[R] source files in temp environment
Hi all,
I often keep code in separate files for organizational purposes, and
source() that code from higher level scripts. One problem is that those
sourced files often create temporary variables that I don't want to keep
around. I could clean up after myself with lots of rm()'s, but that's a
pain, and is messy.
I'm wondering if one solution might be to source the code in a temporary
environment, assign outputs of interest to the .GlobalEnv with <<-, and
then delete the environment afterwards. One way to do this:
file.r:
temp1 = 1
temp2 = 2
desired_var <<- temp1 + temp2
console:
temp_e = new.env()
source("file.r", local = temp_e)
rm(temp_e)
It's a bit messy to create and delete environments, so I tried what
others have referred to:
source("file.r", local = attach(NULL))
This, however, results in a persistent "NULL" environment in the search
path.
> search()
".GlobalEnv""package:bindrcpp" "NULL"
"tools:rstudio" "package:stats" "package:graphics"
"package:grDevices" "package:utils" "package:datasets"
"package:methods" "Autoloads" "package:base"
Of course, functions are built to encapsulate like this (and do so in
their own temporary environment), but in many cases, turning the sourced
code into functions is possible but clunky.
Any thoughts or suggestions would be much appreciated.
Thanks,
Allie
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Re: [R] To implement OO or not in R package, and if so, how to structure it?
Did you read this? https://cran.r-project.org/doc/contrib/Leisch-CreatingPackages.pdf Maybe it could give you some insight in how to create package. That resource is ~9 years old. There are more modern treatments available. You can read mine at http://r-pkgs.had.co.nz. Hadley Thanks both. I'm reading through your new book now Hadley... thanks for that. I'll probably take a shot at building a class to hold one tree per object, and search for objects of a class (per https://stackoverflow.com/questions/5158830/identify-all-objects-of-given-clas-for-further-processing) to implement collections when necessary... It does seem like there might be niche out there for a resource for folks deciding how to structure their package given what they're trying to provide; i.e. should they construct a collection of functions, or class defs, or... Could well exist already, and I may just have missed it... Thanks, Allie __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] To implement OO or not in R package, and if so, how to structure it?
Hello all, I am trying to decide how to structure an R package. Specifically, do I use OO classes, or just provide functions? If the former, how should I structure the objects in relation to the type of data the package is intended to manage? I have searched for, but haven't found, resources that guide one in the *decision* about whether to implement OO frameworks or not in one's R package. I suspect I should, but the utility of the package would be aided by *collections* of objects. R, however, doesn't seem to implement collections. Background: I am writing an R package that will provide a framework for analyzing structural models of trees (as in trees made of wood, not statistical trees). These models are generated from laser scanning instruments and model fitting algorithms, and hence may have aspects that are data-heavy. Furthermore, coputing metrics based on these structures can be computationally heavy. Finally, as a result, each tree has a number of metrics associated with it (which may be expensive to calculate), along with the underlying data of that tree. It will be important as well to perform calculations across many of these trees, as one would do in a dataframe. This last point is important: if one organizes data across potentially thousands of objects, how easy or hard is it to massage properties of those objects into a dataframe for analysis? Thank you in advance for thoughts and pointers. Allie __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Calculating cumulative lengths of hierarchical topology
Hello All, I need to calculate cumulative lengths along a hierarchical network topology (it's a representation of a tree). I can roll my own, but thought that there might be a package out there that would handle hierarchical network topology functions such as this nicely (and that might bring along other useful functions as well). However, I haven't found one after searching. I did find data.tree, which looks quite interesting, but it carries a large overhead that doesn't seem quite appropriate for the relatively simple structure I'm dealing with. Could anyone point me to such a package if one does exist? Thanks very much, Allie Example of the hierarchical topology: len parent_row daughter_row index_num 1 1.7053 02 1 2 1.1653 13 2 3 1.1980 24 3 4 1.1462 35 4 5 1.1346 46 5 6 1.1024 57 6 ... __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Maximum # of DLLs reached, or, how to clean up after yourself?
Hi Henrik,
Thanks for your reply. I didn't realize that floating DLLs were an
issue (good to know). My query is actually a bit more basic. I'm
actually wondering how folks manage their loading and unloading of
packages when calling scripts within scripts.
Quick example:
Script1:
library(package1)
source("script2.r")
# do stuff reliant on package1
detach("package:package1", unload=TRUE)
Script2:
library(package1)
library(package2)
# do stuff reliant on package1 and package2
detach("package:package1", unload=TRUE)
detach("package:package2", unload=TRUE)
Script2 breaks Script1 by unloading package1 (though unloading package2
is ok). I will have to test whether each package is loaded in Script2
before loading it, and use that list when unloading at the end of the
Script2. *Unless there's a better way to do it* (which is my question -
is there?). I'm possibly just pushing the whole procedural scripting
thing too far, but I also think that this likely isn't uncommon in R.
Any thoughts greatly appreciated!
Thanks,
Allie
On 9/13/2016 7:23 PM, Henrik Bengtsson wrote:
In R.utils (>= 2.4.0), which I hope to submitted to CRAN today or
tomorrow, you can simply call:
R.utils::gcDLLs()
It will look at base::getLoadedDLLs() and its content and compare to
loadedNamespaces() and unregister any "stray" DLLs that remain after
corresponding packages have been unloaded.
Until the new version is on CRAN, you can install it via
source("http://callr.org/install#HenrikBengtsson/R.utils@develop";)
or alternatively just source() the source file:
source("https://raw.githubusercontent.com/HenrikBengtsson/R.utils/develop/R/gcDLLs.R";)
DISCUSSION:
(this might be better suited for R-devel; feel free to move it there)
As far as I understand the problem, running into this error / limit is
_not_ the fault of the user. Instead, I'd argue that it is the
responsibility of package developers to make sure to unregister any
registered DLLs of theirs when the package is unloaded. A developer
can do this by adding the following to their package:
.onUnload <- function(libpath) {
library.dynam.unload(utils::packageName(), libpath)
}
That should be all - then the DLL will be unloaded as soon as the
package is unloaded.
I would like to suggest that 'R CMD check' would include a check that
asserts when a package is unloaded it does not leave any registered
DLLs behind, e.g.
* checking whether the namespace can be unloaded cleanly ... WARNING
Unloading the namespace does not unload DLL
* checking loading without being on the library search path ... OK
For further details on my thoughts on this, see
https://github.com/HenrikBengtsson/Wishlist-for-R/issues/29.
Hope this helps
Henrik
On Tue, Sep 13, 2016 at 6:05 AM, Alexander Shenkin wrote:
Hello all,
I have a number of analyses that call bunches of sub-scripts, and in the
end, I get the "maximal number of DLLs reached" error. This has been asked
before (e.g.
http://stackoverflow.com/questions/36974206/r-maximal-number-of-dlls-reached),
and the general answer is, "just clean up after yourself".
Assuming there are no plans to raise this 100-DLL limit in the near future,
my question becomes, what is best practice for cleaning up (detaching)
loaded packages in scripts, when those scripts are sometimes called from
other scripts? One can detach all packages at the end of a script that were
loaded at the beginning of the script. However, if a package is required in
a calling script, one should really make sure it hadn't been loaded prior to
sub-script invocation before detaching it.
I could write a custom function that pushes and pops package names from a
global list, in order to keep track, but maybe there's a better way out
there...
Thanks for any thoughts.
Allie
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[R] Maximum # of DLLs reached, or, how to clean up after yourself?
Hello all, I have a number of analyses that call bunches of sub-scripts, and in the end, I get the "maximal number of DLLs reached" error. This has been asked before (e.g. http://stackoverflow.com/questions/36974206/r-maximal-number-of-dlls-reached), and the general answer is, "just clean up after yourself". Assuming there are no plans to raise this 100-DLL limit in the near future, my question becomes, what is best practice for cleaning up (detaching) loaded packages in scripts, when those scripts are sometimes called from other scripts? One can detach all packages at the end of a script that were loaded at the beginning of the script. However, if a package is required in a calling script, one should really make sure it hadn't been loaded prior to sub-script invocation before detaching it. I could write a custom function that pushes and pops package names from a global list, in order to keep track, but maybe there's a better way out there... Thanks for any thoughts. Allie __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Factors in nlme: singularity in backsolve error
Hello all,
I tried posting on r-sig-ME, but it's not going through. So I thought I
would try here. Apologies if this ends up being a cross-post if it
eventually goes through there
I am parameterizing exponential fits for some metabolic scaling models.
I have done this in lmer already, without problem, using logged
dependent and independent variables. However, I would now like to
incorporate other parameters that aren't necessarily exponentially
related to the dependent variable. Hence, I've turned to nlme, but I
don't have much experience with it. Apologies in advance for newbie
mistakes.
With the code below, I am getting the following error. I'm guessing
that it has something to do with the 'site' factor being misspecified:
Error in nlme.formula(dep ~ scaling_fun(alpha, beta, ind, site), data =
scale_df, :
Singularity in backsolve at level 0, block 1
When I fit a simpler function that does not involve 'site', the model
seems to work correctly.
Any thoughts would be greatly appreciated! I've added the dput object
at the bottom of the email to avoid distraction...
Thanks,
Allie
> head(scale_df)
depind spp site
2 0.28069471 -0.0322841 157A
3 -0.69719050 -1.2568901 183A
4 0.29252012 0.1592420 246A
5 0.72030740 -0.3282789 154A
6 -0.08601891 0.3623756 110A
7 0.30793594 0.2230840 154A
scaling_fun <- function(alpha, beta, ind, site) {
return(beta + ind^alpha + site*(ind^alpha))
}
# results in singularity in backsolve error
nlme(dep ~ trait_scaling_fun(alpha, beta, ind, site),
data = scale_df,
fixed = list(alpha + beta + site ~ 1), random = alpha ~ 1|spp,
start = list(fixed = c(0.7, 0, 1)))
##
# simpler function converges #
##
scaling_fun <- function(alpha, beta, ind) {
return(beta + ind^alpha)
}
nlme(dep ~ scaling_fun(alpha, beta, ind),
data = scale_df,
fixed = list(alpha + beta ~ 1), random = alpha ~ 1|spp,
start = list(fixed = c(0.7, 0)))
# dput for data
scale_df = structure(list(dep = structure(c(0.280694709349609,
-0.697190504779316,
0.29252012378561, 0.720307403285465, -0.0860189064012942, 0.307935942585907,
0.862281389721553, -0.265859454130292, -0.662753116661401,
-0.281590648203109,
1.17791119955669, 0.631729125553481, -0.556750637034717, -0.43297610538,
0.78495323332528, 0.355622302250686, -1.26351337875593, 0.343598303486811,
-1.17350365646135, 0.660405635460007, -0.0444581036277384,
0.722773887452235,
-0.0522058979055465, 0.65594868736652, -0.471798559774723,
0.580581816047275,
0.514408011465886, -0.736138172672309, 0.70774857676606,
-0.0810467855114514,
2.87816317587089, -0.22475032263, -0.497119013269447, 0.031618943500335,
1.93466683745019, 1.0320275291612, 0.874248439252774, -0.327339718896358,
-0.854016320390115, -1.14806351731618, -0.380316794335449,
0.298626272822636,
-0.600084009068698, 0.836832381353764, -1.02141473458357,
-0.0626961141428343,
-1.28013982373819, -0.126310567347687, -0.998914167194147,
-0.966356030272785,
-0.0311625866367497, -0.456212263484603, 2.22345644904786, 1.06808914728274,
2.04676618838053, 2.57057502230498, -1.1354565673953, -0.617861267279932,
-1.29433182429494, 0.0191424880072437, -0.31539529665173,
-0.161941249027648,
-0.582100497448459, 1.62041284412996, 4.12468548155128, 0.181382553309611,
0.395970527486673, 0.949165316445473, 0.536508784640814, 1.88628468601066,
0.460108411105217, 1.50237201805536, -0.248693954731227, 0.604338152411222,
-0.511271387322619, -0.273625967472597, 2.54906943158448, 1.25797640582933,
-0.615499666866161, -0.83022966646613, -0.569798846726899, 1.41607035018281,
0.806876783115155, 3.03500743372039, 0.371311069097266, 0.605523223251687,
0.960528362908707, 0.536545286280021, -1.07783545300095, 0.145069857506269,
-0.390394315762374, -0.524314770428875, -0.205267560118326, 2.8197556390129,
0.548519073742583, 2.25991992849428, -0.274997856331803, -0.748248845217783,
1.27303941400619, 0.23884797601163, -0.582228991340883, -0.380185805876727,
-0.0858712197617979, -0.181441660791883, -0.122600427784157,
1.44111920784939, 0.163470634515893, -0.322754741867578, -1.08355296391174,
-0.27943230825155, -0.367498411981987, -1.25029544932326, 1.96800896885018,
0.741382953698137, 0.525448033325593, 0.58486584900894, -1.39293857038504,
0.0401527810688047, -0.428292900882259, -0.384773565802791,
-0.347537789997483,
0.259461537066455, 1.04953062690743, 0.905652281045827, 0.921052829745329,
0.52450347921673, 1.71595979136317, -0.474652211889487, 0.986966207710898,
-0.256654313404628, 2.99291703386829, -0.874752003654369, 1.01178420482112,
5.77381325416311, -0.167933435302975, -0.746365585369451, 2.80467857407177,
1.95866740218257, -0.503053147492697, -0.0160574809046825,
0.0121332489691898,
0.155574669334708, 0.916506565829058, -0.448074058381429, 0.316834873904141,
1.04981848557227, -0.824609748750358, 1.06744876285501, 0.063863664699137,
-
[R] remove fixed effect in predict.merMod
Hello all,
I've run a model, and now would like to extract residuals. However, I
have set sum-to-zero contrasts for the categorical fixed effect
(contr.sum). Because I am interested in looking at the variation in the
residuals associated with that fixed effect (along with other levels), I
need to calculate residuals setting that fixed effect to zero. Any
thoughts on how to do this?
thanks,
allie
contr.sum.keepnames <- function(...) {
# make deviation contrasts that don't lose the names of the factors
in the model results
# from
https://stackoverflow.com/questions/10808853/why-does-changing-contrast-type-change-row-labels-in-r-lm-summary
conS <- contr.sum(...)
colnames(conS) = rownames(conS)[-length(rownames(conS))]
conS
}
test_df = data.frame(site = rep(LETTERS[1:10], 10), resp = runif(100),
pred = runif(100))
contrasts(test_df$site) = contr.sum.keepnames(levels(test_df$site))
mod = lmer(resp ~ (1 + pred|site) + pred, data = test_df)
residuals = test_df$resp - predict(mod, REform=NA) # I would like the
site effect here to be set to zero
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Re: [R] Fit a smooth closed shape through 4 points
Thanks for your reply, Charles. spline() doesn't seem to fit a closed
shape; rather, it's producing a parabola. Perhaps I'm missing an
argument I should include?
grid.xspline() seems to get close to what I need, but it returns a grob
object - not sure how to work with those as shapes per se.
My goal is to produce a 2D shape from which I can calculate area,
average widths, and other such things. The context is that we have
measured tree crowns in a manner that has produced 4 points such as
these from two offset axes. We want to use the resulting shapes for our
calculations.
(incidentally, my original points were off - here are the correct ones)
shapepoints = structure(list(x = c(8.9, 0, -7.7, 0, 8.9), y = c(0, 2, 0,
-3.8,
0)), .Names = c("x", "y"), row.names = c(NA, -5L), class = "data.frame")
plot(spline(shapepoints))
Thanks,
Allie
On 3/21/2016 1:10 PM, Charles Determan wrote:
Hi Allie,
What is you goal here? Do you just want to plot a curve to the data?
Do you want a function to approximate the data?
You may find the functions spline() and splinefun() useful.
Quick point though, with so few points you are only going to get a very
rough approximation no matter the method used.
Regards,
Charles
On Mon, Mar 21, 2016 at 7:59 AM, Alexander Shenkin mailto:ashen...@ufl.edu>> wrote:
Hello all,
I have sets of 4 x/y points through which I would like to fit
closed, smoothed shapes that go through those 4 points exactly.
smooth.spline doesn't like my data, since there are only 3 unique x
points, and even then, i'm not sure smooth.spline likes making
closed shapes.
Might anyone else have suggestions for fitting algorithms I could
employ?
Thanks,
Allie
shapepoints = structure(c(8.9, 0, -7.7, 0, 0, 2, 0, 3.8), .Dim = c(4L,
2L), .Dimnames = list(NULL, c("x", "y")))
smooth.spline(shapepoints)
# repeat the first point to close the shape
shapepoints = rbind(shapepoints, shapepoints[1,])
smooth.spline(shapepoints)
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[R] Fit a smooth closed shape through 4 points
Hello all,
I have sets of 4 x/y points through which I would like to fit closed,
smoothed shapes that go through those 4 points exactly. smooth.spline
doesn't like my data, since there are only 3 unique x points, and even
then, i'm not sure smooth.spline likes making closed shapes.
Might anyone else have suggestions for fitting algorithms I could employ?
Thanks,
Allie
shapepoints = structure(c(8.9, 0, -7.7, 0, 0, 2, 0, 3.8), .Dim = c(4L,
2L), .Dimnames = list(NULL, c("x", "y")))
smooth.spline(shapepoints)
# repeat the first point to close the shape
shapepoints = rbind(shapepoints, shapepoints[1,])
smooth.spline(shapepoints)
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[R] ggplot: geom_bar not respecting factor order when stacking
Hi all,
ggplot2 (v2.0.0) does not seem to respect factor order when stacking
bars in geom_bar().
##
> dput(temp)
structure(list(phylo_sig = c(0.148740270638472, 0.148740270638472,
0.148740270638472, 0.148740270638472, 0.148740270638472), trait =
c("p_corrected_percent",
"p_corrected_percent", "p_corrected_percent", "p_corrected_percent",
"p_corrected_percent"), value = c(0.031015586683513, 0.0553330412480036,
0.73674222087599, 0.114517508485538, 0.0623916427069555), varlevel =
structure(c(3L,
2L, 4L, 5L, 1L), .Label = c("species", "genus", "family", "plot_code",
"Residual"), class = "factor")), .Names = c("phylo_sig", "trait",
"value", "varlevel"), row.names = c(28L, 62L, 96L, 130L, 164L
), class = "data.frame")
> str(temp)
'data.frame':5 obs. of 4 variables:
$ phylo_sig: num 0.149 0.149 0.149 0.149 0.149
$ trait: chr "p_corrected_percent" "p_corrected_percent"
"p_corrected_percent" "p_corrected_percent" ...
$ value: num 0.031 0.0553 0.7367 0.1145 0.0624
$ varlevel : Factor w/ 5 levels "species","genus",..: 3 2 4 5 1
> ggplot(temp, aes(x=trait, y = value)) + geom_bar(stat = "identity",
aes(fill=varlevel, order = varlevel))
##
The code above results in the correct legend order, but incorrect order
of stacking (https://i.imgur.com/lgAxTFh.png). I have to change the
order of the actual dataframe rows in order to coerce the stacking to work:
##
> temp = temp[c(5,2,1,3,4),]
> ggplot(temp, aes(x=trait, y = value)) + geom_bar(stat = "identity",
aes(fill=varlevel, order = varlevel))
##
This results in correct stacking (https://i.imgur.com/baww43x.png). Any
assistance in getting ggplot to pay attention to the factor ordering
when stacking bars would be much appreciated!
