Displaying 20 results from an estimated 900 matches similar to: "dbFD computing distinct species wrong?"
2018 Jan 10
0
Problem with dbFD function in FD library
Dear all,
I have a question about FD package. I?m trying to calculate functional
diversity indices using insect data. My trait data includes dispersal
ability (0, 0.5, 1), body size (continuous) and five feeding guilds coded
as in percentages (for example; 0,0,0.5,0.5,0) since some of the species
can have two different feeding guilds. However, the package only calculates
when I run ?calc.Frich=
2016 Apr 11
1
Correlation between package output
Hello
I'm currently using the dbFD function of the FD package and i'm having some
things that I can't do.
Is there any way to check the relations between dbFD indexes?
Function cor for example? I can't manage to put the informations correctly
dbFD function gives a lot of output (indexes - nbsp, sing.sp, FRic, FEve,
FDiv, FDis and RaoQ). I want to see the relationships between
2011 Feb 06
2
Subsampling out of site*abundance matrix
Hello,
How can I randomly sample individuals within a sites from a site (row) X
species abundance (column) data frame or matrix? As an example, the matrix
"abund2" made below.
##### (sorry, Im a newbie and this is the only way I know to get an example
on here)
abund1 <- c(150, 300, 0, 360, 150, 300, 0, 240, 150, 0, 60,
0, 150, 0, 540, 0, 0, 300, 0, 240, 300, 300,
2012 Sep 03
1
combing list objects
Hi,
I am trying to combine a long list but I can't work out how to do it, for
example:
abun<-list(rep(0,5),rep(0,7),rep(0,4),rep(0,10))
nb<-c(5,5,1,8)
fill.abun <- function(x, y) {
set <- sample(1:length(x), size = y)
x[set] <- rlnorm(length(set))
return(x)
}
abun <- mapply(fill.abun, abun, nb)
abun
## I want all the data in one
2005 Feb 03
1
Efficient selection and alteration of dataframe records
Hi All,
I am writing a simulation that examines the effects of species
extinctions on ecological communties by sequentially removing
individuals of a given species (sometimes using weighted probabilities)
and replacing the lost individuals with species identities randomly
sampled from the remaining individuals. Thus I use two dataframes. One
contains all the individuals and their species
2012 Sep 28
1
Anova and tukey-grouping
Hello,
I am really new to R and it's still a challenge to me.
Currently I'm working on my Master's Thesis. My supervisor works with SAS
and is not familiar with R at all.
I want to run an Anova, a tukey-test and as a result I want to have the
tukey-grouping ( something like A - AB - B)
I came across the HSD.test in the agricolae-package, but... unfortunately I
do not get an output
2009 Jun 26
1
50993 point distance matrix, too big to as.matrix, looking for another way to calculate point-level summary
Hello, Im working on a 50933 point count bird abundance dataset. I've
succeeded in calculating a distance matrix for this entire set, but I don't
have sufficient memory to convert this to a matrix, as below...
abun.dist <- dist(abun.mat[1:50993,1:235)
test <- rowMeans(as.matrix(abun.dist))
Error in matrix(0, size, size) : too many elements specified
ive been able to run a hclust()
2005 Oct 09
1
1.0.alpha3 plaintext authentication problem
Hello everyone,
Since the upgrade to 1.0.alpha3 I experience a strange problem with
plaintext
authentication. I successfully login first few (2-5) times after the
dovecot restart,
and then on a reason I cannot login any more (both via POP3 and IMAP). I
tried
to find out what could be the reason for this but I failed. Nothing is
changed
inside the user's home directory or
2005 Nov 12
0
Error message in polr
Dear members of the list,
I'm fitting ordinal regressions using polr, and in some models I
get the error copied below. Dependent variable is an ordered factor
of bird abundance categories, and predictors are continuous habitat
variables.
> ro6 <- polr(formula = abun ~ InOmbrot + Oliva.OC + ToCultAr +
DivCulArb + AltitMax + COORXY)
> summary(ro6)
Re-fitting to get Hessian
2010 Nov 10
2
maptools package
A few years back, I wrote some code to plot maps with the maptools
package. Now I am trying to reproduce my results, only to find out
that maptools has been updated and my code no longer works.
