am unable to plot using the usual interactive device.

 > plot(1:10)
This plots in a pdf file "Rplots.pdf" in my working directory.

 > sessionInfo()
R version 2.9.1 (2009-06-26)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

 > dev.cur()
null device
  1
 > capabilities(what = NULL)
jpeg  png tifftcltk  X11 aqua http/ftp  sockets
   FALSEFALSEFALSEFALSEFALSEFALSE TRUE TRUE
  libxml fifo   clediticonv  NLS  profmemcairo
TRUE TRUE TRUE TRUE TRUEFALSEFALSE

 > dev.interactive()
[1] FALSE

Before re-installation, everything was working perfectly.

Please suggest, how do I set the interactive device as default?

Thank in advance,
Regards,
Utkarsh

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--
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] How to set default plotting colors by treatment?


Remko Duursma wrote:

col=c("blue","red")mydfr$[treatment]



Yes, but I would like to use the function for lots of other dataframes
as well, so embedding 'mydfr' in the function is not the ideal
solution...
  
The problem is that the info in 'treatment' is non-constant, and you 
need to either pass on the info into the scope of the function, or you 
need to calculate the values in 'treatment' inside the function. Could 
you provide us with a reproducible example (as suggested in the posting 
guide), that would make it much easier for us to answer you question


veel succes!
Paul


remko

-
Remko Duursma
Post-Doctoral Fellow

Centre for Plants and the Environment
University of Western Sydney
Hawkesbury Campus
Richmond NSW 2753

Dept of Biological Science
Macquarie University
North Ryde NSW 2109
Australia

Mobile: +61 (0)422 096908
www.remkoduursma.com



On Mon, Sep 14, 2009 at 6:08 PM, Polwart Calum (County Durham and
Darlington NHS Foundation Trust)  wrote:
  

# I tried defining a function like this
myplot <- function(...)plot(..., pch=19, col=c("blue","red")[treatment])

# So i can call it like this:
with(mydfr, myplot(Xmeas, Ymeas))

# but:
Error in plot.xy(xy, type, ...) : object 'treatment' not found

  

basically that is something like calling:

myplot( mydfr$Xmeas, mydfr$Ymeas )

So plot doesn't know that treatment is within mydfr...

changing your function to:

myplot <- function(...) {
plot(...,
  pch=19,
  col=c("blue","red")mydfr$[treatment]
 )
}

should work?



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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] How to set default plotting colors by treatment?

I offer my sincere apologies for not reading the e-mail carefully, your 
example is indeed reproducible. When you stop using the 'with' function, 
this is I think what you would like:


myplot2 = function(formula, data, ...) {
   plot(formula, data = data, ..., pch = 19, col = 
c("blue","red")[data$treatment])

}
myplot2(Ymeas~Xmeas, mydfr)

A possible problem occurs when you want to redefine 'pch' or 'col', e.g.:

myplot2(Ymeas~Xmeas, mydfr, pch = 20)
Error in localWindow(xlim, ylim, log, asp, ...) :
 formal argument "pch" matched by multiple actual arguments

cheers and hope this helps,
Paul

Remko Duursma wrote:

The example is reproducible! Did you see the first post?

remko



-
Remko Duursma
Post-Doctoral Fellow

Centre for Plants and the Environment
University of Western Sydney
Hawkesbury Campus
Richmond NSW 2753

Dept of Biological Science
Macquarie University
North Ryde NSW 2109
Australia

Mobile: +61 (0)422 096908
www.remkoduursma.com



On Mon, Sep 14, 2009 at 9:19 PM, Paul Hiemstra  wrote:
  

Remko Duursma wrote:


col=c("blue","red")mydfr$[treatment]



Yes, but I would like to use the function for lots of other dataframes
as well, so embedding 'mydfr' in the function is not the ideal
solution...

  

The problem is that the info in 'treatment' is non-constant, and you need to
either pass on the info into the scope of the function, or you need to
calculate the values in 'treatment' inside the function. Could you provide
us with a reproducible example (as suggested in the posting guide), that
would make it much easier for us to answer you question

veel succes!
Paul


remko

-
Remko Duursma
Post-Doctoral Fellow

Centre for Plants and the Environment
University of Western Sydney
Hawkesbury Campus
Richmond NSW 2753

Dept of Biological Science
Macquarie University
North Ryde NSW 2109
Australia

Mobile: +61 (0)422 096908
www.remkoduursma.com



On Mon, Sep 14, 2009 at 6:08 PM, Polwart Calum (County Durham and
Darlington NHS Foundation Trust)  wrote:

  

# I tried defining a function like this
myplot <- function(...)plot(..., pch=19, col=c("blue","red")[treatment])

# So i can call it like this:
with(mydfr, myplot(Xmeas, Ymeas))

# but:
Error in plot.xy(xy, type, ...) : object 'treatment' not found


  

basically that is something like calling:

myplot( mydfr$Xmeas, mydfr$Ymeas )

So plot doesn't know that treatment is within mydfr...

changing your function to:

myplot <- function(...) {
plot(...,
 pch=19,
 col=c("blue","red")mydfr$[treatment]
)
}

should work?




This message may contain confidential information. If yo...{{dropped:21}}

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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul






--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] installation problem

wesley mathew wrote:

Hello All

I have some problem for installing  XML_2.6-0.tar . I am working in widows
and R version is  R-2.9.1
   >*install.packages("XML")*
After selecting a CRAN mirror
**
*Error :-* Warning: unable to access index for repository
http://cran.pt.r-project.org/bin/windows/contrib/2.9
Warning: unable to access index for repository
http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.9
Warning messages:
1: In open.connection(con, "r") :
  unable to connect to 'cran.r-project.org' on port 80.
2: In getDependencies(pkgs, dependencies, available, lib) :
  package ‘XML’ is not available
**

Hi,

Sounds like either:

- The mirror is broken, try a few others
- You are behind a proxy server, configure you machine to use the proxy 
server

  >*install.packages( "c:/program files/R/XML_2.6-0.tar.gz", type="source",
repos=NULL)*
*Error  :-*  'sh' is not recognized as an internal or external command,
operable program or batch file.

This doesn't work in windows if you have not installed the Rtools 
(http://www.murdoch-sutherland.com/Rtools/). Try to install those first, 
or download and install the windows binary version.

cheers,
Paul

Thanks in advance for your help

Kind Regards

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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] call for input


Martin Batholdy wrote:

Hi,

is there a way to make a call for an input at some point of a process ..?

I don't know how to describe it well ...


like;


please enter your first name:
>


and then, what is typed in should be saved into a variable.

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Hi,

Look at the readline() function.

cheers,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] releasing memory when using the ncdf package

2009-09-15 Thread Paul Hiemstra


Hi,

Try the gc() command.

cheers,
Paul

eric lee wrote:

Hello,

I'm running R 2.7.2 in a windows XP environment and I run the
following in an R console:

library(ncdf)
nc <-open.ncdf('c:/file.nc')
aa <- get.var.ncdf(nc,'var1')

This works fine, but 'aa' takes up about 100mb and I want to release
the memory after using it.  I try:

rm(aa)
close.ncdf(nc)

and look at Windows Task Manager, but the memory hasn't been released.
 Do you know what I should do to release the memory?  Thanks in
advance.

eric

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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] how can we check file empty or not

2009-09-16 Thread Paul Hiemstra


deepak m r wrote:

Hi All,
  I need to check whether the file is empty or not, Please help me
in this regards.
Best regards,
Deepak.M.R

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Hi,

file.info("your_file")$size == 0

cheers,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] How to repeat the names?

2010-02-10 Thread Paul Hiemstra


Hi,

Take a look at rep(), specifically the each = parameter.

cheers,
Paul

Madhavi Bhave wrote:

Dear R helpers
 
I have a city.csv file as given below.
 
'city.csv'

city_name1city_name2
New York CityBuffallo   
 
So I define
 
city_name = read.csv('city.csv')

city1 = city_name$city_name1
city2 = city_name$city_name2
 
My problem is how do I repeat the names one after other say 10 times i.e. my output should be like
 
New York 
City Buffallo
New York 
City Buffallo 
New York 
City Buffallo 
New York City 
...

...
...
...
 
I have tried the following commands 
 
rep(c(city1,city2), 5)
 
and I got the output something like this 
 
[1] 1 1 1 1 1 1 ...
 
If I try
 
rep((city1,city2), 5)
 
Error: unexpected ',' in "rep((city1,"
 
Please guide
 
Regards
 
MAdhavi



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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] Total least squares linear regression

2010-02-10 Thread Paul Hiemstra


Hi,

The wikipedia shows the matrix algebra that calculates Total regression, 
you could put this into R code to solve your problem. Also take a look 
at the pcrcomp or svd function for singular value decmoposition 
implementation. This would probably not be generic, but that is not a 
problem for you.


groet,
Paul

Gnewbee wrote:

Dear all,

After a thorough research, I still find myself unable to find a 
function that does linear regression of 2 vectors of data using the 
"total least squares", also called "orthogonal regression" (see : 
http://en.wikipedia.org/wiki/Total_least_squares) instead of the 
"ordinary least squares" method. Indeed, the "lm" function has a 
"method" argument but the manual says that there is only one option so 
far.
However, since the samples I am studying have the type of relationship 
that requires orthogonal regression, I am bound to use it.


The only thing I've found so far is the "tlsce" function in the "BCE" 
package (see :  http://cran.r-project.org/web/packages/BCE/index.html) 
but I'm not sure it's of general use or designed for the particular 
application of taxonomy, since its arguments are supposed to be matrices.
If any of you knew a function that does this or had a personnal script 
to do this kind of regression, I'd be very grateful.