Thanks,
Allie
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[R] apply function across dataframe columns for non-exclusive groups
Hello all, I've been banging my head over what must be a simple solution. I would like to apply a function across columns of a dataframe for rows grouped across different columns. These groups are not exclusive. See below for an example. Happy to use dplyr, data.table, or whatever. Any guidance appreciated! Thanks, Allie desired algorithm: calculate a/(a+b) for each TRUE and FALSE grouping of columns grp1 and grp2. this_df = data.frame(a = c(1,2,3,4,5), b = c(7,8,9,10,11), grp1 = c(T,T,F,F,F), grp2 = c(F,T,F,T,F)) desired output (doesn't have to be exactly this format, but something along these lines): grp1 T 0.166 grp1 F 0.286 grp2 T 0.25 grp2 F 0.25 __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] Quantifying widths of polygons
Hello all, I am working with data on tree crowns, and this data describes points (verticies) around the polyhedron of the crown volume (think of the crown as a single volume with vertices and faces). I can calculate maximum z distance between any 2 points (maximum depth) and maximum x/y distance (maximum width). These are useful metrics. I would also like to quantify an "average" width of the polygon in 2D space (x/y only), as well as a metric that would describe the "eccentricity" of the polygon. But, I'm not sure how to go about doing that. In general, I've made the polyhedrons and polygons into convex shapes. I have considered getting a centroid, intersecting lines every 10 degrees (for example) going through the centroid with the x/y polygon owin in spatstat, and then analyzing those line lengths. But, I'm not sure that's the right way to go, and maybe there are already tools out there to do this. Any thoughts anyone might have would be very welcome! Thanks, Allie library(rgl) library(spatstat) library(geometry) x = c(1.9,-1.4,1.5,1.8,2.2,0.2,0.6,-0.9,-3.7,1.3,-1.9,-3.4,3.7,2.1,-2.0,-1.9) y = c(-3.1,3.0,1.1,-1.3,1.0,0.0,1.4,1.6,2.3,-3.6,-1.5,-1.3,0.3,-2.1,0.2,-0.3) z = c(5.5,4.5,4.3,4.8,6.7,5.8,7.4,6.2,3.5,2.9,4.0,3.7,3.2,3.0,3.1,8.4) depth = max(z) - min(z) width_max = max(dist(matrix(c(x,y),ncol=2))) xy_win = owin(poly=list(x=x,y=y)) conv_win = convexhull(xy_win) # from here, maybe draw lines every 10 degrees through a centroid? # avg_width = ?? # eccentricity = ?? # 3D plot of crown polyhedron (convex) ps = data.frame(x=x,y=y,z=z) crown.surf = t(convhulln(matrix(c(x,y,z),ncol=3))) open3d() rgl.triangles(ps[crown.surf,1],ps[crown.surf,2],ps[crown.surf,3],col=heat.colors(nrow(ps)),alpha=.2) axes3d() __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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] return named list from foreach
Hello all,
I've been trying to figure out how to return a named list from foreach.
Given that the order of the returned list is guaranteed to be in the
order in which the object is passed to foreach, list members can be
named afterwards. However, I'm wondering if there's a better way to do
it, perhaps with some sort of combine function?
library(doParallel)
library(foreach)
cl <- makeCluster(4)
registerDoParallel(cl)
df = data.frame(nm = letters[11:20], a = 1:10, b=11:20)
out = foreach(i=1:nrow(df)) %dopar% {
a = list(j = sqrt(df[i,]$a), k = sqrt(df[i,]$b))
a
}
How do I name the elements of "out" using the corresponding values df$nm?
thanks,
allie
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[R] expected arguments for rgl.triangles
Hello all, I have a set of points in 3D space that represent vertices of a non-convex polyhedron. I would like to plot this polyhedron, and have been trying to do so with rgl.triangles, but to no avail. I imagine I don't understand what rgl.triangles expects for arguments. I have constructed the triangles myself, and have the three vertices of each triangle. I am then passing these to rgl.triangles in the x,y & z arguments. I end up with unexpected results (see http://i.imgur.com/BaKfzn7.png). Might someone advise me about the structure of arguments that rgl.triangles expects (or perhaps a better way to go about this)? ?rgl.triangles doesn't help much with this particular issue... Thanks, Allie The code, where rows 2,3,4 are one triangle, 5,6,7 the next, etc (apologies - don't know how to serialize a dataframe to make it easy to suck into one's environment): rgl.triangles(tri_df[,1],tri_df[,2],tri_df[,3],col=heat.colors(nrow(tri_df)),alpha=.2) > tri_df x y z 2 -2.9970624 -0.1327280 8.0 3 -1.3358202 3.8762849 4.9 4 3.5380065 0.6652143 9.1 5 -1.3358202 3.8762849 4.9 6 1.4644874 3.6145922 5.3 7 3.5380065 0.6652143 9.1 8 1.4644874 3.6145922 5.3 9 1.9606671 -3.8269811 4.5 10 3.5380065 0.6652143 9.1 11 1.9606671 -3.8269811 4.5 12 -3.5337687 3.6772923 3.9 13 3.5380065 0.6652143 9.1 14 -3.5337687 3.6772923 3.9 15 -5.6586500 1.2726665 3.5 16 3.5380065 0.6652143 9.1 17 -5.6586500 1.2726665 3.5 18 3.8327817 -2.8895994 3.4 19 3.5380065 0.6652143 9.1 20 3.8327817 -2.8895994 3.4 21 6.0806691 -0.4852461 2.2 22 3.5380065 0.6652143 9.1 23 6.0806691 -0.4852461 2.2 24 -0.5109254 -6.7807784 0.5 25 3.5380065 0.6652143 9.1 26 -0.5109254 -6.7807784 0.5 27 2.3503422 -6.2742244 1.8 28 3.5380065 0.6652143 9.1 29 2.3503422 -6.2742244 1.8 30 5.4741865 -1.1803740 0.3 31 3.5380065 0.6652143 9.1 32 5.4741865 -1.1803740 0.3 33 5.712 -0.3589635 2.7 34 3.5380065 0.6652143 9.1 35 5.712 -0.3589635 2.7 36 -3.1939122 -2.4080958 5.4 37 3.5380065 0.6652143 9.1 38 -3.1939122 -2.4080958 5.4 39 -1.4732303 -3.9331403 4.9 40 3.5380065 0.6652143 9.1 41 -1.4732303 -3.9331403 4.9 42 -3.4863074 0.3092904 6.8 43 3.5380065 0.6652143 9.1 44 -3.4863074 0.3092904 6.8 45 0.8019969 -2.2620347 7.2 46 3.5380065 0.6652143 9.1 47 0.8019969 -2.2620347 7.2 48 -2.9970624 -0.1327280 8.0 49 3.5380065 0.6652143 9.1 50 -1.3358202 3.8762849 4.9 51 -2.9970624 -0.1327280 8.0 52 6.4508128 -2.4488802 0.3 53 1.4644874 3.6145922 5.3 54 -1.3358202 3.8762849 4.9 55 6.4508128 -2.4488802 0.3 56 1.9606671 -3.8269811 4.5 57 1.4644874 3.6145922 5.3 58 6.4508128 -2.4488802 0.3 59 -3.5337687 3.6772923 3.9 60 1.9606671 -3.8269811 4.5 61 6.4508128 -2.4488802 0.3 62 -5.6586500 1.2726665 3.5 63 -3.5337687 3.6772923 3.9 64 6.4508128 -2.4488802 0.3 65 3.8327817 -2.8895994 3.4 66 -5.6586500 1.2726665 3.5 67 6.4508128 -2.4488802 0.3 68 6.0806691 -0.4852461 2.2 69 3.8327817 -2.8895994 3.4 70 6.4508128 -2.4488802 0.3 71 -0.5109254 -6.7807784 0.5 72 6.0806691 -0.4852461 2.2 73 6.4508128 -2.4488802 0.3 74 2.3503422 -6.2742244 1.8 75 -0.5109254 -6.7807784 0.5 76 6.4508128 -2.4488802 0.3 77 5.4741865 -1.1803740 0.3 78 2.3503422 -6.2742244 1.8 79 6.4508128 -2.4488802 0.3 80 5.712 -0.3589635 2.7 81 5.4741865 -1.1803740 0.3 82 6.4508128 -2.4488802 0.3 83 -3.1939122 -2.4080958 5.4 84 5.712 -0.3589635 2.7 85 6.4508128 -2.4488802 0.3 86 -1.4732303 -3.9331403 4.9 87 -3.1939122 -2.4080958 5.4 88 6.4508128 -2.4488802 0.3 89 -3.4863074 0.3092904 6.8 90 -1.4732303 -3.9331403 4.9 91 6.4508128 -2.4488802 0.3 92 0.8019969 -2.2620347 7.2 93 -3.4863074 0.3092904 6.8 94 6.4508128 -2.4488802 0.3 95 -2.9970624 -0.1327280 8.0 96 0.8019969 -2.2620347 7.2 97 6.4508128 -2.4488802 0.3 __ 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] dimensions of polyhedrons
Hello all, I have sets of points in (x,y,z) that represent polyhedron vertices (actually tree crowns). I have used convhulln to estimate volumes (the shapes are not necessarily convex, but good enough for now). Now I would like to extract various dimensions of these shapes - horizontal width (max, mean), vertical depth (max, mean), and other metrics. Are there any packages/tools in R that might help me do this? A look around didn't come up with anything. Thanks in advance, Allie __ 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] How to define and calculate volume of 3D polygon?
Hi Folks, I have a set of x,y,z points in 3D space that defines the outline of a tree crown (5 - 15 perimeter points + 1 top & bottom point). I would like to calculate the volume of the corresponding 3D polygon based on those points. I have been able to use geometry::convhulln, but I think this isn't the right algorithm, since the polygon needs to pass through each point in order, and not just snap a rubber-band around the outer points. Any suggestions for alternative algorithms and packages would be most welcome! Thanks, Allie seq x yz 11 -1.7310065 2.4502278 11.1 22 -1.9048260 -0.6096212 9.0 33 2.8652209 0.8891057 11.0 44 2.3929514 -3.4516349 11.2 55 -2.6436343 5.2745803 11.7 66 -4.3521504 4.6924180 11.7 77 6.1441732 -4.8051156 11.6 88 -6.2157823 -3.2193244 8.0 99 1.0024961 -2.8275434 9.0 10 10 -3.9656821 3.0452201 8.0 11 11 4.2070518 -1.5970958 11.0 12 12 -0.9461915 1.2902409 9.8 13 13 2.2792265 0.7517491 11.4 __ 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] Finding files matching full path regex
Hi folks, I'm interested in finding files by matching both filenames and directories via regex. If I have: dir1_pat1/file1.csv dir2_pat1/file2.csv dir2_pat1/file3.txt dir3_pat2/file4.csv I would like to find, for example, all csv files in directories that have "pat1" in their name: dir1_pat1/file1.csv dir2_pat1/file2.csv > list.files(path = ".", pattern = ".*pat1/.*\\.csv", recursive = T) character(0) > list.files(path = ".", pattern = ".*pat1/.*\\.csv", recursive = T, full.names=T) character(0) > list.files(path = ".", pattern = ".*\\.csv", recursive = T, full.names=T) [1] "./dir1_pat1/file1.csv" "./dir2_pat1/file2.csv" "./dir3_pat2/file4.csv" > list.files(path = ".", pattern = "pat1", recursive = T, full.names=T) character(0) I think list.files just runs the regex pattern against the file names, not the full path. I tried full.names=T, but it still matches against the file name only. Suggestions are greatly appreciated. Thank you, Allie [[alternative HTML version deleted]] __ 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] How to vectorize plot graphic?
Thanks Jeff. I'm not sure to which manual you are referring. Nothing like what you mention is found here: http://cran.r-project.org/manuals.html . Perhaps you're referring to The Data Import/Export Manual, but that wouldn't make sense. Googling "R Input/Output manual" doesn't help. Regarding the device, I'm in R-Studio, plotting to the standard device there (I suppose). In any case, I'm not totally sure what the interface between R-Studio's plot window and the R instance is. I think that, as you say, what I'm getting is as expected. I zoom and the plot zooms as expected. So, I guess that part is solved. However, the writing to .wmf as a bitmap instead of a vector is still a mystery to me. Thanks, Allie On 12/1/2013 12:29 PM, Jeff Newmiller wrote: > You have mentioned nothing about the device you are writing the plot to. If > to the default and you are copying it from there as a bitmap, then what you > are describing sounds as expected. Read the R Input/Output manual (again) for > other output options. > --- > Jeff NewmillerThe . . Go Live... > DCN:Basics: ##.#. ##.#. Live Go... > Live: OO#.. Dead: OO#.. Playing > Research Engineer (Solar/BatteriesO.O#. #.O#. with > /Software/Embedded Controllers) .OO#. .OO#. rocks...1k > ----------- > Sent from my phone. Please excuse my brevity. > > Alexander Shenkin wrote: >> Hi Folks, >> >> Using ggplot, I've produced the following graphic: >> http://i.imgur.com/39a139C.png >> >> The graphics in the plot seem to be bitmapped and not vectorized. That >> is, the vertical and horizontal lines jump rows of pixels instead of >> having just nice, angled lines. Any thoughts about how to get these >> graphics vectorized? Or am I misunderstanding something? >> >> Another example: >> >> The code: >> >>require(ggplot2) >> df = data.frame(x = c(1:360), y = sin(seq(0,2*pi*3,length.out = 360))) >>ggplot(df, aes(x=x, y=y)) + geom_line() >> >> produces http://i.imgur.com/mjjSKih.png >> >> Perhaps what I'm dealing with here is my screen resolution. However, I >> use ggsave() to save .wmf files, and those also turn out to be bitmaps >> and not vectors. >> >> Thanks, >> Allie >> >> [[alternative HTML version deleted]] >> >> __ >> 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] How to vectorize plot graphic?
Thanks Carl. Yeah, I can get vectorized graphics out via
ggsave("temp.pdf") too. But I need to add the graphic to a word doc on
windows. Hence the desire to use wmf, which should induce a vector
format (shouldn't it?).
On 12/1/2013 10:39 AM, Carl Witthoft wrote:
> Off the top of my head, I'd suggest trying ggsave() with the extension
> ".svg" . I realize that SVG files are not recognized by some image display
> apps (Microsoft Windows I'm looking at YOU), but IMHO it's the best choice
> for vectorized images.
>
>
> Alexander Shenkin wrote
>> Hi Folks,
>>
>> Using ggplot, I've produced the following graphic:
>> http://i.imgur.com/39a139C.png
>>
>> The graphics in the plot seem to be bitmapped and not vectorized. That
>> is, the vertical and horizontal lines jump rows of pixels instead of
>> having just nice, angled lines. Any thoughts about how to get these
>> graphics vectorized? Or am I misunderstanding something?
>>
>> Another example:
>>
>> The code:
>>
>> require(ggplot2)
>> df = data.frame(x = c(1:360), y = sin(seq(0,2*pi*3,length.out = 360)))
>> ggplot(df, aes(x=x, y=y)) + geom_line()
>>
>> produces http://i.imgur.com/mjjSKih.png
>>
>> Perhaps what I'm dealing with here is my screen resolution. However, I
>> use ggsave() to save .wmf files, and those also turn out to be bitmaps
>> and not vectors.
>>
>> Thanks,
>> Allie
>>
>> [[alternative HTML version deleted]]
>>
>> __
>
>> R-help@
>
>> 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.
>
>
>
>
>
> --
> View this message in context:
> http://r.789695.n4.nabble.com/How-to-vectorize-plot-graphic-tp4681424p4681427.html
> Sent from the R help mailing list archive at Nabble.com.
>
> __
> 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.
>
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] How to vectorize plot graphic?
Hi Folks, Using ggplot, I've produced the following graphic: http://i.imgur.com/39a139C.png The graphics in the plot seem to be bitmapped and not vectorized. That is, the vertical and horizontal lines jump rows of pixels instead of having just nice, angled lines. Any thoughts about how to get these graphics vectorized? Or am I misunderstanding something? Another example: The code: require(ggplot2) df = data.frame(x = c(1:360), y = sin(seq(0,2*pi*3,length.out = 360))) ggplot(df, aes(x=x, y=y)) + geom_line() produces http://i.imgur.com/mjjSKih.png Perhaps what I'm dealing with here is my screen resolution. However, I use ggsave() to save .wmf files, and those also turn out to be bitmaps and not vectors. Thanks, Allie [[alternative HTML version deleted]] __ 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] devtools: rtools not compatible with 3.0.1
Hi Folks, I'm trying to load devtools in R 3.0.1 in order to run the dev version of lme4. I've updated devtools, and just installed Rtools30.exe. However, I get the following warning (in R-Studio, RGui, and R.exe, both x64 and i386): - WARNING: Rtools is required to build R packages, but no version of Rtools compatible with R 3.0.1 was found. (Only the following incompatible version(s) of Rtools were found:3.0) Please download and install the appropriate version of Rtools from http://cran.r-project.org/bin/windows/Rtools/ and then run find_rtools(). - Any ideas? Rtools30.exe is the most recent that I can find. Thanks, Allie R 3.0.1 Win 7 Pro x64 SP1 __ 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] exporting tables to word
Thanks Carlos,
ftable has some internal routines, it seems, that allow it to print out
a flat contigency table in a nice format. Converting to data.frame ends
up messing up the display format, unfortunately.
thanks,
allie
On 4/2/2013 12:41 PM, Carlos Valenzuela wrote:
> You may also want to consider the "rtf" package. It works okay. You would
> have to save your results as a dataframe and you would be able to write
> that object out to an .rtf (or even use an .doc extension, as I have seen
> it done).
>
> For example,
>
> library(rtf)
>
> # Your regression formula
> lmobj<-lm(dv~iv1 + iv2 + iv3, data=dat)
>
> lmresults<-as.data.frame(summary(lmobj)$coefficients)
>
> # Output location for .rtf file
> output<-"filepath/nameoffile.rtf"
>
> # Specify the width, height, font size, etc and margins
> rtfdoc<-RTF(output,width=8.5,height=11,font.size=10,omi=c(1,1,1,1))
>
> addHeader(rtf,title="Title of Table, subtitle="Subtitle")
> addTable(rtfdoc, lmresults, font.size=10, row.names=T, NA.string="-")
> done(rtf)
>
> This is a very crude example so I would suggest looking at the help files
> associated with the "rtf" package to make any modifications, such as adding
> other regression results/tables.
>
> Thanks and hope this helps,
>
> Carlos
>
>
> On Tue, Apr 2, 2013 at 12:13 PM, Alexander Shenkin wrote:
>
>> Thanks Frans,
>>
>> odfTable seems not to like ftable objects. any thoughts?
>>
>> Error: chunk 1 (label = damageTable)
>> Error in UseMethod("odfTable") :
>> no applicable method for 'odfTable' applied to an object of class
>> "ftable"
>>
>>
>> thanks,
>> allie
>>
>> On 4/2/2013 8:09 AM, Frans Marcelissen wrote:
>>> Hi Allie,
>>> My preferred method is by means of odfWeave. Odfweave generates a
>>> libreoffice file, which can directly be transferred to word.
>>> A second way is run R from within spss. Spss has a much better output
>> than
>>> R, but you can use the output system of spss (by means of
>>> spsspivottable.Display())
>>> Frans
>>>
>>>
>>> 2013/4/2 Alexander Shenkin
>>>
>>>> Hello all,
>>>>
>>>> What is your preferred method to export tables (from ftable()) to Word?
>>>> Do you just export to a text file and then copy/paste? Or perhaps via
>>>> HTML output?
>>>>
>>>> Thanks,
>>>> Allie
>>>>
>>>> __
>>>> 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.
>>>>
>>
>> [[alternative HTML version deleted]]
>>
>> __
>> 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.
>>
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] exporting tables to word
Thanks Frans,
odfTable seems not to like ftable objects. any thoughts?
Error: chunk 1 (label = damageTable)
Error in UseMethod("odfTable") :
no applicable method for 'odfTable' applied to an object of class "ftable"
thanks,
allie
On 4/2/2013 8:09 AM, Frans Marcelissen wrote:
> Hi Allie,
> My preferred method is by means of odfWeave. Odfweave generates a
> libreoffice file, which can directly be transferred to word.
> A second way is run R from within spss. Spss has a much better output than
> R, but you can use the output system of spss (by means of
> spsspivottable.Display())
> Frans
>
>
> 2013/4/2 Alexander Shenkin
>
>> Hello all,
>>
>> What is your preferred method to export tables (from ftable()) to Word?
>> Do you just export to a text file and then copy/paste? Or perhaps via
>> HTML output?
>>
>> Thanks,
>> Allie
>>
>> __
>> 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.
>>
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] exporting tables to word
Hello all, What is your preferred method to export tables (from ftable()) to Word? Do you just export to a text file and then copy/paste? Or perhaps via HTML output? Thanks, Allie __ 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] summarize dataframe based on multiple cols, not their combinations
Thanks, John. Your solution gives me:
> ddply(my_df, .(a), summarize, mm = mean(dat), number = length(dat))
a mm number
1 0 14 3
2 1 11 3
I'm looking for (and Ista found a way):
>> a b c mean n
>> 1 1 * * 11 3
>> 2 * 1 * 14 3
>> 3 * * 1 12 3
thanks,
allie
On 3/20/2013 3:24 PM, John Kane wrote:
> Will this do?
>
> library(plyr)
>
> ddply(my_df, .(a), summarize, mm = mean(dat), number = length(dat))
>
> John Kane
> Kingston ON Canada
>
>
>> -Original Message-
>> From: ashen...@ufl.edu
>> Sent: Wed, 20 Mar 2013 14:57:36 -0500
>> To: r-help@r-project.org
>> Subject: [R] summarize dataframe based on multiple cols, not their
>> combinations
>>
>> Hi folks,
>>
>> I'm trying to figure out how to get summarized data based on multiple
>> columns. However, instead of giving summaries for every combination of
>> categorical columns, I want it for each value of each categorical column
>> regardless of the other columns. I could do this with three different
>> commands, but i'm wondering if there's a more elegant way that I'm
>> missing. Thanks!
