Re: [R] OpenOffice ods spreadsheets in R?
David, you are right, I seem not to be able to reproduce the problem with a synthetic file see attached). However, if I run tst<-read.ods(file="test.ods",stringsAsFactors=FALSE) I do not get a data.frame() in tst[[1]], just a vector of the row names: 1> tst[[1]] [1] NA "row1" "row2" "row3" "row4" "row5" I tried to reproduce the "messy" structure of the original file, which is not my fault but how I got the data... Sorry, I can't post the file that actually causes my problems, as it contains all my most important (unpublished) research data... And I don't want to spend hours on finding the exact table lines in many thousands that reproduce the problem, sorry. Anyway, I'll go with the less satisfying solution of exporting all the sheets as .csv (as proposed by Ista and Don, thanks) and see how that goes, just thought there was another solution. Richard, thanks for the tip, I didn't try it, but as far as I can see, it's supposed to run R within OpenOffice? That's not quite what I had in mind, I am using R on different machines and don't want to have to install OpenOffice on each and open it up each time I want to work on the data... Thanks to everyone for the quick and detailed reply! Martin On 10/07/11 02:13, David Winsemius wrote: On Jul 9, 2011, at 8:49 PM, Martin Rittner wrote: I would like to open OpenOffice (LibreOffice) .ods files in R. I've tried the ROpenOffice package from omegahat, but unfortunately, the read.ods() function attempts to use the values of the first column in a worksheet as row names, and thus does not allow duplicates in there (which, even more unfortunately, occur in my files). Also, the function does not allow to forward any other parameters to the called functions, like e.g. row.names=FALSE. Another option read.ods() does not offer is choice of the worksheet(s) to open, but that's a minor issue for me. Now, I could alter the files to fit the function. I could alter the function itself. But before I do any of that, I wanted to ask if someone has a better idea, another approach to ods-files altogether, maybe? I'm not getting the same results as you. Duplicates in the first column do not seem to be causing problems. If you look at the cod for read.ods, you can step through it and modify its behavior to you liking. Perhaps you should post a reproducible example and also the error messages you are getting. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] OpenOffice ods spreadsheets in R?
I would like to open OpenOffice (LibreOffice) .ods files in R. I've tried the ROpenOffice package from omegahat, but unfortunately, the read.ods() function attempts to use the values of the first column in a worksheet as row names, and thus does not allow duplicates in there (which, even more unfortunately, occur in my files). Also, the function does not allow to forward any other parameters to the called functions, like e.g. row.names=FALSE. Another option read.ods() does not offer is choice of the worksheet(s) to open, but that's a minor issue for me. Now, I could alter the files to fit the function. I could alter the function itself. But before I do any of that, I wanted to ask if someone has a better idea, another approach to ods-files altogether, maybe? Thanks, Martin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Reading an ArcGIS raster file
I don't know too much about R myself, but a little about ArcGIS: As far as I know, the .aux files ArcGIS produces do not hold the actual data, but metadata. The actual file should have some other extension (dat, tif, hgz, img, csv... many more), but with rather small datasets the metadata may be larger than the actual data (thanks, ESRI!). As for import of rasterdata in R: I only know of the image() function, which gives an image as tabulated data (which then again may be displayed colourcoded...). I'd be interested in importing rasterfiles (in a defined resolution and scaling) myself (like for plotting rasterfiles on a map), but haven't found a good solution yet (in R, that is)... If you'd have access to ArcGIS, I'd go the other way: let R calculate some rasterdata, import it in the GIS and do the mapping there..? Sorry I can't help you more, I'm rather new to R myself... Martin Juliane Struve wrote: > Dear members, > > How can I read and plot an ArcGIS raster file into R ? The file has extension > .aux and contains floating point bathymetry data. The purpose is to create a > spatial model in R that uses ArcGIS map data. I have managed to read and plot > various shape files into my R project, but I am stuck with this now. I am new > to this list and also to R, so any help would be much appreciated. > > Many thanks and best wishes, > > Juliane > > > > Dr. Juliane Struve > Adjunct Environmental Scientist > Mote Marine Laboratory > Center for Fisheries Enhancement > 1600 Ken Thomson Parkway > Sarasota, Florida, 34236 > (941)388-4441 Ext. 408 > > > > > A Smarter Inbox http://uk.docs.yahoo.com/nowyoucan.html > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Thinking about using two y-scales on your plot?
