Re: [R] Fastest way to extract rows of smaller matrix many times by index to make larger matrix? and multiply columsn of matrix by vector
OK thanks, I thought it probably was, but always worth asking. the multiplication of the columns of M2 by V2 is as intended - not matrix multiplication. On Tue, 14 Sept 2021 at 17:49, Jeff Newmiller wrote: > That is about as fast as it can be done. However you may be able to avoid > doing it at all if you fold V2 into a matrix instead. Did you mean to use > matrix multiplication in your calculation of M3? > > On September 13, 2021 11:48:48 PM PDT, nevil amos > wrote: > >Hi is there a faster way to "extract" rows of a matrix many times to for a > >longer matrix based in a vector or for indices than M[ V, ] > > > >I need to "expand" ( rather than subset) a matrix M of 10-100,000 rows x > >~50 columns to produce a matrix with a greater number (10^6-10^8) of rows > >using a vector V containing the 10^6 -10^8 values that are the indices of > >the rows of M. the output matrix M2 is then multiplied by another vector > V2 > >With the same length as V. > > > >Is there a faster way to achieve these calculations (which are by far the > >slowest portion of a function looped 1000s of times? than the standard M2 > ><- M[ V, ] and M3<-M2*V2, the two calculations are taking a similar time, > >Matrix M also changes for each loop. > > > > > >M<-matrix(runif(50*1,0,100),nrow=1,ncol=50) > >x = 10^7 > >V<-sample(1:1,x,replace=T) > >V2<-(sample(c(1,NA),x,replace=T)) > >print<-(microbenchmark( > >M2<-M[V,], > >M3<-M2*V2, > >times=5,unit = "ms")) > > > > > > > >thanks for any suggestions > > > >Nevil Amos > > > > [[alternative HTML version deleted]] > > > >__ > >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. > > -- > Sent from my phone. Please excuse my brevity. > [[alternative HTML version deleted]] __ 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] Fastest way to extract rows of smaller matrix many times by index to make larger matrix? and multiply columsn of matrix by vector
Hi is there a faster way to "extract" rows of a matrix many times to for a longer matrix based in a vector or for indices than M[ V, ] I need to "expand" ( rather than subset) a matrix M of 10-100,000 rows x ~50 columns to produce a matrix with a greater number (10^6-10^8) of rows using a vector V containing the 10^6 -10^8 values that are the indices of the rows of M. the output matrix M2 is then multiplied by another vector V2 With the same length as V. Is there a faster way to achieve these calculations (which are by far the slowest portion of a function looped 1000s of times? than the standard M2 <- M[ V, ] and M3<-M2*V2, the two calculations are taking a similar time, Matrix M also changes for each loop. M<-matrix(runif(50*1,0,100),nrow=1,ncol=50) x = 10^7 V<-sample(1:1,x,replace=T) V2<-(sample(c(1,NA),x,replace=T)) print<-(microbenchmark( M2<-M[V,], M3<-M2*V2, times=5,unit = "ms")) thanks for any suggestions Nevil Amos [[alternative HTML version deleted]] __ 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] shinyFiles update shinySaveButton filename varaible from server
Is it possible to update the filename variable the shinySaveButton from
the server?
I want to provide a default filename based on a series of choices that the
user has made in the app ( here I have just made a random string to serve
the purpose. how do I feed output$defaultname
so that shinySaveButton( filename = outputSdefaultname )?
library(shiny)
library(shinyFiles)
data <- iris
roots <- c("UserFolder"=".")
ui <- fluidPage(
actionButton("makeName","Make Default File Name"),
shinySaveButton(id = "save", label = "Save file", title = "Save file as
...", filename = "defaultname",filetype=list(csv="csv"))
)
server <- shinyServer(function(input, output, session) {
rv <- reactiveValues()
observeEvent(input$makeName,{
output$defaultname<-paste(letters[sample(1:10,5)],collapse="")
})
observe({
shinyFileSave(input, "save", roots=roots, session=session)
fileinfo <- parseSavePath(roots, input$save)
xx<<-input$save
if (nrow(fileinfo) > 0) {
write.csv(, as.character(fileinfo$datapath))
}
session$allowReconnect("force")
})
})
runApp(list(
ui=ui,
server=server
))
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[R] setting wd to parent directory ("..") of rmd file for all chunks of .Rmd
The Rmarkdown cookbook states that the working directory for r chunks in an
Rmd file is usually the directory containing the file,
however it can be reset using
knitr::opts_knit$set(root.dir =
see:
https://bookdown.org/yihui/rmarkdown-cookbook/working-directory.html#working-directory
I want to set the directory to the parent direcotry of the default directory
usually I would acheive this using setwd("..") so in the rmd I used the
following:
```{r setup, include=FALSE,}
print(getwd())
knitr::opts_knit$set(root.dir = '..')
print(getwd())
```
the print(getwd()) being just to demonstrate the result. There is no
change in the directory.
How do I change the working directory ?
thanks
nevil Amos
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[R] using aws.s3::s3 sync to dowlaod files from public s3 Bucket without credentials?
Hi I am developing a package that reives on some large datasets stored in
aws s3.
I have made the bucket and all objects in the bucket public, but still
cannot sync them to my local directory without providing my AWS key pair.
without these credentials I get a "bucket does not exist" message.
Should it be possible to "see" and use
Sys.setenv("AWS_DEFAULT_REGION" =MYDEFAULTREGION)
aws.s3::s3sync (path ="./", bucket=MYBUCKETNAME,check_region = F,direction
= "download")
to download the bucket contents without providing a keypair where both
bucket and contents are public?
thanks
Nevil Amos
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Re: [R] Plot_ly bar plots - bars span sevral x values when there are missing values.
Hi Rasmus, thanks for that suggestion. It does indeed fix the column widths in this example. the reason it does this is becuase it means that the additonal 0 values added result in values for two adjacent columns. so if adjacent columns are present the "correct" column width is maintained df[c(3,4),]%>%plot_ly( x = ~ x, y = ~ y, type = "bar")%>% layout(xaxis = list(range = c(0,20)), title = "adjcant x values get correct column width") however if there are not tow adjacent columns then the width increases df[c(3,5),]%>%plot_ly( x = ~ x, y = ~ y, type = "bar")%>% layout(xaxis = list(range = c(0,20)), title = "gap between x values column width changes") given this I'm still not sure why the single value example produces a correct column width. for now the generic work around is to pad with y=0 as you suggested. On Wed, 10 Mar 2021 at 05:58, Rasmus Liland wrote: > Dear Nevil, > > Although I am a bit unfamiliar with > plotly, it seems it is possible to plot > two bars side by side at least: > > h <- df[3:4,] > p <- plotly::plot_ly( > data = h, > x = ~ x, > y = ~ y, > type = "bar") > p <- plotly::layout(p=p, > xaxis = list(range = c(0,20)), > title = "example 4 two bars side by side") > plotly::orca(p=p, file="amos4.png") > > Thus, if you want to only plot x=3 and > x=11 you need to set y=0 when x=4:10: > > h <- df[c(3, 11),] > h <- rbind(h, cbind(x=4:10, y=0)) > p <- plotly::plot_ly( > data = h, > x = ~ x, > y = ~ y, > type = "bar") > p <- plotly::layout(p=p, > xaxis = list(range = c(0,20)), > title = "example 2 corrected") > plotly::orca(p=p, file="amos2.png") > > I think this has to do with the xaxis > option in plotly::layout there, and not > with the bar width. > > Best, > Rasmus > [[alternative HTML version deleted]] __ 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] Plot_ly bar plots - bars span sevral x values when there are missing values.
I need to plot a number of bar charts as part of a shiny app. I am using ploty ly x and y values are both numeric x being consecutive integer values. there are often missing values in the data I wish to plot - each plot needs to have a fixed x range. When there are more than a few missing values the bars for the remaining values are being plotted much wider spanning several x values ( see example 2) curiously when there is a single remaining value the bar width is correct (example 3) how can I maintain a constant bar width regardless of number of missing values? I cannot find a bar-width setting. df<-data.frame(x=1:20,y=rnorm(20)^2) #twenty bars each centred above a single x value: df%>%plot_ly( x = ~ x, y = ~ y, type = "bar")%>% layout(xaxis = list(range = c(0,20)), title = "example 1") # this produces wide bars first one spread x= 0-6 second x= 8-14 # expected two column same width as in example 1 centred above x=3 and x=11 df[c(3,11),]%>%plot_ly( x = ~ x, y = ~ y, type = "bar")%>% layout(xaxis = list(range = c(0,20)), title = "example 2 column width expands across multiple x values") # when only a single bar is present it is again the correct width - in this case centred above x=3 df[3,]%>%plot_ly( x = ~ x, y = ~ y, type = "bar")%>% layout(xaxis = list(range = c(0,20)), title = "example 3 correct columns again") [[alternative HTML version deleted]] __ 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] [R-sig-Geo] raster::levels() not working in packaged function.
Many thanks,
That worked, since the NAMESPACE file incudes a warning about editing it
directly I ysed the reoygen tag in the fucntion script
#' @import raster.
On Sun, 1 Nov 2020 at 00:18, Marcelino de la Cruz Rot <
marcelino.delac...@urjc.es> wrote:
> Maybe including
>
> import(raster)
>
> or
>
> importFrom("raster", "levels")
>
> in the package NAMESPACE would help.
>
> Cheers,
>
> Marcelino
>
> El 31/10/2020 a las 13:24, nevil amos escribió:
> > Apologies, I cannot see how to make a rero for this issue.
> >
> > I have a function that uses levels(r) tor return the RAT of a raster "r"
> > when the function is sourced from a script
> > source(".\R\function.r")
> > it works fine.
> > when the function is built into a package and sourced from there
> > library(mypackage) using the same script file to make the package
> > levels(r)[[1]]
> > the same line throws an error, as levels(myraster returns NULL
> >
> > If I modify the script to include the raster namespace:
> > raster::levels(r)[[1]]
> > Then I get the error
> > Error: 'levels<-' is not an exported object from 'namespace:raster'
> >
> >
> > I have also tried just using levels(r) and putting raster as a depends
> > rather than an import in the DESCRIPTION file for the package, this does
> > not solve the error.
> >
> >
> > Any suggestions on how to overcome the problem?
> >
> > many thanks
> >
> > Nevil Amos
> >
> > [[alternative HTML version deleted]]
> >
> > ___
> > R-sig-Geo mailing list
> > r-sig-...@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> > .
>
>
> --
> Marcelino de la Cruz Rot
> Depto. de Biología y Geología
> Física y Química Inorgánica
> Universidad Rey Juan Carlos
> Móstoles España
>
>
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
[R] raster::levels() not working in packaged function.
Apologies, I cannot see how to make a rero for this issue.
I have a function that uses levels(r) tor return the RAT of a raster "r"
when the function is sourced from a script
source(".\R\function.r")
it works fine.
when the function is built into a package and sourced from there
library(mypackage) using the same script file to make the package
levels(r)[[1]]
the same line throws an error, as levels(myraster returns NULL
If I modify the script to include the raster namespace:
raster::levels(r)[[1]]
Then I get the error
Error: 'levels<-' is not an exported object from 'namespace:raster'
I have also tried just using levels(r) and putting raster as a depends
rather than an import in the DESCRIPTION file for the package, this does
not solve the error.
Any suggestions on how to overcome the problem?
many thanks
Nevil Amos
[[alternative HTML version deleted]]
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[R] Return filematrix column by column names instead of column index?
Is there a way to get columns out of a filematrix using the column name
directly in the same way that you can with a regular matrix?
library(filematrix)
M<-t(matrix(1:3,3,4))
colnames(M)<-c("one","two", "three")
M
#Extract column
M[,1]
M[,"one"]
M[,c(1,3)]
M[,c("one","three")]
FM<-fm.create.from.matrix(filenamebase = "test",mat = M)
FM[,1]
colnames(FM)
#extract by column by name does not work
FM[,"one"]
#workaround using grep
#is there a more direct way of doing this to retrieve more than one column?
FM[,grep("one",colnames(FM))]
FM[,c(grep("one",colnames(FM)),grep("three",colnames(FM)))]
many thanks for any suggestions
Nevil Amos
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[R] aws.s3::s3sync Error in curl::curl_fetch_disk(url, x$path, handle = handle) : Failed to open file
I am trying to use aws.s3::s3sync to sync the contents of a bucket to an
aws ec2 instance ( via rstudio server)
my script is as follows I cannot make a repro since that would need to be
run from the instance with my account key and details ( replaced with
xx below).
all files I am trying to sync are under the s3 prefix FAME_FMR which is
the only top level "directory" in the bucket
Have I missed a setting?