>>
>> allie
>>
>>> my_df = data.frame(a = c(1,1,1,0,0,0), b=c(0,0,0,1,1,1),
>> c=c(1,0,1,0,1,0), dat=c(10,11,12,13,14,15))
>>
>>> my_df
>> a b c dat
>> 1 1 0 1 10
>> 2 1 0 0 11
>> 3 1 0 1 12
>> 4 0 1 0 13
>> 5 0 1 1 14
>> 6 0 1 0 15
>>
>>> # not what I want
>>> ddply(my_df, .(a,b,c), function(x) c("mean"=mean(x$dat), "n"=nrow(x)))
>> a b c mean n
>> 1 0 1 0 14 2
>> 2 0 1 1 14 1
>> 3 1 0 0 11 1
>> 4 1 0 1 11 2
>>
>> What I want:
>> a b c mean n
>> 1 1 * * 11 3
>> 2 * 1 * 14 3
>> 3 * * 1 12 3
>>
>> where "*" refers to any value of the other columns.
>>
>> __
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
> FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
> Check it out at http://www.inbox.com/earth
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>
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Re: [R] summarize dataframe based on multiple cols, not their combinations
Nice, thanks Ista!
On 3/20/2013 3:18 PM, Ista Zahn wrote:
> How about
>
> library(reshape2)
> mdf.m <- melt(my_df, measure.vars=c("a", "b", "c"))
> mdf.m <- mdf.m[mdf.m$value > 0, ]
>
> ddply(mdf.m, "variable", function(x) c("mean"=mean(x$dat), "n"=nrow(x)))
>
> ?
>
> Best,
> Ista
>
> On Wed, Mar 20, 2013 at 3:57 PM, Alexander Shenkin wrote:
>> Hi folks,
>>
>> I'm trying to figure out how to get summarized data based on multiple
>> columns. However, instead of giving summaries for every combination of
>> categorical columns, I want it for each value of each categorical column
>> regardless of the other columns. I could do this with three different
>> commands, but i'm wondering if there's a more elegant way that I'm
>> missing. Thanks!
>>
>> allie
>>
>>> my_df = data.frame(a = c(1,1,1,0,0,0), b=c(0,0,0,1,1,1),
>> c=c(1,0,1,0,1,0), dat=c(10,11,12,13,14,15))
>>
>>> my_df
>> a b c dat
>> 1 1 0 1 10
>> 2 1 0 0 11
>> 3 1 0 1 12
>> 4 0 1 0 13
>> 5 0 1 1 14
>> 6 0 1 0 15
>>
>>> # not what I want
>>> ddply(my_df, .(a,b,c), function(x) c("mean"=mean(x$dat), "n"=nrow(x)))
>> a b c mean n
>> 1 0 1 0 14 2
>> 2 0 1 1 14 1
>> 3 1 0 0 11 1
>> 4 1 0 1 11 2
>>
>> What I want:
>> a b c mean n
>> 1 1 * * 11 3
>> 2 * 1 * 14 3
>> 3 * * 1 12 3
>>
>> where "*" refers to any value of the other columns.
>>
>> __
>> 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.
__
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[R] summarize dataframe based on multiple cols, not their combinations
Hi folks,
I'm trying to figure out how to get summarized data based on multiple
columns. However, instead of giving summaries for every combination of
categorical columns, I want it for each value of each categorical column
regardless of the other columns. I could do this with three different
commands, but i'm wondering if there's a more elegant way that I'm
missing. Thanks!
allie
> my_df = data.frame(a = c(1,1,1,0,0,0), b=c(0,0,0,1,1,1),
c=c(1,0,1,0,1,0), dat=c(10,11,12,13,14,15))
> my_df
a b c dat
1 1 0 1 10
2 1 0 0 11
3 1 0 1 12
4 0 1 0 13
5 0 1 1 14
6 0 1 0 15
> # not what I want
> ddply(my_df, .(a,b,c), function(x) c("mean"=mean(x$dat), "n"=nrow(x)))
a b c mean n
1 0 1 0 14 2
2 0 1 1 14 1
3 1 0 0 11 1
4 1 0 1 11 2
What I want:
a b c mean n
1 1 * * 11 3
2 * 1 * 14 3
3 * * 1 12 3
where "*" refers to any value of the other columns.
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[R] extract indep vars from formula
Hello, I'm trying to extract the independent variables from a formula. The closest I've been able to come, aside from rolling my own, is the following: > a = y ~ b * x > attr(terms(formula(a)),"variables") The reason I'm doing this is that I'm building a grid of points that I use to construct a 3-d model prediction surface in rgl. If there are more than two independent variables, I need to set the other ones to 0 in the dataframe for the predict() routine. In order to do that, I need to know what those variables are. I suspect there's a better way to go about doing what I'm doing (perhaps using the model.* family of functions). But, in the meantime, just extracting the independent variables will move me forward. Thanks, Allie __ 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] backreferences in gregexpr
On 11/2/2012 5:14 PM, Gabor Grothendieck wrote:
> On Fri, Nov 2, 2012 at 6:02 PM, Alexander Shenkin wrote:
>> Hi Folks,
>>
>> I'm trying to extract just the backreferences from a regex.
>>
>>> temp = "abcd1234abcd1234"
>>> regmatches(temp, gregexpr("(?:abcd)(1234)", temp))
>> [[1]]
>> [1] "abcd1234" "abcd1234"
>>
>> What I would like is:
>> [1] "1234" "1234"
>>
>> Note: I know I can just match 1234 here, but the actual example is
>> complicated enough that I have to match a larger string, and just want
>> to pass out the backreferenced portion.
>>
>> Any help greatly appreciated!
>>
>
> Try this:
>
>> library(gsubfn)
>> strapplyc(temp, "abcd(1234)")
> [[1]]
> [1] "1234" "1234"
>
Thanks Gabor. Didn't find strapplyc in package gsubfun, but did find
strapply, and that worked well.
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[R] backreferences in gregexpr
Hi Folks,
I'm trying to extract just the backreferences from a regex.
> temp = "abcd1234abcd1234"
> regmatches(temp, gregexpr("(?:abcd)(1234)", temp))
[[1]]
[1] "abcd1234" "abcd1234"
What I would like is:
[1] "1234" "1234"
Note: I know I can just match 1234 here, but the actual example is
complicated enough that I have to match a larger string, and just want
to pass out the backreferenced portion.
Any help greatly appreciated!
Thanks,
Allie
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Re: [R] Which packages are incompatible with 64-bit R?
Thanks Duncan. Here's what I come up with. Anything obviously missing? I'd think there'd be more incompatibilities than just these few... In 32-bit: > pkgs32 = available.packages(type="win.binary") In 64-bit: > pkgs64 = available.packages(type="win.binary") > pkgnames32 = pkgs32[,"Package"] > pkgnames64 = pkgs64[,"Package"] > as.character(pkgnames32[which(is.na(match(pkgnames32, pkgnames64)))]) [1] "RSVGTipsDevice" "RSvgDevice" "eco""rcqp" "sparsenet" "hdf5" On 10/19/2012 8:22 AM, Duncan Murdoch wrote: > On 19/10/2012 8:10 AM, Alexander Shenkin wrote: >> Hi folks, >> >> Despite the pain of migrating to 64-bit R (I have to install 64-bit >> Office also due to RODBC), I'm considering making the leap due to >> memory issues. Is there any place that lists packages that are 64-bit >> incompatible? Or, will I just have to march through all my packages >> and check them one-by-one on CRAN? > > An approximation to that is to call > available.packages(type="win.binary") on both versions, and compare the > lists. Packages may fail to appear for reasons other than > incompatibility, but incompatible packages won't be available in binary > versions. > > Duncan Murdoch __ 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] Which packages are incompatible with 64-bit R?
Hi folks, Despite the pain of migrating to 64-bit R (I have to install 64-bit Office also due to RODBC), I'm considering making the leap due to memory issues. Is there any place that lists packages that are 64-bit incompatible? Or, will I just have to march through all my packages and check them one-by-one on CRAN? Thanks, Allie [[alternative HTML version deleted]] __ 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] bigmemory for dataframes?
System Info: R 2.14.2 Windows 7 Pro x64 SP1 8GB RAM On 10/18/2012 3:42 PM, Alexander Shenkin wrote: > Hi Folks, > > I've been bumping my head against the 4GB limit for 32-bit R. I can't > go to 64-bit R due to package compatibility issues (ROBDC - possible but > painful, xlsReadWrite - not possible, and others). I have a number of > big dataframes whose columns all sorts of data types - factor, > character, integer, etc. I run and save models that keep copies of the > modeled data inside the model objects as well (mle2 objects, to be > specific). > > I'm searching for a way to cache some of these dataframes and objects to > virtual memory (I think I'm using the right terminology...). I've read > around, and while bigmemory and ff and the like would likely suit my > purposes if I were just dealing with numeric matricies, I'm dealing with > dataframes and objects. > > Any thoughts would be greatly appreciated! > > Thanks, > Allie > > __ > 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] bigmemory for dataframes?
Hi Folks, I've been bumping my head against the 4GB limit for 32-bit R. I can't go to 64-bit R due to package compatibility issues (ROBDC - possible but painful, xlsReadWrite - not possible, and others). I have a number of big dataframes whose columns all sorts of data types - factor, character, integer, etc. I run and save models that keep copies of the modeled data inside the model objects as well (mle2 objects, to be specific). I'm searching for a way to cache some of these dataframes and objects to virtual memory (I think I'm using the right terminology...). I've read around, and while bigmemory and ff and the like would likely suit my purposes if I were just dealing with numeric matricies, I'm dealing with dataframes and objects. Any thoughts would be greatly appreciated! Thanks, Allie __ 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] how to know where you've been sourced from
Hello All,
I need a script to perform different actions depending on the file from
which it was source()'d. Thus, my script needs a way to figure out from
whence it was sourced.
There seems to be some relevant information in sys.calls() (see below).
However, I need to get at the name of the file that directly source the
file in question. That is, just one level above. For example, in the
example below, test.r needs to know that it was called by source_test.r.
In this example, the information is in sys.calls()[[4]]. But, if there
are other calls in the stack, I don't imagine it will always be in
sys.calls()[[4]]. Is there a consistent place in sys.calls() or
elsewhere I can look for the sourcing file name?
thanks,
allie
> cat("print(sys.calls())",file="test.r")
> cat("source(\"test.r\")",file="source_test.r")
> cat("source(\"source_test.r\")",file="source_test_parent.r")
> source("source_test_parent.r")
[[1]]
source("source_test_parent.r")
[[2]]
eval.with.vis(ei, envir)
[[3]]
eval.with.vis(expr, envir, enclos)
[[4]]
source("source_test.r")
[[5]]
eval.with.vis(ei, envir)
[[6]]
eval.with.vis(expr, envir, enclos)
[[7]]
source("test.r")
[[8]]
eval.with.vis(ei, envir)
[[9]]
eval.with.vis(expr, envir, enclos)
[[10]]
print(sys.calls())
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[R] remove all terms with interaction factor in formula
Hi Folks, I'm trying to find a way to remove all terms in a formula that contain a particular interaction. For example, in the formula below, I'd like to remove all terms that contain the b:c interaction. > attributes(terms( ~ a*b*c*d))$term.labels [1] "a" "b" "c" "d" "a:b" "a:c" [7] "b:c" "a:d" "b:d" "c:d" "a:b:c" "a:b:d" [13] "a:c:d" "b:c:d" "a:b:c:d" My eventual use is to fit models with the reduced formulas. For example: > my_df = data.frame( iv = runif(100), a=runif(100), b=runif(100), c=runif(100), d=runif(100)) > lm(iv ~ a*b*c*d, data=my_df) I can remove particular terms with update(), but I don't see a way to remove all terms that contain a given combination of factors. Any help would be greatly appreciated. Thanks! Allie __ 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] POSIXct-coerced NA's not considered NA by is.na()
Thanks for your reply, Jim.
On 8/24/2012 12:14 PM, jim holtman wrote:
> I think your first problem is the coersion done by 'c' when you are
> mixing objects of various types: you have POSIXct and character.
Yes, that's something I may have confounded. Still, the warning I'm
getting is "In as.POSIXlt.POSIXct(x, tz) : NAs introduced by coercion".
I'm not sure how c()'s coercion works - the warning seems to indicate
that c() is finding as.POSIXct. That's strange though, since I would
expect to get an error in that case, not just a warning:
> as.POSIXct("b")
Error in as.POSIXlt.character(x, tz, ...) :
character string is not in a standard unambiguous format
> What were your expections?
I was expecting that the NA resulting from the coercion would result in
a TRUE value when being operated on by is.na(). Instead, I got:
> is.na(date_vec[4])
[1] FALSE
>> x <- Sys.time()
>> str(x)
> POSIXct[1:1], format: "2012-08-24 13:12:31"
>> y <- c(x, 'b')
>> str(y)
> POSIXct[1:2], format: "2012-08-24 13:12:31" NA
> Warning message:
> In as.POSIXlt.POSIXct(x, tz) : NAs introduced by coercion
>> dput(y)
> structure(c("1345828351.75", "b"), class = c("POSIXct", "POSIXt"
> ))
>>
>
> Look at the 'dput' and see that what it is trying to do is to use the
> numeric value changed to a character string as a POSIXct value. So I
> am not surprised by the error since it is probably not what you
> wanted. Did you intend to use 'list' instead of 'c'?
I'm a bit confused about how you get that from dput. Here's what I see:
> dput(date_vec)
structure(c("1345831833", "1345831834", NA, "b"), class = c("POSIXct",
"POSIXt"))
Regardless, I do get the same strange is.na() behavior from the following:
> bad_date = "b"
> class(bad_date) = "POSIXct"
> bad_date
[1] NA
Warning message:
In as.POSIXlt.POSIXct(x, tz) : NAs introduced by coercion
> is.na(bad_date) # shouldn't this be TRUE?
[1] FALSE
As nasty as it may be, shouldn't something showing up as "NA" result in
TRUE when being tested by is.na()?
Just to put some context around this, I was investigating this issue as
I was thinking about converting dataframe columns to dates, and
detecting errors in that conversion.
thanks,
Allie
>
> On Fri, Aug 24, 2012 at 9:47 AM, Alexander Shenkin wrote:
>> Hello folks,
>>
>> I found a strangeness while experimenting with POSIXct vectors and
>> lists. It seems that coerced NA's aren't "real" NAs, at least as
>> considered by is.na()?
>>
>>> date_vec = c(as.POSIXct(now()), as.POSIXct(now()+1),NA,"b")
>>> date_vec
>> [1] "2012-08-22 15:00:46 COT" "2012-08-22 15:00:47 COT" NA
>>
>> [4] NA
>> Warning message:
>> In as.POSIXlt.POSIXct(x, tz) : NAs introduced by coercion
>>> date_vec[4]
>> [1] NA
>> Warning message:
>> In as.POSIXlt.POSIXct(x, tz) : NAs introduced by coercion
>>> is.na(date_vec[4])
>> [1] FALSE
>>> is.na(date_vec[3])
>> [1] TRUE
>>> is.POSIXct(date_vec[4])
>> [1] TRUE
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[R] POSIXct-coerced NA's not considered NA by is.na()
Hello folks, I found a strangeness while experimenting with POSIXct vectors and lists. It seems that coerced NA's aren't "real" NAs, at least as considered by is.na()? > date_vec = c(as.POSIXct(now()), as.POSIXct(now()+1),NA,"b") > date_vec [1] "2012-08-22 15:00:46 COT" "2012-08-22 15:00:47 COT" NA [4] NA Warning message: In as.POSIXlt.POSIXct(x, tz) : NAs introduced by coercion > date_vec[4] [1] NA Warning message: In as.POSIXlt.POSIXct(x, tz) : NAs introduced by coercion > is.na(date_vec[4]) [1] FALSE > is.na(date_vec[3]) [1] TRUE > is.POSIXct(date_vec[4]) [1] TRUE __ 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] Sweave: R chunk inside caption?
Hi Folks,
I'm surprised, but I didn't find this question addressed anywhere. I'd
like to generate a LaTeX caption with R code. I've tried the code
below, but I get the following TeX error:
! Argument of \@caption has an extra }.
\par
l.21 }
Any thoughts? Perhaps I'll have to write the "\caption{}" text with R?
thanks!
Sweave document:
\documentclass{article}
\title {test}
\author {me}
\usepackage{Sweave}
\begin {document}
\maketitle
\DeclareGraphicsExtensions{.pdf,.png}
\begin {figure}
<>=
plot(runif(100), runif(100))
@
\caption {
This is the caption with some r-code
<<>>=
2*2
@
}
\label {fig:1}
\end {figure}
\end{document}
TeX document:
\documentclass{article}
\title {test}
\author {me}
\usepackage{Sweave}
\begin {document}
\maketitle
\DeclareGraphicsExtensions{.pdf,.png}
\begin {figure}
\includegraphics{test-fig1}
\caption {
This is the caption with some r-code
\begin{Schunk}
\begin{Sinput}
> 2*2
\end{Sinput}
\begin{Soutput}
[1] 4
\end{Soutput}
\end{Schunk}
}
\label {fig:1}
\end {figure}
\end{document}
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[R] export table in separate file
Hi Folks, I'm using Sweave to generate png & pdf graphics that I then "Import & Link" in a Word document. This let's me create sharable and editable dynamic documents. They are dynamic in that I can regenerate figures when the data changes, and have those figures automatically updated in my Word doc since they're "linked", and not just "imported" in Word. I want to do the same for tables. Right now, I've rolled my own function to turn tables into a png. However, I would like a more robust solution. Is there any way I can turn tables into, say, an HTML table in a separate file that could be linked in Word? I know one can create HTML tables in Sweave and otherwise. The difference is that I need those tables to exist each in their separate file. Any thoughts would be much appreciated. Thanks, Allie __ 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] r-forge down?
Thanks Roy, That's one "R-forge" site, but my impression is that the r-forge.r-project.org site is a different one (and it's the one that hosts the package I'm interested in). Please correct me if those two sites are somehow related. thanks, allie On 8/7/2012 5:29 PM, Roy Mendelssohn wrote: > http://www.rforge.net > > -Roy > > On Aug 7, 2012, at 3:25 PM, Alexander Shenkin wrote: > >> Hi Folks, >> >> I've looked around, haven't found anything, and I'm not sure where else >> to check. I haven't visited R-forge (http://r-forge.r-project.org) in a >> long time. Now that I'm trying, it seems to be down. Anyone know if >> this is a temporary condition, and if so, when it's expected to rise again? >> >> Thanks, >> Allie >> >> __ >> 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. > ** > "The contents of this message do not reflect any position of the U.S. > Government or NOAA." > ** > Roy Mendelssohn > Supervisory Operations Research Analyst > NOAA/NMFS > Environmental Research Division > Southwest Fisheries Science Center > 1352 Lighthouse Avenue > Pacific Grove, CA 93950-2097 > > e-mail: roy.mendelss...@noaa.gov (Note new e-mail address) > voice: (831)-648-9029 > fax: (831)-648-8440 > www: http://www.pfeg.noaa.gov/ > > "Old age and treachery will overcome youth and skill." > "From those who have been given much, much will be expected" > "the arc of the moral universe is long, but it bends toward justice" -MLK Jr. > __ 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] r-forge down?
Hi Folks, I've looked around, haven't found anything, and I'm not sure where else to check. I haven't visited R-forge (http://r-forge.r-project.org) in a long time. Now that I'm trying, it seems to be down. Anyone know if this is a temporary condition, and if so, when it's expected to rise again? Thanks, Allie __ 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] sweave tables as images?
this works - thanks baptiste! i'm working in Sweave right now - perhaps
it will be tough in knitr as you mention.
On 5/25/2012 4:31 PM, baptiste auguie wrote:
> you can open a device that has the exact dimensions of the table,
>
> g = tableGrob(head(iris, 4))
> png("test.png", width=convertWidth(grobWidth(g), "in", value=TRUE),
> height=convertHeight(grobHeight(g), "in",
> value=TRUE),units="in", res=150)
> grid.draw(g)
> dev.off()
>
> Doing this with knitr might be tricky though, since the unit
> conversion opens a blank device window, and you'd want to define some
> hook instead of manually creating the png file.
>
> I have another version of grid.table where you can specify the width
> and height manually [*], e.g to span the full window, but it's not
> necessarily a desirable thing (the spacing between rows and columns
> can become too large).
>
>
> HTH,
>
> baptiste
>
>
> [*] experimental code at https://gist.github.com/2013903
>
> On 26 May 2012 09:16, Alexander Shenkin wrote:
>> Thanks Yihui,
>>
>> That's a great idea, and comes close to the mark, except that I have to
>> use png's in order to "Insert & Link" them as pictures in Word (and
>> hence make the doc both shareable and update when new figures are
>> generated).