Thanks a lot in advance

Gnewbee

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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] How can I associate a list of defined names with the dataframes to be downloaded

2010-02-16 Thread Paul Hiemstra


Alex Levitchi wrote:
Hello 
I am very thankful for the reply from Jim Holtman and David Winsemius, especially for the understandable explanations. it really works. 
Now I get another problem I cannot figure out. 
That is the situation: 
I work in biology. I need to download several files according to an experiment, which can be find out in NCBI GEO, and store them. 
For this I use GEOquery package and getGEO function. 
Each experiment (named GSE) contains several Samples (GSM), which names I extract by names(GSMList()). 
So now I want to make association between the defined names, which represents lowercases names of GSM, having them from names(GSMList()) as 
class(names(GSMList(gse))) 
[1] "character" 

I wrote something like this 
lapply=(i=1:length(names(GSMList(gse))), lgsms[i]=getGEO(names(GSMList(gse))[i])) 
  

Hi Alex,

please read the lapply documentation carefully, don't guess the correct 
syntax. But after looking at the docs of lapply, the examples aren't 
very clear. The correct syntax is somewhere along the lines of this:


geo_list = lapply(names(GSMList), function(name) {
return(getGEO(name) )
 })

you can read this piece code aloud like, "for all names in GSMList do 
the function getGEO and return the results in a list".


cheers,
Paul
but 
"Error: unexpected ',' " or anything else 
if I try to make it directly by associating a name from the list to correspondent GEO file I get this 
lgsms[1]=getGEO(names(GSMList(gse))[1]) #lgsms - list of lowercases names from names(GSMList()) 
File stored at: 
/tmp/RtmpgnMuHv/GSM296650.soft # so it downloaded the file but didn't make the association with the name so I cannot use it. 
Error in lgsms[1] = getGEO(names(GSMList(gse))[1]) : 
incompatible types (from S4 to character) in subassignment type fix 

Generally, working with GEOquery should be done very careful, as previously I also have some problems regarding the characteristics of data extracted from it and the way to convert them in an affordable way. It is a pity, that authors don't give more explanations on it. So I suppose it is also here. 

Kind regards 
Alex Levitchi 



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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] Extending data frame with longer columns

2010-02-17 Thread Paul Hiemstra


Ralf B wrote:

Hi,

I am a beginner in R and have only read a few chapters in the R book,
I was not able to find a solution for this simple problem.

I have an empty data frame:

a=data.frame(name="test")

which I would like to extend in a for-loop (with data extracted from a
database). Ideally I would like to extend the data frame like this:

a["new_1"] = 1:10
a["new_1"] = 1:12
a["new_1"] = 1:14
  
I would first read all the data into a list (maybe using lapply), where 
the columns are the parts of the list. Then you can find out which one 
is longest, and add NA's at the end of the other columns, and than use 
do.call("cbind", list_of_columns) to get the resulting data.frame:


note that I use apply type of constructs a lot, it is sort of one line 
for loop.


# Create a mockup list for this particular example
column_list = lapply(round(runif(5, 1, 10)), function(len_column) {
   rep(len_column, times = len_column)
})

# Find the length of the columns in the list
len_columns = sapply(column_list, length)
# add the NA's
dum = lapply(column_list, function(col) {
  c(col, rep(NA, max(len_columns) - length(col)))
 })
# Make the dataframe
dat = data.frame(do.call("cbind", dum))

it is quite a manual way of doing it, maybe someone else knows of an 
available R function to do it. But this is how I would do it.


cheers,
Paul

R now obviously complains about the changing length of the new
columns. However, I would like to have missing values being added
whenever columns are shorter than a newer (longer) column. How can I
do that?

Thanks,
Ralf

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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] Bayesian Block Kriging?

2010-02-18 Thread Paul Hiemstra


Hi Candan,

As a more general remark, there is a mailing list for spatial data, 
including interpolation, r-sig-geo. This question would be more 
appropriate there. I gave some answers in-line below from what I could 
come up with. Reposting on r-sig-geo would be  a good idea to get more 
response.


cheers,
Paul

Candan Soykan wrote:

Hello,
I'm interested in doing Bayesian kriging using R.  I see that the 
package geoR has a function that will allow one to do this 
(krige.bayes).  However, my data are not in the form of points, but 
rather they are blocks that represent spatial averages (i.e., the 
number of fishing hooks per month in a given lat x long square).  I am 
therefore interested in treating the data as spatial blocks, rather 
than points.  I see that package gstat has a function that will allow 
one to do block kriging (krige).  However, I cannot find a function 
that will allow me to do both, Bayesian and block kriging at the same 
time.  My questions are:


1) Can the function "krige.bayes" be made to accommodate data in areal 
form (rather than point data)? or

possibly, I've never used krige.bayes
2) Does the function "krige" allow for Bayesian inference (i.e., 
priors, posteriors)? or

to my knowledge, no

3) Is there another package that can do both? or

I think not
4) Is there a method for combining functions to do what I would like 
to do?
write a new function that combines both things you want (you question is 
a bit vague)


A response to any and/or all of these questions would be greatly 
appreciated.  Thank you in advance.


Candan Soykan
candan.soy...@noaa.gov

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Re: [R] Extracting values from a list

2010-02-18 Thread Paul Hiemstra


chipmaney schreef:

I have run a kruskal.test() using the by() function, which returns a list of
results like the following (subset of results):

Herb.df$ID: 4-2
   Kruskal-Wallis chi-squared = 18.93, df = 7, p-value = 0.00841

Herb.df$ID: 44-1
Kruskal-Wallis chi-squared = 4.43, df = 6, p-value = 0.6187


So then, how do extract a vector of p-values (i.e., result$p.value) for
every element in the list?



  
If result$p.value normally returns the p value from a kruskal.test 
result you can probably do something like:


vector_pvalues = sapply(result_from_by_list, function(x) x$p.value)

cheers,
Paul

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Re: [R] Plotting multiple table automatically

2010-02-19 Thread Paul Hiemstra


KennyL wrote:

Hi All,

I have a slight issue getting R to plot a series of tables automatically.
Essentially I have a series of tables that I wish to plot. They are named
on_2, on_3 etc. based on the file name when they were read in. I have
filelist <- list.files() to give me list of the table names. I wish to plot
each table, so I was thinking along some kind of for loop as below:

for (i in 1:Number_Files) {
plot(filelist[1])
}

With a few other bits a pieces, however obviously this tries to plot the
character string in filelist, any ideas on how to get R to read the
identically named table and plot that?

Thanks,

Kenny
  

Hi Kenny,

Take a look at parse() if you want it do your way, but consider the 
following much better way. Read the files into a list first not in 
seperate R objects, something like:


list_tables = lapply(list.files(), read.table)
?lapply

and plot:

for(tab %in% list_tables) plot(tab)

cheers,
Paul

--
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] dot-dot-dot as an actual argument

2010-02-19 Thread Paul Hiemstra


Jyotirmoy Bhattacharya wrote:

I could not find any documentation of how dot-dot-dot works when used
as an argument in a function call (rather than as a formal argument in
a definition). I would appreciate some references to the rules
governing situations like:

f1<-function(x,y,...){
  print(x)
}
  

it would print(x), probably complain that y is missing

f2<-function(...){
  f1(...)
}

f2(1,2,3)
  

Hi!

print the .. and see what happens:

f2<-function(...){
 f1(...)
 print(list(...))
}

f2(1,2,3)


In the call above how are the three numbers bound to the individual
formal arguments x and y of f1 rather than f1 being called with a
single pairlist, which is what the documentation says ... is.

And while the example above succeeds, why does the following fail,

library(lattice)
f.barchart <- function(...) {
barchart(...)
}

x <- data.frame(a = c(1,1,2,2), b = c(1,2,3,4), d = c(1,2,2,1))
print(f.barchart(a ~ b, data = x, groups = d))

This gives the error:
Error in eval(expr, envir, enclos) :
  ..3 used in an incorrect context, no ... to look in
  
The problem is that d is a column in x and not a seperate R object. This 
is solved in barchart because the function knows that it needs to look 
in x for d. The problem only is that when the third (group = d) is taken 
from the ... (..3) it doesn't find any R object called d. So it crashes 
with the above error.


cheers,
Paul

Jyotirmoy Bhattacharya

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Re: [R] Extracting values from a list

2010-02-19 Thread Paul Hiemstra


chipmaney wrote:

Thanks, as a follow-up, how do i extract the list element name (ie, 4-2 or 44-1)
  

Look at names(your_list)

cheers,
Paul

thanks,

chipper

Date: Thu, 18 Feb 2010 11:56:45 -0800
From: ml-node+1560750-540257540-69...@n4.nabble.com
To: chipma...@hotmail.com
Subject: Re: Extracting values from a list



Try this:


sapply(x, '[', 'p.value')


On Thu, Feb 18, 2010 at 5:21 PM, chipmaney <[hidden email]> wrote:

  

  

I have run a kruskal.test() using the by() function, which returns a list of



  

results like the following (subset of results):



  

  

Herb.df$ID: 4-2



  

  Kruskal-Wallis chi-squared = 18.93, df = 7, p-value = 0.00841



  





  

Herb.df$ID: 44-1



  

   Kruskal-Wallis chi-squared = 4.43, df = 6, p-value = 0.6187



  

  

  

So then, how do extract a vector of p-values (i.e., result$p.value) for



  

every element in the list?



  

  

  

  

--



  

View this message in context: 
http://n4.nabble.com/Extracting-values-from-a-list-tp1560701p1560701.html
Sent from the R help mailing list archive at Nabble.com.



  

  

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3508 TC Utrecht
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Re: [R] how to generate graph from dataframe?

2010-02-22 Thread Paul Hiemstra


chinna wrote:

I connected to database  and i am accessing the tables  but i dont know how
to generate graphs from the database tables.

can anyone please help me
 i am new to R project
  

Hi,

Take a look at the plot() command. Or you can have a look at the lattice 
or ggplot2 packages. The book R graphics by Paul Murrel is a good book 
on R graphics.


cheers,
Paul

--
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Department of Physical Geography
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University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] (Somewhat) broken EPS files produced

2010-02-22 Thread Paul Hiemstra


Hi Wartan,

Not really an answer to your specific problem, but you could try to use 
pdf instead of eps, in combination ofcourse with pdflatex. I've never 
had problems with pdf nad Sweave. If you need to use eps, than my reply 
is of no help to you :).


cheers,
Paul

Wartan Hachaturow wrote:

Hello.