If not any suggestions on this error?
thanks
Nevil Amos
library(aws.s3)
Sys.setenv("AWS_ACCESS_KEY_ID" = "x",
"AWS_SECRET_ACCESS_KEY" =
"x",
"AWS_DEFAULT_REGION" = "ap-southeast-2")
myBucket<-"ecological-risk-analysis"
myPath<-"~/ShinyApps"
> bucket_exists(myBucket)[1][1] TRUE> dir.exists(myPath)[1] TRUE
>s3sync(path = myPath ,bucket =myBucket)
[998]
"FAME_FMR/HDMS/75m/BinaryThresholded/Satin_Bowerbird_Spp10679_Thresholded_Binary.tif"
[999]
"FAME_FMR/HDMS/75m/BinaryThresholded/Satin_Flycatcher_Spp10366_Thresholded_Binary.tif"
[1000]
"FAME_FMR/HDMS/75m/BinaryThresholded/Scaly_breasted_Lorikeet_Spp10256_Thresholded_Binary.tif"
[ reached getOption("max.print") -- omitted 191 entries ]1191 bucket
objects not found in local directory<== Saving object 'FAME_FMR/' to
'~/ShinyApps/FAME_FMR/'Error in curl::curl_fetch_disk(url, x$path,
handle = handle) :
Failed to open file /home/rstudio/ShinyApps/FAME_FMR/.
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[R] disk.frame change default directory that disk.frames are saved in?
I would like to change the default directory within which all disk frames are saved to a directory on an SSD, which is not the drive there the r tempdir is located. for example instead of saving all disk.frames in tempdir the are all saved in ./media/SSDdrive/DF? Thanks [[alternative HTML version deleted]] __ 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] repeat rows of matrix by number (k) in one colummatrix adding column j with values 1:k
OK sorted - hope these postings might help someone else
Any even faster options would be appreciated still
#seq() does not work but sequence() does
print("rep and sequence")
print(system.time({
j<-NULL
MOut<-NULL
MOut<-M[rep(1:nrow(M), times = M[,4]), ]
j<-sequence(M[,4])
MOut<-cbind(MOut,j)
colnames(Mout)<-c("x","y","z","j")
}))
On Wed, 1 Apr 2020 at 13:42, nevil amos wrote:
> Well,
> I found a way to do it partly using rep(), and one loop that makes it 10x
> or more faster however would still be good to do without the loop at all
> matrix made slightly beigger (1 rows):
>
> M<-matrix(c(1:3
> ), 1,3)
> M<-cbind(M,sample(1:5,size = 1,replace = T))
> #Print(M)
> #Create matrix (Mout) in this case 8 rows with x,y,z in each row of M
> #repeated k times with column j numbered from 1:k
> # ! can do with nested loops but this is very slow ( example below)
> #How do I acheive this quickly without loops?
> print("double loop")
> print(system.time({
> Mout<-NULL
>
> for(i in 1:nrow(M)){
> a=M[i,1:3]
> k=M[i,4]
> for (j in 1:k){
> b=c(a,j)
> Mout<-rbind(Mout,b)
> }
> }
> colnames(Mout)<-c("x","y","z","j")
> }))
>
> print("rep and single loop")
> print(system.time({
> j<-NULL
> MOut<-NULL
> MOut<-M[,1:3][rep(1:nrow(M), times = M[,4]), ]
> for(i in M[,4])(j<-c(j,1:i))
> MOut<-cbind(MOut,j)
> colnames(Mout)<-c("x","y","z","j")
> }))
>
> On Wed, 1 Apr 2020 at 12:18, nevil amos wrote:
>
>> Hi
>>
>> I can achieve this using two for loops but it is slow I need to do this
>> on many matrices with tens of millions of rows of x,y,z and k
>>
>> What is a faster method to achieve this, I cannot use rep as j changes in
>> each row of the new matrix
>> ###
>> M<-matrix(c(1,2,3,4,1,2,3,4,1,2,3,4, 2, 1, 3, 2
>> ), 4,4, dimnames = list(NULL, c("x", "y", "z","k")))
>>
>> Print(M)
>> #Create matrix (Mout) in this case 8 rows with x,y,z in each row of M
>> #repeated k times with column j numbered from 1:k
>> # ! can do with nested loops but this is very slow ( example below)
>> #How do I acheive this quickly without loops?
>> Mout<-NULL
>>
>> for(i in 1:nrow(M)){
>> a=M[i,c("x","y","z")]
>> for (j in 1:M[i,"k"]){
>> b=c(a,j)
>> Mout<-rbind(Mout,b)
>> }
>> }
>> colnames(Mout)[4]<-"j"
>> print(Mout)
>>
>> #
>>
>> Thanks
>>
>> Nevil Amos
>>
>
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Re: [R] repeat rows of matrix by number (k) in one colummatrix adding column j with values 1:k
Well,
I found a way to do it partly using rep(), and one loop that makes it 10x
or more faster however would still be good to do without the loop at all
matrix made slightly beigger (1 rows):
M<-matrix(c(1:3
), 1,3)
M<-cbind(M,sample(1:5,size = 1,replace = T))
#Print(M)
#Create matrix (Mout) in this case 8 rows with x,y,z in each row of M
#repeated k times with column j numbered from 1:k
# ! can do with nested loops but this is very slow ( example below)
#How do I acheive this quickly without loops?
print("double loop")
print(system.time({
Mout<-NULL
for(i in 1:nrow(M)){
a=M[i,1:3]
k=M[i,4]
for (j in 1:k){
b=c(a,j)
Mout<-rbind(Mout,b)
}
}
colnames(Mout)<-c("x","y","z","j")
}))
print("rep and single loop")
print(system.time({
j<-NULL
MOut<-NULL
MOut<-M[,1:3][rep(1:nrow(M), times = M[,4]), ]
for(i in M[,4])(j<-c(j,1:i))
MOut<-cbind(MOut,j)
colnames(Mout)<-c("x","y","z","j")
}))
On Wed, 1 Apr 2020 at 12:18, nevil amos wrote:
> Hi
>
> I can achieve this using two for loops but it is slow I need to do this
> on many matrices with tens of millions of rows of x,y,z and k
>
> What is a faster method to achieve this, I cannot use rep as j changes in
> each row of the new matrix
> ###
> M<-matrix(c(1,2,3,4,1,2,3,4,1,2,3,4, 2, 1, 3, 2
> ), 4,4, dimnames = list(NULL, c("x", "y", "z","k")))
>
> Print(M)
> #Create matrix (Mout) in this case 8 rows with x,y,z in each row of M
> #repeated k times with column j numbered from 1:k
> # ! can do with nested loops but this is very slow ( example below)
> #How do I acheive this quickly without loops?
> Mout<-NULL
>
> for(i in 1:nrow(M)){
> a=M[i,c("x","y","z")]
> for (j in 1:M[i,"k"]){
> b=c(a,j)
> Mout<-rbind(Mout,b)
> }
> }
> colnames(Mout)[4]<-"j"
> print(Mout)
>
> #
>
> Thanks
>
> Nevil Amos
>
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[R] repeat rows of matrix by number (k) in one colummatrix adding column j with values 1:k
Hi
I can achieve this using two for loops but it is slow I need to do this on
many matrices with tens of millions of rows of x,y,z and k
What is a faster method to achieve this, I cannot use rep as j changes in
each row of the new matrix
###
M<-matrix(c(1,2,3,4,1,2,3,4,1,2,3,4, 2, 1, 3, 2
), 4,4, dimnames = list(NULL, c("x", "y", "z","k")))
Print(M)
#Create matrix (Mout) in this case 8 rows with x,y,z in each row of M
#repeated k times with column j numbered from 1:k
# ! can do with nested loops but this is very slow ( example below)
#How do I acheive this quickly without loops?
Mout<-NULL
for(i in 1:nrow(M)){
a=M[i,c("x","y","z")]
for (j in 1:M[i,"k"]){
b=c(a,j)
Mout<-rbind(Mout,b)
}
}
colnames(Mout)[4]<-"j"
print(Mout)
#
Thanks
Nevil Amos
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[R] Cannot view custom tiles made in package tiler in r leaflet - either locally or from github pages server.
I wish to create tiled version of a large number of custom rasters for
viewing in shiny/leaflet apps ( to speed viewing of rasters)
I have produced tiles using package tiler, these can be viewed in the
preview.html, but when uploaded to github pages as described in the
introduction to tiler they do not show up when added as tiles in leaflet.
It is difficult to make a reproducible code here - since the tiles have to
be loaded to be served from the web.
However below I include the code used 1. to produce the tiles and 2, to
view the tiles in my github pages.
I have tried the suggestion of using {-y} in the sever path for TMS, this
makes no difference the background map is displayed but the custom tiles
are not.
Raster used from the package as an example in reality I need to serve many
1x6000 cell geotiffs.
Example code:
library(tiler)
libary(leaflet)
# make tiles in zoom levels 1:6 these tiles have then been uploaded to
github to serve from repository:
#
tile_dir<-"us48lr"
map <- system.file("maps/map_wgs84.tif", package = "tiler")
tile(map,tile_dir , "0-6")
view_tiles(tile_dir)
#no TMS related modifications
tiles <- "https://nevilamos.github.io/TileTest/us48lr/{z}/{x}/{y}.png;
leaflet(
options = leafletOptions(minZoom = 0, maxZoom = 7), width = "100%") %>%
addProviderTiles("Stamen.Toner") %>%
addTiles(urlTemplate=tiles, options = tileOptions(opacity = 0.8)) %>%
setView(-100, 40, 3)
#No tiles displayed
# {-y} and tileOptions(tms=T)
tiles <- "https://nevilamos.github.io/TileTest/us48lr/{z}/{x}/{-y}.png;
leaflet(
options = leafletOptions(minZoom = 0, maxZoom = 7), width = "100%") %>%
addProviderTiles("Stamen.Toner") %>%
addTiles(urlTemplate=tiles, options = tileOptions(opacity = 0.8,tms=T))
%>% setView(-100, 40, 3)
#No tiles displayed
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and provide commented, minimal, self-contained, reproducible code.
[R] reg expr that retains only bracketed text from strings
Hi
I am trying to extract only the text contained in brackets from a vector of
strings
not all of the strings contain closed bracketed text, they should return an
empty string or NA
this is what I have at the moment
mystrings<-c("ABC","A(B)C","AB(C)")
substring(mystrings, regexpr("\\(|\\)", mystrings))
#this returns the whole string if there are no brackets.
[1] "ABC" "(B)C" "(C)"
# my desired desired output:
#[1] "" "(B)" "(C)"
many thanks for any suggestions
Nevil Amos
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and provide commented, minimal, self-contained, reproducible code.
[R] profvis function parse_rprof not being loaded
I have loaded the profvis library but the function parse_ rprof() is
absent.
below is the session info show the absence of the function ( which is
listed in the package help for the current version.)
Documentation for package ‘profvis’ version 0.3.5
DESCRIPTION file.
Help Pages
parse_rprof Parse Rprof output file for use with profvis
pause Pause an R process
print.profvis Print a profvis object
profvis Profile an R expression and visualize profiling data
profvisOutput Widget output function for use in Shiny
renderProfvis Widget render function for use in Shiny
Rsession info:
> library(profvis)
> parse_rprof()
Error in parse_rprof() : could not find function "parse_rprof"
> ls("package:profvis")
[1] "pause" "profvis" "profvisOutput" "renderProfvis"
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
LC_MONETARY=English_Australia.1252
[4] LC_NUMERIC=C LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] profvis_0.3.5
loaded via a namespace (and not attached):
[1] htmlwidgets_1.3 compiler_3.5.2 magrittr_1.5htmltools_0.3.6
tools_3.5.2 yaml_2.2.0 Rcpp_1.0.0 stringi_1.2.4
[9] stringr_1.3.1 digest_0.6.18
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and provide commented, minimal, self-contained, reproducible code.
[R] Mapedit::selectMap in shiny map.
I would like to select polygons from an existing spatial polygon data set
interactively in a shiny leaflet map.