>>
>> thanks,
>> allie
>>
>> On 5/25/2012 2:57 PM, Yihui Xie wrote:
>>> You may take a look at knitr's graphics manual which tells you how you
>>> can automatically crop the white margins:
>>> https://github.com/downloads/yihui/knitr/knitr-graphics.pdf ("Cropping
>>> PDF Graphics").
>>>
>>> I'm not sure if pdfcrop works in this case, though.
>>>
>>> Regards,
>>> Yihui
>>> --
>>> Yihui Xie
>>> Phone: 515-294-2465 Web: http://yihui.name
>>> Department of Statistics, Iowa State University
>>> 2215 Snedecor Hall, Ames, IA
>>>
>>>
>>> On Fri, May 25, 2012 at 2:44 PM, Alexander Shenkin wrote:
>>>> grid.table() works well, but using it in sweave creates graphics with
>>>> very wide margins. I'm sure this has something to do with grid, and not
>>>> just grid.table. Any idea how I can clip the graphic to the edges of
>>>> the table graphic? I've looked into viewports, etc, but I can't seem to
>>>> find anything that will clip a graphic to its edges, perhaps with some
>>>> defined margin.
>>>>
>>>> any help greatly appreciated!
>>>>
>>>> thanks,
>>>> allie
>>
>> __
>> 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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] sweave tables as images?
Thanks Yihui,
That's a great idea, and comes close to the mark, except that I have to
use png's in order to "Insert & Link" them as pictures in Word (and
hence make the doc both shareable and update when new figures are
generated).
thanks,
allie
On 5/25/2012 2:57 PM, Yihui Xie wrote:
> You may take a look at knitr's graphics manual which tells you how you
> can automatically crop the white margins:
> https://github.com/downloads/yihui/knitr/knitr-graphics.pdf ("Cropping
> PDF Graphics").
>
> I'm not sure if pdfcrop works in this case, though.
>
> Regards,
> Yihui
> --
> Yihui Xie
> Phone: 515-294-2465 Web: http://yihui.name
> Department of Statistics, Iowa State University
> 2215 Snedecor Hall, Ames, IA
>
>
> On Fri, May 25, 2012 at 2:44 PM, Alexander Shenkin wrote:
>> grid.table() works well, but using it in sweave creates graphics with
>> very wide margins. I'm sure this has something to do with grid, and not
>> just grid.table. Any idea how I can clip the graphic to the edges of
>> the table graphic? I've looked into viewports, etc, but I can't seem to
>> find anything that will clip a graphic to its edges, perhaps with some
>> defined margin.
>>
>> any help greatly appreciated!
>>
>> thanks,
>> allie
__
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Re: [R] sweave tables as images?
grid.table() works well, but using it in sweave creates graphics with very wide margins. I'm sure this has something to do with grid, and not just grid.table. Any idea how I can clip the graphic to the edges of the table graphic? I've looked into viewports, etc, but I can't seem to find anything that will clip a graphic to its edges, perhaps with some defined margin. any help greatly appreciated! thanks, allie On 5/21/2012 3:33 PM, R. Michael Weylandt wrote: > Take a look at addtable2plot in plotrix or grid.table / tableGrob in > gridExtras. > > Michael > > On Mon, May 21, 2012 at 4:29 PM, Alexander Shenkin wrote: >> Hello folks, >> >> I've been on a journey trying to figure out how to manage documents that >> are amenable to sharing and editing, but that contain dynamic content >> generated by R. I've come to the following solution: I use Sweave to >> generate labeled png & pdf figures, and I "Insert & Link" those figures >> as "Pictures" in a Word 2010 doc. Thus, when data or code changes, I >> regenerate the figures with Sweave, open the Word doc and hit "F9", and >> all the figures are automatically updated. I can send the file around, >> folks can comment and edit, track changes, etc. >> >> Now, however, I'm trying to do the same for tables that I did for >> figures, and it seems a bit more difficult. I can spit out tex tables >> into separate files using the "split=TRUE" chunk option, and I can even >> make those tables into html with xtable(type="html"). Word, however, >> doesn't have the "Insert & Link" option for external text files (which >> makes it such that, if the external file isn't found, Word uses a copy >> stored in the doc). >> >> So, I think it will be better if I can somehow generate the tables as >> images. Is there any way to generate tables as images in separate files >> in Sweave? Or, is there another tree up which I should be barking? >> >> Thanks, >> Allie >> >> __ >> 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] use list as function arguments
Hello Folks,
Is there any way to pass a list into a function such that the function
will use the list as its arguments? I haven't been able to figure that out.
The background: I'm trying to build a function that will apply another
function multiple times, each time with a different set of specified
arguments. I'm trying to figure out how to pass in a list of argument
lists, then loop through the top-level list, passing in the lower-level
list as function arguments.
pseudocode:
b = list( list( arg1 = 1, arg2 = 2 ),
list( arg1 = 3, arg2 = 4 )
)
a <- apply_function(arglist) {
for (i in length(arglist)) {
b(arglist[i])
}
}
Specifically, the actual use I'm trying to implement is a function to
format columns of data frames and matrices independently. What I have
so far is below, but it's not working. Perhaps I'm going about this the
wrong way?
format_cols <- function(x, format_list = list()) {
# usage: length(format_list) must equal ncol(x)
#format list should be a list of lists of key=value pairs
corresponding to format settings for each column
if (is.data.frame(x)) {
newout = data.frame()
} else if (is.matrix(x)) {
newout = matrix()
}
for (i in 1:ncol(x)){
newout = cbind(newout, format(x,format_list[[i]]))
x[,i] = format(x,format_list[[i]])
}
return(newout)
}
Thanks,
Allie
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Re: [R] sweave tables as images?
Thanks Liviu, I've looked into SWord, and while it's an impressive project, I'm concerned that it doesn't quite give me the fine-grain control I'd like over the R environment where it's being executed. It's still in the back of my mind though, and I may indeed go with it at some point. If I understand it correctly, odfWeave doesn't have a path backwards from the odf doc back to the original odfWeave doc (which is the main restriction of all these Sweave/knitr/etc solutions in my use case). Please correct me if I'm wrong about that! Thanks, Allie On 5/22/2012 4:36 AM, Liviu Andronic wrote: > On Mon, May 21, 2012 at 10:29 PM, Alexander Shenkin wrote: >> So, I think it will be better if I can somehow generate the tables as >> images. Is there any way to generate tables as images in separate files >> in Sweave? Or, is there another tree up which I should be barking? >> > Hmm, there are Sweave equivalents for LibreOffice [1] and MS Word [2]. > Have you looked into those? You may find other suggestions in the > ReproducibleResearch Task View [3]. > > Liviu > > [1] http://crantastic.org/packages/odfWeave > [2] http://crantastic.org/packages/SWordInstaller > [3] http://crantastic.org/task_views/ReproducibleResearch __ 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] sweave tables as images?
Thanks Michael - I think grid.table does the trick. On 5/21/2012 3:33 PM, R. Michael Weylandt wrote: > Take a look at addtable2plot in plotrix or grid.table / tableGrob in > gridExtras. > > Michael > > On Mon, May 21, 2012 at 4:29 PM, Alexander Shenkin wrote: >> Hello folks, >> >> I've been on a journey trying to figure out how to manage documents that >> are amenable to sharing and editing, but that contain dynamic content >> generated by R. I've come to the following solution: I use Sweave to >> generate labeled png & pdf figures, and I "Insert & Link" those figures >> as "Pictures" in a Word 2010 doc. Thus, when data or code changes, I >> regenerate the figures with Sweave, open the Word doc and hit "F9", and >> all the figures are automatically updated. I can send the file around, >> folks can comment and edit, track changes, etc. >> >> Now, however, I'm trying to do the same for tables that I did for >> figures, and it seems a bit more difficult. I can spit out tex tables >> into separate files using the "split=TRUE" chunk option, and I can even >> make those tables into html with xtable(type="html"). Word, however, >> doesn't have the "Insert & Link" option for external text files (which >> makes it such that, if the external file isn't found, Word uses a copy >> stored in the doc). >> >> So, I think it will be better if I can somehow generate the tables as >> images. Is there any way to generate tables as images in separate files >> in Sweave? Or, is there another tree up which I should be barking? >> >> Thanks, >> Allie >> >> __ >> 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] sweave tables as images?
Hello folks, I've been on a journey trying to figure out how to manage documents that are amenable to sharing and editing, but that contain dynamic content generated by R. I've come to the following solution: I use Sweave to generate labeled png & pdf figures, and I "Insert & Link" those figures as "Pictures" in a Word 2010 doc. Thus, when data or code changes, I regenerate the figures with Sweave, open the Word doc and hit "F9", and all the figures are automatically updated. I can send the file around, folks can comment and edit, track changes, etc. Now, however, I'm trying to do the same for tables that I did for figures, and it seems a bit more difficult. I can spit out tex tables into separate files using the "split=TRUE" chunk option, and I can even make those tables into html with xtable(type="html"). Word, however, doesn't have the "Insert & Link" option for external text files (which makes it such that, if the external file isn't found, Word uses a copy stored in the doc). So, I think it will be better if I can somehow generate the tables as images. Is there any way to generate tables as images in separate files in Sweave? Or, is there another tree up which I should be barking? Thanks, Allie __ 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] auditing R's memory usage
Hi Folks, I'm running 32-bit R 2.14 in RStudio on my Win 7 x64 system with 8GB RAM. I'm getting memory problems as R wants to swallow more than the 4GB limit. I think I'm stuck at 4GB as I have to use 32-bit R for a number of packages (ODBC, etc). However, I doubt I really need to be using that much memory - I'm probably being very sloppy in my memory management, leaving lots of temporary dataframes around, etc. I'm looking for suggestions about how to audit R's memory usage. Yes, I could go around my code and tie up every loose end. But in the interest of efficiency, I'm wondering about ways I might more intelligently audit R's memory usage. Are there any tools that can tell me what objects are swallowing what amounts of memory? Armed with that information, I can go track down the worst culprits. Thanks, Allie __ 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] rgl.Sweave not producing transparency in pdf plots with alpha
On 5/2/2012 11:40 AM, Duncan Murdoch wrote:
> On 02/05/2012 12:26 PM, Duncan Murdoch wrote:
>> On 02/05/2012 11:00 AM, Alexander Shenkin wrote:
>> > Hi Folks,
>> >
>> > I'm trying to get rgl.Sweave to produce plots with transparency.
>> > However, it just seems to produce opaque plots when pdf is the output
>> > type. Perhaps this is a known issue? I'll just use .png in the
>> > meantime, but wanted to see about this, as I didn't see it in the
>> > documentation (though it's possible I missed it).
>> That uses the rgl.postscript() function, which uses the GL2PS library to
>> convert to PDF. It may be that it doesn't support transparency in your
>> scene. Or perhaps it just hasn't been turned on: GL2PS didn't support
>> transparency when rgl.postscript was written.
>
> I just took a look: transparency is turned off, and when it's turned
> on, it doesn't look very good.
>
> It's possible that there are tuning parameters that could make it look
> good, but I don't know what they are.
>
> Duncan Murdoch
Thanks Duncan, I'll just stick with png for now then.
>
>>
>> Duncan Murdoch
>>
>> >
>> > Thanks,
>> > Allie
>> >
>> >
>> >
>> >
>> > \documentclass{article}
>> > \title {rgl test}
>> > \usepackage{Sweave}
>> > \begin {document}
>> >
>> > This is a test of rgl.sweave's alpha capability.
>> >
>> > \begin{figure}
>> > % uncomment line below for png output (correct transparency)
>> > %<> > resolution=100>>=
>> > <> > resolution=100, outputtype=pdf, pdf=TRUE>>=
>> > library(rgl)
>> > data(volcano)
>> > z<- 2 * volcano# Exaggerate the relief
>> > x<- 10 * (1:nrow(z)) # 10 meter spacing (S to N)
>> > y<- 10 * (1:ncol(z)) # 10 meter spacing (E to W)
>> > zlim<- range(y)
>> > zlen<- zlim[2] - zlim[1] + 1
>> > colorlut<- terrain.colors(zlen) # height color lookup table
>> > col<- colorlut[ z-zlim[1]+1 ] # assign colors to heights for each
>> point
>> > #open3d()
>> > surface3d(x, y, z, color=col, back="lines", alpha=0.75)
>> > @
>> > \end{figure}
>> >
>> > \end{document}
>> >
>> > __
>> > 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.
>>
>
__
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and provide commented, minimal, self-contained, reproducible code.
[R] rgl.Sweave not producing transparency in pdf plots with alpha
Hi Folks,
I'm trying to get rgl.Sweave to produce plots with transparency.
However, it just seems to produce opaque plots when pdf is the output
type. Perhaps this is a known issue? I'll just use .png in the
meantime, but wanted to see about this, as I didn't see it in the
documentation (though it's possible I missed it).
Thanks,
Allie
\documentclass{article}
\title {rgl test}
\usepackage{Sweave}
\begin {document}
This is a test of rgl.sweave's alpha capability.
\begin{figure}
% uncomment line below for png output (correct transparency)
% <>=
<>=
library(rgl)
data(volcano)
z <- 2 * volcano# Exaggerate the relief
x <- 10 * (1:nrow(z)) # 10 meter spacing (S to N)
y <- 10 * (1:ncol(z)) # 10 meter spacing (E to W)
zlim <- range(y)
zlen <- zlim[2] - zlim[1] + 1
colorlut <- terrain.colors(zlen) # height color lookup table
col <- colorlut[ z-zlim[1]+1 ] # assign colors to heights for each point
#open3d()
surface3d(x, y, z, color=col, back="lines", alpha=0.75)
@
\end{figure}
\end{document}
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Re: [R] Coding columns for survival analysis
Jim,
This was very helpful - thank you! I really like the use of diff and
cumsum - those haven't been in my toolkit until now. Your solution came
close, but I needed to keep "NAs" when the tree hadn't been found yet,
or when it had already died. So, for posterity, here's the code I ended
up with:
x <- read.table(text = " tree live1 live2 live3 live4 live5
1 tree1 0 0 0 1 1
2 tree2 0 0 1 1 0
3 tree3 0 1 1 0 0
4 tree4 1 1 0 0 0
5 tree4 1 1 1 1 0 # another test condition
6 tree5 1 0 0 0 0", header = TRUE)
# get matrix of data columns
z <- as.matrix(x[, -1])
# process each row
a <- t( apply(z, 1, function(.row) {
.row[is.na(.row)] = 0 # replace NAs with 0's so that
diff works correctly - not a problem in this example, but it is in the
real data
diffs = diff(c(0, .row))
alive <- .row
found <- diffs == 1
die <- diffs == -1
statevec <- rep(1,length(.row))
statevec <- statevec + alive # 2 where alive
statevec <- statevec + found # 3 where found
statevec <- statevec + die * 3 # 4 where dead
c(NA, "alive", "found", "mort")[statevec]
})
)
a
[,1][,2][,3][,4][,5]
1 NA NA NA "found" "alive"
2 NA NA "found" "alive" "mort"
3 NA "found" "alive" "mort" NA
4 "found" "alive" "mort" NA NA
5 "found" "alive" "alive" "alive" "mort"
6 "found" "mort" NA NA NA
Best,
Allie
On 4/13/2012 7:01 PM, jim holtman wrote:
> try this:
>
>> x <- read.table(text = " tree live1 live2 live3 live4 live5
> +1 tree1 0 0 0 1 1
> +2 tree2 0 0 1 1 0
> +3 tree3 0 1 1 0 0
> +4 tree4 1 1 0 0 0
> +6 tree4 1 1 1 1 0 # another test condition
> +5 tree5 1 0 0 0 0", header = TRUE)
>>
>> # get matrix of data columns
>> z <- as.matrix(x[, -1])
>> # process each row
>> a <- apply(z, 1, function(.row){
> + # determine where found (will be a 2)
> + found <- pmin(cumsum(.row) + 1, 3) # cannot be greater than 3
> + # determined where it died
> + die <- cumsum(diff(c(0, .row)) != 0)
> + # replace value at die == 2 with 4
> + found[die == 2] <- 4
> + c(NA, "found", "alive", "mort")[found]
> + })
>> t(a) # result
> [,1][,2][,3][,4][,5]
> 1 NA NA NA "found" "alive"
> 2 NA NA "found" "alive" "mort"
> 3 NA "found" "alive" "mort" "mort"
> 4 "found" "alive" "mort" "mort" "mort"
> 6 "found" "alive" "alive" "alive" "mort"
> 5 "found" "mort" "mort" "mort" "mort"
>>
>
>
> On Fri, Apr 13, 2012 at 4:53 PM, Alexander Shenkin wrote:
>> Hello Folks,
>>
>> I have 5 columns for thousands of tree records that record whether that
>> tree was alive or dead. I want to recode the columns such that the cell
>> reads "found" when a live tree is first observed, "alive" for when a
>> tree is found alive and is not just found, and "mort" when it was
>> previously alive but is now dead.
>>
>> Given the following:
>>
>>> tree_live = data.frame(tree =
>> c("tree1","tree2","tree3","tree4","tree5"), live1 = c(0,0,0,1,1), live2
>> = c(0,0,1,1,0), live3 = c(0,1,1,0,0), live4 = c(1,1,0,0,0), live5 = c(1,
>> 0, 0, 0, 0))
>>
>> tree live1 live2 live3 live4 live5
>>1 tree1 0 0 0 1 1
>>2 tree2 0 0 1 1 0
>>3 tree3 0 1 1 0 0
>>4 tree4 1 1 0 0 0
>>5 tree5 1 0 0 0 0
>>
>> I would like to end up with the following:
>>
>>> tree_live_recode
>>
>> live1 live2 live3 live4 live5
>>1NANANA found alive
>>2NANA found aliv
[R] Coding columns for survival analysis
Hello Folks,
I have 5 columns for thousands of tree records that record whether that
tree was alive or dead. I want to recode the columns such that the cell
reads "found" when a live tree is first observed, "alive" for when a
tree is found alive and is not just found, and "mort" when it was
previously alive but is now dead.
Given the following:
> tree_live = data.frame(tree =
c("tree1","tree2","tree3","tree4","tree5"), live1 = c(0,0,0,1,1), live2
= c(0,0,1,1,0), live3 = c(0,1,1,0,0), live4 = c(1,1,0,0,0), live5 = c(1,
0, 0, 0, 0))
tree live1 live2 live3 live4 live5
1 tree1 0 0 0 1 1
2 tree2 0 0 1 1 0
3 tree3 0 1 1 0 0
4 tree4 1 1 0 0 0
5 tree5 1 0 0 0 0
I would like to end up with the following:
> tree_live_recode
live1 live2 live3 live4 live5
1NANANA found alive
2NANA found alive mort
3NA found alive mort 0
4 found alive mort 0 0
5 found mort 0 0 0
I've accomplished the recode in the past, but only by going over the
dataset multiple times in messy and inefficient fashion. I'm wondering
if there are concise and efficient ways of going about it?
(I haven't been using the Survival package for my analyses, but I'm
starting to look into it.)
Thanks,
Allie
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] How do Sweave users collaborate with Word users?
Thanks for the heads up, Paul. That's good to know. I happen to be in academics, as are my collaborators, but I could imagine running into problems down the road. The good thing seems to be that it's just the users who want to interact with R who need the software. If collaborators are just touching the text, or are inserting graphics of their own, then sounds like things are still good. But, that's just my impression from the brief description I've seen online. Thanks, Allie On 4/9/2012 7:42 AM, Paul Bivand wrote: > If you're considering SWord, you should remember that the licence is > not the normal R licence and in commercial use will require a > commercial licence. While some academic disciplines use Word etc, the > issue may be more common outside academia. > > For those of us where such requirements involve a procurement process, > the need to purchase something when other users (and the > administration) are happy with their Word/Excel solutions may be an > insurmountable barrier. > > Good luck > > Paul Bivand > Centre for Economic and Social Inclusion (a non-profit organisation) > London > > > > On 9 April 2012 13:23, Richard M. Heiberger wrote: >> You might want to consider SWord, which provides similar facilities for the >> Word and R >> user. Word-oriented co-authors can modify the Word part of the document >> without >> impacting the R part of the document. >> >> SWord is by Thomas Baier tho...@statconn.com, author of the statconnDCOM >> interface >> that is underneath RExcel. See rcom.univie.ac.at for information and >> download and to >> sign up on the rcom email list. >> >> Rich >> >> On Sat, Apr 7, 2012 at 4:54 PM, Alexander Shenkin wrote: >> >>> Hello All, >>> >>> I'm getting my workflow switched over to Sweave, which is very cool. >>> However, I collaborate with folks (as many of you must as well) who use >>> Word to Track Changes amongst a group while crafting a paper. In the >>> simplest case, there will just be two people (one Sweave user and one >>> Word user) editing a paper. >>> >>> I'm wondering, how do Sweave users go about this? I could convert a >>> sweave file to a .docx easily enough via an intermediary pdf, rtf, html >>> or otherwise. However, once the file has been marked up with changes, >>> the challenge is to migrate those (accepted) changes back to the sweave >>> document. Perhaps the most straightforward way is to manually >>> back-propagate changes, but I imagine that could be a painstaking process. >>> >>> Ideally, I imagine a tool that puts invisible tags in the word document >>> when it is originally produced from Sweave, and is then able to >>> propagate changes back to that sweave file after markup. I'd be >>> pleasantly surprised if such a tool existed. >>> >>> Perhaps there are other ways of making this work. Any thoughts are >>> kindly appreciated! >>> >>> Thanks, >>> Allie >>> >>> __ >>> 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<http://www.r-project.org/posting-guide.html> >>> and provide commented, minimal, self-contained, reproducible code. >>> >>[[alternative HTML version deleted]] >> >> __ >> 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-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] How do Sweave users collaborate with Word users?
