Subject: Marine Geospatial Ecology Tools (MGET) help
Text archives
| From: | "Arthur Knight" <> |
|---|---|
| To: | "Ben Best" <>, "Jason Roberts" <> |
| Cc: | <> |
| Subject: | RE: [mget-help] Additional advice on MGET please |
| Date: | Mon, 7 Jun 2010 07:20:22 +1000 |
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Thank you Ben and Jason for this detailed
advice and material. It is very timely and helpful, and I am
very impressed by the level of integration you have been able to achieve
between ArcGIS and the statistical software. I think these tools will prove
invaluable for the work I am proposing. In the short term I will use your
information to facilitate my proposal for a framework for aquatic connectivity
assessment in The proposal will undergo some internal
review before it can be released to a wider community, but I would welcome your
input and advice in due course, so I will keep in contact. Thank you again. Regards, Arthur Knight. From:
Ben Best [mailto:] Hi Arthur, On Fri, Jun 4, 2010 at 11:55 AM, Jason Roberts <> wrote: Hi Arthur, It sounds like you have some very specific ideas in mind
for your project. Discussing them with Ben, as he recommends, might be the
quickest way to determine if MGET will be of use to you. But based on your
description, I identified four areas that MGET might help you with: 1. Converting
data to ArcGIS-readable formats. MGET has various tools for this. Whether they
will be useful depends on what input data you will be using. Many oceanographic
datasets are distributed in HDF or NetCDF format. ArcGIS has trouble with these
and MGET can help you convert them to Arc format. There are some examples here. 2. Fitting
statistical models and creating predictive maps from rasters representing model
covariates. MGET interoperates with R to fit GLMs and GAMs. Once a model is
fitted, you can evaluate its performance using ROC analysis and then create
maps of the predicted response. MGET does the work of reading your rasters,
running them though the prediction functions in R, and creating outputs
representing the response. There is a worked example here. As Ben mentioned, we have not yet ported his CART
implementation from ArcRstats to MGET. It is likely that we will complete that
job in the next few months, as well as an implementation of RandomForests for
evaluating the importance of predictor variables in tree-based models. 3. Incorporating
R code into ArcGIS geoprocessing workflows. MGET includes generic geoprocessing
tools for executing R code within geoprocessing models. If you have
fragements of R code that need to run at different steps in an ArcGIS workflow,
this can be a convenient way to orchestrate the flow, even if nothing else in
MGET is useful to you. 4. Efficiently
building connectivity networks and calculating least-cost paths between sites.
These are the ConnMod tools that Ben has been updating in preparation for
incorporation into MGET. It is best if he explains the details of them. I will also forward you a copy of the following paper which
gives an overview of MGET’s software architecture and an example of #2
above. Roberts, J.J., B.D. Best, D.C. Dunn, E.A. Treml, and P.N.
Halpin (2010). Marine Geospatial Ecology Tools: An integrated framework for
ecological geoprocessing with ArcGIS, Python, R, MATLAB, and C++. Environmental
Modelling & Software 25: 1197-1207 doi:10.1016/j.envsoft.2010.03.029. Best regards, Jason From: Ben Best [mailto:] Sent: Thursday, June 03, 2010 10:33 PM Hi
Arthur,
On Thu,
Jun 3, 2010 at 8:43 PM, Arthur Knight <>
wrote: Hi. I am writing a review and framework for a new connectivity approach
to assessing wetlands in However I have not heard back from Ben about accessing further
information and I could really do with that information now. Please let me know if you feel the MGET
software is appropriate for the sort of analysis I am
interested in (see below). I would also be interested in hearing if
you know of other researchers who are using your software for wetland
connectivity assessment and management applications, as this would help to
consolidate my decision on the software. Regards Arthur Knight. ------------- Hi Ben. Do you have any advice for me about the most suitable software from
your suite of applications? I would appreciate your advice. Regards Arthur Knight. From: Arthur Knight Hi Ben. I have had a quick look at MGET and I thought it had a lot of tools
not relevant to my area of interest. My work requirement is to develop new, more consistent and generally
applicable assessment and mapping methods for hydrologic and ecologic
connectivity between terrestrial aquatic ecosystems for management
applications. This encompasses runoff-runon processes, defined flows and
rainfall but applying it across the rather large The techniques will be linked to existing mapping and inventory
data including DEMs and stream networks. A significant amount of the data will be stochastic in nature but
evaluated within a landscape model stratified by eco-hydrological sub-regions.
Given that the task is a multi-scaled spatio-temporal problem, I felt a more
defendable approach would be to include CART styled modelling to evaluate the
significance of connectivity characteristics for the inundation of different
wetland types with different environmental conditions and reference periods of
assessment. Scott Goetz and Patrick and Claire Jantz (Remote Sensing of
Environment 113 (2009) 1421-1429 published a terrestrial habitat graph theory
based connectivity study for I am an SPLUS (similar to R) and ArcGIS user/programmer so I am
particularly interested in exploring how your software might be integrated into
our scientific and knowledge based systems. We also map and model estuarine and marine systems out to 3
nautical miles from the coast. Please let me know if you feel the MGET
software is more appropriate for evaluation. I would also be interested in hearing if
you know of other researchers who are using your software for wetland
connectivity assessment and management applications. Regards Arthur Knight. From: Ben Best [mailto:] Hi
Arthur, On Thu,
May 20, 2010 at 8:35 PM, Arthur Knight <>
wrote: Hi. I am
interested in your ArcRstats Version 0.7. I have downloaded the zip file (from
your .duke.edu/geospatial/software site) but my system tells me the zip
file is corrupt, and it will not open. Could you
please confirm the status of the file for download? Thank
you. Arthur
Knight. ________________________________________________________ Dr Arthur
Knight Senior
Biodiversity Planning Officer Biodiversity
and Resource Management, Natural Resources and Environment Telephone 07 5451 2247 Facsimile 07
5451 2260 Email: Department
of Environment and Resource Management Centenary
Square, 52-64 Currie Street Nambour Q 4560 ________________________________________________________ Dr Arthur
Knight Senior
Biodiversity Planning Officer Biodiversity
and Resource Management, Natural Resources and Environment Telephone 07 5451 2247 Facsimile 07
5451 2260 Email: Department
of Environment and Resource Management Centenary
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