The process is straightforward in leaflet/ mapedit, however I need to
include the procedure in a shiny app map interface. I cannot work out how
to incorporate the selectMap() in the shiny app. An error is returned:
Here is some toy code showing the code in using leaflet locally:
library(mapedit)
library(leaflet)
options(stringsAsFactors = F)
bounds <- c(5.956063, 10.49511, 45.81706, 47.80848 )
lf <- leaflet() %>%
addTiles()%>%
addPolygons(data =gadmCHE,
label = ~NAME_1,
layerId = ~NAME_1)
selected <-selectMap(lf)
##the above works fine and returns a dataframe giving the ids of the
selected polygons.
##however the code below - trying to implement in shiny fails with "Can’t
call runApp() from within runApp(). If your application code contains
runApp(), please remove it.
library(shiny)
library(leaflet)
library(mapedit)
ui <- fluidPage(
leafletOutput(“mymap”)
)
server <- function(input, output, session) {
lf<-leaflet() %>%
addTiles()%>%
addPolygons(data =gadmCHE,
label = ~NAME_1,
layerId = ~NAME_1)
output$mymap <- renderLeaflet({selectMap(lf)
})
}
shinyApp(ui, server)
##How do I achieve the same in a shiny map?
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[R] Identifying attributes of specific foreach task on error.
I am running foreach to reclassify a large number of rasters.
I am getting the Error in { : task 1359 failed - "cannot open the
connection"
How do I get the attributes ( in this case files being read and written)
for that specific task?
It runs fine until that point presumably there is a problem with the input
or output file name, but I cannot determine which file it refers to.
cheers
Nevil Amos
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and provide commented, minimal, self-contained, reproducible code.
[R] clusterR (fun=aggregate) error number of items to replace is not a multiple of replacement length
I am getting the above error with clusterR and aggregate: works fine without parralell: library(raster) r-raster(matrix(data = sample(c(1:10,NA),1,replace=T),100,100),xmn=0, xmx=1000,ymn=0,ymx=1000) beginCluster() Parr_agg-clusterR(r,fun=aggregate,args=list(fact=3,fun=modal,expand=TRUE,na.rm=TRUE)) endCluster() agg-aggregate(r,3,fun=modal,na.rm=TRUE) plot(agg) [[alternative HTML version deleted]] __ 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] clusterR (fun=aggregate) error number of items to replace is not a multiple of replacement length
Apoligies. did not read help properly it states: Among other functions, it does _not_ work with ... (dis)aggregate On Mon, Apr 20, 2015 at 4:54 PM, nevil amos nevil.a...@gmail.com wrote: I am getting the above error with clusterR and aggregate: works fine without parralell: library(raster) r-raster(matrix(data = sample(c(1:10,NA),1,replace=T),100,100),xmn=0, xmx=1000,ymn=0,ymx=1000) beginCluster() Parr_agg-clusterR(r,fun=aggregate,args=list(fact=3,fun=modal,expand=TRUE,na.rm=TRUE)) endCluster() agg-aggregate(r,3,fun=modal,na.rm=TRUE) plot(agg) [[alternative HTML version deleted]] __ 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] How to run sequential Rscript command for windows command line with a batch file.
Hi, I need to run multiple iterations of a script to which I am supplying a single numeric argument I can open the command prompt window and enter a single command: C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 18 and it runs OK and saves the outputs. Similarly if I run the same single command from a batch file it works fine however If I have multiple lines in the batch file eg: C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 18 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 19 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 20 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 22 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 23 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 24 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 25 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 26 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 27 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 28 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 29 C:\Program Files\R\R-3.1.0\bin\x64\Rscript.exe myScript.R.R 30 it pauses after running the first line only. How do I get all lines in this batch file to run sequentially? thanks [[alternative HTML version deleted]] __ 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 TRUE only for first match of values between matrix and vector.
I wish to return True in a matrix for only the first match of a value per row where the value equals that in a vector with the same number of values as rosw in the matrix eg: A-matrix(c(2,3,2,1,1,2,NA,NA,NA,5,1,0,5,5,5),5,3) B-c(2,1,NA,1,5) desired result: [,1] [,2] [,3] [1,] TRUE FALSE FALSE [2,] FALSE NA FALSE [3,]NA NANA [4,] TRUE NA FALSE [5,] FALSE TRUE FALSE however A==B returns: [,1] [,2] [,3] [1,] TRUE TRUE FALSE [2,] FALSE NA FALSE [3,]NA NANA [4,] TRUE NA FALSE [5,] FALSE TRUE TRUE and apply(A,1,function(x) match (B,x)) returns [,1] [,2] [,3] [,4] [,5] [1,]1 NA1 NA NA [2,]3 NA NA11 [3,] NA222 NA [4,]3 NA NA11 [5,] NA NA332 thanks [[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] return the name of source.
Thanks this does it: script.name - basename(sys.frame(1)$ofile) On Tue, Aug 27, 2013 at 4:07 PM, Henrik Bengtsson h...@biostat.ucsf.eduwrote: See findSourceTraceback() of R.utils. /Henrik On Mon, Aug 26, 2013 at 10:58 PM, peter dalgaard pda...@gmail.com wrote: On Aug 27, 2013, at 07:12 , nevil amos wrote: Is there a fuction that will allow me to retrun the filename for a script from within that script. Not a standard one, but you should be able to get at it via a bit of breaking and entering: sys.status() and friends (sys.calls, sys.frames) give you access to the evaluation frame of source() which contains a variable called file. -pd fir instance If I have a script myscript.r: FileName-unknown.fucntion() print(FileName) and run it source(myscript.r) will return myscript.r Thanks Nevil Amos [[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. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.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. [[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] return the name of source.
Is there a fuction that will allow me to retrun the filename for a script from within that script. fir instance If I have a script myscript.r: FileName-unknown.fucntion() print(FileName) and run it source(myscript.r) will return myscript.r Thanks Nevil Amos [[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] return output to console for copying as input
I want to print a vector of strings to the console formatted as if it were input X-c(a,b,c) X [1] a b c what I would like to get is the.function(X) a,b,c what is the function? cheers Nevil amos [[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] Problem i9ncreasing memory to jvm for XLConnect
I am using some r scripts to reformat a large data set that needs to be saved into xls format. I am getting the Out of Memory Error (Java) despite having set a large memory in the first line of the script ( on opening R and before loading any libraries) I am using R version 2.15.2 (2012-10-26) -- Trick or Treat Platform: x86_64-w64-mingw32/x64 (64-bit) On 64 Bit window 7 machine with 12G of ram. When I run the script to increase memory for jvm it is not increasing the memory but remaining at 244MB ( presumably the remainder of the initial 256mb once JVM is loaded... the script and out put is as follows rm(list = ls()) options(java.parameters = -Xmx4096m,stringsAsFactors=F) library(XLConnect) Loading required package: XLConnectJars Loading required package: rJava XLConnect 0.2-3 by Mirai Solutions GmbH http://www.mirai-solutions.com , http://miraisolutions.wordpress.com print(xlcMemoryReport()) Amount of free memory in the Java Virtual Machine (JVM): 244.0936 MB How do I increase the memory? thanks [[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] Problem i9ncreasing memory to jvm for XLConnect
Thanks for those suggestions. There was no previous part of the session . I opened r then ran the script as seen. In this case the rm(list = ls()) was superfluous - I just tend to have it at the beginning of scripts to remove any rubbish if I have run previous stuff in the session. It would be nice if the xlcFreeMemory() gave the maximum available. On Tue, Jun 11, 2013 at 11:02 PM, Anthony Damico ajdam...@gmail.com wrote: the rm(list = ls()) at the top of your snippet makes me wonder if you had loaded any packages (like XLConnect) that use Java in a previous part of the session? i believe you must designate the ram allocation for java prior to loading any java-related packages, and clearing out your objects will not act as a reset.. i'm also not sure if the memory report shows what's currently allocated or the actual maximum.. i've had success with increasing the allocation on windows in the past, even though the initial memory report said only ~120mb. be sure to execute the xlcFreeMemory() command after any big runs-- it's the java-equivalent of gc() also you should be able to use options( java.parameters = -Xmx4g ) unless you love multiplying by 1024 :) On Tue, Jun 11, 2013 at 3:21 AM, nevil amos nevil.a...@gmail.com wrote: I am using some r scripts to reformat a large data set that needs to be saved into xls format. I am getting the Out of Memory Error (Java) despite having set a large memory in the first line of the script ( on opening R and before loading any libraries) I am using R version 2.15.2 (2012-10-26) -- Trick or Treat Platform: x86_64-w64-mingw32/x64 (64-bit) On 64 Bit window 7 machine with 12G of ram. When I run the script to increase memory for jvm it is not increasing the memory but remaining at 244MB ( presumably the remainder of the initial 256mb once JVM is loaded... the script and out put is as follows rm(list = ls()) options(java.parameters = -Xmx4096m,stringsAsFactors=F) library(XLConnect) Loading required package: XLConnectJars Loading required package: rJava XLConnect 0.2-3 by Mirai Solutions GmbH http://www.mirai-solutions.com , http://miraisolutions.wordpress.com print(xlcMemoryReport()) Amount of free memory in the Java Virtual Machine (JVM): 244.0936 MB How do I increase the memory? thanks [[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. [[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] merge without NA last
I am trying to create a merge where the first value contains NA values. I wish to retain these in order. however when I use all.x=T and sort=F they are retained but na values are placed last: X-data.frame(k1=c(A,NA,C,B)) print (X) k1 1A 2 NA 3C 4B Y-data.frame(k2=c(1,2,3),k3=c(A,B,C)) Z-merge(X,Y, by.x=1,by.y=2,all.x=T,sort=F) print (Z) k1 k2 1A 1 2C 3 3B 2 4 NA NA The result I need is k1 k2 1A 1 2 NA NA 3C 3 4B 2 how do I prevent NA c=values being sorted to last - I need to retain values in position. thanks Nevil Amos [[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] Default for boot in mantel{ecodist} was Re: Size of subsample in ecodist mantel()
How do I use pboot to set the level of resampling (size of each resample) in mantel()? if I enter a value for pboot then the ulim==llim X-dist(1:100) Y-dist(1:100+50*rnorm(100)) length(X) [1] 4950 print(mantel(X~Y,nperm=1000,nboot=1000,pboot=10)) mantelr pval1 pval2 pval3 llim.2.5% ulim.97.5% 0.1396906 0.001 1.000 0.001 0.1396906 0.1396906 if I do not set a value for pboot then as expected ulimllim print(mantel(X~Y,nperm=1000,nboot=1000)) mantelr pval1 pval2 pval3 llim.2.5% ulim.97.5% 0.1396906 0.001 1.000 0.001 0.1005011 0.1805416 many thanks Nevil Amos [[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] Size of subsample in ecodist mantel()
Thanks Sarah, It is not clear to me exactly how I set this value. if I enter a value for pboot then the ulim==llim X-dist(1:100) Y-dist(1:100+50*rnorm(100)) length(X)[1] 4950 print(mantel(X~Y,nperm=1000,nboot=1000,pboot=10)) mantelr pval1 pval2 pval3 llim.2.5% ulim.97.5% 0.1396906 0.001 1.000 0.001 0.1396906 0.1396906 if I do not set a value for pboot then as expected ulimllim print(mantel(X~Y,nperm=1000,nboot=1000)) mantelr pval1 pval2 pval3 llim.2.5% ulim.97.5% 0.1396906 0.001 1.000 0.001 0.1005011 0.1805416 What is the default for pboot? this does not appear to be dealt with in help for mantel On Thu, Jun 28, 2012 at 8:35 PM, Sarah Goslee sarah.gos...@gmail.comwrote: You can set it using the pboot argument. Sarah On Thursday, June 28, 2012, nevil amos wrote: What is the size of the boostrapped subsample in ecodist mantel() thanks [[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. -- Sarah Goslee http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org [[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] Size of subsample in ecodist mantel()
What is the size of the boostrapped subsample in ecodist mantel() thanks [[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] VEGAN ordistep, stepwise model selection in CCA - familywise error correction.
I am using VEGAN ordistep function for stepwise model selection. By default the Pin and Pout values are set to .05 and .1 Is it appropriate to use a family wise correction ( such as bonferroni or one of the alternatives) to adjust these values where there are several (5-10), potentially correlated variables in the model selection process? -- Nevil Amos Molecular Ecology Research Group Australian Centre for Biodiversity Monash University CLAYTON VIC 3800 Australia [[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] removing only rows/columns with na value from square ( symmetrical ) matrix.