Thanks Rich, While it doesn't tickle me the way sweave/knitr does, SWord sounds more or less like the thing I'm looking for. However, poking around http://rcom.univie.ac.at/ and http://www.statconn.com doesn't reveal any download links. It seems as though SWord has been pulled from their lineup? Not sure - I've shot them an email to inquire. Thanks, Allie On 4/9/2012 7:23 AM, Richard M. Heiberger wrote: > You might want to consider SWord, which provides similar facilities > for the Word and R > user. Word-oriented co-authors can modify the Word part of the > document without > impacting the R part of the document. > > SWord is by Thomas Baier tho...@statconn.com > <mailto:tho...@statconn.com>, author of the statconnDCOM interface > that is underneath RExcel. See rcom.univie.ac.at > <http://rcom.univie.ac.at> for information and download and to > sign up on the rcom email list. > > Rich > > On Sat, Apr 7, 2012 at 4:54 PM, Alexander Shenkin <mailto:ashen...@ufl.edu>> wrote: > > Hello All, > > I'm getting my workflow switched over to Sweave, which is very cool. > However, I collaborate with folks (as many of you must as well) > who use > Word to Track Changes amongst a group while crafting a paper. In the > simplest case, there will just be two people (one Sweave user and one > Word user) editing a paper. > > I'm wondering, how do Sweave users go about this? I could convert a > sweave file to a .docx easily enough via an intermediary pdf, rtf, > html > or otherwise. However, once the file has been marked up with changes, > the challenge is to migrate those (accepted) changes back to the > sweave > document. Perhaps the most straightforward way is to manually > back-propagate changes, but I imagine that could be a painstaking > process. > > Ideally, I imagine a tool that puts invisible tags in the word > document > when it is originally produced from Sweave, and is then able to > propagate changes back to that sweave file after markup. I'd be > pleasantly surprised if such a tool existed. > > Perhaps there are other ways of making this work. Any thoughts are > kindly appreciated! > > Thanks, > Allie > > __ > R-help@r-project.org <mailto: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 > <http://www.r-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code. > > [[alternative HTML version deleted]] __ 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] How do Sweave users collaborate with Word users?
This sounds neat, and I wish you the best of luck with it. While I'm sure it'll be great for folks who are already curious enough to dive into Sweave or knitr, my guess is that coaxing collaborators into using markdown with SVN or GIT instead of passing around a Word file with Track Changes is going to be a tough sell, to put it lightly. I'll keep my eyes out for emerging sweave/knitr <-> word solutions (note the double arrow), but sounds like manual change-synchronization is the only game in town right now, alas. Thanks, Allie On 4/7/2012 4:29 PM, Yihui Xie wrote: > I cannot reply in detail at the moment, but we have a proposal to the > Google Summer of Code this year which will address the collaboration > issue. The basic idea is to write everything in plain text with > markdown (including R code), and compile the file with the knitr > package, then convert it to Word or whatever other formats with > pandoc, which is an extremely powerful document converter. You can see > a simple example here for how knitr works with markdown: > http://yihui.name/knitr/demo/upload/ Since everything is in plain > text, it is easy to collaborate through a version control system like > SVN or GIT. Markdown is easy to write and cleaner compared to Word. > > Regards, > Yihui > -- > Yihui Xie > Phone: 515-294-2465 Web: http://yihui.name > Department of Statistics, Iowa State University > 2215 Snedecor Hall, Ames, IA > > > > On Sat, Apr 7, 2012 at 3:54 PM, Alexander Shenkin wrote: >> Hello All, >> >> I'm getting my workflow switched over to Sweave, which is very cool. >> However, I collaborate with folks (as many of you must as well) who use >> Word to Track Changes amongst a group while crafting a paper. In the >> simplest case, there will just be two people (one Sweave user and one >> Word user) editing a paper. >> >> I'm wondering, how do Sweave users go about this? I could convert a >> sweave file to a .docx easily enough via an intermediary pdf, rtf, html >> or otherwise. However, once the file has been marked up with changes, >> the challenge is to migrate those (accepted) changes back to the sweave >> document. Perhaps the most straightforward way is to manually >> back-propagate changes, but I imagine that could be a painstaking process. >> >> Ideally, I imagine a tool that puts invisible tags in the word document >> when it is originally produced from Sweave, and is then able to >> propagate changes back to that sweave file after markup. I'd be >> pleasantly surprised if such a tool existed. >> >> Perhaps there are other ways of making this work. Any thoughts are >> kindly appreciated! >> >> Thanks, >> Allie >> >> __ >> 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] How do Sweave users collaborate with Word users?
Hello All, I'm getting my workflow switched over to Sweave, which is very cool. However, I collaborate with folks (as many of you must as well) who use Word to Track Changes amongst a group while crafting a paper. In the simplest case, there will just be two people (one Sweave user and one Word user) editing a paper. I'm wondering, how do Sweave users go about this? I could convert a sweave file to a .docx easily enough via an intermediary pdf, rtf, html or otherwise. However, once the file has been marked up with changes, the challenge is to migrate those (accepted) changes back to the sweave document. Perhaps the most straightforward way is to manually back-propagate changes, but I imagine that could be a painstaking process. Ideally, I imagine a tool that puts invisible tags in the word document when it is originally produced from Sweave, and is then able to propagate changes back to that sweave file after markup. I'd be pleasantly surprised if such a tool existed. Perhaps there are other ways of making this work. Any thoughts are kindly appreciated! Thanks, Allie __ 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] Rgui maintains open file handles after Sweave error
Reproducibility is important, and as I mentioned in a previous email, there are probably ways I could avoid running the entire script over and over again with each sweave compilation. Still, relying on saved workspaces, temporary files or caches still has some of the issues that working in the main environment does. Specifically, you're not working with the base data all the way through the final analyses each time you run the sweave doc. To produce those workspace, files or caches requires a run of scripts. If those scripts have changed, or if your data have changed, then your workspace, files and/or cache is then just as out of date as your workspace. Saving workspaces, files and/or caches still requires care that they're not saved after having been modified by the command line, etc. I think that working with saved workspaces, files and/or caches is probably less prone to "pollution" than working in the main environment, but it's far from failsafe. As long as the final sweave doc is run with scripts from beginning to end, getting the sweave doc up to snuff by working more quickly in the main environment is acceptable IMHO. So is working with the other methods above. Best, Allie On 4/5/2012 12:34 PM, Yihui Xie wrote: > Well, I do not think it is a good practice (in terms of reproducible > research) to keep on running Sweave in the same R session, because > your previous run and your current workspace could "pollute" your next > run. To make sure a document compiles on its own, it is better always > to start a new clean R session. If you run into speed issues (e.g. you > have chunks which require intensive computing), you can consider using > cache, which the knitr package has reasonably good support. > > Regards, > Yihui > -- > Yihui Xie > Phone: 515-294-2465 Web: http://yihui.name > Department of Statistics, Iowa State University > 2215 Snedecor Hall, Ames, IA > > > > On Thu, Apr 5, 2012 at 12:26 PM, Alexander Shenkin wrote: >> Yep, I'm using RStudio, and have used Tinn-R in the past. RStudio does >> start a new R session when processing a sweave document via the RStudio >> GUI. In my case, this presented a problem for the reasons I stated >> before (i.e. that I need to run sweave in the main environment, not a >> new one). Hence, I'm running Sweave from the command line, and >> processing the tex doc via TeXworks (from MiKTeX). I sent the RStudio >> team a feature request to add an option to be able to run Sweave in the >> main environment (perhaps while maintaining the default of running it in >> a separate environment). >> >> Allie >> __ 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] Rgui maintains open file handles after Sweave error
Yep, I'm using RStudio, and have used Tinn-R in the past. RStudio does
start a new R session when processing a sweave document via the RStudio
GUI. In my case, this presented a problem for the reasons I stated
before (i.e. that I need to run sweave in the main environment, not a
new one). Hence, I'm running Sweave from the command line, and
processing the tex doc via TeXworks (from MiKTeX). I sent the RStudio
team a feature request to add an option to be able to run Sweave in the
main environment (perhaps while maintaining the default of running it in
a separate environment).
Allie
On 4/5/2012 12:12 PM, Yihui Xie wrote:
> In terms of editors, I think RStudio is pretty good
> (http://www.rstudio.org/download/preview). Or LyX
> (http://yihui.name/knitr/demo/lyx/), or TeXmaker, WinEdit
> (http://yihui.name/knitr/demo/editors/)... All of them start a new R
> session when weaving the document, and all support one-click
> compilation. In all, anything but Windows Notepad.
>
> Regards,
> Yihui
> --
> Yihui Xie
> Phone: 515-294-2465 Web: http://yihui.name
> Department of Statistics, Iowa State University
> 2215 Snedecor Hall, Ames, IA
>
>
>
> On Thu, Apr 5, 2012 at 11:22 AM, Duncan Murdoch
> wrote:
>> On 04/04/2012 3:25 PM, Alexander Shenkin wrote:
>>>
>>> Hello Folks,
>>>
>>> When I run the document below through sweave, rgui.exe/rsession.exe
>>> leaves a file handle open to the sweave-001.pdf graphic (as verified by
>>> process explorer). Pdflatex.exe then crashes (with a Permission Denied
>>> error) because the graphic file is locked.
>>>
>>> This only seems to happen when there is an error in the sweave document.
>>> When there are no errors, no file handles are left open. However, once
>>> a file handle is stuck open, I can find no other way of closing it save
>>> for quitting out of R.
>>>
>>> Any help would be greatly appreciated! It would be nice to be able to
>>> write flawless sweave every time, but flawed as I am, I am having to
>>> restart R continuously.
>>
>>
>> I'd suggest a different workflow, in which you run a new copy of R every
>> time you want to Sweave a document. The files will be closed when that copy
>> dies, and the results are less likely to be affected by the current state of
>> your workspace (assuming you don't load an old workspace in the new copy).
>>
>> For example, when I'm working on a Sweave document, I spend my time in my
>> text editor, and get it to run R to process the file whenever I want to see
>> what the output looks like.
>>
>> The only real disadvantages to this approach that I can think of are that
>> you need to figure out how to tell your text editor to run R (and that might
>> be hard if you're using a poor editor like Windows Notebook, but is usually
>> easy), and it will run a tiny bit slower because you need to start up R
>> every time.
>>
>> Duncan Murdoch
>>
>>
>>> Thanks,
>>> Allie
>>>
>>>
>>> OS: Windows 7 Pro x64 SP1
>>>
>>>
>>>> sessionInfo()
>>> R version 2.14.2 (2012-02-29)
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>>
>>> test.Rnw:
>>>
>>> \documentclass{article}
>>> \title {file handle test}
>>> \author{test author}
>>> \usepackage{Sweave}
>>> \begin {document}
>>> \maketitle
>>>
>>> \SweaveOpts{prefix.string=sweave}
>>>
>>> \begin{figure}
>>> \begin{center}
>>>
>>> <>=
>>> df = data.frame(a=rnorm(100), b=rnorm(100), group = c("g1",
>>> "g2", "g3", "g4"))
>>> plot(df$a, df$y, foo)
>>> @
>>>
>>> \caption{test figure one}
>>> \label{fig:one}
>>> \end{center}
>>> \end{figure}
>>> \end{document}
>>>
>>>
>>>
>>> Sweave command run:
>>>
>>> Sweave("test.Rnw", syntax="SweaveSyntaxNoweb")
>>>
>>>
>>>
>>> Sweave.sty:
>>>
>>> \NeedsTeXFormat{LaTeX2e}
>>> \ProvidesPackage{Sweave}{}
>>>
>>> \RequirePackage{ifthen}
>>> \newboolean{Sweave@gin}
>>> \setboolean{Sweave@gin}{true}
>>> \newboolean{Sweave@ae}
>>> \setboolean{Sweave@ae}{true}
>>>
>>> \DeclareOption{nogin}{\setboolean{Sweave@gin}{fa
Re: [R] Rgui maintains open file handles after Sweave error
Thanks for the nice ideas, Duncan. I think that would work nicely in
most cases. The major issue with that workflow in my case is that the
scripts to set up my workspace take around a half-hour to run (I really
wish CUDA was working with my setup!), so running R each time in that
case is time-consuming.
Perhaps I should be working more with intermediate files, or perhaps
writing the workspace out to an .Rdata file and reading that in the
sweave document instead of running the entire data-prep script.
Thanks,
Allie
On 4/5/2012 11:22 AM, Duncan Murdoch wrote:
> On 04/04/2012 3:25 PM, Alexander Shenkin wrote:
>> Hello Folks,
>>
>> When I run the document below through sweave, rgui.exe/rsession.exe
>> leaves a file handle open to the sweave-001.pdf graphic (as verified by
>> process explorer). Pdflatex.exe then crashes (with a Permission Denied
>> error) because the graphic file is locked.
>>
>> This only seems to happen when there is an error in the sweave document.
>> When there are no errors, no file handles are left open. However, once
>> a file handle is stuck open, I can find no other way of closing it save
>> for quitting out of R.
>>
>> Any help would be greatly appreciated! It would be nice to be able to
>> write flawless sweave every time, but flawed as I am, I am having to
>> restart R continuously.
>
> I'd suggest a different workflow, in which you run a new copy of R every
> time you want to Sweave a document. The files will be closed when that
> copy dies, and the results are less likely to be affected by the current
> state of your workspace (assuming you don't load an old workspace in the
> new copy).
>
> For example, when I'm working on a Sweave document, I spend my time in
> my text editor, and get it to run R to process the file whenever I want
> to see what the output looks like.
>
> The only real disadvantages to this approach that I can think of are
> that you need to figure out how to tell your text editor to run R (and
> that might be hard if you're using a poor editor like Windows Notebook,
> but is usually easy), and it will run a tiny bit slower because you need
> to start up R every time.
>
> Duncan Murdoch
>
>> Thanks,
>> Allie
>>
>>
>> OS: Windows 7 Pro x64 SP1
>>
>>
>> > sessionInfo()
>> R version 2.14.2 (2012-02-29)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>>
>> test.Rnw:
>>
>> \documentclass{article}
>> \title {file handle test}
>> \author{test author}
>> \usepackage{Sweave}
>> \begin {document}
>> \maketitle
>>
>> \SweaveOpts{prefix.string=sweave}
>>
>> \begin{figure}
>> \begin{center}
>>
>> <>=
>> df = data.frame(a=rnorm(100), b=rnorm(100), group = c("g1",
>> "g2", "g3", "g4"))
>> plot(df$a, df$y, foo)
>> @
>>
>> \caption{test figure one}
>> \label{fig:one}
>> \end{center}
>> \end{figure}
>> \end{document}
>>
>>
>>
>> Sweave command run:
>>
>> Sweave("test.Rnw", syntax="SweaveSyntaxNoweb")
>>
>>
>>
>> Sweave.sty:
>>
>> \NeedsTeXFormat{LaTeX2e}
>> \ProvidesPackage{Sweave}{}
>>
>> \RequirePackage{ifthen}
>> \newboolean{Sweave@gin}
>> \setboolean{Sweave@gin}{true}
>> \newboolean{Sweave@ae}
>> \setboolean{Sweave@ae}{true}
>>
>> \DeclareOption{nogin}{\setboolean{Sweave@gin}{false}}
>> \DeclareOption{noae}{\setboolean{Sweave@ae}{false}}
>> \ProcessOptions
>>
>> \RequirePackage{graphicx,fancyvrb}
>> \IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
>>
>>
>> \ifthenelse{\boolean{Sweave@gin}}{\setkeys{Gin}{width=0.8\textwidth}}{}%
>> \ifthenelse{\boolean{Sweave@ae}}{%
>>\RequirePackage[T1]{fontenc}
>>\RequirePackage{ae}
>> }{}%
>>
>> \DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
>> \DefineVerbatimEnvironment{Soutput}{Verbatim}{}
>> \DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
>>
>> \newenvironment{Schunk}{}{}
>>
>> \newcommand{\Sconcordance}[1]{%
>>\ifx\pdfoutput\undefined%
>>\csname newcount\endcsname\pdfoutput\fi%
>>\ifcase\pdfoutput\special{#1}%
>>\else\immediate\pdfobj{#1}\fi}
>>
>> __
>> 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] Rgui maintains open file handles after Sweave error
Here is Dr. Leisch's advice for dealing with open handles (and it works):
> On 4/5/2012 4:22 AM, Friedrich Leisch wrote:
> ...
> You need to close the pdf device, not an open connection:
>
> R> Sweave("test.Rnw")
> Writing to file test.tex
> Processing code chunks with options ...
> 1 : keep.source term verbatim pdf
>
> Error: chunk 1
> Error in plot.xy(xy, type, ...) : object 'foo' not found
> R> ls()
> [1] "col.yellowbg" "df"
> R> dev.list()
> pdf
> 2
> R> dev.off()
> null device
> 1
> Best,
> Fritz
On 4/4/2012 2:52 PM, Alexander Shenkin wrote:
> Thanks for the reply, Henrik. Process Explorer still shows the file
> handle as being open, but R only shows the following:
>
>> showConnections(all=TRUE)
> description class mode text isopen can read can write
> 0 "stdin" "terminal" "r" "text" "opened" "yes""no"
> 1 "stdout""terminal" "w" "text" "opened" "no" "yes"
> 2 "stderr""terminal" "w" "text" "opened" "no" "yes"
>>
>
> On 4/4/2012 2:45 PM, Henrik Bengtsson wrote:
>> See ?closeAllConnections
>>
>> Suggestion to the maintainer of Sweave: "atomify" the figure
>> generation, e.g. use { pdf(); on.exit(dev.off()); {...}; } or similar,
>> instead of { pdf(); {...}; dev.off(); } possibly by leaving a copy of
>> the fault figure file for troubleshooting.
>>
>> /Henrik
>>
>> On Wed, Apr 4, 2012 at 12:25 PM, Alexander Shenkin wrote:
>>> Hello Folks,
>>>
>>> When I run the document below through sweave, rgui.exe/rsession.exe
>>> leaves a file handle open to the sweave-001.pdf graphic (as verified by
>>> process explorer). Pdflatex.exe then crashes (with a Permission Denied
>>> error) because the graphic file is locked.
>>>
>>> This only seems to happen when there is an error in the sweave document.
>>> When there are no errors, no file handles are left open. However, once
>>> a file handle is stuck open, I can find no other way of closing it save
>>> for quitting out of R.
>>>
>>> Any help would be greatly appreciated! It would be nice to be able to
>>> write flawless sweave every time, but flawed as I am, I am having to
>>> restart R continuously.
