Displaying 20 results from an estimated 8000 matches similar to: "removeing only rows/columns with "na" value from square ( symmetrical ) matrix."
2012 Apr 10
7
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 "\$"
>
2012 Jan 11
2
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
2010 May 20
1
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
2010 May 04
7
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
2012 Jan 21
2
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
2011 Oct 16
2
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
2010 Sep 21
1
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
2013 Aug 27
1
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]]
2020 Oct 31
2
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
2010 Oct 12
2
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
2011 Dec 03
1
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
2010 Apr 29
5
reduce size of pdf
is there a way to reduce the size of pdf files in R: ?
compression?
lower dpi ?
or some other option?
2010 Dec 17
1
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
2010 May 07
1
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
2011 Sep 12
1
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')
2010 Jun 01
1
Printing page nmbers in multi-page pdf
Is it possible to print page numbers in pdf() with multiple pages?
thanks
Nevil Amos
2010 Apr 29
1
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) {
>
>
>
2023 Nov 14
1
data.frame weirdness
In that case identical should be FALSE but it is TRUE
identical(a1, a2)
## [1] TRUE
On Tue, Nov 14, 2023 at 8:58?AM Deepayan Sarkar
<deepayan.sarkar at gmail.com> wrote:
>
> They differ in whether the row names are "automatic":
>
> > .row_names_info(a1)
> [1] -3
> > .row_names_info(a2)
> [1] 3
>
> Best,
> -Deepayan
>
> On Tue, 14 Nov
2023 Nov 14
1
data.frame weirdness
Also why should that difference result in different behavior?
On Tue, Nov 14, 2023 at 9:38?AM Gabor Grothendieck
<ggrothendieck at gmail.com> wrote:
>
> In that case identical should be FALSE but it is TRUE
>
> identical(a1, a2)
> ## [1] TRUE
>
>
> On Tue, Nov 14, 2023 at 8:58?AM Deepayan Sarkar
> <deepayan.sarkar at gmail.com> wrote:
> >
> >
2023 Nov 14
1
data.frame weirdness
On Tue, 14 Nov 2023 at 09:41, Gabor Grothendieck
<ggrothendieck at gmail.com> wrote:
>
> Also why should that difference result in different behavior?
That's justifiable, I think; consider:
> d1 = data.frame(a = 1:4)
> d2 = d3 = data.frame(b = 1:2)
> row.names(d3) = c("a", "b")
> data.frame(d1, d2)
a b
1 1 1
2 2 2
3 3 1
4 4 2
> data.frame(d1,