[R-sig-eco] Biostatistics 1.0.0 run in latest RStudio
Carl Von Ende
cvonende @end|ng |rom n|u@edu
Tue Jan 26 08:01:50 CET 2021
Dear Rob,
Ahh - now I see. Thanks very much.
Best,
Carl
On 1/25/21, 5:01 AM, "R-sig-ecology on behalf of r-sig-ecology-request using r-project.org" <r-sig-ecology-bounces using r-project.org on behalf of r-sig-ecology-request using r-project.org> wrote:
Send R-sig-ecology mailing list submissions to
r-sig-ecology using r-project.org
To subscribe or unsubscribe via the World Wide Web, visit
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
or, via email, send a message with subject or body 'help' to
r-sig-ecology-request using r-project.org
You can reach the person managing the list at
r-sig-ecology-owner using r-project.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of R-sig-ecology digest..."
Today's Topics:
1. Re: Biostatistics 1.0.0 run in latest RStudio (Carl Von Ende)
(R Knell)
2. Do You Have Anything Against Using ISO DATA? (Skipton Woolley)
----------------------------------------------------------------------
Message: 1
Date: Sun, 24 Jan 2021 16:02:44 +0000
From: R Knell <r.knell using qmul.ac.uk>
To: "r-sig-ecology using r-project.org" <r-sig-ecology using r-project.org>
Subject: Re: [R-sig-eco] Biostatistics 1.0.0 run in latest RStudio
(Carl Von Ende)
Message-ID:
<DB6PR07MB34163B859DD5DA348AF532A7DFBE0 using DB6PR07MB3416.eurprd07.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
>Dear Dr. Knell,
>Thanks very much for creating the package Biostatistics 1.0.0. Have you run the Biostatistics 1.0.0 tutorial in the most recent version of RStudio (Version >1.4.1103). When I try, the tutorial seems to hang-up at "Multiple choice quizzes in the Descriptive and Exploratory Statistics: Introduction." There is no "Next" button >available. But perhaps I am doing something wrong? I have not used a "Tutorial" tab before.
>
>Best,
>
>Carl von Ende
>Dept. Biol. Sciences
>Northern Illinois University
>DeKalb, IL 60115
>cvonende using niu.edu<mailto:cvonende using niu.edu>
Dear Carl
Sorry for the slight confusion there. You just need to exit that tutorial and move on to the next one.
The introduction does need a bit of work to make it clearer I realise now.
Best wishes
Rob
Rob Knell
Reader in Evolutionary Ecology
School of Biological and Chemical Sciences
Queen Mary University of London
Research website http://webspace.qmul.ac.uk/rknell/
Photography https://flic.kr/s/aHskkA3UQJ
r.knell using qmul.ac.uk<mailto:r.knell using qmul.ac.uk>
[[alternative HTML version deleted]]
------------------------------
Message: 2
Date: Mon, 25 Jan 2021 03:08:26 +0000
From: Skipton Woolley <skipton.woolley using utas.edu.au>
To: "Alexandre%20F.%20Souza\"%20" <alexsouza.cb.ufrn.br using gmail.com>
Cc: Lista%20de%20discussao%20R-sig-ecology%20
<r-sig-ecology using r-project.org>
Subject: [R-sig-eco] Do You Have Anything Against Using ISO DATA?
Message-ID:
<ME2PR01MB38571769423594563F1EF1E7B8BD0 using ME2PR01MB3857.ausprd01.prod.outlook.com>
Content-Type: text/plain; charset="utf-8"
Hi Alexandre,
If you are interested in model-based bioregionalisation there are several attractive options
available in R. With colleagues, I have been trying to develop and implement model-based
bioregionalisation to maintain species information and uncertainty throughout the modelling
process.
Here are a few papers which might be of interest to you.