I've been able to fix the first part of it by forcing
spb <- maptools:::read.shape("/home/sasha/Documents/maps/spb.shp")
(as read.shape has been deprecated)
but now when I do
plot(spb,
2009 Oct 19
1
updating columns using other column as reference
Dear R-gurus,
Just supose I have a dara.frame that looks like
myDF<-read.table(stdin(),head=T,sep=",")
codID,namesp,k1,k2,k3,k4
1,spA,2,5,6,3
2,spB,4,5,4,6
3,spC,2,1,5,6
4,spC,5,4,3,2
5,spD,1,2,3,4
6,spE,2,4,3,1
I need to update the columns k1-k4 with the namesp, but
considering the math between Kx and codID.
My desired output must looks like:
codID,namesp,k1,k2,k3,k4
2009 Oct 26
1
defining number of samples
dear all
i am trying to perform t-test (t.test) in R
here i am putting the commands and answer i got
> t.test(Ht_cm[from_treeline=='above'][type=='SD'],Ht_cm[from_treeline=='below'][type=='SD'])
Welch Two Sample t-test
data: Ht_cm[from_treeline == "above"][type == "SD"] and Ht_cm[from_treeline == "below"][type ==
2005 Dec 23
1
WMP mp3 stream trouble
Hello everyone,
I made a big effort to provide an mp3 stream on my site to please the
unenlightened masses, and then I see in my logs that it doesn't work
in Windows Media Player. Doh! There's no Windows machine around to
test on so if anyone could help me out, I'd be very grateful. I
couldn't find anything in the list's archive or on the web in general,
sorry.
Details:
2012 Jan 05
2
Bayesian estimate of prevalence with an imperfect test
Hi all!
I'm new to this forum so please excuse me if I don't conform perfectly to
the protocols on this board!
I'm trying to get an estimate of true prevalence based upon results from an
imperfect test. I have various estimates of se/sp which could inform my
priors (at least upper and lower limits even if with a uniform distribution)
and found the following code on this website..
2012 Aug 24
3
Euclidean distance function
Hi,
I should preface this problem with a statement that although I am sure this
is a really easy function to write, I have tried and failed to get my head
around writing functions in R. I can use R where functions exist to do what
I want done, but have found myself completely incapable of writing them
myself.
The problem is that I have a table with several rows of species and several
columns of
2009 Apr 11
1
data argument and environments
I'm having difficulty with an environmental issue: I have an additive
model fitting function
with a typical call that looks like this:
require(quantreg)
n <- 100
x <- runif(n,0,10)
y <- sin(x) + rnorm(n)/5
d <- data.frame(x,y)
lam <- 2
f <- rqss(y ~ qss(x, lambda = lam), data = d)
this is fine when invoked as is; x and y are found in d, and lam is
found the
2019 Aug 07
1
#include_next <stdio.h> not found
Dear All,
Just when I thought I had the plague of gfortran-9 under control, I made the tactical error
of allowing my mac mini to ?upgrade? to macOS 10.14.6 which apparently also upgraded
Xcode to 10.3. In consequence I?m having difficulty building my packages. The current
symptom is:
/usr/local/clang7/bin/clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG
2009 Nov 05
3
performing operations on a dataframe
Hey all,
I feel like the solution to this problem should be relatively simple, but
for some reason I can't find answers or come up with my own solution.
Given the dataframe:
(SpA and SpB not important, want to look at distribution of cooccurance for
each year)
Year SpA SpB Coocc
2000 0
2000 2
2000 1
2001 8
2001 2
2001 0
2001 0
2002 1
2002 2
How can I apply different functions to
2009 Apr 16
0
FD: R package to measure functional diversity indices
Dear useRs,
The FD package is intended for ecologists interested in functional
diversity (FD). It measures different functional diversity indices
from multiple traits (any type of traits). The first version of FD
(1.0-0) is now available on CRAN:
http://cran.r-project.org/web/packages/FD/
The main functions of FD are:
dbFD: Compute different multidimensional FD indices
gowdis: Gower
2009 Apr 16
0
FD: R package to measure functional diversity indices
Dear useRs,
The FD package is intended for ecologists interested in functional
diversity (FD). It measures different functional diversity indices
from multiple traits (any type of traits). The first version of FD
(1.0-0) is now available on CRAN:
http://cran.r-project.org/web/packages/FD/
The main functions of FD are:
dbFD: Compute different multidimensional FD indices
gowdis: Gower