I'm writing some simple text using sweave, and faced a strange problem
with eps files produced for my plots (one example attached).
Individual eps files are interpreted by ghostscript just fine, and
show up without errors. But once I try to include them into main
LaTeX/Sweave document (using regular \includegraphics, produced by
Sweave),
ghostscript gives me this error on those files:

Error: /undefinedresult in --stringwidth--
Operand stack:
   (600)   0.5
Execution stack:
   %interp_exit   .runexec2   --nostringval--   --nostringval--
--nostringval--   2   %stopped_push   --nostringval--
--nostringval--   --nostringval--   false   1   %stopped_push   1878
1   3   %oparray_pop   1877   1   3   %oparray_pop   1861   1   3
%oparray_pop   1755   1   3   %oparray_pop   --nostringval--
%errorexec_pop   .runexec2   --nostringval--   --nostringval--
--nostringval--   2   %stopped_push   --nostringval--
--nostringval--
Dictionary stack:
   --dict:1157/1684(ro)(G)--   --dict:0/20(G)--   --dict:82/200(L)--
--dict:178/300(L)--   --dict:91/200(L)--
Current allocation mode is local
Current file position is 207944
GPL Ghostscript 8.71: Unrecoverable error, exit code 1

What might be the problem?

P.S. I get exactly the same behavior on Debian/sid and OS X.

  



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Re: [R] generating reports from database through R

2010-02-23 Thread Paul Hiemstra


durga chennu wrote:

Hi,

after some research now i am connecting to the database
.but i am not getting any reports can u please tell me any suggestions
or ideas.



Regards
chinna.

[[alternative HTML version deleted]]

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Hi Chinna,

Please be much more specific as to what you want, both in terms of the 
analysis and the report. Please read the posting guide carefully, 
sticking to it will get you much better responses from the mailing list.


cheers,
Paul

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Re: [R] export graphics for editing in Illustrator

2010-02-23 Thread Paul Hiemstra


Ivan Calandra wrote:

Dear R users,

I would like to edit my graphics in Illustrator. I know that I can set 
up almost every graph parameter in R, but the time I will spend 
searching for the correct settings might not be worth since I'm quite 
used to Illustrator and since I will in any case use Illustrator to 
prepare for publication.


Up to now, I've used savePlot() with type=("eps") but I'm unable to 
dissociate every part of the plot in Illustrator.


Is there a better way to do it? Another function, another package, or 
a completely different approach? I'm of course open to all suggestions.


For info, I run R2.10 on Windows XP

Thanks in advance
Ivan

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Hi,

I mostly use pdf to store my results from R. In R code it would look like:

pdf("bla.pdf")
plot commands...
dev.off()

I can read these pds into Inkscape (opensource vector drawing program) 
and edit all the indvidual lines and such. I can imagine Illustrator 
should also be able to read these pdfs.


cheers,
Paul

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Re: [R] Boot R


Cassiano wrote:

Hello,

This is my first post, and my english is not very good, but I will try...

I have a problem with boot the R. After that I install ubuntu 9.10 the R
don't run. When I open the terminal and digit R, appear the message:

*/usr/lib/R/bin/exec/R: error while loading shared libraries:
libgfortran.so.3: cannot open shared object file: No such file or directory*
  

Hi,

R tries to find libgfortran.so.3, which it cannot find. Either it's not 
on your computer, or it's the wrong version. Check if it is installed:


dpkg -l | grep libgfortran

If this last command does not return anything, you need to install using:

sudo apt-get update
sudo apt-get install libgfortran3

probably it is not installed by default and this will solve the problem.

cheers,
Paul


What's happening?
Can anyone help me?

Thank you

  



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Re: [R] two questions for R beginners


Ivan Calandra wrote:

Since you want input from beginners, here are some thoughts

I had and still have two big problems with R:
- this vectorization thing. I've read many manuals (including R 
inferno), but I'm still not completely clear about it. In simple 
examples, it's fine. But when it gets a bit more complex, then...
Related to it, the *apply functions are still a bit difficult to 
understand. When I have to use them, I just try one and see what 
happens. I don't understand them well enough to know which one I need.
- the second problem is where to find the functions/packages I need. 
There are many options, and that's actually the problem. R Wiki, 
Rseek, RSiteSearch, Crantastic, etc... When you start with R, you 
discover that the capabilities of R are almost unlimited and you don't 
really know where to start, where to find what you need.


As noted in earlier posts, the mailing list is really great, but some 
people are really hard with beginners. It was noted in a discussion a 
few days ago, but it looks like some don't realize how difficult it is 
at the beginning to formulate a good question, clear, with 
self-contained example and so on. Moreover, not everybody speaks 
English natively. I don't mean that you must help, even when the 
question is really vague and not clear and whatever. I'm just saying 
that if you don't want to help (whatever the reason), you don't have 
to say it badly. But in any cases, the mailing list is still really 
helpful. As someone noted (sorry I erased the email so I don't 
remember who), it might be a good idea to split it.

Hi everyone,

My 2ct about the mailing list :). I understand that beginners have a 
hard time formulating a good question. But the problem is that we can't 
answer the question when it is unclear. So either I:


- Don't bother answering
- Try do discuss with the author of the question, taking lots of time to 
find out what exactly is the question.

- Send a "read the posting guide" answer

I mostly do the first, as I have to get things done during my PhD :). So 
this leaves us with kind of a problem, the person mailing the list 
doesn't have the knowledge to ask the right question, the list can't 
answer properly and consequently, the person mailing the list still 
doesn't get the information he/she needs. We could start an R-beginner 
mailing list, but this would also suffer from this problem. What do you 
guys think?


Maybe the mailing list is not the right medium for really basic stuff. 
For that I would recommend a good R-book or (better) a course in R or 
(even better) some colleagues who work with R that you can ask questions to.


cheers,
Paul


Hope that's what you wanted
Ivan


Le 2/26/2010 08:39, Dieter Menne a écrit :


Patrick Burns wrote:
  

* What were your biggest misconceptions or
stumbling blocks to getting up and running
with R?


 

(This derives partly from teaching)

The fact that this xapply-stuff was not idempotent (worse: not 
always) and

that you need a monster like do.call() to straighten this out. Nowadays,
plyr comes close.

The concept of environment. With S it was worse, though.

That you cannot change values "passed by reference". I noted that the 
latter

is no problem for students who have not worked with c(++/#) before. That
there is only one return-result in functions.

"[" and the likes as an operator.

10 years ago, when I started, the message was: S4 is the future, S3 is
legacy. So I learned S4. Only to never use is in self-written code 
later.

Might be different for BioConductor people.

That sometimes you can use vectors not in data= (lattice), and 
sometimes not

(ggplot2). Still a VERY confusing inconsistency.

The "why-does-this-not-print" FAQ.

Why does par(oma..) not work with lattice?

Dieter





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Phone:  +3130 253 5773 Wed-Fri
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Re: [R] two questions for R beginners


Ivan Calandra wrote:

You are definitely right...
What to do with bad beginner's questions is not a simple issue.

If a "beginner's mailing list" is created, who will answer to such 
questions? And moreover, the beginners won't take advantage of the other 
questions (I've personally learned a lot trying to understand the 
questions and answers to other's problems). And also, as you said, the 
problems might persist.
The beginner's mailing list might be good in one aspect though: the 
"experts" who subscribe to it would be willing to help the beginners to 
get started with R, knowing that the questions might not be clearly stated.


As you pointed out, the mailing list is not the best for basic stuff 
(the question is of course "what is basic?"). Not everybody knows some 
colleagues who work with R (I'm personally the 1st one to use R in my lab).
I think, somehow and I have no idea how, documentation and guidance to 
search for help should be more accessible as soon as you start with R. 
Maybe a _*clear*_ section on the R homepage or in the "introduction to 
R" manual like "where to find help", including all of the most common 
and useful resources available (from "?" and RSiteSearch() to R Wiki and 
Crantastic).
  

Hi Ivan (and list),

I think the main problem is not as much that there isn't structure in 
the way R provides documentation / tutorials, but that people have a 
hard time finding the structure. There are task views for certain 
specific fields, but I think a lot of beginners do not know that they 
exist. There are separate mailing lists for specific fields, but I often 
see geographical (my field of expertise) oriented questions on R-help 
that would fit much better on R-sig-geo.


So I think a "O my God, I've downloaded R and what now" tutorial might 
be a good idea to put very close to the download button of R on CRAN. 
This tutorial would focus not on how to do things in R, but would 
provide guidance to the most obvious sources of information such as Task 
views, specific mailing lists, ways to search list archives, information 
for beginners how to write a good e-mail etc. I think for a lot of 
beginners it is not as much the answer to a specific question that they 
need, but more guidance how to look for answers themselves.


But at the end of the day, R is still not very easy to learn when coming 
from GUI oriented stats programs. In addition, to become reasonably 
fluent in R, you need spend at least a few hours a week on it. SO I 
think we can ease the pain for beginners, but not take away that it 
takes quite some time to become fluent in R.


cheers,
Paul

I hope that this whole discussion might help to make the R world better.
Thank you Patrick for initiating it!
Regards,
Ivan

Le 2/26/2010 15:09, Paul Hiemstra a écrit :
  

Ivan Calandra wrote:


Since you want input from beginners, here are some thoughts

I had and still have two big problems with R:
- this vectorization thing. I've read many manuals (including R 
inferno), but I'm still not completely clear about it. In simple 
examples, it's fine. But when it gets a bit more complex, then...
Related to it, the *apply functions are still a bit difficult to 
understand. When I have to use them, I just try one and see what 
happens. I don't understand them well enough to know which one I need.
- the second problem is where to find the functions/packages I need. 
There are many options, and that's actually the problem. R Wiki, 
Rseek, RSiteSearch, Crantastic, etc... When you start with R, you 
discover that the capabilities of R are almost unlimited and you 
don't really know where to start, where to find what you need.


As noted in earlier posts, the mailing list is really great, but some 
people are really hard with beginners. It was noted in a discussion a 
few days ago, but it looks like some don't realize how difficult it 
is at the beginning to formulate a good question, clear, with 
self-contained example and so on. Moreover, not everybody speaks 
English natively. I don't mean that you must help, even when the 
question is really vague and not clear and whatever. I'm just saying 
that if you don't want to help (whatever the reason), you don't have 
to say it badly. But in any cases, the mailing list is still really 
helpful. As someone noted (sorry I erased the email so I don't 
remember who), it might be a good idea to split it.
  