Model-based bioregionalisation perspective piece:
https://academic.oup.com/bioscience/article/70/1/48/5670754?login=true
Comparison of model-based methods:
https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13447
Vegetation classification (bioregionalisation) using Regions of Common Profiles.
https://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.13088
[https://onlinelibrary.wiley.com/cms/asset/2bdffdcb-f397-4884-a522-117552992254/jbi.2017.44.issue-12.cover.gif]<https://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.13088>
Simultaneous vegetation classification and mapping at large spatial scales<https://onlinelibrary.wiley.com/doi/abs/10.1111/jbi.13088>
Aim Multivariate mixture models offer the ability to streamline the typically multi�\stage process of vegetation classification and mapping into a single, simultaneous analytical step. Our aim is to ...
onlinelibrary.wiley.com
[https://besjournals.onlinelibrary.wiley.com/cms/asset/660a90cf-3de4-44bc-aac9-6b796528810d/mee3.v11.10.cover.gif]<https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13447>
Determining marine bioregions: A comparison of quantitative approaches - Hill - 2020 - Methods in Ecology and Evolution - Wiley Online Library<https://besjournals.onlinelibrary.wiley.com/doi/abs/10.1111/2041-210X.13447>
Areas that contain ecologically distinct biological content, called bioregions, are a central component to spatial and ecosystem�\based management. We review and describe a variety of commonly used...
besjournals.onlinelibrary.wiley.com
There is code available for the second paper here:
https://github.com/Hillna-IMAS/Bioregion_Methods/tree/v1.1
The RCP approach can be implemented using the RCPmod package (on cran) or the updated ecomix package https://github.com/skiptoniam/ecomix which is still in development - but should be on cran soon.
ecomix has all the functionality of RCPmod, but with some additional functions to make interpretation of these models a little easier.
Anyway, I hope your bioregionalisation work goes well. I'd be happy to help with ecomix related questions if you decide to apply such methods.
Cheers,
Skip.
Dear R-Sig Colleagues,
I am performing a bioregionalization of the Cerrado woody flora in central
Brazil.
I am following the steps
Produce a dissimilarity matrix from species x site matrix
Perform a NMDS on the dissimilarity matrix
Interpolate each NMDS axis with Kriging
Partition the stacked interpolated rasters with K-means
I am willing to change the k-means by the ISO DATA method implemented in
ArcGis, which takes an initial number of groups (the same used for the
k-means classification). The ISODATA algorithm has some further refinements
by splitting and merging of clusters. Clusters are merged if either the
number of members (pixel) in a cluster is less than a certain threshold or
if the centers of two clusters are closer than a certain threshold.
Clusters are split into two different clusters if the cluster standard
deviation exceeds a predefined value and the number of members (pixels) is
twice the threshold for the minimum number of members. It implements a set
of rule-of-thumb procedures that have been incorporated into an iterative
classification algorithm. Many of the steps used in the algorithm are based
on the experience obtained through experimentation. The ISODATA algorithm
is a modification of the k-means clustering algorithm and is supposed to
overcome the disadvantages of k-means.
The classification produced preserved the main patterns found in kmeans
while reducing the number of groups.
However, I have not found anything in the literature of bioregionalization
using ISO DATA, only kmeans. Do you know of any reasons I should not use
ISO DATA for this aim?
Thank you very much in advance for any inputs,
Best,
Alexandre
--
Dr. Alexandre F. Souza
Professor Associado
Chefe do Departamento de Ecologia
Universidade Federal do Rio Grande do Norte
CB, Departamento de Ecologia
Campus Universit��rio - Lagoa Nova
59072-970 - Natal, RN - Brasil
lattes: lattes.cnpq.br/7844758818522706<http://lattes.cnpq.br/7844758818522706>
http://www.esferacientifica.com.br<http://www.esferacientifica.com.br>
https://www.youtube.com/user/alexfadigas<https://www.youtube.com/user/alexfadigas>
http://www.docente.ufrn.br/alexsouza<http://www.docente.ufrn.br/alexsouza>
orcid.org/0000-0001-7468-3631<http://orcid.org/0000-0001-7468-3631> <http://www.docente.ufrn.br/alexsouza<http://www.docente.ufrn.br/alexsouza>>
Dr. Skipton Woolley
IMAS, University of Tasmania.
Ph: 0419 990 927
University of Tasmania Electronic Communications Policy (December, 2014).
This email is confidential, and is for the intended recipient only. Access, disclosure, copying, distribution, or reliance on any of it by anyone outside the intended recipient organisation is prohibited and may be a criminal offence. Please delete if obtained in error and email confirmation to the sender. The views expressed in this email are not necessarily the views of the University of Tasmania, unless clearly intended otherwise.
[[alternative HTML version deleted]]
------------------------------
Subject: Digest Footer
_______________________________________________
R-sig-ecology mailing list
R-sig-ecology using r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
------------------------------
End of R-sig-ecology Digest, Vol 154, Issue 14
**********************************************
More information about the R-sig-ecology
mailing list