Yes the matrix is symmetric Gabor provided a partial solution: Try this: ix - na.action(na.omit(replace(M, upper.tri(M), 0))) M[-ix, -ix] However this removes all rows containing an NA in the lower half of the matrix - even if the corresponding column has also been removed I I have revised the example to show this. thanks all for you help in the below case I would like to retain row and column [c(1:5,7,8,10:12),c(1:5,7,8,10:12)] M-matrix(sample(144),12,12) M[10,9]-NA M-as.matrix(as.dist(M)) N=M #the above rows are to create the symmetric matrix M and a copy N M[6,]-NA M[,6]-NA #above two rows - make corresponding row and column NA print (M) ix - na.action(na.omit(replace(M, upper.tri(M), 0))) M-M[-ix, -ix] print (M) print (however what I would like to retain is the maximum amout of data while removing rows or columns containing NA ie:) print(N [c(1:5,7,8,10:12),c(1:5,7,8,10:12)]) -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com thanks to all On 21/05/2012, at 1:10 AM, peter dalgaard wrote: On May 20, 2012, at 16:37 , Bert Gunter wrote: Your problem is not well-defined. In your example below, why not remove rows 1,2,6, and 10, all of which contain NA's? Is the matrix supposed to be symmetric? YES Do NA's always occur symmetrically? YES ...and even if they do, how do you decide whether to remove row/col 9 or row/col 10 in the example? (Or, for that matter, between (1 and 2) and 6. In that case you might chose to remove the smallest no. of row/cols but in 9 vs. 10, the situation is completely symmetric.) You either need to rethink what you want to do or clarify your statement of it. -- Bert On Sun, May 20, 2012 at 7:17 AM, Nevil Amos nevil.a...@monash.edu wrote: I have some square matrices with na values in corresponding rows and columns. M-matrix(1:2,10,10) M[6,1:2]-NA M[10,9]-NA M-as.matrix(as.dist(M)) print (M) 1 2 3 4 5 6 7 8 9 10 1 0 2 1 2 1 NA 1 2 1 2 2 2 0 1 2 1 NA 1 2 1 2 3 1 1 0 2 1 2 1 2 1 2 4 2 2 2 0 1 2 1 2 1 2 5 1 1 1 1 0 2 1 2 1 2 6 NA NA 2 2 2 0 1 2 1 2 7 1 1 1 1 1 1 0 2 1 2 8 2 2 2 2 2 2 2 0 1 2 9 1 1 1 1 1 1 1 1 0 NA 10 2 2 2 2 2 2 2 2 NA 0 How do I remove just the row/column pair( in this trivial example row 6 and 10 and column 6 and 10) containing the NA values? so that I end up with all rows/ columns that are not NA - e.g. 1 2 3 4 5 7 8 9 1 0 2 1 2 1 1 2 1 2 2 0 1 2 1 1 2 1 3 1 1 0 2 1 1 2 1 4 2 2 2 0 1 1 2 1 5 1 1 1 1 0 1 2 1 7 1 1 1 1 1 0 2 1 8 2 2 2 2 2 2 0 1 9 1 1 1 1 1 1 1 0 if i use na omit I lose rows 1,2,6, and 9 which is not what I want. thanks -- Nevil Amos Molecular Ecology Research Group Australian Centre for Biodiversity Monash University CLAYTON VIC 3800 Australia [[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. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ 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. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com [[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] removeing only rows/columns with na value from square ( symmetrical ) matrix.
I have some square matrices with na values in corresponding rows and columns. M-matrix(1:2,10,10) M[6,1:2]-NA M[10,9]-NA M-as.matrix(as.dist(M)) print (M) 1 2 3 4 5 6 7 8 9 10 1 0 2 1 2 1 NA 1 2 1 2 2 2 0 1 2 1 NA 1 2 1 2 3 1 1 0 2 1 2 1 2 1 2 4 2 2 2 0 1 2 1 2 1 2 5 1 1 1 1 0 2 1 2 1 2 6 NA NA 2 2 2 0 1 2 1 2 7 1 1 1 1 1 1 0 2 1 2 8 2 2 2 2 2 2 2 0 1 2 9 1 1 1 1 1 1 1 1 0 NA 10 2 2 2 2 2 2 2 2 NA 0 How do I remove just the row/column pair( in this trivial example row 6 and 10 and column 6 and 10) containing the NA values? so that I end up with all rows/ columns that are not NA - e.g. 1 2 3 4 5 7 8 9 1 0 2 1 2 1 1 2 1 2 2 0 1 2 1 1 2 1 3 1 1 0 2 1 1 2 1 4 2 2 2 0 1 1 2 1 5 1 1 1 1 0 1 2 1 7 1 1 1 1 1 0 2 1 8 2 2 2 2 2 2 0 1 9 1 1 1 1 1 1 1 0 if i use na omit I lose rows 1,2,6, and 9 which is not what I want. thanks -- Nevil Amos Molecular Ecology Research Group Australian Centre for Biodiversity Monash University CLAYTON VIC 3800 Australia [[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] How to remove $ (Dollar sign) from string
How do I remove a $ character from a string sub() and gsub() with $ or \$ as pattern do not work. sub($,,ABC$DEF) [1] ABC$DEF sub(\$,,ABC$DEF) Error: '\$' is an unrecognized escape in character string starting \$ sub(\$,,ABC$DEF) Error: unexpected input in sub(\ Thanks -- Nevil Amos Molecular Ecology Research Group Australian Centre for Biodiversity Monash University CLAYTON VIC 3800 Australia [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Extracting part of anova.cca()
I have an anova.cca() output. If it is possible I would like to extract the table it contains as a data frame ie myAnova Permutation test for rda under reduced model Terms added sequentially (first to last) Model: rda(formula = mygenind@tab ~ mds3dCS_NULL + mds3dTRE_25_2_CS25 + mydata$LAT.x + mydata$LONG.x + mydata$Hab_Config + mds3dTRE_25_100_CS25 + mydata$TreeCov + mydata$Site_No + mds3dSFW_EO_100_CS25 + mds3dSFW_EO_5000_CS25 + mydata$Landscape + mds3dSFW_TH_10_CS25, scale = T, na.action = na.omit) Df Var F N.Perm Pr(F) mds3dCS_NULL3 6.527 2.6380 99 0.01 ** mds3dTRE_25_2_CS25 3 5.596 2.2616 99 0.01 ** mydata$LAT.x1 1.892 2.2939 99 0.01 ** mydata$LONG.x 1 1.891 2.2929 99 0.01 ** mydata$Hab_Config 2 2.772 1.6807 99 0.01 ** mds3dTRE_25_100_CS253 3.952 1.5970 99 0.01 ** mydata$TreeCov 1 1.272 1.5418 99 0.01 ** mydata$Site_No 1 1.345 1.6306 99 0.01 ** mds3dSFW_EO_100_CS253 3.741 1.5120 99 0.01 ** mds3dSFW_EO_5000_CS25 3 3.410 1.3783 99 0.01 ** mydata$Landscape8 9.300 1.4094 99 0.01 ** mds3dSFW_TH_10_CS25 3 3.658 1.4785 99 0.01 ** Residual 139 114.644 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 I would like to extract as a table: Df Var F N.Perm Pr(F) mds3dCS_NULL3 6.527 2.6380 99 0.01 ** mds3dTRE_25_2_CS25 3 5.596 2.2616 99 0.01 ** mydata$LAT.x1 1.892 2.2939 99 0.01 ** mydata$LONG.x 1 1.891 2.2929 99 0.01 ** mydata$Hab_Config 2 2.772 1.6807 99 0.01 ** mds3dTRE_25_100_CS253 3.952 1.5970 99 0.01 ** mydata$TreeCov 1 1.272 1.5418 99 0.01 ** mydata$Site_No 1 1.345 1.6306 99 0.01 ** mds3dSFW_EO_100_CS253 3.741 1.5120 99 0.01 ** mds3dSFW_EO_5000_CS25 3 3.410 1.3783 99 0.01 ** mydata$Landscape8 9.300 1.4094 99 0.01 ** mds3dSFW_TH_10_CS25 3 3.658 1.4785 99 0.01 ** Residual 139 114.644 Is this possible? what is the syntax? I have looked at str(myAnova) but cannot see how to get the table with variable names included Many thanks Nevil Amos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Terms with zero variance included in ordistep best model?
Below I have pasted the outputs of an ordistep() on an rda() I noticed in the final fitting of the ordistep() that two terms mydata$TreeCov and mydata$HabConfig were still included but had variance of 0 and therefore P was not calculated. Why are they still included in the final model? thanks Nevil Amos myOrdistepBoth Call: rda(formula = mygenind@tab ~ mds3dCS_NULL + mds3dTRE_25_2_CS25 + mydata$LAT.x + mydata$Hab_Config + mds3dTRE_25_100_CS25 + mydata$TreeCov + mydata$Site_No + mds3dSFW_EO_100_CS25 + mds3dSFW_EO_5000_CS25 + mydata$Landscape + mds3dSFW_TH_10_CS25 + mydata$LONG.x, scale = T, na.action = na.omit) Inertia Proportion Rank Total 160. 1. Constrained45.3560 0.2835 32 Unconstrained 114.6440 0.7165 139 Inertia is correlations Some constraints were aliased because they were collinear (redundant) Eigenvalues for constrained axes: RDA1 RDA2 RDA3 RDA4 RDA5 RDA6 RDA7 RDA8 RDA9 RDA10 RDA11 RDA12 RDA13 RDA14 RDA15 RDA16 RDA17 RDA18 RDA19 RDA20 RDA21 RDA22 RDA23 RDA24 RDA25 3.3489 3.2291 2.8211 2.5129 2.2606 2.1062 2.0834 1.8720 1.7727 1.6680 1.6072 1.5512 1.5100 1.4314 1.3802 1.2427 1.1497 1.1153 1.0547 1.0287 0.9814 0.9361 0.9168 0.8851 0.7577 RDA26 RDA27 RDA28 RDA29 RDA30 RDA31 RDA32 0.7150 0.7056 0.6436 0.6098 0.5643 0.4806 0.4140 Eigenvalues for unconstrained axes: PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 3.433 3.098 3.057 2.912 2.866 2.743 2.669 2.586 (Showed only 8 of all 139 unconstrained eigenvalues) anova(myOrdistepBoth,by=term) Permutation test for rda under reduced model Terms added sequentially (first to last) Model: rda(formula = mygenind@tab ~ mds3dCS_NULL + mds3dTRE_25_2_CS25 + mydata$LAT.x + mydata$Hab_Config + mds3dTRE_25_100_CS25 + mydata$TreeCov + mydata$Site_No + mds3dSFW_EO_100_CS25 + mds3dSFW_EO_5000_CS25 + mydata$Landscape + mds3dSFW_TH_10_CS25 + mydata$LONG.x, scale = T, na.action = na.omit) Df Var F N.Perm Pr(F) mds3dCS_NULL3 6.527 2.6380 99 0.01 ** mds3dTRE_25_2_CS25 3 5.596 2.2616 99 0.01 ** mydata$LAT.x1 1.892 2.2939 99 0.01 ** mydata$Hab_Config 2 2.858 1.7325 99 0.01 ** mds3dTRE_25_100_CS253 4.314 1.7435 99 0.01 ** mydata$TreeCov 1 1.238 1.5008 99 0.01 ** mydata$Site_No 1 1.304 1.5806 99 0.01 ** mds3dSFW_EO_100_CS253 3.834 1.5497 99 0.01 ** mds3dSFW_EO_5000_CS25 3 3.344 1.3515 99 0.01 ** mydata$Landscape8 9.711 1.4717 99 0.01 ** mds3dSFW_TH_10_CS25 3 3.702 1.4961 99 0.01 ** mydata$LONG.x 1 1.037 1.2569 99 0.06 . Residual 139 114.644 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 anova(myOrdistepBoth,by=margin) Permutation test for rda under reduced model Marginal effects of terms Model: rda(formula = mygenind@tab ~ mds3dCS_NULL + mds3dTRE_25_2_CS25 + mydata$LAT.x + mydata$Hab_Config + mds3dTRE_25_100_CS25 + mydata$TreeCov + mydata$Site_No + mds3dSFW_EO_100_CS25 + mds3dSFW_EO_5000_CS25 + mydata$Landscape + mds3dSFW_TH_10_CS25 + mydata$LONG.x, scale = T, na.action = na.omit) Df Var F N.Perm Pr(F) mds3dCS_NULL3 3.519 1.4222199 0.00500 ** mds3dTRE_25_2_CS25 3 3.663 1.4805199 0.00500 ** mydata$LAT.x1 1.185 1.4364199 0.00500 ** mydata$Hab_Config 0 0.000 0. 0 mds3dTRE_25_100_CS253 3.569 1.4423199 0.00500 ** mydata$TreeCov 0 0.000 0. 0 mydata$Site_No 1 1.251 1.5170199 0.00500 ** mds3dSFW_EO_100_CS253 3.303 1.3348199 0.00500 ** mds3dSFW_EO_5000_CS25 3 3.395 1.3721199 0.01000 ** mydata$Landscape8 9.573 1.4508199 0.00500 ** mds3dSFW_TH_10_CS25 3 3.658 1.4785199 0.00500 ** mydata$LONG.x 1 1.037 1.2569 1399 0.03571 * Residual 139 114.644 --- Signif. codes: 0 *** 0.001 ** 0.01 * 0.05 . 0.1 1 [[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] replacing + in string
I am trying to replace + in a string with another character I am getting odd results using sub and gsub X-one + two gsub(+,plus,X) [1] plusoplusnpluseplus plus+plus plustpluswplusoplus sub(+,plus,X) [1] plusone + two X-one ~ two it seems to work fine with other characters: sub(~,plus,X) [1] one plus two How do I enable + to be recognised as a normal character? thanks Nevil Amos __ 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] DEMEtics expected run time for calculating DEST CI
What would be the expected runtime for DEMEtics calculating pairwise Dest and CI with 1000 bootstraps for 600 individuals 9 loci in 48 populations? I am currently running it on a fairly fast unix computer and the estimated completion time is approximately 6 weeks. The manual suggested that I might expect hours to days. Have I got a setting wrong somewhere? D.Jost(filename=spp,object=T,format.table=T) many thanks Nevil Amos __ 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] Vegan(ordistep) error: Error in if (aod[1, 5] = Pin) { : missing value where TRUE/FALSE needed
Whilst the constrained proportion was 0 in the example below I am getting the
error in cases where this is not so. See new output pasted below
[1] ORDISTEP RDA1 BOTH WAYS
[1]
[1] SFW ALL Adult
[1] mds3dSFW_EO_100_CS25 mds3dSFW_EO_5000_CS25 mds3dSFW_TH_10_CS25
mds3dSFW_TH_2_CS25
Call: rda(formula = mygenind@tab ~ mds3dTRE_25_100_CS25 + mds3dTRE_25_10_CS25 +
mds3dTRE_25_2_CS25 + mds3dTRE_25_5_CS25 + mydata$TreeCov + mydata$Hab_Config +
mydata$Site_No + mydata$Landscape + mds3dCS_NULL + mydata$LAT.x +
mydata$LONG.x, na.action
= na.omit)
Inertia Proportion Rank
Total 4.5099 1.