>>>
>>> Thanks,
>>> Allie
>>>
>>>
>>> OS: Windows 7 Pro x64 SP1
>>>
>>>
>>>> sessionInfo()
>>> R version 2.14.2 (2012-02-29)
>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>
>>>
>>> test.Rnw:
>>>
>>>\documentclass{article}
>>>\title {file handle test}
>>>\author{test author}
>>>\usepackage{Sweave}
>>>\begin {document}
>>>\maketitle
>>>
>>>\SweaveOpts{prefix.string=sweave}
>>>
>>>\begin{figure}
>>>\begin{center}
>>>
>>><>=
>>>df = data.frame(a=rnorm(100), b=rnorm(100), group = c("g1",
>>> "g2", "g3", "g4"))
>>>plot(df$a, df$y, foo)
>>>@
>>>
>>>\caption{test figure one}
>>>\label{fig:one}
>>>\end{center}
>>>\end{figure}
>>>\end{document}
>>>
>>>
>>>
>>> Sweave command run:
>>>
>>>Sweave("test.Rnw", syntax="SweaveSyntaxNoweb")
>>>
>>>
>>>
>>> Sweave.sty:
>>>
>>>\NeedsTeXFormat{LaTeX2e}
>>>\ProvidesPackage{Sweave}{}
>>>
>>>\RequirePackage{ifthen}
>>>\newboolean{Sweave@gin}
>>>\setboolean{Sweave@gin}{true}
>>>\newboolean{Sweave@ae}
>>>\setboolean{Sweave@ae}{true}
>>>
>>>\DeclareOption{nogin}{\setboolean{Sweave@gin}{false}}
>>>\DeclareOption{noae}{\setboolean{Sweave@ae}{false}}
>>>\ProcessOptions
>>>
>>>\RequirePackage{graphicx,fancyvrb}
>>>\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
>>>
>>>\ifthenelse{\boolean{Sweave@gin}}{\setkeys{Gin}{width=0.8\textwidth}}{}%
>>>\ifthenelse{\boolean{Sweave@ae}}{%
>>> \RequirePackage[T1]{fontenc}
>>> \RequirePackage{ae}
>>>}{}%
>>>
>>>\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
>>>\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
>>>\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
>>>
>>>\newenvironment{Schunk}{}{}
>>>
>>>\newcommand{\Sconcordance}[1]{%
>>> \ifx\pdfoutput\undefined%
>>> \csname newcount\endcsname\pdfoutput\fi%
>>> \ifcase\pdfoutput\special{#1}%
>>> \else\immediate\pdfobj{#1}\fi}
>>>
>>> __
>>> 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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rgui maintains open file handles after Sweave error
Thanks for the reply, Henrik. Process Explorer still shows the file
handle as being open, but R only shows the following:
> showConnections(all=TRUE)
description class mode text isopen can read can write
0 "stdin" "terminal" "r" "text" "opened" "yes""no"
1 "stdout""terminal" "w" "text" "opened" "no" "yes"
2 "stderr""terminal" "w" "text" "opened" "no" "yes"
>
On 4/4/2012 2:45 PM, Henrik Bengtsson wrote:
> See ?closeAllConnections
>
> Suggestion to the maintainer of Sweave: "atomify" the figure
> generation, e.g. use { pdf(); on.exit(dev.off()); {...}; } or similar,
> instead of { pdf(); {...}; dev.off(); } possibly by leaving a copy of
> the fault figure file for troubleshooting.
>
> /Henrik
>
> On Wed, Apr 4, 2012 at 12:25 PM, Alexander Shenkin wrote:
>> Hello Folks,
>>
>> When I run the document below through sweave, rgui.exe/rsession.exe
>> leaves a file handle open to the sweave-001.pdf graphic (as verified by
>> process explorer). Pdflatex.exe then crashes (with a Permission Denied
>> error) because the graphic file is locked.
>>
>> This only seems to happen when there is an error in the sweave document.
>> When there are no errors, no file handles are left open. However, once
>> a file handle is stuck open, I can find no other way of closing it save
>> for quitting out of R.
>>
>> Any help would be greatly appreciated! It would be nice to be able to
>> write flawless sweave every time, but flawed as I am, I am having to
>> restart R continuously.
>>
>> Thanks,
>> Allie
>>
>>
>> OS: Windows 7 Pro x64 SP1
>>
>>
>>> sessionInfo()
>> R version 2.14.2 (2012-02-29)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>>
>> test.Rnw:
>>
>>\documentclass{article}
>>\title {file handle test}
>>\author{test author}
>>\usepackage{Sweave}
>>\begin {document}
>>\maketitle
>>
>>\SweaveOpts{prefix.string=sweave}
>>
>>\begin{figure}
>>\begin{center}
>>
>><>=
>>df = data.frame(a=rnorm(100), b=rnorm(100), group = c("g1",
>> "g2", "g3", "g4"))
>>plot(df$a, df$y, foo)
>>@
>>
>>\caption{test figure one}
>>\label{fig:one}
>>\end{center}
>>\end{figure}
>>\end{document}
>>
>>
>>
>> Sweave command run:
>>
>>Sweave("test.Rnw", syntax="SweaveSyntaxNoweb")
>>
>>
>>
>> Sweave.sty:
>>
>>\NeedsTeXFormat{LaTeX2e}
>>\ProvidesPackage{Sweave}{}
>>
>>\RequirePackage{ifthen}
>>\newboolean{Sweave@gin}
>>\setboolean{Sweave@gin}{true}
>>\newboolean{Sweave@ae}
>>\setboolean{Sweave@ae}{true}
>>
>>\DeclareOption{nogin}{\setboolean{Sweave@gin}{false}}
>>\DeclareOption{noae}{\setboolean{Sweave@ae}{false}}
>>\ProcessOptions
>>
>>\RequirePackage{graphicx,fancyvrb}
>>\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
>>
>>\ifthenelse{\boolean{Sweave@gin}}{\setkeys{Gin}{width=0.8\textwidth}}{}%
>>\ifthenelse{\boolean{Sweave@ae}}{%
>> \RequirePackage[T1]{fontenc}
>> \RequirePackage{ae}
>>}{}%
>>
>>\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
>>\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
>>\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
>>
>>\newenvironment{Schunk}{}{}
>>
>>\newcommand{\Sconcordance}[1]{%
>> \ifx\pdfoutput\undefined%
>> \csname newcount\endcsname\pdfoutput\fi%
>> \ifcase\pdfoutput\special{#1}%
>> \else\immediate\pdfobj{#1}\fi}
>>
>> __
>> 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.
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Rgui maintains open file handles after Sweave error
Hello Folks,
When I run the document below through sweave, rgui.exe/rsession.exe
leaves a file handle open to the sweave-001.pdf graphic (as verified by
process explorer). Pdflatex.exe then crashes (with a Permission Denied
error) because the graphic file is locked.
This only seems to happen when there is an error in the sweave document.
When there are no errors, no file handles are left open. However, once
a file handle is stuck open, I can find no other way of closing it save
for quitting out of R.
Any help would be greatly appreciated! It would be nice to be able to
write flawless sweave every time, but flawed as I am, I am having to
restart R continuously.
Thanks,
Allie
OS: Windows 7 Pro x64 SP1
> sessionInfo()
R version 2.14.2 (2012-02-29)
Platform: i386-pc-mingw32/i386 (32-bit)
test.Rnw:
\documentclass{article}
\title {file handle test}
\author{test author}
\usepackage{Sweave}
\begin {document}
\maketitle
\SweaveOpts{prefix.string=sweave}
\begin{figure}
\begin{center}
<>=
df = data.frame(a=rnorm(100), b=rnorm(100), group = c("g1",
"g2", "g3", "g4"))
plot(df$a, df$y, foo)
@
\caption{test figure one}
\label{fig:one}
\end{center}
\end{figure}
\end{document}
Sweave command run:
Sweave("test.Rnw", syntax="SweaveSyntaxNoweb")
Sweave.sty:
\NeedsTeXFormat{LaTeX2e}
\ProvidesPackage{Sweave}{}
\RequirePackage{ifthen}
\newboolean{Sweave@gin}
\setboolean{Sweave@gin}{true}
\newboolean{Sweave@ae}
\setboolean{Sweave@ae}{true}
\DeclareOption{nogin}{\setboolean{Sweave@gin}{false}}
\DeclareOption{noae}{\setboolean{Sweave@ae}{false}}
\ProcessOptions
\RequirePackage{graphicx,fancyvrb}
\IfFileExists{upquote.sty}{\RequirePackage{upquote}}{}
\ifthenelse{\boolean{Sweave@gin}}{\setkeys{Gin}{width=0.8\textwidth}}{}%
\ifthenelse{\boolean{Sweave@ae}}{%
\RequirePackage[T1]{fontenc}
\RequirePackage{ae}
}{}%
\DefineVerbatimEnvironment{Sinput}{Verbatim}{fontshape=sl}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{}
\DefineVerbatimEnvironment{Scode}{Verbatim}{fontshape=sl}
\newenvironment{Schunk}{}{}
\newcommand{\Sconcordance}[1]{%
\ifx\pdfoutput\undefined%
\csname newcount\endcsname\pdfoutput\fi%
\ifcase\pdfoutput\special{#1}%
\else\immediate\pdfobj{#1}\fi}
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] summaryBy: transformed variable on RHS of formula?
Hi Folks, I'm trying to cut my data inside the summaryBy function. Perhaps formulas don't work that way? I'd like to avoid adding another column if possible, but if I have to, I have to. Any ideas? Thanks, Allie require(doBy) df = dataframe(a <- rnorm(100), b <-rnorm(100)) summaryBy(a ~ cut(b,c(-100,-1,1,100)), data=df) # preferred solution, but it throws an error # Error in `[.data.frame`(data, , rh.var, drop = FALSE) : undefined columns selected df$c = cut(b,c(-100,-1,1,100)) summaryBy(a ~ c, data=df) # works fine __ 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] dot products
Hello,
I need to take a dot product of each row of a dataframe and a vector.
The number of columns will be dynamic. The way I've been doing it so
far is contorted. Is there a better way?
dotproduct <- function(dataf, v2) {
apply(t(t(as.matrix(a)) * v2),1,sum) #contorted!
}
df = data.frame(a=c(1,2,3),b=c(4,5,6))
vec = c(4,5)
dotproduct(df, vec)
thanks,
allie
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Vectorizing a loop
Hello Folks,
I'm trying to vectorize a loop that processes rows of a dataframe. It
involves lots of conditionals, such as "If column 10 == 3, and if column
3 is True, and both column 5 and 6 are False, then set column 4 to True".
So, for example, any ideas about vectorizing the following?
df = data.frame( list(a=c(1,2,3,4), b=c("a","b","c","d"), c=c(T,F,T,F),
d=NA, e=c(F,F,T,T)) )
for (i in 1:nrow(df)) {
if (df[i,3] %in% c(FALSE,NA) & (df[i,1] > 2 | df[i,5]) ) {
df[i,4] = 1
}
if (df[i,5] %in% c(TRUE, NA) & df[i,2] == "b") {
df[i,4] = 2
df[i,5] = T
}
}
Thanks,
Allie
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] strange date problem - May 3, 1992 is NA
On 6/22/2011 4:09 PM, Brian Diggs wrote:
> On 6/22/2011 1:37 PM, Alexander Shenkin wrote:
>> On 6/22/2011 3:34 PM, Brian Diggs wrote:
>>> On 6/22/2011 12:09 PM, Luke Miller wrote:
>>>> For what it's worth, I cannot reproduce this problem under a nearly
>>>> identical instance of R (R 2.12.1, Win 7 Pro 64-bit). I also can't
>>>> reproduce the problem with R 2.13.0. You've got something truly weird
>>>> going on with your particular instance of R.
>>>>
>>>>
>>>>> is.na(strptime("5/3/1992", format="%m/%d/%Y"))
>>>> [1] FALSE
>>>>> is.na(strptime("5/2/1992", format="%m/%d/%Y"))
>>>> [1] FALSE
>>>>> sessionInfo()
>>>> R version 2.12.1 (2010-12-16)
>>>> Platform: i386-pc-mingw32/i386 (32-bit)
>>>>
>>>> locale:
>>>> [1] LC_COLLATE=English_United States.1252
>>>> [2] LC_CTYPE=English_United States.1252
>>>> [3] LC_MONETARY=English_United States.1252
>>>> [4] LC_NUMERIC=C
>>>> [5] LC_TIME=English_United States.1252
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> other attached packages:
>>>> [1] rj_0.5.2-1 lattice_0.19-17
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] grid_2.12.1 rJava_0.8-8 tools_2.12.1
>>>
>>> Like Luke, I can not reproduce what you see in (an old installation of)
>>> R 2.12.1 (and it also didn't have rj, lattice, grid, rJava, or tools
>>> attached or loaded in any way).
>>>
>>> My vague gut feeling is it might be a timezone/daylight savings time
>>> related issue (though usually times have to be involved). At least,
>>> that is a common problem with weird things happening with dates.
>>>
>>> What do you get as output for the following?
>>>
>>> Sys.timezone()
>>> Sys.info()
>>> conflicts()
>>> dput(strptime("5/3/1992", format="%m/%d/%Y"))
>>> dput(as.POSIXct(strptime("5/3/1992", format="%m/%d/%Y")))
>>> dput(strptime("5/2/1992", format="%m/%d/%Y"))
>>> dput(as.POSIXct(strptime("5/2/1992", format="%m/%d/%Y")))
>>
>>> Sys.timezone()
>> [1] "COT"
>>> Sys.info()
>> sysname release
>> version nodename machine
>> "Windows" "7 x64" "build 7601,
>> Service Pack 1" "machine_name""x86"
>> login user
>>"username" "username"
>>> conflicts()
>> [1] "untangle.specials" "body<-""format.pval"
>> "round.POSIXt" "trunc.POSIXt" "units"
>>> dput(strptime("5/3/1992", format="%m/%d/%Y"))
>> structure(list(sec = 0, min = 0L, hour = 0L, mday = 3L, mon = 4L,
>> year = 92L, wday = 0L, yday = 123L, isdst = -1L), .Names = c("sec",
>> "min", "hour", "mday", "mon", "year", "wday", "yday", "isdst"
>> ), class = c("POSIXlt", "POSIXt"))
>>> dput(as.POSIXct(strptime("5/3/1992", format="%m/%d/%Y")))
>> structure(NA_real_, class = c("POSIXct", "POSIXt"), tzone = "")
>>> dput(strptime("5/2/1992", format="%m/%d/%Y"))
>> structure(list(sec = 0, min = 0L, hour = 0L, mday = 2L, mon = 4L,
>> year = 92L, wday = 6L, yday = 122L, isdst = 0L), .Names = c("sec",
>> "min", "hour", "mday", "mon", "year", "wday", "yday", "isdst"
>> ), class = c("POSIXlt", "POSIXt"))
>>> dput(as.POSIXct(strptime("5/2/1992", format="%m/%d/%Y")))
>> structure(704782800, class = c("POSIXct", "POSIXt"), tzone = "")
>>
>
> Fun :)
>
> So, not being familiar with COT, I looked it up to see what/when the
> daylight savings times switch overs are/were.
>
> http://www.timeanddate.com/worldclock/timezone.html?n=41&syear=1990
>
Re: [R] strange date problem - May 3, 1992 is NA
On 6/22/2011 3:34 PM, Brian Diggs wrote:
> On 6/22/2011 12:09 PM, Luke Miller wrote:
>> For what it's worth, I cannot reproduce this problem under a nearly
>> identical instance of R (R 2.12.1, Win 7 Pro 64-bit). I also can't
>> reproduce the problem with R 2.13.0. You've got something truly weird
>> going on with your particular instance of R.
>>
>>
>>> is.na(strptime("5/3/1992", format="%m/%d/%Y"))
>> [1] FALSE
>>> is.na(strptime("5/2/1992", format="%m/%d/%Y"))
>> [1] FALSE
>>> sessionInfo()
>> R version 2.12.1 (2010-12-16)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] rj_0.5.2-1 lattice_0.19-17
>>
>> loaded via a namespace (and not attached):
>> [1] grid_2.12.1 rJava_0.8-8 tools_2.12.1
>
> Like Luke, I can not reproduce what you see in (an old installation of)
> R 2.12.1 (and it also didn't have rj, lattice, grid, rJava, or tools
> attached or loaded in any way).
>
> My vague gut feeling is it might be a timezone/daylight savings time
> related issue (though usually times have to be involved). At least,
> that is a common problem with weird things happening with dates.
>
> What do you get as output for the following?
>
> Sys.timezone()
> Sys.info()
> conflicts()
> dput(strptime("5/3/1992", format="%m/%d/%Y"))
> dput(as.POSIXct(strptime("5/3/1992", format="%m/%d/%Y")))
> dput(strptime("5/2/1992", format="%m/%d/%Y"))
> dput(as.POSIXct(strptime("5/2/1992", format="%m/%d/%Y")))
> Sys.timezone()
[1] "COT"
> Sys.info()
sysname release
version nodename machine
"Windows" "7 x64" "build 7601,
Service Pack 1" "machine_name""x86"
login user
"username" "username"
> conflicts()
[1] "untangle.specials" "body<-""format.pval"
"round.POSIXt" "trunc.POSIXt" "units"
> dput(strptime("5/3/1992", format="%m/%d/%Y"))
structure(list(sec = 0, min = 0L, hour = 0L, mday = 3L, mon = 4L,
year = 92L, wday = 0L, yday = 123L, isdst = -1L), .Names = c("sec",
"min", "hour", "mday", "mon", "year", "wday", "yday", "isdst"
), class = c("POSIXlt", "POSIXt"))
> dput(as.POSIXct(strptime("5/3/1992", format="%m/%d/%Y")))
structure(NA_real_, class = c("POSIXct", "POSIXt"), tzone = "")
> dput(strptime("5/2/1992", format="%m/%d/%Y"))
structure(list(sec = 0, min = 0L, hour = 0L, mday = 2L, mon = 4L,
year = 92L, wday = 6L, yday = 122L, isdst = 0L), .Names = c("sec",
"min", "hour", "mday", "mon", "year", "wday", "yday", "isdst"
), class = c("POSIXlt", "POSIXt"))
> dput(as.POSIXct(strptime("5/2/1992", format="%m/%d/%Y")))
structure(704782800, class = c("POSIXct", "POSIXt"), tzone = "")
>
>
>> On Wed, Jun 22, 2011 at 2:40 PM, Alexander Shenkin
>> wrote:
>>> On 6/22/2011 1:34 PM, Sarah Goslee wrote:
>>>> On Wed, Jun 22, 2011 at 2:28 PM, David
>>>> Winsemius wrote:
>>>>>
>>>>> On Jun 22, 2011, at 2:03 PM, Sarah Goslee wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> On Wed, Jun 22, 2011 at 11:40 AM, Alexander Shenkin
>>>>>> wrote:
>>>>>>>>
>>>>>>>> is.na(strptime("5/2/1992", format="%m/%d/%Y"))
>>>>>>>
>>>>>>> [1] FALSE
>>>>>>>>
>>>>>>>> is.na(strptime("5/3/1992", format="%m/%d/%Y"))
>>>>>>>
>>>>>>> [1] TRUE
>>>>>>
>>>>>> I c
Re: [R] strange date problem - May 3, 1992 is NA
Wow. Setting my timezone to UTC -5 Bogota (where there is no daylight
savings time), I get the error:
> is.na(strptime("5/3/1992", format="%m/%d/%Y"))
[1] TRUE
But setting it to UTC -5 East Coast Time (whether or not I tell windows
to adjust for DST) I get:
> is.na(strptime("5/3/1992", format="%m/%d/%Y"))
[1] FALSE
Can others test this on their systems? How strange. I wonder how much
tropical forest carbon this will account for. :-)
Thanks,
Allie
On 6/22/2011 3:23 PM, William Dunlap wrote:
> The isdst value -1 doesn't seem right. Shouldn't it
> be either 0 (not daylight savings time) or 1 (yes dst)?
> I've only seen isdst==-1 when all the other entries
> were NA (that happens when the string doesn't match
> the format).
>
> In the parts of the US where daylight savings time is
> used the switchover took place near the beginning of
> April in 1992, so you should have isdst=1 by May 3.
> Perhaps you have an odd timezone file on your machine.
>
> Bill Dunlap
> Spotfire, TIBCO Software
> wdunlap tibco.com
>
>> -Original Message-
>> From: Alexander Shenkin [mailto:ashen...@ufl.edu]
>> Sent: Wednesday, June 22, 2011 1:07 PM
>> To: William Dunlap
>> Subject: Re: [R] strange date problem - May 3, 1992 is NA
>>
>> Hi Bill,
>>
>> Thanks for your reply. The results look almost identical to my eyes,
>> except for the mysterious "TRUE"...
>>
>>> methods("is.na")
>> [1] is.na.data.frame is.na.numeric_version is.na.POSIXlt
>>> trace(methods("is.na"), quote(cat(" is.na: class(x)=",
>> class(x), "\n")))
>> Tracing function "is.na.data.frame" in package "base"
>> Tracing function "is.na.numeric_version" in package "base"
>> Tracing function "is.na.POSIXlt" in package "base"
>> [1] "is.na.data.frame" "is.na.numeric_version" "is.na.POSIXlt"
>>> z <- strptime("5/3/1992", format="%m/%d/%Y")
>>> is.na(z)
>> Tracing is.na.POSIXlt(z) on entry
>> is.na: class(x)= POSIXlt POSIXt
>> [1] TRUE
>>> str(unclass(z))
>> List of 9
>> $ sec : num 0
>> $ min : int 0
>> $ hour : int 0
>> $ mday : int 3
>> $ mon : int 4
>> $ year : int 92
>> $ wday : int 0
>> $ yday : int 123
>> $ isdst: int -1
>>
>>
>>> sessionInfo()
>> R version 2.12.1 (2010-12-16)
>> Platform: i386-pc-mingw32/i386 (32-bit)
>>
>> locale:
>> [1] LC_COLLATE=English_United States.1252
>> [2] LC_CTYPE=English_United States.1252
>> [3] LC_MONETARY=English_United States.1252
>> [4] LC_NUMERIC=C
>> [5] LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> loaded via a namespace (and not attached):
>> [1] tools_2.12.1
>>
>> thanks,
>> allie
>>
>> On 6/22/2011 1:50 PM, William Dunlap wrote:
>>> What do you get for the following commands, which
>>> show which is.na method is getting called and
>>> the internal structure of the dataset made
>>> by strptime?
