Displaying 20 results from an estimated 2000 matches similar to: "(no subject)"
2004 Feb 23
1
dendrogram ultrametrics
Dear R-help listers,
Is anyone aware of a function that outputs dendrogram ultrametrics?
Cheers, Lisa.
PS please reply to me personally as well as to the list because the
website wasn't letting me subscribe for some reason. thanks...
Lisa Holman
Research Officer, Vegetation Dynamics
Policy & Science Division
NSW Department of Environment & Conservation
PO Box 1967, Hurstville 2220.
2007 Aug 28
1
subcripts on data frames (PR#9885)
I'm not sure if this is a bug, or if I'm doing something wrong.
=20
=46rom the worms dataframe, which is at in a file called worms.txt at
=20
http://www.imperial.ac.uk/bio/research/crawley/therbook
<http://www.imperial.ac.uk/bio/research/mjcraw/therbook/index.htm>=20
=20
the idea is to extract a subset of the rows, sorted in declining order
of worm density, with only the maximum
2008 Jul 06
1
What is my replication unit? Lmer for binary longitudinal data with blocks and two treaments.
First I would like to say thank you for taking the time to read it.Here is my
problem.
I am running a lmer analysis for binary longitudinal (repeated measures)
data.
Basically, I manipulated fruits and vegetation to two levels each(present
and absent) and I am trying to access how these factors affect mice foraging
behavior. The design consist of 12 plots, divided in 3 blocks. So each
block
2010 Oct 24
1
best predictive model for mixed catagorical/continuous variables
Would anybody be able to advise on which package would offer the best
approach for producing a model able to predict the probability of species
occupation based upon a range of variables, some of them catagorical (eg.
ten soil types where the numbers assigned are not related to any
qualitative/quantitative continuum or vegetation type) and others continuous
such as field size or vegetation height.
2009 Dec 13
0
cross validation/GAM/package Daim
Dear r-helpers,
I estimated a generalized additive model (GAM) using Hastie's package GAM.
Example:
gam1 <- gam(vegetation ~ s(slope), family = binomial, data=aufnahmen_0708, trace=TRUE)
pred <- predict(gam1, type = "response")
vegetation is a categorial, slope a numerical variable.
Now I want to assess the accurancy of the model using k-fold cross validation.
I found the
2010 May 26
1
Fill a matrix using logical arguments?
Hello all,
I am going slightly mad trying to create a table for running
co-correspondence analysis.
What I have is seed bank and vegetation data, and my aim is to see if
the vegetation found in a site (containing several seed bank samples)
can predict the composition of a seed bank sample within that site. So
for this I need two tables with matching rows.
I have created an empty matrix,
2010 Nov 12
1
repeated measure test
Hi,
This is a question regarding technique rather than an R specific issue. I
have been asked to evaluate a 30+ year long term continuous survey of bird
presence/absence data that has an associated ocular estimate of the
vegetation community percent coverage. The data are organized by
subpopulations (5), and by year ( 1991 - present). We are interested in
gaining understanding on whether bird
2008 Jul 11
0
GroupedData for three way randomized block. LME
I am trying to fit a formula to my data, but I just can't find the right way
to do it.
My experiment consists of manipulating FRUITS and VEGETATION to two levels
each(intact or removed) on 12 experimental plots.
This leaves me with 4 treatment combinations
Fruit intact Vegetation removed
Fruit int. Veget int.
Fruit rem. Veget rem.
Fruit rem. Veget. intac
those treatements are distributed
2011 Sep 23
0
vegan rda na adaptation
Dear R users,
I know, the topic is more related to the r-sig-ecology. I decided to
post it to the r-help as some specific topics of my question deals
with NA-values and RDA (R vegan) and an adaptated RDA code due to a
specific study design (including a second matrix).
I am calculating a RDA for a dependent matrix (different variables for
tree performance) and different explanatory
2008 Jul 19
1
wroung groupedData despite reading Bates and Pinheiro 3 times
Hi everyone. I am trying to add a formula to my data using the groupedData
function.
My experiment consists of randomized block design using fruits, vegetation
and time as factors. The idea is to see if fruits, vegetation and time
explain the abundance of mice. I am using tree density as a covariate.
So I tried to fit the following structure to my data.