Constrained1.2635 0.2802 29
Unconstrained 3.2464 0.7198 142
Inertia is variance
Some constraints were aliased because they were collinear (redundant)
Eigenvalues for constrained axes:
RDA1 RDA2 RDA3 RDA4 RDA5 RDA6 RDA7 RDA8
RDA9RDA10RDA11
0.173325 0.126065 0.093396 0.086910 0.072219 0.063064 0.062034 0.058022
0.050743 0.045038 0.043567
RDA12RDA13RDA14RDA15RDA16RDA17RDA18RDA19
RDA20RDA21RDA22
0.039200 0.035363 0.033358 0.029372 0.028224 0.025715 0.024484 0.024007
0.021999 0.020480 0.018853
RDA23RDA24RDA25RDA26RDA27RDA28RDA29
0.017277 0.015510 0.015091 0.012845 0.011089 0.009377 0.006886
Eigenvalues for unconstrained axes:
PC1PC2PC3PC4PC5PC6PC7PC8
0.2037 0.1710 0.1670 0.1450 0.1343 0.1155 0.1120 0.1015
(Showed only 8 of all 142 unconstrained eigenvalues)
Error in if (aod[1, 5] = Pin) { : missing value where TRUE/FALSE needed
In addition: There were 50 or more warnings (use warnings() to see the first 50)
traceback()
6: ordistep(myrda0, scope = formula(myrda1), direction = both,
Pin = 0.05, Pout = 0.1) at #55
5: eval(expr, envir, enclos) at #55
4: eval(expr, pf) at #55
3: withVisible(eval(expr, pf)) at #55
2: evalVis(expr) at #55
1: capture.output(ordistep(myrda0, scope = formula(myrda1), direction = both,
Pin = 0.05, Pout = 0.1)) at #55
Cheers
Nevil Amos
Nevil Amos nevil.amos at monash.edu writes:
I am getting the following erro rmessage in ordistep. I have a number of
similarly structured datasets using ordistep in a loop, and the message
only occurs for some of the datasets.
I cannot include a reproducible sample - the specific datasets where this
is occur ing are fairly large and there are several pcnm's in the rhs of
the formula.
Error in if (aod[1, 5] = Pin) { : missing value where TRUE/FALSE needed
Nevil,
It seems to me that the source of the problem appears in this table:
Inertia Proportion Rank
Total 1.8110 1.
Conditional0.8681 0.4793 32
Constrained0. 0.0
Unconstrained 0.9429 0.5207 29
Inertia is variance
Some constraints were aliased because they were collinear (redundant)
The key point is that Constrained component is completely alaised (Inertia
0,
Rank 0) and therefore it cannot be analysed in permutation tests. You get the
same error message with this model:
mod - rda(dune ~ Moisture + Condition(Moisture), dune.env)
and for the same reason. In your case, PCNM's seem to explain everything and
there is nothing left for other variables, and therefore you cannot analyse
them.
Cheers, Jari Oksanen
I can see how to fix this in vegan. All I can do is to handle these cases
smoothly and with comprehensible error messages, though. They cannot be
handled
with permutation tests since there is nothing to do if Constrained component
is zeroed.
Cheers, Jari Oksanen
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Error message in vegan ordistep
I am getting the following erro rmessage in ordistep. I have a number of
similarly structured datasets using ordistep in a loop, and the message only
occurs for some of the datasets.
I cannot include a reproducible sample - the specific datasets where this is
occur ing are fairly large and there are several pcnm's in the rhs of the
formula.
thanks for any pointers that may allow me to track down the cause of the error.
Nevil Amos
Error in if (aod[1, 5] = Pin) { : missing value where TRUE/FALSE needed
In addition: There were 50 or more warnings (use warnings() to see the first 50)
traceback()
9: ordistep(myrda0, scope = formula(myrda1), direction = both,
Pin = 0.05, Pout = 0.1) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
8: eval(expr, envir, enclos) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
7: eval(expr, pf) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
6: withVisible(eval(expr, pf)) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
5: evalVis(expr) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
4: capture.output(ordistep(myrda0, scope = formula(myrda1), direction = both,
Pin = 0.05, Pout = 0.1)) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
3: eval.with.vis(expr, envir, enclos)
2: eval.with.vis(ei, envir)
1:
source(~/Documents/Dropbox/thesis/CH3/Analysis/RDAPARTIALSexandAgeConnectandGEOGraphy2.R)
print(myrda1)
Call: rda(formula = mygenind@tab ~ pcnmTRE_25_100_CS25 + pcnmTRE_25_10_CS25 +
pcnmTRE_25_2_CS25 +
pcnmTRE_25_5_CS25 + mydata$TreeCov + mydata$Hab_Config + pcnmEYR_EO_100_CS25 +
pcnmEYR_EO_5000_CS25 + pcnmEYR_TH_10_CS25 + pcnmEYR_TH_2_CS25 + mydata$Site_No
+ mydata$Landscape
+ Condition(pcnmCS_NULL + mydata$LAT.x + mydata$LONG.x), na.action = na.omit)
Inertia Proportion Rank
Total 1.8110 1.
Conditional0.8681 0.4793 32
Constrained0. 0.0
Unconstrained 0.9429 0.5207 29
Inertia is variance
Some constraints were aliased because they were collinear (redundant)
Eigenvalues for unconstrained axes:
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8
0.16008 0.14733 0.12183 0.09054 0.07380 0.06971 0.05578 0.04215
(Showed only 8 of all 29 unconstrained eigenvalues)
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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] Vegan(ordistep) error: Error in if (aod[1, 5] = Pin) { : missing value where TRUE/FALSE needed
I am getting the following erro rmessage in ordistep. I have a number of
similarly structured datasets using ordistep in a loop, and the message
only occurs for some of the datasets.
I cannot include a reproducible sample - the specific datasets where this
is occur ing are fairly large and there are several pcnm's in the rhs of
the formula.
thanks for any pointers that may allow me to track down the cause of the
error.
Error in if (aod[1, 5] = Pin) { : missing value where TRUE/FALSE needed
In addition: There were 50 or more warnings (use warnings() to see the
first 50)
traceback()
9: ordistep(myrda0, scope = formula(myrda1), direction = both,
Pin = 0.05, Pout = 0.1) at
RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
8: eval(expr, envir, enclos) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
7: eval(expr, pf) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
6: withVisible(eval(expr, pf)) at
RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
5: evalVis(expr) at RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
4: capture.output(ordistep(myrda0, scope = formula(myrda1), direction =
both,
Pin = 0.05, Pout = 0.1)) at
RDAPARTIALSexandAgeConnectandGEOGraphy2.R#86
3: eval.with.vis(expr, envir, enclos)
2: eval.with.vis(ei, envir)
1:
source(~/Documents/Dropbox/thesis/CH3/Analysis/RDAPARTIALSexandAgeConnectandGEOGraphy2.R)
print(myrda1)
Call: rda(formula = mygenind@tab ~ pcnmTRE_25_100_CS25 + pcnmTRE_25_10_CS25
+ pcnmTRE_25_2_CS25 +
pcnmTRE_25_5_CS25 + mydata$TreeCov + mydata$Hab_Config +
pcnmEYR_EO_100_CS25 +
pcnmEYR_EO_5000_CS25 + pcnmEYR_TH_10_CS25 + pcnmEYR_TH_2_CS25 +
mydata$Site_No + mydata$Landscape
+ Condition(pcnmCS_NULL + mydata$LAT.x + mydata$LONG.x), na.action =
na.omit)
Inertia Proportion Rank
Total 1.8110 1.
Conditional0.8681 0.4793 32
Constrained0. 0.0
Unconstrained 0.9429 0.5207 29
Inertia is variance
Some constraints were aliased because they were collinear (redundant)
Eigenvalues for unconstrained axes:
PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8
0.16008 0.14733 0.12183 0.09054 0.07380 0.06971 0.05578 0.04215
(Showed only 8 of all 29 unconstrained eigenvalues)
--
Nevil Amos
Molecular Ecology Research Group
Australian Centre for Biodiversity
Monash University
CLAYTON VIC 3800
Australia
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[R] partial mantel tests in ecodist with intential NA values.