Hi everyone,

My 2ct about the mailing list :). I understand that beginners have a 
hard time formulating a good question. But the problem is that we 
can't answer the question when it is unclear. So either I:


- Don't bother answering
- Try do discuss with the author of the question, taking lots of time 
to find out what exactly is the question.

- Send a "read the posting guide" answer

Re: [R] two questions for R beginners


Thomas Adams wrote:

Paul,

I think your point "you need [to] spend at least a few hours a week on 
it" is key. Since I am not doing statistics daily, more in fits & 
starts as my latest project -may- require, my approach has been more 
task oriented. A less-than-ideal approach. So, I think your suggestion 
is on-the-mark.


Tom
I also see co-workers who would like to work with R, see the benefit of 
R etc, but don't have the time to learn and maintain R. But I'm not 
really sure how to fix this, it seems impossible to have both easy, 
intuitive  to use and power and flexibility.


cheers,
Paul



Paul Hiemstra wrote:

Ivan Calandra wrote:

You are definitely right...
What to do with bad beginner's questions is not a simple issue.

If a "beginner's mailing list" is created, who will answer to such 
questions? And moreover, the beginners won't take advantage of the 
other questions (I've personally learned a lot trying to understand 
the questions and answers to other's problems). And also, as you 
said, the problems might persist.
The beginner's mailing list might be good in one aspect though: the 
"experts" who subscribe to it would be willing to help the beginners 
to get started with R, knowing that the questions might not be 
clearly stated.


As you pointed out, the mailing list is not the best for basic stuff 
(the question is of course "what is basic?"). Not everybody knows 
some colleagues who work with R (I'm personally the 1st one to use R 
in my lab).
I think, somehow and I have no idea how, documentation and guidance 
to search for help should be more accessible as soon as you start 
with R. Maybe a _*clear*_ section on the R homepage or in the 
"introduction to R" manual like "where to find help", including all 
of the most common and useful resources available (from "?" and 
RSiteSearch() to R Wiki and Crantastic).
  

Hi Ivan (and list),

I think the main problem is not as much that there isn't structure in 
the way R provides documentation / tutorials, but that people have a 
hard time finding the structure. There are task views for certain 
specific fields, but I think a lot of beginners do not know that they 
exist. There are separate mailing lists for specific fields, but I 
often see geographical (my field of expertise) oriented questions on 
R-help that would fit much better on R-sig-geo.


So I think a "O my God, I've downloaded R and what now" tutorial 
might be a good idea to put very close to the download button of R on 
CRAN. This tutorial would focus not on how to do things in R, but 
would provide guidance to the most obvious sources of information 
such as Task views, specific mailing lists, ways to search list 
archives, information for beginners how to write a good e-mail etc. I 
think for a lot of beginners it is not as much the answer to a 
specific question that they need, but more guidance how to look for 
answers themselves.


But at the end of the day, R is still not very easy to learn when 
coming from GUI oriented stats programs. In addition, to become 
reasonably fluent in R, you need spend at least a few hours a week on 
it. SO I think we can ease the pain for beginners, but not take away 
that it takes quite some time to become fluent in R.


cheers,
Paul
I hope that this whole discussion might help to make the R world 
better.

Thank you Patrick for initiating it!
Regards,
Ivan

Le 2/26/2010 15:09, Paul Hiemstra a écrit :
 

Ivan Calandra wrote:
  

Since you want input from beginners, here are some thoughts

I had and still have two big problems with R:
- this vectorization thing. I've read many manuals (including R 
inferno), but I'm still not completely clear about it. In simple 
examples, it's fine. But when it gets a bit more complex, then...
Related to it, the *apply functions are still a bit difficult to 
understand. When I have to use them, I just try one and see what 
happens. I don't understand them well enough to know which one I 
need.
- the second problem is where to find the functions/packages I 
need. There are many options, and that's actually the problem. R 
Wiki, Rseek, RSiteSearch, Crantastic, etc... When you start with 
R, you discover that the capabilities of R are almost unlimited 
and you don't really know where to start, where to find what you 
need.


As noted in earlier posts, the mailing list is really great, but 
some people are really hard with beginners. It was noted in a 
discussion a few days ago, but it looks like some don't realize 
how difficult it is at the beginning to formulate a good question, 
clear, with self-contained example and so on. Moreover, not 
everybody speaks English natively. I don't mean that you must 
help, even when the question is really vague and not clear and 
whatever. I'm just saying that if you don't want to help

Re: [R] Boot R


Cassiano wrote:

I think I have 'libgfortran'.
After that I digit 'dpkg -l | grep libgfortran' in terminal, I got this
message:

ii  libgfortran2   4.2.4-5ubuntu1
Runtime library for GNU Fortran applications
ii  libgfortran2-dbg   4.2.4-5ubuntu1
Runtime library for GNU Fortran applications
ii  libgfortran3   4.4.1-4ubuntu9
Runtime library for GNU Fortran applications
ii  libgfortran3-dbg   4.4.1-4ubuntu9
Runtime library for GNU Fortran applications


And the error continue:

/usr/lib/R/bin/exec/R: error while loading shared libraries:
libgfortran.so.3: cannot open shared object file: No such file or directory

  

if you do:

sudo updatedb
locate libgfortran | grep so

does it find the file? And in which path?

cheers,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] Boot R


Cassiano wrote:

I think I have 'libgfortran'.
After that I digit 'dpkg -l | grep libgfortran' in terminal, I got this
message:

ii  libgfortran2   4.2.4-5ubuntu1
Runtime library for GNU Fortran applications
ii  libgfortran2-dbg   4.2.4-5ubuntu1
Runtime library for GNU Fortran applications
ii  libgfortran3   4.4.1-4ubuntu9
Runtime library for GNU Fortran applications
ii  libgfortran3-dbg   4.4.1-4ubuntu9
Runtime library for GNU Fortran applications


And the error continue:

/usr/lib/R/bin/exec/R: error while loading shared libraries:
libgfortran.so.3: cannot open shared object file: No such file or directory

  

Cassiano wrote:
After sudo updatedb - nothing

after locate libgfortran | grep so

//usr/lib/libgfortran.so.2
/usr/lib/libgfortran.so.2.0.0
/usr/lib/libgfortran.so.3.0.0
/usr/lib/debug/usr/lib/libgfortran.so.2.0.0
/usr/lib/debug/usr/lib/libgfortran.so.3.0.0
/usr/lib/gcc/i486-linux-gnu/4.4/libgfortran.so
/
My reply:
The point is that R is expecting /usr/lib/libgfortran.so.3 but your 
computer has /usr/lib/libgfortran.so.3.0.0. A trick is to make a 
symbolic link from /usr/lib/libgfortran.so.3 to 
/usr/lib/libgfortran.so.3.0.0. /usr/lib/libgfortran.so only points to 
/usr/lib/libgfortran.so.3.0.0 in that case:


sudo ln -s /usr/lib/libgfortran.so.3.0.0 /usr/lib/libgfortran.so.3

This should fix the problem.

cheers,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] R Experts

2010-03-01 Thread Paul Hiemstra


Hi,

Maybe the R version Ryan is using is very old?

cheers,
Paul

Erik Iverson wrote:



Ryan Kinzer wrote:

Erik

Thanks for helping.  Both of them are factors.



That's the problem, they need to be of class Date.  See the R NEWS 
article about Date classes in Volume 4/1.


http://cran.r-project.org/doc/Rnews/

I don't see how they could be factors though, since you shouldn't be 
able to subtract two factors from each other without a warning at least?


e.g., when I make up factors f1  and f2

>f1 - f2



Warning message:
In Ops.factor(f1, f2) : - not meaningful for factors

We would have to have a small, reproducible example to know for sure 
what's going on...


Best Regards,
Erik

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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] two questions for R beginners

2010-03-01 Thread Paul Hiemstra


Jack Siegrist wrote:

My biggest impediment, as a scientist without previous programming
experience, is that the R help is not beginner-friendly. I think it is
probably great for experienced programmers and for the people who helped to
create the software, to help them  remember what they did, but I think it is
very difficult for a newcomer without a strong programming background to
learn about a new function or to discover the name of a function that you
are pretty sure should already exist. Maybe this wouldn’t matter for most
programming languages, but as free statistics software R is obviously going
to attract many scientists who want to get an analysis done and have varying
levels of experience with programming. 
  

Hi Jack,

A problem more or less is that the R community consists primarily of 
volunteers. People who answer questions to the help list in their spare 
time or during company time. This also holds for many of the online 
material. A program like Mathematica has a company providing the online 
material, they hire people to do this work. I don't use this as an 
excuse for R, but it might explain why the R community is what it is.


In reply to the 'bashing' of new users. I agree that sometimes the 
experts answering the questions can be blunt, but most often it is in 
response to questions that are very hard to answer. As I said earlier in 
this mail thread, asking the right question already involves some of the 
knowledge to answer the question. So to get good, informative responses 
a user needs some level already.


I do want to point out that there is a posting guide for the mailing 
list that gives a quite detailed instructions, like give the exact error 
(don't just say, R crashes). Provide traceback() and sessionInfo() etc, 
etc. And a lot of posters do not adhere to these rules.


cheers,
Paul


I found it much easier to learn how to use Mathematica, using only the
online help. With R I had to buy several books to get a handle on it, which
is fine, but even the books that I have found to be most useful tend to be
didactically lacking—either too cursory or mired in unexplained programming
jargon. They are OK just not great.

What I think would be very helpful is an introduction to programming using
R, preferably a big thick college textbook that takes at least a semester to
go through, which should be a prerequisite for going through the
Introduction to R available on CRAN.

Also to do any analysis on real data you have to use the apply family of
functions to perform different functions by groups. A long introduction to
these functions, with lots of comparisons and contrasts between them would
be very helpful.

