A statistical question, not specific to R.
I'm asking for a pointer for a source of definitive descriptions of what
types of data are best summarized by the arithmetic, geometric, and harmonic
means.
As an aquatic ecologist I see regulators apply the geometric mean to
geochemical concentrations
On Mon, 2 Nov 2020, mehdi heydari wrote:
I want to do SEM on my dataset (plant ecology) in R. Can you introduce
someone to help me?
Mehdi,
I highly recommend Jim Grace's book, "Structural Equation Modeling and
Natural Systems" and his 2008 paper, "Structural Equation Modeling for
On Thu, 18 Jun 2020, Manuel Spínola wrote:
I teach mainly to wildlife ecology students.
Manuel,
I'm a stream ecologist/fluvial geomorphologist but have run my sole
environmental consulting practice for the past 27 years.
I was using several datasets from different sources for homeworks and
On Thu, 18 Jun 2020, Manuel Spínola wrote:
I teach statistics to students in ecology and environmental sciences
fields and I would like to know if you could point me in the right
direction of sources of ecological/environmental datasets within and
outside packages, especially for
On Tue, 4 Sep 2018, g.cerritelli wrote:
I have data on the heading kept by an animal during a migratory movement.
I would like to represet this data not using a circular plot but on a
xy-plot, to represent the change of kept directions over time.
Giulia,
Without knowing what question(s)
On Thu, 25 Jun 2015, Gian Maria Niccolò Benucci wrote:
I am working on a fungal dataset with 151 OTUs distributed in 20 samples.
I have imported it as phyloseq object and as normal species matrix as well
to work with the vegan package. I am trying to find a way to get relative
abundances at
On Mon, 16 Mar 2015, Ludovico Frate wrote:
I would like to analyse the differences in life form (Raunki??)
composition between two populations. The two populations (plant
communities) were sampled randomly and the presence of plant species were
recorded. So for each plot I have the frequency
On Mon, 16 Mar 2015, Ludovico Frate wrote:
No, I'm interested in the whole plot composition! I would like to
understand if there are differences in terms of life forms composition
beteween two groups of plots (each group has 70 plots). A simple t-test or
other non parametric tests do not work
On Tue, 17 Feb 2015, Marc Taylor wrote:
A colleague of mine is doing some basic descriptive analyses of algal
community data (e.g. MDS, PCA), and we got to talking about how his data
(percent coverage) might be transformed before the calculation of distance
matrices. This may be desirable in
The compositional data sets have few observations: 4 to 7 rows each, but
there are 5 parts (columns) for each row.
I tried to use the robCompositions function pcaCoDa(). There was an error
and warning generated:
( winters.biplot - pcaCoDa(winters.coda) )
Error in princomp.default(xilr,
Data sets have been scaled and closed using acomp(). The dist() function
returns a matrix of Aitchison distances row-by-row in the data set. Example:
2004 2005 20062011 2012
20050.5917687
20060.70849411.1382195
20110.5796871
On Mon, 13 Oct 2014, Rich Shepard wrote:
2004 2005 20062011 2012
20050.5917687
20060.70849411.1382195 20110.57968710.35033940.9175847
20121.36156700.80987641.76824540.9206943
20131.49556971.2024123
On Fri, 10 Oct 2014, separ...@yahoo.com wrote:
It is not clear whether you need a supervised or an unsupervised model.
Clustering is unsupervised: it will classify compositions in hierarchical
groups regardless the label (countries, regions). If this is what you
intend, you might compute the
The documentation for packages compositions and robCompositions describe
distance measures and (in the former package) clustering. However, all the
examples, and the function syntax, apply to a single data set.
This works well with geochemical and official statistical data when the
goal is
For a data set of count proportions, testing for fit to a multivariate
normal distribution is done with the function dnorm.acomp() in package
'compositions'. The function's calling parameters are the data set, mean,
and variance.
Example data set:
dput(win.acomp)
structure(c(0.0667,
On Tue, 30 Sep 2014, separ...@yahoo.com wrote:
See Filzmoser et al. (2009)
http://www.statistik.tuwien.ac.at/forschung/SM/SM-2009-2.pdf
Serge-Étienne,
I'll carefully read this; have not found it in my literature surches.
Filzmoser et al. (2009) wrote that Some measures like the standard
On Fri, 26 Sep 2014, Serge-Étienne Parent wrote:
If your data are compositions, you will probably use acomp (for Aitchison
composition) to close the simplex between 0 and 1.
Serge-Étienne,
The composistions are proportions based on the total of the individual
groups counts so the simplex
On Fri, 26 Sep 2014, Kari Lintulaakso wrote:
you might be interested of http://www.compositionaldata.com/.
Karl,
Yes, I am familiar with that Web site. I was disappointed that the forum
lacked any activity. No response to my posts.
They have a forum for CoDa related questions. There
The data sets to be analyzed are proportions based on counts. Each row is
closed; the proportions total 1.00. I understand the need to transform the
raw data to a CoDA simplex, and my reading strongly suggests that the
isometric log ratio (ilr) function is the most appropriate for these data.
On Wed, 30 Jul 2014, Bruce Miller wrote:
I have valid ranges for the known species FA (forearm measurements) and
Fc(minimum) and Fc (maximum). So I do two separate runs with the data
using the lm model one with FA~Fcmin and one FA~Fcmax.