Richie, A plot of the actual temperature during a year (or thousands of years, as people in palaeoclimate-studies are rather used to) is just so much more intuitive, than some correlation-coefficients or such. I know I'm largely speaking to statisticians in this forum, but in Earth Sciences, most people aren't... I see the use of correlation coefficients and -plots in proofing that an apparent correlation is "real", but the first question upon presenting any statistic analysis is always "What does the DATA look like?". Of course, these plots could be plotted separately with a common x-axis, it's just a matter of saving space and of being used to that kind of graph. I can't imagine anyone being falsely lead to a thought like "oh gosh, the temperature is much higher/bigger/more than the precipitation!" - that makes no sense. I do see the point in graphs where values are plotted together, whose possible interaction with each other might lead to wrong conclusions. Then, it might not be obvious that one is drawing a senseless conclusion. Best regards, Martin Richard Cotton wrote: > > thegeologician wrote: > >> ... very often time-series plots of some values are >> given rather to show the temporal correlation of these, than to show the >> actual numerical values! The same applies for plots of some sample >> values over distance (eg. element concentration over a sample or >> investigation area). In this case one is more interested in whether some >> values change simultaneously, than what the actual values at every point >> are. >> >> In the mentioned plot (see link below), the temporal evolution of the >> mean temperature and of the precipitation over a year is the important >> information. >> >> > > If temporal correlation is what you are interested in, then why not plot > that? If you also care about the evolution of temperature and > precipitation, then these can be plotted on individual graphs, to give three > graphs in total, each with a common x-axis (time), and each showing one > variable of interest on its y-axis. This way the problems of multiple > y-axes are avoided. > > > - > Regards, > Richie. > > Mathematical Sciences Unit > HSL > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Thinking about using two y-scales on your plot?
Hello all, I know I'm not making friends with this, but: I absolutely see the point in dual-(or more!)-y-axis plots! I find them quite informative, and I see them often. In Earth-Sciences (and I very generously include atmospheric sciences here, as Johannes has given an example of a meteorological plot...) very often time-series plots of some values are given rather to show the temporal correlation of these, than to show the actual numerical values! The same applies for plots of some sample values over distance (eg. element concentration over a sample or investigation area). In this case one is more interested in whether some values change simultaneously, than what the actual values at every point are. In the mentioned plot (see link below), the temporal evolution of the mean temperature and of the precipitation over a year is the important information. No-one would get confused or yield wrong conclusions, if the curves would intersect somewhere else, only because of a shift of one y-axis relative to the other!? (which was proposed to be one of the great dangers of dual-scaled axes in the article Hadley posted) On the other hand, you would never express temperature in terms of a percentage of some arbitrary start value, if you could give it just in plain °C!? (as was proposed as a workaround in the article mentioned) An awkward scale like this makes the actual graph much harder to read, not easier, as proposed. Furthermore, since the observed values in Earth Sciences often show a cyclic behavior, the graphs would still cross each other over and over again, no matter what the scale was. So my conclusion for now: I'd answer the Question "are dual-scaled axes in graphs ever the best solution?" with a definitive YES. Maybe only in some specialized applications, but - yes. I strongly expect this discussion to go on (as I've read frequently here that these kind of graphs are considered very "inappropriate"..) and I am happy to learn to do better graphs, if you can show me to be wrong... Greetings, Martin Johannes Hüsing wrote: > I wonder how long it will take until metereologists will see the light. > > http://www.zoolex.org/walter.html > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplot2: bug in geom_ribbon + log scale!?
'works nicely with loging the values. Thank you very much! Keep on the great work, the more I use ggplot2, the more I love it! Greetings, Martin [EMAIL PROTECTED] wrote: > Yes, that's a bug in the current version (fixed in the development > version) - the problem is that the min and max aesthetics aren't being > correctly scaled. You can fix it by explicitly logging those values, > or I can send you the development version off list if you remind me of > your OS. > > Hadley > > On 2/17/08, Martin Rittner <[EMAIL PROTECTED]> wrote: > >> Hi everyone, Hadley, >> >> it seems there's a bug in geom_ribbon() when using it in a log-scaled plot: >> >> d<-data.frame(x=c(1:20),y1=rnorm(20)+3,y2=rnorm(20)+5) >> p<-ggplot() >> p<-p+geom_ribbon(data=d,aes(x=d[["x"]],min=d[["y1"]],max=d[["y2"]])) >> p<-p+geom_line(data=d,aes(x=d[["x"]],y=d[["y1"]]),colour="blue") >> p<-p+geom_line(data=d,aes(x=d[["x"]],y=d[["y2"]]),colour="red") >> p2+scale_y_continuous() >> >> ...gives the plot I want, only with my actual data, I'd need it in >> log-scale: >> >> p2+scale_y_log10() >> >> shifts the ribbon far above the actual data (factor 1000, if I see it >> right, but I haven't tested it with different data to check on that...). >> >> I'm using the latest version of ggplot2 (0.5.7). >> >> Has anyone any suggestions for a workaround/patch? >> >> Many Thanks, Martin >> >> __ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. >> >> > > > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] ggplot2: bug in geom_ribbon + log scale!?