A few random examples concerning the R help: 


In my version of R (2.7.0 on Windows XP) typing
  

?+


doesn’t do anything, but then if you type in the next line
+ ?sum
you get the “Arithmetic Operators” help page.
If you had just typed
  

?sum

in the first place you get the “Sum of Vector Elements” help page. 


Most examples in the R help pages use way to many other functions to be
useful to a beginner. If an example uses 10 other functions besides the one
being described, chances are a beginner won’t know what one of them does,
which can set off a chain of having to look up other irrelevant functions.

Some function names in the base package are goofy, such as “rowsum” which is
used to “compute column sums across rows”, not to be confused with “rowSums”
which computes row sums.

  



--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] Simple Linear Autoregressive Model with R Language


Emil Davtyan wrote:

Hello -

I need to do simple linear autoregressive model with R software for my
thesis. I looked into all your documentation and I am not able to find
anything too helpful. Can someone help me with the codes?

Thanks
Emil


  
	[[alternative HTML version deleted]]


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Hi,

Google "R ar model", the first hit gives:

http://stat.ethz.ch/R-manual/R-patched/library/stats/html/ar.html

cheers,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] two questions for R beginner


Brandon Zicha wrote:

What were your biggest misconceptions or
stumbling blocks to getting up and running
with R?


Easy.  I terms of materials I have been unable to find good books that 
introduce users to R from the perspective of someone familiar only 
with packages like SPSS or STATA, or not familiar with statistics 
packages at all.  Even introduction texts use jargon without 
introducing it.


I think that R-help files should be more thorough than they are, and 
contain more examples.  I thought that STATA help files were sparse!  
The notion that 'R is a user community and thus they do this in their 
spare time' is no excuse for those creating new tools for R not 
developing complete help files.  It doesn't take that much time 
relative to actually creating the new function.

Hi Brandon,

I would disagree with your point that documentation doesn't take much 
time. Writing documentation that is suitable for both the advanced user 
(being a reference, and thus preferably short) and the beginning user 
(being sort of a tutorial, and thus prefererably longer) is quite a 
challenge, comparable to writing a good paper. Apart from the fact that 
it takes quite a while, it is also not much fun. Often people develop 
packages for their own research and put the software online so others 
can benefit, they don;t need the documentation themselves and don't get 
paid to write the documentation.


So saying 'it's no excuse' really goes too far in my view. R is free, 
you did not pay several thousands of euros giving you the right for good 
support. Even the support is free through the mailing list. You can get 
a paid version of R at Revelution Computing. Then you can call them if 
there are problems. I'm not meaning to offend anybody, but I didn't 
agree with "is no excuse for those creating new tools for R not 
developing complete help files".  Partly the strength of R is in the 
open source, but sometimes, as with documentation, this can bite you. 
But I think the R docs aren't that bad, I've seen proprietary software 
that a worse job than R.


my 2euro on the subject :),

Cheers,
Paul


In terms of actual R use - creating, using, and manipulating data are 
the biggest frustration for those of the 'spreadsheet generation'.  I 
get the impression that one needs to not merely understand, but be 
fully fluent in the jargon of matrix mathematics to even know what is 
going on half the time.  I find myself - even now - using 'rules of 
thumb' that 'seemed to work' rather than fully understanding what I am 
doing.  It is particularly discouraging when many of those 'intro 
books' suggest using something besides R for data manipulation - how 
clumsy is that!?


I find the actual programming syntax itself is the easiest part to 
master.  It is certainly more flexible - but without a particularly 
sufficient increase in complexity - than trying to write script in 
SPSS and STATA.


Brandon Zicha

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PLEASE do read the posting guide 
http://www.R-project.org/posting-guide.html

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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] two questions for R beginner

nity is much looser, much more open source. Probably the R 
core team would be the closest thing we have.


What do you think?

Best,

Brandon Z


On Mar 2, 2010, at 1:16 PM, Paul Hiemstra wrote:


Brandon Zicha wrote:

What were your biggest misconceptions or
stumbling blocks to getting up and running
with R?


Easy.  I terms of materials I have been unable to find good books 
that introduce users to R from the perspective of someone familiar 
only with packages like SPSS or STATA, or not familiar with 
statistics packages at all.  Even introduction texts use jargon 
without introducing it.


I think that R-help files should be more thorough than they are, and 
contain more examples.  I thought that STATA help files were 
sparse!  The notion that 'R is a user community and thus they do 
this in their spare time' is no excuse for those creating new tools 
for R not developing complete help files.  It doesn't take that much 
time relative to actually creating the new function.

Hi Brandon,

I would disagree with your point that documentation doesn't take much 
time. Writing documentation that is suitable for both the advanced 
user (being a reference, and thus preferably short) and the beginning 
user (being sort of a tutorial, and thus prefererably longer) is 
quite a challenge, comparable to writing a good paper. Apart from the 
fact that it takes quite a while, it is also not much fun. Often 
people develop packages for their own research and put the software 
online so others can benefit, they don;t need the documentation 
themselves and don't get paid to write the documentation.


So saying 'it's no excuse' really goes too far in my view. R is free, 
you did not pay several thousands of euros giving you the right for 
good support. Even the support is free through the mailing list. You 
can get a paid version of R at Revelution Computing. Then you can 
call them if there are problems. I'm not meaning to offend anybody, 
but I didn't agree with "is no excuse for those creating new tools 
for R not developing complete help files".  Partly the strength of R 
is in the open source, but sometimes, as with documentation, this can 
bite you. But I think the R docs aren't that bad, I've seen 
proprietary software that a worse job than R.


my 2euro on the subject :),

Cheers,
Paul


In terms of actual R use - creating, using, and manipulating data 
are the biggest frustration for those of the 'spreadsheet 
generation'.  I get the impression that one needs to not merely 
understand, but be fully fluent in the jargon of matrix mathematics 
to even know what is going on half the time.  I find myself - even 
now - using 'rules of thumb' that 'seemed to work' rather than fully 
understanding what I am doing.  It is particularly discouraging when 
many of those 'intro books' suggest using something besides R for 
data manipulation - how clumsy is that!?


I find the actual programming syntax itself is the easiest part to 
master.  It is certainly more flexible - but without a particularly 
sufficient increase in complexity - than trying to write script in 
SPSS and STATA.


Brandon Zicha

__
R-help@r-project.org mailing list
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http://www.R-project.org/posting-guide.html

and provide commented, minimal, self-contained, reproducible code.



--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul






--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

__
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Re: [R] Random real numbers


frederik vanhaelst wrote:

Hi,

How could i generate random real numbers between 0 en 2*pi?

Thanks,

Frederik

[[alternative HTML version deleted]]

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Googeling for "R generate random number" gave this as a second hit (on 
my machine):


http://blog.revolution-computing.com/2009/02/how-to-choose-a-random-number-in-r.html

cheers,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] error in R

2010-03-03 Thread Paul Hiemstra


Hi Frederik,

There is no need for the double for loop:

b[,5] <- sin(runif(5,0,2*pi))

As to your question, check the values i and k take. In the first 
iteration of the second loop k == 0, and R does not support an index 
equal to 0. The problem is in 1:n-1, this gives 0- 4, in stead do 
1:(n-1). Better is to skip the double for loop altogether and vectorization.


cheers,
Paul

frederik vanhaelst wrote:

Hi,

I want put some values in the last column of  a matrix b. But every time
again there comes the same error on the screen...

  

b <- array(0, c(5,5))
m<-matrix(runif(20,0,2*pi),5) # the sinus of this kind of values i


want put in the last column of b, m is a 5*4 matrix
  

n<-5
for(i in 1:n){


+ a2<-1
+ for(k in 1: n-1){
+ a2<-a2*sin(m[i,k])
+ }
+ b[i,n]<-a2
+ }
Error in b[i, n] <- a2 : replacement has length zero
Is there someone who see the problem?

Thanks a lot,

Frederik

[[alternative HTML version deleted]]

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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] Redhat Linux Install

2010-03-08 Thread Paul Hiemstra

Marc Schwartz wrote:

On Mar 5, 2010, at 3:45 PM, Ryan Garner wrote:

I just installed R on Redhat Linux at work for the first time and have two
questions.

1. I tried to install R to have png and cairo capabilities and was
unsuccessful. Before running make, I ran ./configure --with-libpng=yes
--with-x=no --with-cairo=yes --with-readline-yes . R installed fine, but
when I run R and type capabilities()

capabilities()

jpeg pngtiff tcltk X11 aqua http/ftp
sockets
TRUE TRUE TRUE TRUEFALSEFALSE TRUE TRUE
l ibxmlfifo cledit iconv NLS profmemcairo
TRUEFALSE TRUE TRUE TRUE TRUEFALSE

Why are png and cairo still FALSE?

2. I would also like to have X11 enabled. From reading the message board,
the consesus seems to be to install xorg-dev. I'm unable to do this because
I don't have root or super user priveleges. But if I'm able to log into my
work servers with PuTTY and Xming and run xemacs or xvim, does this mean
that X11 is already installed somewhere? If so, how do I specify this when
doing ./configure?

There is conflicting information here.

You specified --with-x=no, yet you want X. You indicate that you "installed R",
yet you do not have root access.

In order to compile R from source and have the functionality that you seem to want, you will need either have root access to install the required libraries or have the SysAdmin do so. In order to install R using the defaults, you need to have root access or have your SysAdmin do so.

The required libraries are the 'dev' or development versions of the RPMs for
each of the components such as libpng, cairo, readline and X. These contain the
header files (.h) that are required to compile R from source and support these
features. These issues are described in the R Installation and Administration
manual:

http://cran.r-project.org/doc/manuals/R-admin.html

The easier option would be to have the SysAdmin simply use the available RPMs
for R rather than compiling from source. I presume that by Red Hat Linux, you
mean RHEL. You can point your SysAdmin to the EPEL
(http://fedoraproject.org/wiki/EPEL) which provides pre-built RPMs for R,
installable by using 'yum'.