I would like to perform partial mantel tests on only within group values, with between group values assigned to NA. This is possible in package ncf partial.mantel.test, however this sues a different permutation to that used in ecodist.ecodist will not accept data with NA values, returning a matrix is not square error. is it possible to perform this test in ecodist? many thanks Nevil Amos library(ecodist) library(ncf) x-sample(1:1000,20) y-sample(1:1000,20) z-sample(1:1000,20) M1-as.matrix( distance(x)) M2 -as.matrix( distance(y )) M3-as.matrix( distance(z )) D1-(lower(M1)) D2-(lower(M2)) D3-(lower(M3)) mantel(D1 ~ D2+D3, nperm=1000) mantelr pval1 pval2 pval3 llim.2.5% ulim.97.5% 0.09014696 0.1030 0.8980 0.1840 0.01857311 0.18468621 partial.mantel.test(M1,M2,M3,quiet=T) $MantelR r12 r13 r23 r12.3 r13.2 0.08977575 0.02170997 -0.01561346 0.09014696 0.02320821 $p [1] 0.09590410 0.30769231 0.47552448 0.09490509 0.30169830 $call [1] partial.mantel.test(M1 = M1, M2 = M2, M3 = M3, quiet = T) attr(,class) [1] partial.Mantel M1[1:10,11:20]-NA M1[11:20,1:10]-NA D1-(lower(M1)) mantel(D1 ~ D2+D3, nperm=1000) Error in mantel(D1 ~ D2 + D3, nperm = 1000) : Matrix not square. partial.mantel.test(M1,M2,M3,quiet=T) $MantelR r12 r13 r23r12.3r13.2 0.054906562 0.003446670 -0.015613460 0.054967403 0.004310979 $p [1] 0.2837163 0.4275724 0.4555445 0.2857143 0.4235764 $call [1] partial.mantel.test(M1 = M1, M2 = M2, M3 = M3, quiet = T) attr(,class) [1] partial.Mantel Warning message: In partial.mantel.test(M1, M2, M3, quiet = T) : Missing values exist; Pairwise deletion will be used __ 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 plot CI's (llim ulim) on ecodist mgram
I would like to put confidence intervals on a mantel corellogram they are already calculated in the pmgram object but I am unsure how I get the x value in order to plot them? package(ecodist) X-1:100 Y-rnorm(1:100) Z-rnorm(1:100) XY-dist(data.frame(X,Y)) YX-dist(data.frame(Y,X)) my.mgram-mgram(XY,XZ) plot(my.mgram) print(my.mgram) print(my.mgram) $mgram lag ngroup mantelr pvalllim ulim [1,] 3.770055672 0.500012737 0.001 0.49689923 0.504301550 [2,] 11.310165691 0.383960457 0.001 0.38000201 0.387324434 [3,] 18.850274584 0.232086251 0.001 0.22670074 0.237501735 [4,] 26.390384587 0.114097397 0.001 0.10243901 0.122973735 [5,] 33.930494463 -0.003113351 0.835 -0.01928101 0.008839295 [6,] 41.470603468 -0.106354446 0.001 -0.12682280 -0.089539628 [7,] 49.010713357 -0.181250278 0.001 -0.20154017 -0.164863572 [8,] 56.550823348 -0.266397615 0.001 -0.28498271 -0.251134864 [9,] 64.090933252 -0.298705798 0.001 -0.31421396 -0.284154643 [10,] 71.631042228 -0.353134525 0.001 -0.36468910 -0.341422330 [11,] 79.171152147 -0.337181781 0.001 -0.34854961 -0.322161075 [12,] 86.711262108 -0.334465576 0.001 -0.35500933 -0.309763543 [13,] 94.251371 43 -0.238965642 0.001 -0.26437371 -0.196038662 $resids [1] NA attr(,class) [1] mgram Thanks Nevil Amos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to format Rsuperscript 2 followed by = value
I am trying to put an R2 value with R2 formatted with a superscript 2 followed by = and the value : the first mtext prints the R2 correctly formatted but follows it with =round(summary(mylm)$r.squared,3))) as text the second prints R^2 = followed by the value of round(summary(mylm)$r.squared,3))). how do I correctly write the expression to get formatted r2 followed by the value? x=runif(10) y=runif(10) summary(mylm-lm(y~x)) plot(x,y) abline(mylm) mtext(expression(paste(R^2,=,round(summary(mylm)$r.squared,3))),1) mtext(paste(expression(R^2),=,round(summary(mylm)$r.squared,3)),3) thanks Nevil Amos __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to format R superscript 2 followed by = value
I am trying to put an R2 value with R2 formatted with a superscript 2 followed by = and the value : the first mtext prints the R2 correctly formatted but follows it with =round(summary(mylm)$r.squared,3))) as text the second prints R^2 = followed by the value of round(summary(mylm)$r.squared,3))). how do I correctly write the expression to get formatted r2 followed by the value? x=runif(10) y=runif(10) summary(mylm-lm(y~x)) plot(x,y) abline(mylm) mtext(expression(paste(R^2,=,round(summary(mylm)$r.squared,3))),1) mtext(paste(expression(R^2),=,round(summary(mylm)$r.squared,3)),3) thanks Nevil Amos __ 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 get xlab and ylab in bold?
A very basic query This code plots OK the axis values are in bold but the axis labels are not. how do I get them in bold too? thanks Nevil Amos plot(c(1,1),xlim=c(0,450),ylim=c(0.7,1.4),xlab=Distance (cells) from edge of grid,ylab=Resistance distance, type=l,col=white,lwd=2,font=2,family='sans') __ 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] lm.fit error in scatterplot matrix
I am getting the following error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases when running the command scatterplotMatrix(~THL+WL+BD+TL+Mass|SEX_,by.group=TRUE,plot.points=T,smooth=F,main=spp,) it works fine without the by group option I assume there are some cases with too few values, how can I get the loop containing this line to skip errors and move on to the next case? [[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] How to add label to lines()
I am plotting a number of lines on a standard plot. I would like to add labels at the end (rhs) of each line. is there a way to do this other than defining the individual xy coordinates and placing each label using text() Thanks Nevil Amos __ 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 assemble data frame of unknown number of columns in loop
How do I assemble ad data fame, consisting of columns form other data
frames identified in a loop? cbind is not working as the initial data
fame has 0 columns and rows.
ModList-dir(./MODEL_DISTS/)
ModList-ModList[grep(pattern=3COLUMNS,ModList)]
ALL_MODELS-data.frame()
for (i in ModList){
+ X-read.table(file=paste(./MODEL_DISTS/,i,sep=))
+ BASE=sub(3COLUMNS, , i, fixed = TRUE)
+ names(X)-c(FromSiteID,ToSiteID,CS_RESISTANCE)
+ ALL_MODELS-cbind(ALL_MODELS,X[3])
+ }
Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 0, 2080
thanks
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[R] how to keep keep matching column in output of merge
How do I keep the linking column[s] in a merge()? I need to use the values again in a further merge. thanks Nevil Amos __ 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 keep keep matching column in output of merge
Apologies, it is there! On 5/01/2011 1:26 AM, Sarah Goslee wrote: Hi Nevil, We really need an example here of what you're doing, since merge() does keep the id column by default. x- data.frame(id = c(a, b, c, NA), x=c(1,2,3,4)) y- data.frame(id1 = c(NA, a, d, c), y=c(101, 102, 103, 104)) merge(x, y) id x y 1 a 1 102 2 b 2 101 3 c 3 104 4 d 4 103 Sarah On Tue, Jan 4, 2011 at 8:31 AM, Nevil Amosnevil.a...@gmail.com wrote: How do I keep the linking column[s] in a merge()? I need to use the values again in a further merge. thanks Nevil Amos __ 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] Change legend position in s.value {ade4}
How do I change the postion of the legend in s.value {ade4} from the
defaul , bootom left?
thanks
Nevil Amos
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[R] how to change number of characters per line for print() to sink()?
I am using r to read and reformat data that is then saved to a text file using sink(), the file has a number of initial lines of comments and summary data followed by print of a data.frame with no row names. for example a-c(100:120) b-c(rnorm(100:120)) c-c(rnorm(200:220)) mydata-data.frame(rbind(a,b,c)) sink(datafile.txt) cat(comments about my data \n) cat(other calculations returned as separate text comments on a line \n) print(mydata,row.names=F) sink() I need the content of the text file to keep each row of the data frame on a single line thus (with intervening columns present of course) datafile.txt comments about my data other calculations returned as separate text comments on a line X1 X2 X3 X4 X5 X6 . X19 X20 X21 100.000 101.00 102.000 103.000 104.000 105.000 ..118.000 119.000 120.000 -0.3380570 -1.400905 1.0396499 -0.5802181 -0.2340614 0.6044928 ...-0.4854702 -0.3677461 -1.2033173 -0.9002824 1.544242 -0.8668653 0.3066256 0.2490254 -1.6429223 . 0.0861146 0.4276929 -0.3408604 How doI change setting for print() or use another function to keep each row of the data frame as a single line ( of greater length up to approx 300 characters) instead of wrapping the data frame into multiple lines of text? The problem : I end up with the data frame split into several sections one under another thus datafile.txt comments about my data other calculations returned as separate text comments on a line X1 X2 X3 X4 X5 X6 100.000 101.00 102.000 103.000 104.000 105.000 -0.3380570 -1.400905 1.0396499 -0.5802181 -0.2340614 0.6044928 -0.9002824 1.544242 -0.8668653 0.3066256 0.2490254 -1.6429223 X7 X8 X9 X10 X11 X12 106.000 107. 108.000 109.000 110.000 111.000 0.3152427 0.15093494 -0.3316172 -0.3603724 -2.0516402 -0.4556241 -0.6502265 -0.08842649 -0.3775335 -0.4942572 -0.0976565 -0.7716651 X13 X14 X15 X16 X17X18 112.000 113.000 114.000 115.000 116. 117.00 0.8829135 0.8851043 -0.7687383 -0.9573476 -0.03041968 1.425754 0.2666777 0.6405255 0.2342905 -0.7705545 -1.18028004 1.303601 X19 X20 X21 118.000 119.000 120.000 -0.4854702 -0.3677461 -1.2033173 0.0861146 0.4276929 -0.3408604 __ 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] filling large matrix( or dist object) with values from small matrix.
The script below provides a trivial example of filling a large matrix
with values from a small one with corresponding row and column details.
this is fine for a small example but too slow for many large examples (
my small matrices are 65x65 and my large matrices up to 900x900, and I
have many permutations to fill.
is there a more efficient way to achieve this
M-as.matrix(as.dist(matrix(x,nrow=4,ncol=4,dimnames=list(c(A,B,C,D),c(A,B,C,D)
N-matrix(NA,nrow=8,ncol=8,dimnames=list(c(A,B,C,D,A,B,C,D),c(A,B,C,D,A,B,C,D)))
for (r in 1:nrow(N)){
for (c in 1:(ncol(N))){
N[r,c]=M[rownames(N)[r],colnames(N)[c]]
}
}
thanks
Nevil Amos
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[R] how to find names referring to parts of an R object. particlualry w.r.t capscale
This is both a very general, and a specific question. either answer will help me a lot. I know the object$part syntax is used to retrieve parts of an object for instance myMantel$signif will return the the p value of mantel() and myMantel$statistic the mantel r. Is there any way of listing such components of all objects. at the moment I would like to be able to extract the variance, p value etc for a capscle to tabulate the automatically but would also like to know if the re is a simple way to establish the way to refer to all individual sub parts of a object? thanks Nevil Amos __ 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] NA handling problem in capscale (vegan)
I am having a problem with NA handling in capscale function. as I understand it from the help capscale should permit NA values when na.action=na.mit or na.exclude, however I am getting the error Error in X[nas, , drop = FALSE] : incorrect number of dimensions trivial example is pasted below. library(vegan) mydist- matrix(1:25, 5, 5) mydata-matrix(rnorm(1:25),5,5) mydata[3,1]-NA mydata-data.frame(mydata) capscale(mydist~X1+X2+Condition(X3),data=mydata,na.action = na.omit) Thanks Nevil Amos __ 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] repeatability/intraclass with nested levels
I have a spectrophotometric dataset with repeated measures of a value
at 200 wavelengths for each of 150 individuals.
I would like to use the repeated samples to at each wavelength to look
at measurement/observer error, compared to difference between
individuals error
I have looked at doing this with icc{irr} or using an anova approach,
but I am unclear how to acheive this given that there is a nested
structure- the value varies between wavelengths within individuals.
Many thanks
Nevil Amos
data is structured thus:
ANWC_NO Wavelength Repeatvalue
1 00239300 r1 0.079501
2 00239302 r1 0.084113
3 00239304 r1 0.087697
202 11157300 r1 0.008449
203 11157302 r1 0.009489
204 11157304 r1 0.010142
403 11158300 r1 0.026999
404 11158302 r1 0.029612
405 11158304 r1 0.030271
604 11159300 r1 0.032784
66934 38711300 r3 0.062081
66935 38711302 r3 0.065137
66936 38711304 r3 0.067092
67135 38712300 r3 0.029389
67136 38712302 r3 0.030192
67137 38712304 r3 0.030860
67336 38993300 r3 0.045720
67337 38993302 r3 0.048060
67338 38993304 r3 0.051898
67537 38994300 r3 0.051815
67538 38994302 r3 0.055162
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[R] conditioning variables in dbRDA
I am using cascaple() in vegan, is it permissible to have more than one conditioning variable thus capscale(DIST~varaible1+variable2+Conditon(varaible3+variable4), data=mydata) many thanks Nevil Amos __ 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] partial dbRDA or CCA with two distance objects in Vegan.