Hi everyone, Hadley, it seems there's a bug in geom_ribbon() when using it in a log-scaled plot: d<-data.frame(x=c(1:20),y1=rnorm(20)+3,y2=rnorm(20)+5) p<-ggplot() p<-p+geom_ribbon(data=d,aes(x=d[["x"]],min=d[["y1"]],max=d[["y2"]])) p<-p+geom_line(data=d,aes(x=d[["x"]],y=d[["y1"]]),colour="blue") p<-p+geom_line(data=d,aes(x=d[["x"]],y=d[["y2"]]),colour="red") p2+scale_y_continuous() ...gives the plot I want, only with my actual data, I'd need it in log-scale: p2+scale_y_log10() shifts the ribbon far above the actual data (factor 1000, if I see it right, but I haven't tested it with different data to check on that...). I'm using the latest version of ggplot2 (0.5.7). Has anyone any suggestions for a workaround/patch? Many Thanks, Martin __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] ggplot2 used in a function - variable scope/environment
Hi Hadley,
that helps perfectly! The actual solution, given my former example, would be
mapping=aes(x=names(da)[1],y=c)
I read about aes_string() sometime, but I didn't realize it was the
solution to this problem... As often, PEBKAC!
Many Thanks!
Martin
hadley wickham wrote:
> Hi Martin,
>
> Two comments:
>
> * ggplot always requires the data to be plotted to be stored in a
> data.frame, not the environment - this makes it possible to (e.g.)
> save self contained plot objects - but that isn't the problem here,
> the problem is setting up the appropriate mapping
>
> * aes_string makes it easier to build up aesthetic mappings
> programmatically - aes_string(x = names(data)[1], y = names(data)[c])
>
> Does that help?
>
> Hadley
>
> On Fri, Feb 15, 2008 at 2:21 PM, Martin Rittner
> <[EMAIL PROTECTED]> wrote:
>> Hi everybody!
>>
>> I'm trying to use ggplot2 to return a plot from a function (so I can add
>> something or alter it then). Unfortunately, if I add a mapping to a
>> layer in the function, the variable *name* is stored in the layer,
>> rather than the variable's *value* - so that after the function returns
>> the ggplot2-object, it doesn't plot because the variable don't exist in
>> the environment calling the function.. e.g:
>>
>> my function does something like:
>>
>> getPlot<-function(da=NULL,...){
>> #1st column holds x-values, others hold data series to plot...
>> co<-as.character(names(da))
>> co<-co[2:length(co)]
>>
>> pl<-ggplot(data=da)
>> pl<-pl+scale_y_log10()+scale_x_continuous()
>> for(c in co){
>>
>> pl<-pl+geom_line(x=da[[1]],y=da[[c]],mapping=aes(x=da[[1]],y=da[[c]]))
>> }
>>
>> return(pl)
>> }
>>
>> I need to add every layer separately, because I want to be able to
>> explicitly define attributes for every data series (colour, size... e.g.
>> highlight only two specific out of 10 series...).
>>
>> Anyway, my problem is this:
>>
>> d<-data.frame(x=seq(0.0,1.0,length=5),y1=rnorm(5),y2=rnorm(5))
>> p<-getPlot(da=d)
>> p
>>
>> returns with
>>
>> Error in data.frame(..., check.names = FALSE) :
>>arguments imply differing number of rows: 0, 5
>>
>> and the plot object contains:
>>
>> Title:
>> Labels: x=, y=
>> ---
>> Data:x, y1, y2 [5x3]
>> Mapping:
>> Scales: y,x -> y,x
>> $margins
>> [1] FALSE
>>
>> $facets
>> [1] ". ~ ."