The goal is to provide the predicted (estimated) values
On Tue, 13 May 2014, Zbigniew Ziembik wrote:
or (commercial):
Aitchison, J. 2003. The Statistical Analysis of Compositional Data. The
Blackburn Press.
There's also: Analyzing Compositional Data with R by van den Boogaart, K.
Gerald,Tolosana-Delgado, Raimon. Published by Springer in their
I have data frames on which I want to calculate the default Bray-Curtis
dissimilarity matrix using vegdist() in the vegan package. The data are
proportions of individuals in each of 5 categories with the first column as
the collection date. One such data frame is:
sampdate filter gather
I've read the docs for anosim, adonis, and mrpp and am currently reading
the vegan tutorial. Toward the end of the anosim and mprr docs the author
writes that each has potential shortcomings and recommends the adonis
package be used instead. This leads to my two questions:
1) Why are anosin
On Mon, 4 Nov 2013, Jari Oksanen wrote:
To serve the people?
Jari,
Ah, altriism is not dead. :-)
I have suggested in the documentation that adonis() usually is better, but
it also suffers from similar problems as these alternatives. My analysis
suggests that adonis() is more robust and
On Mon, 4 Nov 2013, Angel wrote:
Hello Rich, I may be able to provide some insight into this...
I would think they are included because of familiarity and different usage
scenario's.
Angel,
I assumed this to be the case and appreciate your insights into what those
are.
ANOSIM/MRPP
On Fri, 19 Apr 2013, Mauricio Zambrano-Bigiarini wrote:
I asked about the SWAT/GRASS GIS interface to the SWAT team, and they told
me that it is still available, but is not being updated. Unfortunately,
they moved into ArcGIS :(
Mauricio,
Yeah, they did that a while ago for some unknown
On Mon, 10 Dec 2012, Sarah Goslee wrote:
... get.taxonomic() no longer has an outputFile argument.
I've read the get.taxonomic() description in bio.infer.pdf and it works
... to a point. There are 3 taxa currently not in the ITIS database (a
freshwater worm, a midge, and one chironomid for
Following the example in Lester Yuan's 2007 paper in the Journal of
Statistical Software I've bumped into a fence and need help getting over it.
My data is in the same data frame format as his bcnt.OR data set:
head(bioinfer)
SVN Taxon CountValue
1 WP220110711
On Mon, 10 Dec 2012, Sarah Goslee wrote:
2007 is forever ago in software years: get.taxonomic() no longer has
an outputFile argument.
Sarah,
Ah, so!
If you can't figure out how to adapt the code in the JSS article by
reading the help files,
I've read the .pdf that comes with the
On Thu, 6 Dec 2012, alfredo tello wrote:
Check out the R package Vegan tutorial by Jari Oksanen:
http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf. Vegan has
several functions which I believe should allow you to address some of your
questions.
Alfredo,
I will certainly do this.
I
On Thu, 6 Dec 2012, Alan Haynes wrote:
Theres a book coming out next May by Otto Wildi called Data Analysis in
Vegetation Ecology 2nd Edition which includes a lot of R code. While its
aimed at vegetation ecology, a lot of the principles in the book can be
generalised to community analysis in
On Thu, 6 Dec 2012, Ian R Waite wrote:
Just my two cents, HTH
Ian,
Thank you.
Rich
--
Richard B. Shepard, Ph.D. | Integrity - Credibility - Innovation
Applied Ecosystem Services, Inc. |
http://www.appl-ecosys.com Voice: 503-667-4517 Fax: 503-667-8863
I left academia and basic ecological research decades ago and now work
with environmental data collected by companies in compliance with regulatory
permit requirements. I've bought and read (mostly) all the books I could
find on ecological analyses using R (all but one of Alain Zuur's books,
On Wed, 16 May 2012, Highland Statistics Ltd wrote:
There is a limit to what can be done with stats. Do you really want to
analyse data that has been collected by different folks, labs, etc.? Any
change over time may actually reflect a lab effect.
Alain,
Within the ivory tower of academic
On Wed, 16 May 2012, Highland Statistics Ltd wrote:
Non-normality of your response variable is not a reason to apply a data
transformation.
Alain,
I was exploring whether a transformation might be useful. Turns out that
it's not useful.
It all depends, and no sensible answer can be
On Tue, 15 May 2012, Brian S Cade wrote:
You could try quantile regression from the quantreg package.
Brian,
That looks like a plan.
Thank you,
Rich
--
Richard B. Shepard, Ph.D. | Integrity - Credibility - Innovation
Applied Ecosystem Services, Inc. |Helping Ensure Our
On Tue, 15 May 2012, salvadorsanchezcolon wrote:
I would suggest that you look at zero-inflated models for continuous
responses.
Salvador,
Good suggestion.
Thanks,
Rich
--
Richard B. Shepard, Ph.D. | Integrity - Credibility - Innovation
Applied Ecosystem Services, Inc. |
On Tue, 15 May 2012, tom_phili...@nps.gov wrote:
Are those true zeros, or below detection limit values?
Tom,
Recorded as a combination of both. Data were collected over ~31 years by
different folks, analyzed by different labs, and stored in spreadsheets
(gak!) with no standardized
On Mon, 10 Oct 2011, Dave Roberts wrote:
I want to compare the results of the two sampling exercises in order to
test the performance of the two sampling techniques.
I would try something pretty direct. Any appeal to differences in
dissimilarities confounds the effects with the particular
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