In addition to Marc, CRAN also provides .rpm version of R [1]. It could
be that these are newer than the ones on EPEL, but I'm not sure.

cheers,
Paul

[1] http://cran.r-project.org/bin/linux/redhat/

If you can use ssh to login to the server using PuTTY and that supports X as
you indicate, then it means that the server has been configured to support 'X
forwarding' and that your ssh login is using the '-X' option to request it on
your end of the connection. This means that the server supports X, but may or
may not have the X related development RPMs installed, which as I note, are
required to compile R from source and support X. Xming, on the other hand, I
believe provides its own X server implementation, which potentially brings
other issues into play. I have not used it, so would defer to others on the
details.

HTH,

Marc Schwartz

Re: [R] Removing Zeros from matrix

2010-03-09 Thread Paul Hiemstra


Dimitris Rizopoulos wrote:

one approach is the following:

mat <- matrix(rnorm(100*45), 100, 45)
mat[sample(100*45, 50)] <- 0

index <- rowMeans(mat == 0) == 0
mat[index, ]

Dimitris,

You use quite a complicated syntax to get the index. I think the 
following syntax using apply is more easy to understand:


# Note, MARGIN equal to 1 means loop over rows
# If any member of a row is zero
index = apply(mat == 0, MARGIN = 1, any)
# If all members of a row are zero
index = apply(mat == 0, MARGIN = 1, all)

cheers and hope it helps,
Paul



I hope it helps.

Best,
Dimitris


On 3/9/2010 11:05 AM, ogbos okike wrote:

Hi Everybody,
I have a matrix of about 45 columns. Some of the rows contain zeros. 
Using
data1<-data[complete.cases(data),], I can remove the "NA" rows. But 
I am

unable to tackle that of zeros.
Can anybody give me an idea of how to remove rows containing zeros in a
matrix.
Thanks so much
Best
Ogbos

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--
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] IMPORTANT - To remove the null elements from a vector

2010-03-09 Thread Paul Hiemstra


barbara.r...@uniroma1.it wrote:

I have a vector that have null elements. How to remove these elements?
For example:
x=[10 0 30 40 0 0] I want the vector y=[10 30 40]
Thanks
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and, to add to the options already posted:

subset(x, x != 0)

cheers,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] Removing Zeros from matrix

2010-03-09 Thread Paul Hiemstra


Dimitris Rizopoulos wrote:



On 3/9/2010 1:36 PM, Paul Hiemstra wrote:

Dimitris Rizopoulos wrote:

one approach is the following:

mat <- matrix(rnorm(100*45), 100, 45)
mat[sample(100*45, 50)] <- 0

index <- rowMeans(mat == 0) == 0
mat[index, ]

Dimitris,

You use quite a complicated syntax to get the index. I think the
following syntax using apply is more easy to understand:


well, this way is much more efficient to compute, especially if you 
have many rows. Compare the following to see the difference:


mat <- matrix(rnorm(2*1e06), 1e06, 2)
mat[sample(2*1e06, 50)] <- 0

system.time(index1 <- !apply(mat == 0, MARGIN = 1, any))

system.time(index2 <- rowMeans(mat == 0) == 0 )

all.equal(index1, index2)
Point taken, I totally agree that for large matrices you should use your 
approach. Didn't know that it made such a difference, great to learn 
something new :). But I still like the other syntax more ;).


cheers,
Paul



Best,
Dimitris



# Note, MARGIN equal to 1 means loop over rows
# If any member of a row is zero
index = apply(mat == 0, MARGIN = 1, any)
# If all members of a row are zero
index = apply(mat == 0, MARGIN = 1, all)

cheers and hope it helps,
Paul



I hope it helps.

Best,
Dimitris


On 3/9/2010 11:05 AM, ogbos okike wrote:

Hi Everybody,
I have a matrix of about 45 columns. Some of the rows contain zeros.
Using

data1<-data[complete.cases(data),], I can remove the "NA" rows. But
I am

unable to tackle that of zeros.
Can anybody give me an idea of how to remove rows containing zeros 
in a

matrix.
Thanks so much
Best
Ogbos

[[alternative HTML version deleted]]

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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] How to select partially (not completely) unique rows?

2009-06-30 Thread Paul Hiemstra


Hi Mark,

If you convert the data.frame to a Spatial class (see the sp-package 
documentation) you can use the function zerodist to find spatial 
locations that are at the same locations.


cheers,
Paul

Mark Na wrote:

Dear R-helpers,

I know how to use unique to select unique rows, e.g.

unique.rows<-unique(dataframe)

but I would like to select those rows that are unique only only TWO of my
dataframe's columns (so, two rows with the same value on these two columns
would not be kept, even if they had different values in other columns).

For example, I have a dataframe with 10 columns, two of which are LATITUDE
and LONGITUDE. I wish to keep only one row per unique combination of these
two columns, so I've tried:

unique.latlong<-extracted[unique(paste(extracted$latitude,extracted$longitude)),]

but this is returning a dataframe of missing values (NAs).

Could anyone point me in the right direction?

Thanks! Mark Na

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--
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] mapping states with colors

2009-07-03 Thread Paul Hiemstra


Hi,

You could have a look at the sp-package, it provides R-classes for 
spatial data. In addition, it also provides very nice plotting 
facilities. To read your data into these sp classes you can use the 
rgdal package. There is also an R mailing list specifically for 
geographic data (r-sig-geo) which might be a more suitable place to get 
good replies.


cheers,
Paul

Donald Braman wrote:

Hi folks,
I'm just learning how to use maps.  As an initial foray, I'm mapping the
states that have "duty to retreat" (blue) and "stand your ground" (red)
self-defense standards.  Here is my extremely naive script:

dtr <- c('alabama', 'arizona', 'conneticut', 'delaware', 'dist of columbia'
, 'hawaii', 'maryland', 'massachusetts', 'minnesota', 'missouri', 'nebraska'
, 'new hampshire', 'new jersey', 'new mexico', 'new york', 'north carolina'
, 'north dakota', 'ohio', 'pennsylvania', 'rhode island', 'virginia',
'wyoming', 'arkansas', 'vermont')


syg <-  c( 'alaska', 'california', 'colorado', 'florida', 'georgia', 'idaho'
, 'illinois', 'indiana', 'iowa', 'kansas', 'kentucky', 'louisiana', 'maine'
, 'michigan', 'mississippi', 'montana', 'nevada', 'oklahoma', 'oregon', 'south
carolina', 'south dakota', 'tennessee', 'texas', 'utah', 'washington', 'west
va', 'wisconsin')


map('state', proj='bonne', param=50,

region = c(syg, dtr),

fill=TRUE,

col=c('red', 'blue'))

Obviously that doesn't work.  A couple questions:

1. How do I get Alaska & Hawaii on the map?
2. How to I set the col atttribute for a subset of the states I'm mapping?

Many thanks in advance for any help!

Don

Donald Braman
http://www.culturalcognition.net
http://ssrn.com/author=286206
http://www.law.gwu.edu/Faculty/profile.aspx?id=10123

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--
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] Mathematical annotation axis in lattice

2009-07-07 Thread Paul Hiemstra


Hi Albart,

This bugged me also for quite some time. After some experiments the 
following syntax worked best:


library(lattice)
a = 0.11
xyplot(1:10~10:11, xlab = as.expression(bquote(R^2~" equals "~.(a

With the combination of as.expression and bquote you can mix text, math 
expression and the content of objects (in the case here of a). Read the 
documentation of bquote for more details.


cheers,
Paul

Coster, Albart wrote:

Dear list,

making mathematical expressions in plots is not difficult: expression(phi[1]) 
for example. At this moment I am stuck in creating a vector of expressions:

pos <- 1:10
lab <- letters[pos]

Now, I would like to create a vector of expressions which I could use for labeling the x-axis of a lattice plot. 


ll <- as.expression(paste(pos," phi[",lab,"]",sep = "")

xyplot(1:10~11:10,scales = list(x = list(labels = ll,at = 1:10)))

does not work. I read about the function substitute, but that did not solve it.

Could you recommend me how I should do this? 


Thanks in advance,

Albart Coster

Wageningen Universiteit
Netherlands

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--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] changing point style in xyplots depending on groups

2009-07-10 Thread Paul Hiemstra


Thomas von Känel wrote:

hi,
i've got the following and would like to set the point style for A, B 
and C myself (eg pch=1, 6 and 16)


library(lattice)
df <- data.frame(x  = log(c(1, 0.5 ,0.2 ,0.12 ,0.06, 1, 0.5 ,0.2, 
0.12,0.06, 1, 0.5 ,0.2 ,0.12,0.06)),
   y  = c(1, 2, 5, 14, 24, 51, 50, 50, 49, 54, 100, 101, 103, 97, 
95),
   gr = 
c('A','A','A','A','A','B','B','B','B','B','C','C','C','C','C'))

xyplot(df$y~df$x,groups=df$gr)

thanks in advance for any help
Tom von Känel
Human Genetics
Uni Berne

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Making pch not one value but a list of numbers should work, in this case 
do not use the groups variable:


xyplot(x~y, df, pch = c(1,1,1,1,1,3,3,3,3,3,5,5,5,5,5))

cheers,
Paul

--
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] Problems generating image from tiff file

2009-07-17 Thread Paul Hiemstra


Hi Mehdi,

PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

I don't mean to rude, but you seem to lack basic knowledge regarding the 
use of spatial data in R. Starting to use R is hard, but please ask your 
supervisor to help you or try and read more information on the internet. 
Some hints:


The Spatial taskview:
http://cran.r-project.org/web/views/Spatial.html

The R tips wiki:
http://wiki.r-project.org/rwiki/doku.php?id=tips:spatial-data

Or read the sp-documentation:
?sp
vignette("sp")

In addition, there is a mailing list specifically for geographic data 
and analysis in R, r-sig-geo. This is a much better place for your type 
of questions.


I also have some comments inline below.

cheers and good luck with your R adventures!
Paul

Mehdi Khan wrote:

I imported the attached tiff file and converted the coordinate system to
long lat and graphed it:

californiatiff<- readGDAL("california1.tif")
proj4string(californiatiff)
  

What is the outcome of this command?

rasterprojection <- spTransform(californiatiff, CRS("+proj=longlat")

It seems that you reproject a grid here. Remember that when reprojecting 
a grid, the grid structure is lost. The squares in the grid in the new 
projection aren't squares anymore. So the output of spTransform is no 
longer a grid (SpatialGrid or SpatialPixels) but a point dataset 
(SpatialPoints).


however, when using the plot command for rasterprojection, 
The sp-objects are plotted not using the plot command, but using the 
spplot command. If you are using this, this is not obvious from your e-mail.