>>>
>>>> methods("is.na")
>>> [1] is.na.data.frame is.na.numeric_version is.na.POSIXlt
>>>> trace(methods("is.na"), quote(cat(" is.na: class(x)=", class(x),
>>> "\n")))
>>> Tracing function "is.na.data.frame" in package "base"
>>> Tracing function "is.na.numeric_version" in package "base"
>>> Tracing function "is.na.POSIXlt" in package "base"
>>> [1] "is.na.data.frame" "is.na.numeric_version" "is.na.POSIXlt"
>>>> z <- strptime("5/3/1992", format="%m/%d/%Y")
>>>> is.na(z)
>>> Tracing is.na.POSIXlt(z) on entry
>>> is.na: class(x)= POSIXlt POSIXt
>>> [1] FALSE
>>>> str(unclass(z))
>>> List of 9
>>> $ sec : num 0
>>> $ min : int 0
>>> $ hour : int 0
>>> $ mday : int 3
>>> $ mon : int 4
>>> $ year : int 92
>>> $ wday : int 0
>>> $ yday : int 123
>>> $ isdst: int 1
>>>
>>>
>>>
>>> Bill Dunlap
>>> Spotfire, TIBCO Software
>>> wdunlap tibco.com
>>>
>>>> -Original Message-
>>>> From: r-help-boun...@r-project.org
>>>> [mailt
Re: [R] strange date problem - May 3, 1992 is NA
On 6/22/2011 1:34 PM, Sarah Goslee wrote:
> On Wed, Jun 22, 2011 at 2:28 PM, David Winsemius
> wrote:
>>
>> On Jun 22, 2011, at 2:03 PM, Sarah Goslee wrote:
>>
>>> Hi,
>>>
>>> On Wed, Jun 22, 2011 at 11:40 AM, Alexander Shenkin
>>> wrote:
>>>>>
>>>>> is.na(strptime("5/2/1992", format="%m/%d/%Y"))
>>>>
>>>> [1] FALSE
>>>>>
>>>>> is.na(strptime("5/3/1992", format="%m/%d/%Y"))
>>>>
>>>> [1] TRUE
>>>
>>> I can't reproduce your problem on R 2.13.0 on linux:
>>
>> I also cannot reproduce it on a Mac with 2.13.0 beta
>
> Which strongly suggests that you should start by upgrading your R
> installation if at all possible.
>
> I'd also recommend trying it on a default R session, with no extra
> packages loaded, and no items in your workspace. It's possible that
> something else is interfering.
>
> On linux, that's achieved by typing R --vanilla at the command line.
> I'm afraid I don't know how to do it for Windows, but should be
> similarly straightforward.
>
Thanks Sarah. Still getting the problem. I should surely upgrade, but
still, not a bad idea to get to the bottom of this, or at least have it
documented as a known issue. BTW, I'm on Windows 7 Pro x64.
(running Rgui.exe --vanilla):
> is.na(strptime("5/3/1992", format="%m/%d/%Y"))
[1] TRUE
> is.na(strptime("5/2/1992", format="%m/%d/%Y"))
[1] FALSE
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
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Re: [R] strange date problem - May 3, 1992 is NA
On 6/22/2011 1:03 PM, Sarah Goslee wrote:
> Hi,
>
> On Wed, Jun 22, 2011 at 11:40 AM, Alexander Shenkin wrote:
>>> is.na(strptime("5/2/1992", format="%m/%d/%Y"))
>> [1] FALSE
>>> is.na(strptime("5/3/1992", format="%m/%d/%Y"))
>> [1] TRUE
>
> I can't reproduce your problem on R 2.13.0 on linux:
>
>> strptime("5/2/1992", format="%m/%d/%Y")
> [1] "1992-05-02"
>> is.na(strptime("5/2/1992", format="%m/%d/%Y"))
> [1] FALSE
>> strptime("5/3/1992", format="%m/%d/%Y")
> [1] "1992-05-03"
>> is.na(strptime("5/3/1992", format="%m/%d/%Y"))
> [1] FALSE
>
> My suspicion is that you imported the data from a spreadsheet and
> there's some formatting glitch that's not showing up. If you type the
> string "5/3/1992" into the command by hand, do you still get the same
> result?
Copy and pasting the above lines reproduces the problem on my setup.
> If so, then we need to know your OS and version of R, at least.
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid grDevices datasets splines graphics stats tcltk
utils methods base
other attached packages:
[1] ggplot2_0.8.9 proto_0.3-8 reshape_0.8.4 plyr_1.4
svSocket_0.9-51 TinnR_1.0.3 R2HTML_2.2 Hmisc_3.8-3
survival_2.36-2
loaded via a namespace (and not attached):
[1] cluster_1.13.2 digest_0.4.2lattice_0.19-17 svMisc_0.9-61
tools_2.12.1
>
>> Any idea what's going on with this? Running strptime against all dates
>> from around 1946, only 5/3/1992 was converted as "NA". Even stranger,
>> it still seems to have a value associated with it (even though is.na
>> thinks it's NA):
>>
>>> strptime("5/3/1992", format="%m/%d/%Y")
>> [1] "1992-05-03"
>
> This makes no sense to me.
>
> Sarah
>
>
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[R] strange date problem - May 3, 1992 is NA
> is.na(strptime("5/2/1992", format="%m/%d/%Y"))
[1] FALSE
> is.na(strptime("5/3/1992", format="%m/%d/%Y"))
[1] TRUE
Any idea what's going on with this? Running strptime against all dates
from around 1946, only 5/3/1992 was converted as "NA". Even stranger,
it still seems to have a value associated with it (even though is.na
thinks it's NA):
> strptime("5/3/1992", format="%m/%d/%Y")
[1] "1992-05-03"
Thanks,
Allie
R
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[R] reproduction archives
Hello Folks, As some of my old code broke when an updated package changed its interface, I started thinking about reproduction of analyses. It's not good enough to save our code - we have to save the package versions those analyses used as well as the R-core. I saw a couple references to "reproduction archives" around, but nothing specific. Is there any good way to package up code along with the relevant packages and R version in order to guarantee that we can reproduce our results in the future? I suppose that one could make note of all package versions, etc, but automating the process would mean that it would be followed more often. (also, tracking down those packages and installing them all just to reproduce a result could be an undertaking). Thanks, Allie __ 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] holding objects in dataframes
Hello list, I need to keep track of objects that are related to particular observations. In this case, I need to keep track of polygons that are associated with observations. What I would ideally have is one column of a dataframe hold a "polygonal" object (from the spatstat package). My question: I seem to have managed to do it, but as I haven't read that dataframes are supposed to be able to hold list elements or objects this way, I wanted to ask if I'm violating things here in a way such that my code may break in future R releases. (that is, am i relying on non-guaranteed behavior). My other option is to created a named list or something along those lines, and just match() the dataframe and named list when i need access to the related objects. Please see below for the code. Thoughts and suggestions are greatly appreciated! By tinkering around, I've found that dataframe columns do seem to be able to hold list elements: a=data.frame(i=c(1,2),j=c(3,4)) z=list(x=c(1,2,3)) a$k=NA a[1,]$k=z > str(a) 'data.frame': 2 obs. of 3 variables: $ i: num 1 2 $ j: num 3 4 $ k:List of 2 ..$ : num 1 2 3 ..$ : logi NA Extending that behavior, I can attach "polygonal" objects to dataframes it seems: library(spatstat) a=data.frame( a=c(1,2), b=c(3,4) ) a$polygons=NA a[1,]$polygons = list(disc(radius=50)) > str(a) 'data.frame': 2 obs. of 3 variables: $ a : num 1 2 $ b : num 3 4 $ polygons:List of 2 ..$ :List of 5 .. ..$ type : chr "polygonal" .. ..$ xrange: num -50 50 .. ..$ yrange: num -50 50 .. ..$ bdry :List of 1 .. .. ..$ :List of 4 .. .. .. ..$ x : num 50 49.9 49.8 49.5 49 ... .. .. .. ..$ y : num 0 2.45 4.9 7.34 9.75 ... .. .. .. ..$ area: num 7851 .. .. .. ..$ hole: logi FALSE .. ..$ units :List of 3 .. .. ..$ singular : chr "unit" .. .. ..$ plural: chr "units" .. .. ..$ multiplier: num 1 .. .. ..- attr(*, "class")= chr "units" .. ..- attr(*, "class")= chr "owin" ..$ : logi NA > area.owin(a[1,]$polygons[[1]]) [1] 7850.828 thanks, allie __ 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] RODBC for 64-bit R with 32-bit Access
Hello Folks,
I do hope this is the correct place to post (and not in R-SIG-DB). I have
spent the better part of a day searching for an answer to this question, and
have yet to resolve it.
I am trying to query an .accdb Access database (with 32-bit Office 2007
currently residing on the machine) with 64-bit R via RODBC. There seem to
be some conflicting accounts as to whether or not this is possible.
Ripley's ODBC Connectivity PDF and the odbcConnect docs indicate it is not
possible (copied below for reference). However, this thread (
http://r.789695.n4.nabble.com/RODBC-Access-Excel-driver-location-for-64-bit-Win7-td2542550.html)
seems to indicate that it may be possible by using
c:\windows\sysWOW64\odbcad32.exe:
"For 64-bit WIn 7, I needed to use the ODBC in
c:\windows\sysWOW64\odbcad32.exe. I configured RODBC in the 'usual' way for
the 64-bit ODBC (i.e., per the R Import/Export manual) and everything is
fine."
I have tried creating DSN's using c:\windows\sysWOW64\odbcad32.exe and
referencing those with RODBC, but I come up with errors:
> library(RODBC);
> channel <- odbcConnect("myDSN");
Warning messages:
1: In odbcDriverConnect("DSN=myDSN") :
[RODBC] ERROR: state IM014, code 0, message [Microsoft][ODBC Driver
Manager] The specified DSN contains an architecture mismatch between the
Driver and Application
2: In odbcDriverConnect("DSN=myDSN") : ODBC connection failed
If anyone knows any more about this issue, I would be grateful for the
information!
Thanks,
Allie
R 2.12.0
Windows 7 Pro x64
Access 2007
from Ripley's ODBC Connectivity
"32-bit Windows drivers for Access 2007 and Excel 2007 are bundled with
Office 2007 but can be installed separately via the installer
AccessDatabaseEngine.exe available from The Access/Excel 2010 versions
at ... have a 64-bit version: however the 64-bit drivers cannot be installed
alongside 32-bit versions of Office (as far as we know, and defnitely not
for Office 2007)."
odbcConnect docs:
"You must have the 32-bit drivers when using 32-bit R and the 64-bit drivers
when using 64-bit R: otherwise there will be a cryptic message about a
driver not being found. And the 64-bit drivers cannot be installed alongside
32-bit Microsoft Office, and vice versa."
[[alternative HTML version deleted]]
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[R] dmultinomial
Hello All,
I'm trying to run a maximum likelihood analysis using dmultinomial (i'm
avoiding dmultinom as I'd like to run it with vectors for the ML stuff).
However, I'm having a hard time getting even the simplest example
running. Any help would be greatly appreciated.
> library(mc2d)
> dmultinomial(x=c(0,0,1),prob=c(1,1,1),size=1,log=TRUE)
Error in if (ncol(x) != K) stop("x[] and prob[] must be equal length
vectors or equal col matrix.") :
argument is of length zero
# Once I get the simple stuff above running, I'd like to be able to do
the following:
> testmat=rmultinomial(4, 1, prob)
> testmat
[,1] [,2] [,3]
[1,]100
[2,]001
[3,]001
[4,]001
> dmultinomial(x=testmat,prob=prob,size=1,log=TRUE)
Error in if (!is.null(size) && nrow(size) != n) size <- matrix(t(size), :
missing value where TRUE/FALSE needed
thanks,
allie
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and provide commented, minimal, self-contained, reproducible code.
[R] dmultinomial
Hello All,
I'm trying to run a maximum likelihood analysis using dmultinomial (i'm
avoiding dmultinom as I'd like to run it with vectors for the ML stuff).
However, I'm having a hard time getting even the simplest example
running. Any help would be greatly appreciated.
> library(mc2d)
> dmultinomial(x=c(0,0,1),prob=c(1,1,1),size=1,log=TRUE)
Error in if (ncol(x) != K) stop("x[] and prob[] must be equal length
vectors or equal col matrix.") :
argument is of length zero
# Once I get the simple stuff above running, I'd like to be able to do
the following:
> testmat=rmultinomial(4, 1, prob)
> testmat
[,1] [,2] [,3]
[1,]100
[2,]001
[3,]001
[4,]001
> dmultinomial(x=testmat,prob=prob,size=1,log=TRUE)
Error in if (!is.null(size) && nrow(size) != n) size <- matrix(t(size), :
missing value where TRUE/FALSE needed
thanks,
allie
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and provide commented, minimal, self-contained, reproducible code.
[R] translate vector of numbers to indicies of 0/1 matrix
Hello All, Searched around, haven't found a decent solution. I'd like to translate a vector of numbers to a matrix (or to a list of vectors) such that the vector values would serve as indicies of the 1's in an otherwise-zero-filled matrix (or list of vectors). For example: > a = c(1,3,3,4) # perform operation [,1] [,2] [,3] [,4] [1,]1000 [2,]0010 [3,]0010 [4,]0001 Any help greatly appreciated! thanks, allie __ 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] finding euclidean proximate points in two datasets
On 5/20/2010 9:18 AM, David Winsemius wrote:
>
> On May 20, 2010, at 10:02 AM, Alexander Shenkin wrote:
>
>> Hello all,
>>
>> I've been pouring through the various spatial packages, but haven't come
>> across the right thing yet.
>
> There is a SIG for such questions.
thanks - just joined it.
>> Given a set of points in 2-d space X, i'm trying to find the subset of
>> points in Y proximate to each point in X. Furthermore, the proximity
>> threshold of each point in X differs (X$threshold). I've constructed
>> this myself already, but it's horrificly slow with a dataset of 40k+
>> points in one set, and a 700 in the other.
>>
>> A very inefficient example of what I'm looking for:
>
> Not really a reproducible example. If euclidean_dist is a function ,
> then it is not one in any of the packages I have installed.
it's not reproducible - i'll make a better effort to include
reproducible code in the future. and that function is just one i would
have written, but didn't want to clog the email with code. Anyway, here
is a reproducible example:
X = data.frame(x=c(1,2,3), y=c(2,3,1), threshold=c(1,2,4))
Y = data.frame(x=c(5,2,3,4,2,5,2,3), y=c(5,2,2,4,1,2,3,1))
proximate=list()
i=1
for (pt in 1:length(X$x)) {
proximate[[i]] <- sqrt((X[pt,]$x - Y$x)^2 + (X[pt,]$y - Y$y)^2) >
X[pt,]$threshold
i=i+1
}
proximate
>>
>>for (pt in X$idx) {
>>proximity[i] = euclidian_dist(X[pt]$x, X[pt]$y, Y$x, Y$y) <
>> X$threshold
>> i = i+1
>>}
>>
>
> Have you considered first creating a subset of candidate points that are
> within "threshold" of each reference point on both coordinates. That
> might sidestep a lot of calculations on points that are easily
> eliminated on a single comparison. Then you could calculate distances
> within that surviving subset of points. On average that should give you
> an over 50% "hit rate":
>
>> (4/3)*pi*0.5^3
> [1] 0.5235988
That's a nice idea. I'll still be waiting quite a while while my
machine cranks, but not as long. Still - I suspect there would be much
bigger gains if there were tailored packages. I'll re-post over on
sig-geo about that. thanks.
>> Perhaps crossdist() in spatstat is what I should use, and then code a
>> comparison with X$threshold after the cross-distances are computed.
>> However, I was wondering if there was another tool I should be
>> considering. Any and all thoughts are very welcome. Thanks in advance.
>>
>> Thanks,
>> Allie
>> --
>> Alexander Shenkin
>> PhD Candidate
>> School of Natural Resources and Environment
>> University of Florida
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] finding euclidean proximate points in two datasets
Hello all,
I've been pouring through the various spatial packages, but haven't come
across the right thing yet.
Given a set of points in 2-d space X, i'm trying to find the subset of
points in Y proximate to each point in X. Furthermore, the proximity
threshold of each point in X differs (X$threshold). I've constructed
this myself already, but it's horrificly slow with a dataset of 40k+
points in one set, and a 700 in the other.
A very inefficient example of what I'm looking for:
for (pt in X$idx) {
proximity[i] = euclidian_dist(X[pt]$x, X[pt]$y, Y$x, Y$y) <
X$threshold
i = i+1
}
Perhaps crossdist() in spatstat is what I should use, and then code a
comparison with X$threshold after the cross-distances are computed.
However, I was wondering if there was another tool I should be
considering. Any and all thoughts are very welcome. Thanks in advance.
Thanks,
Allie
--
Alexander Shenkin
PhD Candidate
School of Natural Resources and Environment
University of Florida
http://snre.ufl.edu/people/students.asp
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Re: [R] export dataframe's column classes to a list
It does indeed! thank you very much, and thanks to mark leeds as well,
who emailed me off list with a similar solution.
On 5/19/2010 3:49 PM, Peter Alspach wrote:
> Tena koe Allie
>
> Does
>
> sapply(myframe, class)
>
> do what you want?
>
> Peter Alspach
>
>
>> -Original Message-
>> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-
>> project.org] On Behalf Of Alexander Shenkin
>> Sent: Thursday, 20 May 2010 8:19 a.m.
>> To: r-help@r-project.org
>> Subject: [R] export dataframe's column classes to a list
>>
>> Hi Folks,
>>
>> I want to export a dataframe's column classes to a list so that I can
>> reinstantiate the dataframe from a CSV file in the future. (I know
>> about save(), which I'm using in addition to this).
>>
>> what I want to do is the following:
>> write.csv(myframe);
>> col_classes = get_col_classes(myframe);
>> write.csv(col_classes, "column_classes")
>>
>> ... time passes, R gets closed, etc ...
>>
>> col_classes = read.csv("column_classes")
>> new_myframe = read.csv("myfile.csv", colClasses = col_classes)
>>
>>
>> My question is how to construct the "get_col_classes()" function
>>
> above.
>
>> Any thoughts are greatly appreciated!
>>
>> Thanks,
>> Allie
>>
>> --
>> Alexander Shenkin
>> PhD Candidate
>> School of Natural Resources and Environment
>> University of Florida
>>
>> http://snre.ufl.edu/people/students.asp
>>
>> __
>> 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.
>>
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] export dataframe's column classes to a list
Hi Folks,
I want to export a dataframe's column classes to a list so that I can
reinstantiate the dataframe from a CSV file in the future. (I know
about save(), which I'm using in addition to this).
what I want to do is the following:
write.csv(myframe);
col_classes = get_col_classes(myframe);
write.csv(col_classes, "column_classes")
... time passes, R gets closed, etc ...
col_classes = read.csv("column_classes")
new_myframe = read.csv("myfile.csv", colClasses = col_classes)
My question is how to construct the "get_col_classes()" function above.
Any thoughts are greatly appreciated!
Thanks,
Allie
--
Alexander Shenkin
PhD Candidate
School of Natural Resources and Environment
University of Florida
http://snre.ufl.edu/people/students.asp
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] timing a function
You could also put the call to system.time inside the function itself:
f = function(x) {
system.time({
... #function's code
ret_val = ...
}); flush.console();
return ret_val;
}
i s'pose you'd miss out on the time taken to jump to the function code,
return the value, etc, but for functions that are heavy at all, that
wouldn't trip you up.
allie
On 5/17/2010 2:06 PM, Barry Rowlingson wrote:
> On Mon, May 17, 2010 at 6:24 PM, Peter Ehlers wrote:
>
>
>> Try
>> system.time(y <- f(x))
>>
>> and see ?"=".
>>
>> -Peter Ehlers
>>
> Ah ha. That explains the curly brackets I saw in a posting with
> system.time on stack overflow just now:
>
> system.time({y=f(x)})
>
> works as expected since the {} pair make a new code block. Also you
> can then time more than one statement:
>
> system.time({y=f(x);z=g(y)})
>
> - gives the total time for f(x) and g(y).
>
> Barry
>
> __
> 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.