I am trying to use the cca/rda/capscale functions in vegan to analyse genetic distance data ( provided as a dist object calculated using dist.genpop in package adegenet) with geographic distance partialled out ( provided as a distance object using dist function in veganthis method is attempting to follow the method used by Geffen et al 2004 as suggested by Legendre and . FORTIN (2010). I cannot see how to introduce the Conditioning ( partialled) second dist matrix. as you can see from the code snippet below, the two dist objects are of the same dimensions. - I get an error using capscale: Error in qr.fitted(Q, Xbar) : 'qr' and 'y' must have the same number of rows or cca Error in weighted.mean.default(newX[, i], ...) : 'x' and 'w' must have the same length when using a conditioning distance object instead of a variable (Clade) of the same length as the constraints ( Latitude and Longitude) I would be grateful, for any pointers on this, ie which test is the appropriate one to use ( I believe capscale since it is similar to distance-based redundancy analysis (Legendre Anderson 1999)) and whether this test is indeed equivalent to the approach suggested by Legendre Fortin, (Geffen et al used DISTLM). many thanks Nevil Amos ACB Monash University references (Geffen, E., M. J. Anderson, et al. (2004). Climate and habitat barriers to dispersal in the highly mobile grey wolf. Molecular Ecology 13(8): 2481-2490.) LEGENDRE, P. and M.-J. FORTIN (2010). Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Molecular ecology resources early copy online Snippet from analysis script: Gen_Dist-dist.genpop(mygenpop,method=2,diag=F,upper=F) str(Gen_Dist) Class 'dist' atomic [1:666] 0.866 0.757 0.813 0.872 0.887 ... ..- attr(*, Labels)= Named chr [1:37] 4879 4883 4884 4885 ... .. ..- attr(*, names)= chr [1:37] 01 02 03 04 ... ..- attr(*, Size)= int 37 ..- attr(*, call)= language dist.genpop(x = mygenpop, method = 2, diag = F, upper = F) ..- attr(*, Diag)= logi FALSE ..- attr(*, Upper)= logi FALSE ..- attr(*, method)= chr Edwards str(geog) Class 'dist' atomic [1:666] 6.61 4.19 14.6 16.71 16.68 ... ..- attr(*, Size)= int 37 ..- attr(*, Labels)= chr [1:37] 2 5 6 7 ... ..- attr(*, Diag)= logi FALSE ..- attr(*, Upper)= logi FALSE ..- attr(*, method)= chr euclidean ..- attr(*, call)= language dist(x = XY) myDbRDA-cca(Gen_Dist ~ Latitude+Longitude+Condition(Clade),data = mydata) myDbRDA-cca(Gen_Dist ~ Latitude+Longitude+Condition(geog),data = mydata) Error in weighted.mean.default(newX[, i], ...) : 'x' and 'w' must have the same length __ 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] partial dbRDA or CCA with two distance objects in Vegan.
Thanks for that, just to confirm I therefore need to use: #if #geogdist is a geographic distance matrix #gen_dist is a genetic distance matrix #env_var are environmental variables mypcnm-pcnm(geogdist) mydbRDA-capscale(gen_dist~env_var+Condition(mypcnm$vectors)) cheers Nevil On 22/09/2010 1:34 AM, Jari Oksanen wrote: On 21/09/10 17:40 PM, Nevil Amosnevil.a...@gmail.com wrote: I am trying to use the cca/rda/capscale functions in vegan to analyse genetic distance data ( provided as a dist object calculated using dist.genpop in package adegenet) with geographic distance partialled out ( provided as a distance object using dist function in veganthis method is attempting to follow the method used by Geffen et al 2004 as suggested by Legendre and . FORTIN (2010). I cannot see how to introduce the Conditioning ( partialled) second dist matrix. as you can see from the code snippet below, the two dist objects are of the same dimensions. - I get an error using capscale: Error in qr.fitted(Q, Xbar) : 'qr' and 'y' must have the same number of rows or cca Error in weighted.mean.default(newX[, i], ...) : 'x' and 'w' must have the same length when using a conditioning distance object instead of a variable (Clade) of the same length as the constraints ( Latitude and Longitude) I would be grateful, for any pointers on this, ie which test is the appropriate one to use ( I believe capscale since it is similar to distance-based redundancy analysis (Legendre Anderson 1999)) and whether this test is indeed equivalent to the approach suggested by LegendreFortin, (Geffen et al used DISTLM). Nevil, You cannot use cca() for dissimilarity data. If you have dissimilarity data, you must use capscale() which runs db-RDA. Even there, your constraints (variables on the right hand side of the formula) must be rectangular data and not dissimilarities. AFAIK, people have changed their dissimilarities into a PCNM structure when they want to partial out the distance effect. That is one of the few original possibilities since data must be rectangular (rows and columns). Cheers, jari oksanen __ 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 un-crosstabulate data without changing numeric values to text?
I have a large amount of data read in from over 140 excel files in the
format of x. r1 to r5 are repeat measures for a given Wavelength and
ANWC_NO.
I need to rearrange x into 3 columns, ANWC_NO,Wavelegth, value ie
ANWC_NOWavelength r1
ANWC_NOWavelength,r2
ANWC_NOWavelength r3
etc...
I can rearrange the data using the code below, however all the columns
end up as strings, not numeric values. I cannot then summaries the
data, ( whcih I need to do in bins of wavelanght for each ANWC_NO)
x
Wavelength r1 r2 r3 r4 r5 ANWC_NO
1300 0.003126 0.005382 0.001094 0.012529 0.005632 39239
2302 0.004924 0.006280 0.002366 0.015234 0.006204 39239
3304 0.004769 0.005960 0.002759 0.015856 0.006804 39239
4306 0.005181 0.006717 0.004033 0.017380 0.007675 39239
5308 0.005872 0.008083 0.004429 0.018334 0.008504 39239
6310 0.007164 0.010775 0.005949 0.019952 0.009594 39239
y =NULL
rows-nrow(x)
for(r in 1:rows){
+ for(c in 2:6){
+ row-c(c(x[r,7]),as.numeric(c(x[r,1])),as.numeric(c(x[r,c])))
+ y-rbind(y,row)
+ }}
colnames(y)-c(ANWC_NO,WAVELENGTH,VALUE)
head (y)
ANWC_NO WAVELENGTH VALUE
row 39239 300 0.003126
row 39239 300 0.005382
row 39239 300 0.001094
row 39239 300 0.012529
row 39239 300 0.005632
row 39239 302 0.004924
mean(y$VALUE)
Error in y$VALUE : $ operator is invalid for atomic vectors
how do I get the data arranged in three columns but maintaining
WavelENGTH and the values as numeric in a data.frame?
Many thanks
Nevil Amos
Monash University
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and provide commented, minimal, self-contained, reproducible code.
[R] mapproject Lambert in metres
I have the following script to convert Longitude and Latitude into lambert projection ( adapted from Geneland manual). How do I get the proejction with units in metres rather than whatever they are currently? alos is it possible to add a fualse XY so that all values are positive ( all my lattidudes are south ie negative) Many thanks Nevil Amos Monash University LONGLAT is a headerless two column file of longitude and latitude such as 141 -32 142 -35 136 -20 ## load packages require(mapproj) require(maps) ## read raw data coord.lonlat - LONGLAT ## convert (Lon,Lat) coordinates into Lambert mapproj.res - mapproject(x=coord.lonlat[,1], y=coord.lonlat[,2], projection=lambert, param=c(min(coord.lonlat[,2]),max(coord.lonlat[,2]))) ## save planar coordinates as a two-column matrix coord.lamb - cbind(mapproj.res$x,mapproj.res$y) __ 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 output text to sink without initial line number [1], and data frame line by line without column names
I want to output a text file assembeld from various soruces within r (
actually as a genepop file)
the output should be formatted line 1 text comment
line 2:n selected
column names from data frame
line n+1on lines of
selected columns from data frame one row at a time
I have the following code, but cannot see how to remove the line numbers
and omit column names form the line by line data frame output
col1-c(2,45,67)
col2-c(a,B,C)
col3-c(234,44,566)
mydf-as.data.frame(cbind(col1,col2,col3))
n-ncol(mydf)
nr-nrow(mydf)
sink(test.txt)
print(I will be including text of various sorts in this file so cannot
use print table or similar command)
for (i in 1:n){
print(colnames(mydf[i]),quote=F) }
for (j in 1:nr){
print(mydf[j,c(2:n)],quote=F,row.names=F)}
sink()
The test.txt contains:
[1] I will be including text of various sorts in this file so cannot
use print table or similar command
[1] col1
[1] col2
[1] col3
col2 col3
a 234
col2 col3
B 44
col2 col3
C 566
what I would like in test.txt is:
I will be including text of various sorts in this file so cannot use
print table or similar command
col1
col2
col3
a 234
B 44
C 566
Many thanks
Nevil Amos
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Re: [R] How to output text to sink from data frame line by line without column names
OK I see how to remove the line numbers[1] etc by using cat instead of
print, but cannot work out how to remove the column names from the data
frame output
On 13/06/2010 4:21 PM, Nevil Amos wrote:
I want to output a text file assembeld from various soruces within r (
actually as a genepop file)
the output should be formatted line 1 text comment
line 2:n selected
column names from data frame
line n+1on lines
of selected columns from data frame one row at a time
I have the following code, but cannot see how to remove the line
numbers and omit column names form the line by line data frame output
col1-c(2,45,67)
col2-c(a,B,C)
col3-c(234,44,566)
mydf-as.data.frame(cbind(col1,col2,col3))
n-ncol(mydf)
nr-nrow(mydf)
sink(test.txt)
print(I will be including text of various sorts in this file so
cannot use print table or similar command)
for (i in 1:n){
print(colnames(mydf[i]),quote=F) }
for (j in 1:nr){
print(mydf[j,c(2:n)],quote=F,row.names=F)}
sink()
The test.txt contains:
[1] I will be including text of various sorts in this file so cannot
use print table or similar command
[1] col1
[1] col2
[1] col3
col2 col3
a 234
col2 col3
B 44
col2 col3
C 566
what I would like in test.txt is:
I will be including text of various sorts in this file so cannot use
print table or similar command
col1
col2
col3
a 234
B 44
C 566
Many thanks
Nevil Amos
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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 get a list of subdirectories in the wd?
How do I get a list of subdirectories only, not files, in a directory dir.create(test) setwd(test) dir.create(adir) dir.create(bdir) file.create(afile) dir() returns [1] adir afile bdir in need to return [1] adir bdir cheers Nevil Amos __ 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] Printing page nmbers in multi-page pdf
Is it possible to print page numbers in pdf() with multiple pages? thanks Nevil Amos __ 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] warning In fun(...) : no DISPLAY variable so Tk is not available
I am getting the above warning following loading of Geneland 3.1.5 on unix , while a simple plot sends output to the pdf file ( see attached code) no output results from Geneland functions, resulting in empty pdf files library (Geneland) Loading required package: RandomFields Loading required package: fields Loading required package: spam Package 'spam' is loaded. Spam version 0.21-0 (2010-03-13). Type demo( spam) for some demos, help( Spam) for an overview of this package. Help for individual functions is optained by adding the suffix '.spam' to the function name, e.g. 'help(chol.spam)'. Attaching package: 'spam' The following object(s) are masked from 'package:base': backsolve, forwardsolve, norm Try help(fields) for an overview of this library fields web: http://www.image.ucar.edu/Software/Fields Loading required package: mapproj Loading required package: maps Loading required package: snow Loading required package: tcltk Loading Tcl/Tk interface ... done ooo oGeneland is loaded o o o o* Please * o o o oRegister on o ohttp://folk.uio.no/gillesg/Geneland/register.php o o o oSee manual ono ohttp://folk.uio.no/gillesg/Geneland/Geneland.htmlo o o oThis is Geneland-3.1.5 o o o ooo Warning message: In fun(...) : no DISPLAY variable so Tk is not available pdf(test.pdf) plot(1:10,1:10) dev.off() null device __ 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 install an archived version of a package in windows
How do I install an archived version of a package - in this case Geneland 3.1.5 in windows? The archived versions are available on CRAN and tar.gz. I can downland this, but then the only option to install a local copy is utils:::menuInstallLocal() or install from local zip file in the console packages menu, this does not work wither with the downlaoded tar.gz, or if I unzip it and save all its contents as Genland_3.1.5.zip in the R/bin direcotry. What do I need to do? thanks Nevil Amos __ 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] Geneland error on unix: Error in MCMC(........ :, unused argument(s) (ploidy = 2, genotypes = geno)
I am receiving the above error ( full r session output below) the
script runs OK in windows. and genotypes and ploidy are both
correct arguments
any suggestions would be most welcome
Nevil Amos
MERG/ACB
Monash University School of Biological Sciences
library(Geneland)
Loading required package: RandomFields
Loading required package: fields
Loading required package: spam
Package 'spam' is loaded. Spam version 0.21-0 (2010-03-13).