>
2012 Oct 04
4
Creating vegetation distance groups from one column
Hi R listers,
I am trying to group distances of nests to the vegetation into classes that
are define by (0-5m, 6-10m, 11-15m, 16-20m, 21-25m, 26-30m, 31-35m, 36-40m,
41-45m, 46-50m, 51-55m, 56-60m). Each row is a nest and all the distances to
the vegetation is in a column.
In plyr, I have tried - below script but I think I am going about this the
wrong way and am not successful.
#Veg index
2007 Sep 05
1
ecological meaning of randomForest vegetation classification?
Hi, everyone,
I haven't found anything similar in the forum, so here's my problem (I'm no
expert in R nor statistics):
I have a data set of 59.000 cases with 9 variables each (fractional
coverage of 9 different plant types, such as deciduous broad-leaved
temperate trees or evergreen tropical trees etc.), which was generated by a
vegetation model.
In order to evaluate the quality of
2001 Nov 13
0
VEGAN: R functions for vegetation ecologists
A colleague has just passed me this interesting
address:
http://cc.oulu.fi/~jarioksa/softhelp/vegan.html
"Vegan: R functions for vegetation ecologists"
"Vegan package is intended to help vegetation ecologists and
other community ecologists to use R. It is not a completely
self-contained package, but it complements other R functions.
.../...
At this first stage, vegan implements
2006 Jul 21
2
rpart unbalanced data
Hello all,
I am currently working with rpart to classify vegetation types by spectral
characteristics, and am comming up with poor classifications based on the fact
that I have some vegetation types that have only 15 observations, while others
have over 100. I have attempted to supply prior weights to the dataset, though
this does not improve the classification greatly. Could anyone supply some
2008 Apr 18
2
Correspondence and detrended correspondence analysis
Hi,
I hope someone knows the answer to this or has a real good reference about it (I am using Legendre & Legendre, Numerical Ecology, 1998).... My data is a data.frame with locations as rows and vegetation assemblages / species as columns. I've done a PCA, a correspondance analysis (CA) using ca in ca package and a detrended correspondance analysis (DCA) using decorana from vegan package.
2009 Apr 02
1
Time series analysis with irregular time-series
Dear R users
I am currently investigating time series analysis using an irregular time series. Our study is looking at vegetation change in areas of alien vegetation growth after clearing events. The irregular time series is sourced from Landsat ETM+ data, over a six year period I have 38 scenes. For certain periods I have monthly data while for others, images are up to three months apart. So far
2012 Apr 14
2
master thesis
Hi,
For my master thesis I have 24 micro-plots on which I did measurements during 3 months.
The measurements were:
- Rainfall and runoff events throughout 3monts (runoff being dependant on the rainfall, a coefficient (%) has been made per rainfall event and per 3 months)
- Soil texture (3 different textures were differentiated)
- Slope (3 classes of slopes)
- Stoniness (one time measurement)
2008 Mar 04
1
simplifying a GLM-removing categorical variables
Hi,
Thanks for reading this mesage!
I have created a GLM (using the quasipoisson family) and am now trying to
simplify it. One of my explanatory variables is categorical (vegetation
type, with 6 different levels). In the model, 5 of the 6 levels are
significant and one is not.
How should I simplify my model? Do I need to take out the whole category
(i.e. all of vegetation type), or just the
2009 Mar 09
1
rcorr.cens Goodman-Kruskal gamma
Dear r-helpers!
I want to classify my vegetation data with hierachical cluster analysis.
My Dataset consist of Abundance-Values (Braun-Blanquet ordinal scale; ranked) for each plant species and relev?.
I found a lot of r-packages dealing with cluster analysis, but none of them is able to calculate a distance measure for ranked data.
Podani recommends the use of Goodman and Kruskals' Gamma for
2006 Sep 12
1
Transformation of a data frame
Dear R-helpers,
Apologies in advance for this (probably) simple question. I've searched the
R Archive and can't seem to find a solution to my problem.
I have a data frame of vegetation quadrat data with the following format:
Q S C
1 A 5
1 B 10
1 C 50
1 D 10
2 A 20
2 E 10
2 C 40
3 D 5
3 F 1
3 G 5
3 B 75
Where Q is the sample (vegetation quadrats), S is the species and C is the