I get a blob.  I
can see the outline of the state of california and nevada, but rather than
being able to see the geographic features, it is just a monocolor blob. 
My

suspicion is that since it is a list of coordinates and another column that
contains attributes, I need to turn it into a polygon.  I've tried the
following codes but none work:

  

rasterprojection2<-SpatialPolygons(rasterprojection)


You are trying to convert a grid to a polygon, this is not possible.

Error in is.vector(X) :
  trying to get slot "Polygons" from an object of a basic class ("integer")
with no slots

 rasterprojection2<- Polygons(rasterprojection)
Error in as.vector(x, "list") :
  cannot coerce type 'S4' to vector of type 'list'

Essentially, all I need to do is to connect the coordinates into polygons.
What am I doing wrong?
  
You used readgdal to read the tif file. If you want polygons, get a 
shapefile and read it using readOGR or readShapeLines or readShapePoly.

Thank you!
  



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--
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
http://intamap.geo.uu.nl/~paul

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Re: [R] Problems generating image from tiff file

2009-07-18 Thread Paul Hiemstra


Hi Mehdi,

No problem, we all have to start somewhere! Glad to have helped.

If you take a look at 
http://wiki.r-project.org/rwiki/doku.php?id=tips:spatial-data:spatial_data_visualization 
you will find some tips on how to plot spatial data using spplot. 
Including how to plot a grid together with a polygon.


good luck and cheers,
Paul

Mehdi Khan schreef:

Paul,

Thank you very much for your explanation.  I have only been using R 
for GIS purposes for about a week, so my expertise in the field is 
shallow.  Your explanation helped me out and I was able to plot the 
tif file simply by using the spplot command.


The reason I was projecting it was that I am trying to project a 
separate shape file on top of the tif--and the coordinates of the two 
files are different. 

What I ended up doing was using spTransform to change the coordinate 
system of the shape file into that of the tif file, and used the image 
() and plot commands to graph them on top of one another.


I'm definately a novice when it comes to R, but I am learning.  Thanks 
a lot!



On Fri, Jul 17, 2009 at 12:25 AM, Paul Hiemstra <mailto:p.hiems...@geo.uu.nl>> wrote:


Hi Mehdi,


PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

I don't mean to rude, but you seem to lack basic knowledge
regarding the use of spatial data in R. Starting to use R is hard,
but please ask your supervisor to help you or try and read more
information on the internet. Some hints:

The Spatial taskview:
http://cran.r-project.org/web/views/Spatial.html

The R tips wiki:
http://wiki.r-project.org/rwiki/doku.php?id=tips:spatial-data

Or read the sp-documentation:
?sp
vignette("sp")

In addition, there is a mailing list specifically for geographic
data and analysis in R, r-sig-geo. This is a much better place for
your type of questions.

I also have some comments inline below.

cheers and good luck with your R adventures!
Paul


Mehdi Khan wrote:

I imported the attached tiff file and converted the coordinate
system to
long lat and graphed it:

californiatiff<- readGDAL("california1.tif")
proj4string(californiatiff)
 


What is the outcome of this command?

rasterprojection <- spTransform(californiatiff,
CRS("+proj=longlat")
   


It seems that you reproject a grid here. Remember that when
reprojecting a grid, the grid structure is lost. The squares in
the grid in the new projection aren't squares anymore. So the
output of spTransform is no longer a grid (SpatialGrid or
SpatialPixels) but a point dataset (SpatialPoints).


however, when using the plot command for rasterprojection,

The sp-objects are plotted not using the plot command, but using
the spplot command. If you are using this, this is not obvious
from your e-mail.

I get a blob.  I
can see the outline of the state of california and nevada, but
rather than
being able to see the geographic features, it is just a
monocolor blob. My
suspicion is that since it is a list of coordinates and
another column that
contains attributes, I need to turn it into a polygon.  I've
tried the
following codes but none work:

 


rasterprojection2<-SpatialPolygons(rasterprojection)
   


You are trying to convert a grid to a polygon, this is not possible.

Error in is.vector(X) :
 trying to get slot "Polygons" from an object of a basic class
("integer")
with no slots

 rasterprojection2<- Polygons(rasterprojection)
Error in as.vector(x, "list") :
 cannot coerce type 'S4' to vector of type 'list'

Essentially, all I need to do is to connect the coordinates
into polygons.
What am I doing wrong?
 


You used readgdal to read the tif file. If you want polygons, get
a shapefile and read it using readOGR or readShapeLines or
readShapePoly.

Thank you!
 




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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:

Re: [R] Show representation of a data structure

2009-07-21 Thread Paul Hiemstra


bwgoudey schreef:

  I'm currently working with some large complex data structures eg list of
lists of data_frames containing lots more variables and lists etc.
Sometimes, I'd like to be able to bring up a simple representation of the
structure I'm working with, minus all of the values it contains (so simply
printing the variable doesn't work as its too hard to see structure when
there are 1000s of values being printed).  I know there is a function in R
that allows you to do something like this but I cannot remember what it is
and my searching has turned up nothing. Does anyone know the function I'm
talking about or have any other useful suggestions as to what I can do?
  
   Thanks
  

Hi,

Try summary() or str() on the object.

cheers,
Paul

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Re: [R] animated grid graphics

2009-07-21 Thread Paul Hiemstra


Hi,

Drawing grid graphics always takes long, I would write the images to 
png's and make the animation. If you use Linux I can suggest some nice 
tools to do this. This movie is also much more compatible with all kinds 
of machines. It might be that you can get your grid animation working on 
your own computer, but if another user has a less powerfull machine he 
might not have a smooth animation.


Good luck!
Paul

Unternährer Thomas schreef:

I need to make a fairly complex animated graphic and decided to use grid for it.
A very simple example of what I need:

##==
library(grid)
grid.newpage()
pushViewport(plotViewport())
pushViewport(viewport(xscale = extendrange(c(0, 100)),
  yscale = extendrange(c(0, 100
grid.xaxis()
grid.yaxis()

rectNames <- paste("r", 1:100, sep = "")
for (i in 1:100) {
  grid.rect(x = unit(sample(0:100, 1), "native"),
y = unit(sample(0:100, 1), "native"),
width = 0.1, height = 0.1, name = rectNames[i])
}

for (i in 1:100) {
  grid.remove(rectNames[i])
}
##==

The problem here is that removing grid objects is very slow, at least in the 
way I use it. Is it possible to remove all objects at once (or to use some

technique similar to double buffering)?


A second way to do it would be to remove a viewport and all its children from
the current viewport tree. Is this possible? Example:

##==
grid.newpage()
pushViewport(plotViewport())
pushViewport(viewport(xscale = extendrange(c(0, 100)), 
  yscale = extendrange(c(0, 100

grid.xaxis()
grid.yaxis()

pushViewport(viewport(xscale = extendrange(c(0, 100)), 
 yscale = extendrange(c(0, 100)),

 name = "plotVP"))
for (i in 1:100) {
  grid.rect(x = unit(sample(0:100, 1), "native"), 
y = unit(sample(0:100, 1), "native"),

width = 0.1, height = 0.1, name = paste("r", i, sep = ""))
}

*remove("plotVP")*??
##==


Another approach would be to save every single plot as an image and use 
something like imagemagick to produce an animated gif, but I was just wondering

if it's possible by using grid only (no need to use it outside of R).

Thanks in advance

Thomas

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Re: [R] animated grid graphics


Allan Engelhardt wrote:

On 21/07/09 14:00, Paul Hiemstra wrote:

Hi,

Drawing grid graphics always takes long, I would write the images to 
png's and make the animation. If you use Linux I can suggest some 
nice tools to do this. 


Please do suggest!  I was thinking about a similar problem.

Allan.

Hi Allan and Jeremy,

I use the jpeg2yuv and mpg2enc commands to create an mpg movie from a 
series of jpeg's, in this case created using R. The command to produce 
the mpg movie looks something like:


ls *.jpg | jpeg2yuv -f 25 -I p | mpg2enc -q3 -M2 2048 -o animation.mpg

These tools are part of the ffmpeg project (http://ffmpeg.org/) an I 
think they are part of the debian (and maybe ubuntu) repositories. 
Another cool tool is yuvmotionfps, it allows you to interpolation 
between frame, see http://jcornet.free.fr/linux/yuvmotionfps.html.


cheers and good luck,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] Multi-line comments?


Mark Knecht wrote:

Hi,
   I looked in the language definition and was surprised. Is there
really no multi-line/block comment defined in R?

   I wanted to comment out 20 lines that I'm moving to a function but
didn't want to delete them. Is there no defined way to get around
using a # on each of the 20 lines?

Thanks,
Mark

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Hi,

This issue has come up before, and as far as I know there is no 
multiline comment. However, there are a few ways of commenting out 
larges pieces of code.


- Use a good text editor, Kate (KDE) allows you to select the 20 lines 
and press Ctrl-D to comment them all at once.

- Use a setup like:
if(FALSE) {
line1
...
line20
}

And set FALSE to TRUE if you want to let the code be executed.

These are probably not the only ones, but this is what I could think of 
right now.


cheers and good luck,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] All possible linear models given multiple explaining variables


Thomas A. Groen wrote:

Hi,
 
I would like to have a script/function (or write one) that can calculate the

linear models for all possible combinations of explaining variables.
Eventually I would like to end up with a data base (or data frame) giving
for each model the R2, R2adj, AIC etc.
Currently I'm a bit stuck while writing my own script using the lm()
function from the base package. Also, I haven't fund any function (yet) that
can do this as well. Perhaps these functions/scripts already exist? I would
be very grateful to any suggestions and thoughts.
 
kind regards,

Thomas

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Hi,

Take a look at the step() command.

cheers,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] Multi-line comments?