>
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] pnmath on windows
Hello All, I'd like to enable threaded computing on my system (windows 7 pro x64) if possible. pnmath seems to be the most accepted solution out there for the time being, but it requires compiling. Are there binaries for windows available that don't require manual compiliation? If not, does anyone know what the bottleneck there is? That is, what keeps me from compiling it myself and handing it to a friend with another windows system? Thanks, Allie -- Alexander Shenkin PhD Candidate School of Natural Resources and Environment University of Florida http://snre.ufl.edu/people/students.asp __ 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] R for windows 64 bit
Hi Alessia, Note that, while your physical limit might be 6 GB, Windows memory management allows more memory than that to be allocated (aka Virtual Memory, or at least that's what they called it in XP). Windows swaps out memory from RAM to the hard disk and back when necessary (please excuse the explanation if you already know all this). For processing large vectors, this swapping might bring your system to a standstill. Regardless, the "maximum" memory for a windows process is larger than the physical RAM you have available. allie On 1/12/2010 6:27 AM, alessia matano wrote: > Fine, it worked. I will try in this way. > > Just the last question and I won't bother you further today. My > machine right now has just 6 giga of RAM (it will be increased to 16 > in a few days), and I see that with this experimental version > memory.limit is 6135. > > How is the command to increase the memory usage until the maximum I > can (5 giga?). If I am writing memory.limit(5000) it still gives me > the error: > > don't be silly! Your machine has a 4Gb address limit > > which is quite odd. > > Many thanks > Best > A. > > 2010/1/12 alessia matano : > >> ok, perfect! >> I will try with it...many many thanks. Have you got there also the >> quantreg package, which has actually the same problem of sparseM >> (32bit version)? >> >> best >> alessia >> >> 2010/1/12 Uwe Ligges : >> >>> >>> On 12.01.2010 12:09, alessia matano wrote: >>> I am sorry, I know it is an experimental version, and I have been misleading saying a new version. Therefore, I will wait for when they will be available officially, since it is just a few days. >>> Or just use today my private repository I indicated in the other mail. >>> >>> Uwe Ligges >>> >>> >>> However, I tried also to go to the cran pages and download them and insert into the library. For quantreg it worked, for sparseM it did not probably because it's a win32 version, as you said. 2010/1/12 Prof Brian Ripley: > On Tue, 12 Jan 2010, alessia matano wrote: > > >> Dear all, >> >> I just download and set this new version of R. I am now trying to >> download the packages I need which are sperseM and quantreg. I >> downloaded and insert into the library file the quantreg pacjkage and >> it seems to work. However, when I try to do the same with sparseM I >> get the following error message: >> >> Loading required package: SparseM >> Error in inDL(x, as.logical(local), as.logical(now), ...) : >> unable to load shared library >> 'C:/PROGRA~1/R/R-211~1.0DE/library/SparseM/libs/SparseM.dll': >> LoadLibrary failure: %1 non è un'applicazione di Win32 valida. >> >> >> Any help for it? >> > Please do refer to the posting referred to in that thread (and Henrique, > please do not post just the URL without the explanations). > > https://stat.ethz.ch/pipermail/r-devel/2010-January/056301.html > > You cannot mix 32-bit Windows binary packages with this experimental port > (it is not a 'new version'): you need to install from the package > sources. > If that is too difficult for you, please do not try to use unsupported > experimental builds (and Uwe Ligges may have some binary packages > available > for test in a few days). > > > >> Thanks a lot >> alessia >> >> 2010/1/11 Henrique Dallazuanna: >> >>> Try this version (beta of development version): >>> >>> http://www.stats.ox.ac.uk/pub/RWin/Win64/R-2.11.0dev-win64.exe >>> >>> On Mon, Jan 11, 2010 at 2:29 PM, alessia matano >>> wrote: >>> Dear all, do you know if there is any particular version of R to implement with windows 64 bit, in such a way to increase the amount of memory it can use? How should I increase the memory, and more importantly to set a higher max vector size? It still stops me saying "Could not allocate vector of size 145" thanks to all alessia __ 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. >>> >>> >>> -- >>> Henrique Dallazuanna >>> Curitiba-Paraná-Brasil >>> 25° 25' 40" S 49° 16' 22" O >>> >>> >> __ >> 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-gu
Re: [R] Avoiding loops
Though, from my limited understanding, the 'apply' family of functions
are actually just loops. Please correct me if I'm wrong. So, while
more readable (which is important), they're not necessarily more
efficient than explicit 'for' loops.
allie
On 9/2/2009 3:13 AM, Phil Spector wrote:
> Here's one way (assuming your data frame is named dat):
>
>with(dat,
> data.frame(a,t(sapply(a,function(x){
>apply(dat[a - x >= -5 & a - x <=
> 0,c('b','c')],2,sum)}
>
>
> - Phil Spector
> Statistical Computing Facility
> Department of Statistics
> UC Berkeley
> spec...@stat.berkeley.edu
>
>
>
> On Tue, 1 Sep 2009, dolar wrote:
>
>>
>> Would like some tips on how to avoid loops as I know they are slow in R
>>
>> i've got a data frame :
>>
>> a b c
>> 1 5 2
>> 4 6 9
>> 5 2 3
>> 8 3 2
>>
>> What i'd like is to sum for each value of a, the sum of b and the sum
>> of c
>> where a equal to or less than (with a distance of 5)
>>
>> i.e. for row three
>> we have a=5
>> i'd like to sum up b and sum up c with the above rule
>> since 5, 4 and 1 are less than (within a distance of 5) or equal to
>> 5, then
>> we should get the following result:
>>
>> a b c
>> 5 13 14
>>
>> the overall result should be
>> a b c
>> 1 5 2
>> 4 11 11
>> 5 13 14
>> 8 11 14
>>
>> how can i do this without a loop?
>> --
>> View this message in context:
>> http://www.nabble.com/Avoiding-loops-tp25251376p25251376.html
>> Sent from the R help mailing list archive at Nabble.com.
>>
>> __
>> 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.
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Re: [R] Regular expression to define contents between parentheses
Hi Judith,
This probably isn't the only way to do it, but:
gsub("\\(.*?\\)", "", myvector, perl=TRUE)
seems to do the trick.
The problem is that regular expressions are greedy, so you were matching
everything between the first and last parens, as you noticed. Putting
the question mark there makes it a "minimal" matching operation.
Apparently this is only implemented in perl regex's, or at least in that
syntax. Hence the 'perl=TRUE'.
hth,
allie
On 8/25/2009 3:17 PM, Judith Flores wrote:
> Hello dear R-helpers,
>
>I haven't been able to figure out of find a solution in the R-help
> archives about how to delete all the characters contained in groups of
> parenthesis. I have a vector that looks more or less like this:
>
> myvector<-c("something (80 km/h, sd) & more (6 kg/L,sd)", "somethingelse (48
> m/s, sd) & moretoo (50g/L , sd)")
>
> I want to extract all the strings that are not contained in parenthesis, the
> goal would be to obtain the following new vector:
>
> subvector<-c("something & more", "somethingelse & moretoo")
>
> I tried the following, but this pattern seems to enclose all that is included
> between the first opened parenthesis and the last closed parethesis, which
> makes sense, but it's not what I need:
>
> subvector<-gsub("\\((.*)\\)","",myvector
>
>
> Your help will be very appreciated.
>
> Thank you,
>
> Judith
>
> __
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> 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.
>
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Re: [R] Convert list to data frame while controlling column types
On 8/24/2009 2:06 AM, Petr PIKAL wrote:
> Hi
>
> r-help-boun...@r-project.org napsal dne 23.08.2009 17:29:48:
>
>> On 8/23/2009 9:58 AM, David Winsemius wrote:
>>> I still have problems with this statement. As I understand R, this
>> should be impossible. I have looked at both you postings and neither of
>> them clarify the issues. How can you have blanks or spaces in an R
>> numeric vector?
>>
>>
>> Just because I search numeric columns doesn't mean that my regex matches
>> them! I posted some info on my data frame in an earlier email:
>>
>> str(final_dataf)
>> 'data.frame': 1127 obs. of 43 variables:
>> $ block : Factor w/ 1 level "2": 1 1 1 1 1 1 1 1 1 1 ...
>> $ treatment : Factor w/ 4 levels "I","M","N","T": 1 1 1 1 1 1 ...
>> $ transect : Factor w/ 1 level "4": 1 1 1 1 1 1 1 1 1 1 ...
>> $ tag: chr NA "121AL" "122AL" "123AL" ...
>> ...
>> $ h1 : num NA NA NA NA NA NA NA NA NA NA ...
>> ...
>>
>> You can see that I do indeed have some numeric columns. And while I
>
> Well, AFAICS you have a data frame with 3 columns which are factors and 1
> which is character. I do not see any numeric column. If you want to change
> block and transect to numeric you can use
>
> df$block <- as.numeric(as.character(df$block))
If you take a closer look at my data frame listing, you'll see that it
is "1127 obs. of 43 variables". I edited the column listing for
readability, and you'll see even in my editing listing I do indeed have
one numeric column - "h1". And as I mentioned earlier, I use
colClasses, so no need to change anything to numeric here.
>
>> search them for spaces, I only do so because my dataset isn't so large
>> as to require me to exclude them from the search. If my dataset grows
>> too big at some point, I will exclude numeric columns, and other columns
>> which cannot hold blanks or spaces.
>>
>> To clarify further with an example:
>>
>>> df = data.frame(a=c(1,2,3,4,5),b=c("a","","c","d"," "))
>>> df = as.data.frame(lapply(df, function(x){ is.na(x) <-
>> + grep('^\\s*$',x); return(x) }), stringsAsFactors = FALSE)
>>> df
>> ab
>> 1 1a
>> 2 2
>> 3 3c
>> 4 4d
>> 5 5
>
> which can be done also by
> df[,2] <- levels(df[,2])[1:2]<-NA
>
> but maybe with less generalization
Yes - my point was to show how I looped through an entire data frame
looking for \\s*, even when some of the columns were numeric. I gave
this simple example with a 2-column data frame to illustrate that point.
>>> str(df)
>> 'data.frame': 5 obs. of 2 variables:
>> $ a: num 1 2 3 4 5
>> $ b: Factor w/ 5 levels ""," ","a","c",..: 3 NA 4 5 NA
>>
>> And one final clarification: I left out "as.data.frame" in my previous
>> solution. So it now becomes:
>>
>>> final_dataf = as.data.frame(lapply(final_dataf, function(x){ is.na(x)
>> + <- grep('^\\s*$',x); return(x) }), stringsAsFactors = FALSE)
>
> Again not too much of clarification, in your first data frame second
> column is a factor with some levels you want to convert to NA, which can
> be done by different approaches.
This clarification was to show the code that worked (for posterity), as
my previous post left out an argument. It seems that perhaps you missed
the previous emails.
> Your final_dataf is same as df.
Yes, that is the point. As I mentioned in the first email of this
thread, I was trying to get around as.data.frame's automatic conversion
routines, in order to retain the original column types. And it turned
out that gsub() was more of the problem than as.data.frame() was.
Please refer to the earlier emails for more information on that.
> Columns which shall be numeric and are read as factor/character by
> read.table likely contain some values which strictly can not be considered
> numeric. You can see them quite often in Excel like programs and some
> examples are
>
> 1..2, o.5, 12.o5 and or spaces, "-" e.t.c.
>
> and you usually need handle them by hand.
>
> Regards
> Petr
>
>> Hope that clarifies things, and thanks for your help.
>>
>> Thanks,
>> Allie
>>
>>
>> On 8/23/2009 9:58 AM, David Winsemius wrote:
>>> On Aug 23, 2009, at 2:47 AM, Alexander Shenkin wrote:
>>>
>>>> On 8/21/200
Re: [R] Convert list to data frame while controlling column types
On 8/23/2009 9:58 AM, David Winsemius wrote:
> I still have problems with this statement. As I understand R, this
should be impossible. I have looked at both you postings and neither of
them clarify the issues. How can you have blanks or spaces in an R
numeric vector?
Just because I search numeric columns doesn't mean that my regex matches
them! I posted some info on my data frame in an earlier email:
str(final_dataf)
'data.frame': 1127 obs. of 43 variables:
$ block : Factor w/ 1 level "2": 1 1 1 1 1 1 1 1 1 1 ...
$ treatment : Factor w/ 4 levels "I","M","N","T": 1 1 1 1 1 1 ...
$ transect : Factor w/ 1 level "4": 1 1 1 1 1 1 1 1 1 1 ...
$ tag: chr NA "121AL" "122AL" "123AL" ...
...
$ h1 : num NA NA NA NA NA NA NA NA NA NA ...
...
You can see that I do indeed have some numeric columns. And while I
search them for spaces, I only do so because my dataset isn't so large
as to require me to exclude them from the search. If my dataset grows
too big at some point, I will exclude numeric columns, and other columns
which cannot hold blanks or spaces.
To clarify further with an example:
> df = data.frame(a=c(1,2,3,4,5),b=c("a","","c","d"," "))
> df = as.data.frame(lapply(df, function(x){ is.na(x) <-
+ grep('^\\s*$',x); return(x) }), stringsAsFactors = FALSE)
> df
ab
1 1a
2 2
3 3c
4 4d
5 5
> str(df)
'data.frame': 5 obs. of 2 variables:
$ a: num 1 2 3 4 5
$ b: Factor w/ 5 levels ""," ","a","c",..: 3 NA 4 5 NA
And one final clarification: I left out "as.data.frame" in my previous
solution. So it now becomes:
> final_dataf = as.data.frame(lapply(final_dataf, function(x){ is.na(x)
+ <- grep('^\\s*$',x); return(x) }), stringsAsFactors = FALSE)
Hope that clarifies things, and thanks for your help.
Thanks,
Allie
On 8/23/2009 9:58 AM, David Winsemius wrote:
>
> On Aug 23, 2009, at 2:47 AM, Alexander Shenkin wrote:
>
>> On 8/21/2009 3:04 PM, David Winsemius wrote:
>>>
>>> On Aug 21, 2009, at 3:41 PM, Alexander Shenkin wrote:
>>>
>>>> Thanks everyone for their replies, both on- and off-list. I should
>>>> clarify, since I left out some important information. My original
>>>> dataframe has some numeric columns, which get changed to character by
>>>> gsub when I replace spaces with NAs.
>>>
>>> If you used is.na() <- that would not happen to a true _numeric_ vector
>>> (but, of course, a numeric vector in a data.frame could not have spaces,
>>> so you are probably not using precise terminology).
>>
>> I do have true numeric columns, but I loop through my entire dataframe
>> looking for blanks and spaces for convenience.
>
> I still have problems with this statement. As I understand R, this
> should be impossible. I have looked at both you postings and neither of
> them clarify the issues. How can you have blanks or spaces in an R
> numeric vector?
>
>
>>
>>> You would be well
>>> advised to include the actual code rather than applying loose
>>> terminology subject you your and our misinterpretation.
>>
>> I did include code in my previous email. Perhaps you were looking for
>> different parts.
>>
>>>
>>> ?is.na
>>>
>>>
>>> I am guessing that you were using read.table() on the original data, in
>>> which case you should look at the colClasses parameter.
>>>
>>
>> yep - I use read.csv, and I do use colClasses. But as I mentioned
>> earlier, gsub converts those columns to characters. Thanks for the tip
>> about is.na() <-. I'm now using the following, thus side-stepping the
>> whole "controlling as.data.frame's column conversion" issue:
>>
>> final_dataf = lapply(final_dataf, function(x){ is.na(x) <-
>> + grep('^\\s*$',x); return(x) })
>
>
> Good that you have a solution.
>
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
>
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Re: [R] Convert list to data frame while controlling column types
On 8/21/2009 3:04 PM, David Winsemius wrote:
>
> On Aug 21, 2009, at 3:41 PM, Alexander Shenkin wrote:
>
>> Thanks everyone for their replies, both on- and off-list. I should
>> clarify, since I left out some important information. My original
>> dataframe has some numeric columns, which get changed to character by
>> gsub when I replace spaces with NAs.
>
> If you used is.na() <- that would not happen to a true _numeric_ vector
> (but, of course, a numeric vector in a data.frame could not have spaces,
> so you are probably not using precise terminology).
I do have true numeric columns, but I loop through my entire dataframe
looking for blanks and spaces for convenience.
> You would be well
> advised to include the actual code rather than applying loose
> terminology subject you your and our misinterpretation.
I did include code in my previous email. Perhaps you were looking for
different parts.
>
> ?is.na
>
>
> I am guessing that you were using read.table() on the original data, in
> which case you should look at the colClasses parameter.
>
yep - I use read.csv, and I do use colClasses. But as I mentioned
earlier, gsub converts those columns to characters. Thanks for the tip
about is.na() <-. I'm now using the following, thus side-stepping the
whole "controlling as.data.frame's column conversion" issue:
final_dataf = lapply(final_dataf, function(x){ is.na(x) <-
+ grep('^\\s*$',x); return(x) })
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Re: [R] Convert list to data frame while controlling column types
Thanks everyone for their replies, both on- and off-list. I should
clarify, since I left out some important information. My original
dataframe has some numeric columns, which get changed to character by
gsub when I replace spaces with NAs. Thus, in going back to a
dataframe, those (now character) columns get converted to factors. I
recently added stringsAsFactors to get characters to make things a bit
easier. I wrote the column-type reset function below, but it feels
kludgey, so was wondering if there was some other way to specify how one
might want as.data.frame to handle the columns.
str(final_dataf)
'data.frame': 1127 obs. of 43 variables:
$ block : Factor w/ 1 level "2": 1 1 1 1 1 1 1 1 1 1 ...
$ treatment : Factor w/ 4 levels "I","M","N","T": 1 1 1 1 1 1 1 1 1 1 ...
$ transect : Factor w/ 1 level "4": 1 1 1 1 1 1 1 1 1 1 ...
$ tag: chr NA "121AL" "122AL" "123AL" ...
...
$ h1 : num NA NA NA NA NA NA NA NA NA NA ...
...
reset_col_types <- function (df, col_types) {
# Function to reset column types in dataframes. col_types can be
constructed
# by using lapply(class,df)
coerce_fun = list (
"character" = `as.character`,
"factor" = `as.factor`,
"numeric" = `as.numeric`,
"integer" = `as.integer`,
"POSIXct" = `as.POSIXct`,
"logical" = `as.logical` )
for (i in 1:length(df)) {
df[,i] = coerce_fun[[ col_types[i] ]]( df[,i] ) #apply coerce
function
}
return(df)
}
col_types = lapply(final_dataf, class)
col_types = lapply(col_types, function(x) x[length(x)]) # for posix,
take the more specified class
names(col_types)=NULL
col_types = unlist(col_types)
final_dataf = as.data.frame(lapply(final_dataf, function(x)
gsub('^\\s*$',NA,x)), stringsAsFactors = FALSE)
final_dataf = reset_col_types(final_dataf, col_types)
Thanks,
Allie
On 8/21/2009 10:54 AM, Steve Lianoglou wrote:
> Hi Allie,
>
> On Aug 21, 2009, at 11:47 AM, Alexander Shenkin wrote:
>
>> Hello all,
>>
>> I have a list which I'd like to convert to a data frame, while
>> maintaining control of the columns' data types (akin to the colClasses
>> argument in read.table). My numeric columns, for example, are getting
>> converted to factors by as.data.frame. Is there a way to do this, or
>> will I have to do as I am doing right now: allow as.data.frame to coerce
>> column-types as it sees fit, and then convert them back manually?
>
> This doesn't sound right ... are there characters buried in your
> numeric columns somewhere that might be causing this?
>
> I'm pretty sure this shouldn't happen, and a small test case here goes
> along with my intuition:
>
> R> a <- list(a=1:10, b=rnorm(10), c=LETTERS[1:10])
> R> df <- as.data.frame(a)
> R> sapply(df, is.factor)
> a b c
> FALSE FALSE TRUE
>
> Can you check to see if your data's wonky somehow?
>
> -steve
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
> | Memorial Sloan-Kettering Cancer Center
> | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>
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[R] Convert list to data frame while controlling column types
Hello all, I have a list which I'd like to convert to a data frame, while maintaining control of the columns' data types (akin to the colClasses argument in read.table). My numeric columns, for example, are getting converted to factors by as.data.frame. Is there a way to do this, or will I have to do as I am doing right now: allow as.data.frame to coerce column-types as it sees fit, and then convert them back manually? Thanks, Allie __ 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] Symbolic references - passing variable names into functions
Hello All,
I am trying to write a function which would operate on columns of a
dataframe specified in parameters passed to that function.
f = function(dataf, col1 = "column1", col2 = "column2") {
dataf$col1 = dataf$col2 # just as an example
}
The above, of course, does not work as intended. In some languages one
can force evaluation of a variable, and then use that evaluation as the
variable name. Thus,
> a = "myvar"
> (operator)a = 1
> myvar
[1] 1
Is there some operator which allows this symbolic referencing in R?
Thanks,
Allie
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