>>
>> ---
>> geom_line: (colour=black, size=1, linetype=1, x=NA, y=NA) + (x=c(0,
>> 0.25, 0.5, 0.75, 1), y=c(0.180036717548597, -0.369556903134046,
>> -0.924474152821948, -2.40773640658189, 0.801471591443009))
>> stat_sort: (...=) + (x=c(0, 0.25, 0.5, 0.75, 1), y=c(0.180036717548597,
>> -0.369556903134046, -0.924474152821948, -2.40773640658189,
>> 0.801471591443009))
>> position_identity: ()
>> mapping: (x=da[[1]], y=da[[c]])
>>
>> geom_line: (colour=black, size=1, linetype=1, x=NA, y=NA) + (x=c(0,
>> 0.25, 0.5, 0.75, 1), y=c(-1.59744511956184, -0.9333541477049,
>> 1.88697835844878, 0.921829569181679, -0.741077741846118))
>> stat_sort: (...=) + (x=c(0, 0.25, 0.5, 0.75, 1), y=c(-1.59744511956184,
>> -0.9333541477049, 1.88697835844878, 0.921829569181679, -0.741077741846118))
>> position_identity: ()
>> mapping: (x=da[[1]], y=da[[c]])
>>
>> Note the mappings, they refer to "da" and "c" (defined in the function)
>> which are not available in the calling environment. Any Idea how I can
>> avoid the problem/paste the actual values in, like it did for the
>> geometry and the statistics?
>>
>> Thanks, Martin
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] ggplot2 used in a function - variable scope/environment
Hi everybody!
I'm trying to use ggplot2 to return a plot from a function (so I can add
something or alter it then). Unfortunately, if I add a mapping to a
layer in the function, the variable *name* is stored in the layer,
rather than the variable's *value* - so that after the function returns
the ggplot2-object, it doesn't plot because the variable don't exist in
the environment calling the function.. e.g:
my function does something like:
getPlot<-function(da=NULL,...){
#1st column holds x-values, others hold data series to plot...
co<-as.character(names(da))
co<-co[2:length(co)]
pl<-ggplot(data=da)
pl<-pl+scale_y_log10()+scale_x_continuous()
for(c in co){
pl<-pl+geom_line(x=da[[1]],y=da[[c]],mapping=aes(x=da[[1]],y=da[[c]]))
}
return(pl)
}
I need to add every layer separately, because I want to be able to
explicitly define attributes for every data series (colour, size... e.g.
highlight only two specific out of 10 series...).
Anyway, my problem is this:
d<-data.frame(x=seq(0.0,1.0,length=5),y1=rnorm(5),y2=rnorm(5))
p<-getPlot(da=d)
p
returns with
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 0, 5
and the plot object contains:
Title:
Labels: x=, y=
---
Data:x, y1, y2 [5x3]
Mapping:
Scales: y,x -> y,x
$margins
[1] FALSE
$facets
[1] ". ~ ."
---
geom_line: (colour=black, size=1, linetype=1, x=NA, y=NA) + (x=c(0,
0.25, 0.5, 0.75, 1), y=c(0.180036717548597, -0.369556903134046,
-0.924474152821948, -2.40773640658189, 0.801471591443009))
stat_sort: (...=) + (x=c(0, 0.25, 0.5, 0.75, 1), y=c(0.180036717548597,
-0.369556903134046, -0.924474152821948, -2.40773640658189,
0.801471591443009))
position_identity: ()
mapping: (x=da[[1]], y=da[[c]])
geom_line: (colour=black, size=1, linetype=1, x=NA, y=NA) + (x=c(0,
0.25, 0.5, 0.75, 1), y=c(-1.59744511956184, -0.9333541477049,
1.88697835844878, 0.921829569181679, -0.741077741846118))
stat_sort: (...=) + (x=c(0, 0.25, 0.5, 0.75, 1), y=c(-1.59744511956184,
-0.9333541477049, 1.88697835844878, 0.921829569181679, -0.741077741846118))
position_identity: ()
mapping: (x=da[[1]], y=da[[c]])
Note the mappings, they refer to "da" and "c" (defined in the function)
which are not available in the calling environment. Any Idea how I can
avoid the problem/paste the actual values in, like it did for the
geometry and the statistics?
Thanks, Martin
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