Type demo( spam) for some demos, help( Spam) for an overview
of this package.
Help for individual functions is optained by adding the
suffix '.spam' to the function name, e.g. 'help(chol.spam)'.
Attaching package: 'spam'
The following object(s) are masked from 'package:base':
backsolve, forwardsolve, norm
Try help(fields) for an overview of this library
fields web: http://www.image.ucar.edu/Software/Fields
Loading required package: mapproj
Loading required package: maps
Loading required package: snow
Loading required package: tcltk
Loading Tcl/Tk interface ... done
ooo
oGeneland is loaded o
o o
o* Please * o
o o
oRegister on o
ohttp://www2.imm.dtu.dk/~gigu/Geneland/register.php o
o o
oSee manual ono
ohttp://www2.imm.dtu.dk/~gigu/Geneland/#Manualo
o o
oType citation(Geneland) for a quick citation guide o
o o
oSee http://www2.imm.dtu.dk/~gigu/Geneland/# o
ofor additional referenceso
o o
oThis is Geneland-3.2.1 o
o o
ooo
Warning message:
In fun(...) : no DISPLAY variable so Tk is not available
DIRLIST-c(Adult_ALL
NO_ANW/)#,Adult_Or_ANW/,Adult_Females/,Adult_Males/)
for(d in DIRLIST){
+ theWd- paste(/nfs/monash/home/namos/Rwork/,d,sep=)
+ setwd(theWd)
+ SPP.CODES -EYR#c(BT,EYR,FH,SPP,STP)
+ for (sp in SPP.CODES){
+ path.sp- paste(theWd,sp,/,sep=)
+ dir.create(path.sp)
+ GENO.TABLE-paste(theWd,sp,geno,sep=)
+ XY.TABLE-paste(theWd,sp,xy,sep=)
+ MINPOP=1
+ MAXPOP=25
+ INITPOP=1
+ NITS=50
+ THIN=NITS/1000
+ nrun - 10
+ burnin - 200
+ geno-noquote(read.table(GENO.TABLE))
+ coord-read.table(XY.TABLE)
+
+ ## Loop for multiple runs
+
+ for(irun in 1:nrun)
+ {
+ ## define path to MCMC directory
+
+ path.mcmc - paste(path.sp,irun,/,sep=)
+ dir.create(path.mcmc)
+ MCMC(coordinates=coord, ploidy=2, genotypes=geno, varnpop=T,
npopmax=MAXPOP, npopinit=MINPOP, spatial=T, freq.model=Correlated,
nit=NITS, thinning=500, rate.max=nrow(geno), delta.coord=100,
path.mcmc=path.mcmc)
+ ## MCMC postprocessing
+ PostProcessChain(coordinates=coord,path.mcmc=path.mcmc,genotypes=geno,
nxdom=50,nydom=50,burnin=burnin)
+ }
+ ## Computing average posterior probability
+
+ lpd - rep(NA,nrun)
+ for(irun in 1:nrun)
+ {
+ path.lpd - paste(path.mcmc,log.posterior.density.txt,sep=)
+ lpd[irun] - mean(scan(path.lpd)[-(1:burnin)])
+ }
+ ## Runs sorted by decreasing average posterior probability:
+ order(lpd,decreasing=TRUE)
+
+ #pdf(Number of pops.pdf,((210-10)/25.4),((297-10)/25.4))
+ #theWd-getwd()
+ ##setwd(theWd)
+ #par(mfrow = c(5, 2),cex=0.25)
+ #for(irun in 1:nrun)
+ #
+ #{
+ #
+ ###Below is code form the Geneland Plotnpop function
+ #fileparam - paste(path.mcmc, parameters.txt, sep = )
+ #param - as.matrix(read.table(fileparam))
+ #thinning - as.numeric(param[param[, 1] == thinning, 3])
+ #filenpop - paste(path.mcmc, populations.numbers.txt, sep = )
+ #npop - scan(filenpop)
+ # sub - -(1:burnin)
+ #
+ #plot((1:length(npop)) * thinning, npop, type = l,ylab = Number of
classes, xlab = Index of MCMC iteration Whole
chain,main=paste(path.mcmc,\n,Run:, irun, sep = ), ylim = c(1,
max(npop)+ 0.5))
+ #hist(npop[sub], plot = TRUE, prob = TRUE, breaks = seq(0.5,max(npop)
+ 0.5, 1), xlab = paste(Nb. of pop. along the chain (after a burnin of
, burnin, x, thinning, i t.), sep = ), main = Number of
populations long the chain after burnin)
+ #
+ #
+ #}
+ #dev.off()
+ }
+ }
Error in MCMC(coordinates = coord, ploidy = 2, genotypes = geno, varnpop
= T, :
unused argument(s) (ploidy = 2, genotypes = geno)
Execution halted
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[R] writing string values from a matrix to a file without enclosing quotes
I am trying to format data for the Geneland package I need to write a series of paired numbers and paired 000 to a plain ascii file without surrounding the numerals with quotes, the original data is in a matrix formatted paired strings, and written to file using write.table(x,output filename,col.names=F,row.names=F) thus 77 79 132 132 000 000 179 181 132 132 150 150 179 179 132 132 000 000 179 179 132 134 150 152 however I need the output file without the quotes but retaining 000 not reducing it to 0 thus 77 79 132 132 000 000 179 181 132 132 150 150 179 179 132 132 000 000 179 179 132 134 150 152 How might I achieve this? Thanks Nevil Amos __ 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 replace all NA values in a data.frame with another ( not 0) value
I need to replace NA occurrences in multiple columns in a data.frame with 000/000 how do I achieve this? Thanks Nevil Amos __ 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 replace all NA values in a data.frame with another ( not 0) value
Thanks, this works, replacing the NA values with the 000/000' string. On 4/05/2010 11:20 PM, Muhammad Rahiz wrote: Hi Nevil, You can try a method like this x - c(rnorm(5),rep(NA,3),rnorm(5)) # sample data dat - data.frame(x,x) # make sample dataframe dat2 - as.matrix(dat) # conver to matrix y - which(is.na(dat)==TRUE) # get index of NA values dat2[y] - 000/000 # replace all na values with 000/000 Muhammad Nevil Amos wrote: I need to replace NA occurrences in multiple columns in a data.frame with 000/000 how do I achieve this? Thanks Nevil Amos __ 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] using get and paste in a loop to return objects for object names listed a strings
I am trying to create a heap of boxplots, by looping though a series of
factors and variables in a large data.frame suing paste to constrcut the
facto and response names from the colnames
I thought I could do this using get()
however it is not working what am I doing wrong?
thanks
Nevil Amos
sp.codes=levels(data.all$CODE_LETTERS)
for(spp in sp.codes) {
data.sp=subset(data.all,CODE_LETTERS==spp)
responses = colnames(data.all)[c(20,28,29,19)]
#if (spp==BT) responses = colnames(data.all)[c(19,20,26:29)]
groups=colnames (data.all)[c(9,10,13,16,30)]
data.sp=subset(data.all,CODE_LETTERS==spp)
for (response in responses){
for (group in groups){
r-get(paste(data.sp$,response,sep=))
g-get(paste(data.sp$,group, sep=))
print (r)
print(g)
boxplot(r ~g)
}}}
Error in get(paste(data.sp$, response, sep = )) :
object 'data.sp$Hb' not found
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Re: [R] using get and paste in a loop to return objects for object names listed a strings
Thanks for that, the package looks very useful. It gave me the answer
in a roundabout way - reminded me I needed to sue attach() so that the
get () was only dealing with the objects in data.frame, rather than
using the data.frame$factorname
I therefore managed to sort a work around, but will be looking at ggplot
2 for other things
the work around and the head of the data file is shown below
head(data.all)
Line Capture_ID Landscape_Name Band_text Bird_IDDate
CODE_LETTERS Site_Name Age_Class SEX_ Capture_Number Mass Season
SEASON_CLASS EVC Moult Sine_Julian Cosine_Julian HCT Hb
Site_Cond Logs_Length
10 10 10 Axe Creek 42605012275 7/11/2007
0:00 YTH Ax1 AF 1 21.5
Spring SS Heathy Dry Forest N -0.80 0.59
0.48 NA43 5
13 13 13 Axe Creek 37136021170 8/11/2007
0:00 YTH Ax1 AF 1 21.5
Spring SS Heathy Dry Forest N -0.79 0.61
0.53 20.443 5
19 19 21 Axe Creek 37136031171 9/11/2007
0:00 YTH Ax1 AF 1 19.5
Spring SS Heathy Dry Forest N -0.78 0.62
0.53 NA43 5
30 30 34 Axe Creek 37136041172 10/11/2007
0:00 YTH Ax1 UM 1 24.5
Spring SS Heathy Dry Forest Y -0.76 0.63
NA NA43 5
31 31 35 Axe Creek 37136051173 10/11/2007
0:00 YTH Ax1 UU 1 NA
Spring SS Heathy Dry Forest U -0.76 0.63
NA NA43 5
32 32 36 Axe Creek 37136061174 10/11/2007
0:00 YTH Ax1 UM 1 23.5
Spring SS Heathy Dry Forest U -0.76 0.63
0.50 NA43 5
Litter_Cov Understorey TreeCov H.L WBC BCI CCIPca1 YEAR
Hab_Config
10 22.5 650.35 NA NA NANA 2007 D
13 22.5 650.35 NA NA -3.11592 0.6215803 2007 D
19 22.5 650.35 NA NA NANA 2007 D
30 22.5 650.35 NA NA NANA 2007 D
31 22.5 650.35 NA NA NANA 2007 D
32 22.5 650.35 NA NA NANA 2007 D
sp.codes=levels(data.all$CODE_LETTERS)
for(spp in sp.codes) {
data.sp=subset(data.all,CODE_LETTERS==spp)
responses = colnames(data.all)[c(20,28,29,19)]
#if (spp==BT) responses = colnames(data.all)[c(19]#,20,26:29)]
groups=colnames (data.all)[c(9,10)]# ,13,16,30
attach(data.sp)
for (response in responses){
for (group in groups){
g=get(group)
r=get(response)
boxplot(r ~g, main=spp,xlab=group,ylab=response)
}
}
detach(data.sp)
}
On 29/04/2010 7:05 PM, Paul Hiemstra wrote:
Nevil Amos wrote:
I am trying to create a heap of boxplots, by looping though a series
of factors and variables in a large data.frame suing paste to
constrcut the facto and response names from the colnames
I thought I could do this using get()
however it is not working what am I doing wrong?
You don't give a reproducible example, this makes it hard to answer
your question.
But not really in response to your question, take a look at histogram
from the lattice package or geom_boxplot from the ggplot2 package.
These functions can do all the work for you of drawing boxplots for a
series of factors and variables in a large data.frame. This saves you
a lot of time.
cheers,
Paul
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[R] reduce size of pdf
is there a way to reduce the size of pdf files in R: ? compression? lower dpi ? or some other option? __ 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] reduce size of pdf
The file is a large number of scatterplot matrices (120pp of 4x4 matrix) the individual plots may have up to several hudred points. I am already using the useDingbats but the files are still very large - I can reduce them about 50% in cute.pdf by changing the dpi setting but it would be good to handle directly in R They need to be screen/ draft print quality only not for publication. They are being used to ciruclate to a number of people for discussion On 30/04/2010 2:20 AM, Greg Snow wrote: It would help if we knew how big your pdf is and why it is big. Can you show an example or at least describe the process used to generate the file and what you goals are in creating/displaying the file? __ 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.