Erik Iverson schreef:
What editor are you all using to write R code?  Many will have ways of doing what you want, e.g., comment-region (bound  by default to M-; through comment-dwim) in Emacs. 
  

I use Kate, the advanced text editor in KDE.
Paul

-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On 
Behalf Of Michael Knudsen
Sent: Wednesday, July 22, 2009 9:55 AM
To: Mark Knecht
Cc: r-help
Subject: Re: [R] Multi-line comments?

On Wed, Jul 22, 2009 at 4:30 PM, Mark Knecht wrote:

  

  I wanted to comment out 20 lines that I'm moving to a function but
didn't want to delete them. Is there no defined way to get around
using a # on each of the 20 lines?



Just like you, I have been longing for that myself. It seems that the
answer is negative, so I have ended up using

if (1==0)
{
   # code goes here
}

although is not really nice to look at.




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Re: [R] Re ading Image Files

2009-07-23 Thread Paul Hiemstra


cotixan wrote:

Hello, I'm rather new to R and I want to do some image analysis. Is there a
way to read jpeg files into a matrix like matlab's imread?
  

http://cran.r-project.org/web/packages/rimage/index.html

--
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] PDF Compression

2009-07-30 Thread Paul Hiemstra


Hi,

You could have a look at exporting the pdfs using the Cairo package.

cheers,
Paul

David Keegan schreef:

Hi,

I am generating a large number of graphs with pdf() and
incorporating them in pdf document using pdflatex.

According to the pdf() help:

   'pdf' writes uncompressed PDF.  It is primarily intended for
   producing PDF graphics for inclusion in other documents, and
   PDF-includers such as 'pdftex' are usually able to handle
   .compression.

But pdflatex incorporates the R graphs without compressing them.
They appear in the final document in cleartext, almost but not identical
to what was generated by R.

I tried the latex settings "\\pdfcompresslevel=9",
"\\pdfobjcompresslevel=3". They reduced the overall size of
the final document slightly, but didn't cause the embedded R
graphs to be compressed.

Can anyone suggest how I can get pdflatex to compress the R
graphs while embedding them? My output files are very big,
and I know they would be substantially smaller if the R
graphs were compressed.

Regards,
David



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Re: [R] R-installation regarding.

2010-03-23 Thread Paul Hiemstra


Hi Frederick,

The development files for readline are not available. Install them to 
get this working. For debian/ubuntu the package to install is called 
libreadline-dev or something. SUSE's package manager might have a 
similar package. Alternatively you can skip installing R from source and 
use binary packages that are available in .dev, .rpm etc from CRAN [1]. 
This ensures you have the latest version of R and that upgrading is done 
through the package manager of SUSE, minimizing your work.


cheers,
Paul

[1] http://cran.r-project.org/bin/linux/suse/

fredrick devadoss wrote:

Hello All,

I am new to R and tried to install R in Linux system (OS: Open SUSE). After 
untar the source code, changed the directory, and typed the command 
./configure, it was checking a list...finally it gave an error message. Here 
with i have enclosed the error message.

Check-list goes like this:

checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (/usr/i586-suse-linux/bin/ld) supports shared 
libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... yes
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (/usr/i586-suse-linux/bin/ld) supports 
shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... no
checking readline/history.h presence... no
checking for readline/history.h... no
checking readline/readline.h usability... no
checking readline/readline.h presence... no
checking for readline/readline.h... no
checking for rl_callback_read_char in -lreadline... no
checking for main in -lncurses... yes
checking for rl_callback_read_char in -lreadline... no
checking for history_truncate_file... no
configure: error: --with-readline=yes (default) and headers/libs are not 
available

Can anyone help me in this regard?

Expecting your reply and thanks in advance.

Warm regards
Fredrick.

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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] pdf files in loops

2010-04-01 Thread Paul Hiemstra


James Rome wrote:

On 3/31/2010 10:01 PM, Berwin A Turlach wrote:

G'day James,

On Wed, 31 Mar 2010 21:44:31 -0400
James Rome  wrote:


  
I need to make a bunch of PDF files of histograms. 
  


[...]

  

What am I doing wrong?
  


http://cran.ms.unimelb.edu.au/doc/FAQ/R-FAQ.html#Why-do-lattice_002ftrellis-graphics-not-work_003f

HTH.

Cheers,

Berwin

--
I got it. Thanks. I forgot to assign the graph to a variable. :-(

for( gate in gatelist) {
outfile = paste("../", airport, "/", airport, "taxiHistogram", gate,
".pdf", sep="")
pdf(file = outfile, width = 10, height=8, par(lwd=1))   
title=paste("Taxi time for Arrival Gate", gate, "by Runway at", airport)

gdf = mdf[mdf$ArrivalGate == gate, ]
gdf$tt= gdf$TaxiTime/60   
g = histogram(~(gdf$tt) | gdf$Runway, data=gdf, type="count",

ylab="Count",breaks=20, main=title,
   xlab="taxi time (min)",  par.strip.text=list(cex=0.7))
print(g)
dev.off()   
}


works. Is there a way to make all the plots pages in one pdf file?
  

Hi,

Put the pdf() and the dev.off() outside the loop and the plots will be 
on separate pages in the same pdf file.


pdf()
loop
dev.off()

cheers,
Paul

Thanks,
Jim

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University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] interpolating between lat/long position data with time

2010-04-10 Thread Paul Hiemstra


cbarcelo wrote:

Hello,
I am currently working with satellite tracking data for an organism with
irregularly spaced location data in space and time (point data is
occasionally spaced by 1-10 days). I have 4 columns of data, Lat, Long,
Date, Time. I would like to linearly interpolate my data set so that I have
one position per day with attached time stamps. I am fairly new to R, any
pointers on code for this would be most helpful!
Thanks!
  

Hi,

Take a look at the Spatial Task view, this provides an introduction to 
all kinds spatial data processing in R. In addition, the R-sig-geo 
mailing list is a more suitable list to ask this question, you will 
probably get more response there.


cheers,
Paul

--
Drs. Paul Hiemstra
Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] Adding country boundaries on field map plots

2010-04-11 Thread Paul Hiemstra


zow...@ncst.go.ke wrote:

Hi R users,

What is the command  for adding (or how do we add) country boundaries on 
r-spatial plots. 

Thanks  


ZABLONE OWITI
 GRADUATE STUDENT
Nanjing University of Information, Science and Technology
College of International Education
Add: 219 Ning Liu Rd, Nanjing, Jiangsu, 21004, P.R. China

Website: www.nuist.edu.cn

 


[[alternative HTML version deleted]]

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Hi,

You have to be more specific, in particular you need to provide some 
code that takes us to the step where you would want to add the country 
boundaries. In addition, the r-sig-geo mailing list might be a better 
place to ask this question.


If you use spplot, look at the sp.layout argument.

cheers,
Paul

--
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] using BLAT in r

2010-04-11 Thread Paul Hiemstra


Fahim wrote:

I am trying to use blat in R. I couldn't find any package in CRAN or
bioconductor. I downloaded the windows executable from Jim Kent's (from
ucsc) webpage. I was wondering how to use/call these executables or
functions embedded in these executables. 
I am seeking for some direction or some material that addresses such

problem.
Help appreciated. 
Thanks


-Fahim Mohammad 
cecs, univ of Louisville
  

Hi Fahim,

The easiest way I can see is to use system() to call the executable. 
Probably BLAT uses some text parameter files to specify what it needs to 
do. Write an R function that generates the BLAT parameters files, run 
BLAT and process the result using another function, something like this:


writeParameterfile()
system(blat)
getOutcomes()

Another option, a hard one though, is to link the source code of BLAT 
directly into R. But I think using system is a good alternative.


cheers,
Paul

--
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Department of Physical Geography
Faculty of Geosciences
University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] histogram


Santosh wrote:

Dear R gurus...

How do I control "smoothing" of a density plot in panel.densityplot when
using histogram?

Thanks much,
Santosh

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Hi,

From ?panel.densityplot, argument darg, I was referred to ?density. I 
think the 'bw' argument is what you need. Pass it to panel.densityplot 
in the darg argument.


cheers,
Paul

--
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Department of Physical Geography
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University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] R interactive input like C++


余舟 wrote:

Huhu,

Thank you for all you guys. readline works.

I hope R can be more and more powerful to deal with strings.
  

Strings and power come from regular expressions, check out ?regexpr.

cheers,
Paul

Thank you so much;
Zhou

2010/4/14 Erik Iverson 

  

David Scott wrote:



Erik Iverson wrote:

  

?? wrote:



Thank you for your reply.

My objective is simple. Assume  I have a constant vector, say Vector. in
C++ code, I want to do:


int index;
cout<<"Please enter the index of the element you want to look at Vector
:";
cin>>index
cout<  

Isn't that what the file argument of ?scan says?  I think?

file: the name of a file to read data values from.  If the
  specified file is ‘""’, then input is taken from the keyboard
  (or whatever ‘stdin()’ reads if input is redirected or R is
  embedded).




I think the required function is readline which prompts for user input.

?readline


  

Great, didn't know that one.  The example in ?readline is hilarious.




[[alternative HTML version deleted]]

  



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--
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University of Utrecht
Heidelberglaan 2
P.O. Box 80.115
3508 TC Utrecht
Phone:  +3130 274 3113 Mon-Tue
Phone:  +3130 253 5773 Wed-Fri
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Re: [R] Question about R mode


djack...@miners.utep.edu wrote:

Hello all,

I am using R to perform certain calculations on huge amounts of data.  In short 
I need a function that does the mode function, ie returns the most common 
element.  I looked at the mode function in R but it seems to return the type of 
the data element you give it.  Does such a method exist?  I have tried googling 
this to no avail as all the results lead me back to the mode function I do not 
want.
  

I googled for "R calculate mode", the first hit was this result:

http://www.mail-archive.com/r-help@r-project.org/msg30197.html

this is probably what you want.

cheers,
Paul

Thanks,

Don
 		 	   		  
	[[alternative HTML version deleted]]


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University of Utrecht
Heidelberglaan 2
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Phone:  +3130 253 5773 Wed-Fri
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Re: [R] histogram