Open MarkACantrell opened 7 years ago
evilkermit
commented
7 years ago Perhaps we could add a mask environmental layer that only gets used when looking at aquatic species? We would need a way to know which species are aquatic, though, to make sure that we only use that layer when it's appropriate.
MarkACantrell
commented
7 years ago That might work.
Also, check with Mark Endries mark_endries@fws.gov. He has been working with MaxEnt models for several hundred species across NC, including GRSM. He may have used NHD+ data to predict aquatic species.
Some wholly aquatic species may require a new raster layer of potential habitats for prediction.
Thanks, Mark
Sent from my iPhone
On Aug 26, 2016, at 3:02 AM, John Duggan notifications@github.com wrote:
Perhaps we could add a mask environmental layer that only gets used when looking at aquatic species? We would need a way to know which species are aquatic, though, to make sure that we only use that layer when it's appropriate.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/nationalparkservice/npmap-species/issues/131#issuecomment-242659642, or mute the thread https://github.com/notifications/unsubscribe-auth/AUQ4mF8pJjSPh0GMa6BcyW9jHu7mkfX7ks5qjp2bgaJpZM4Jtafw .
tpcolson
commented
7 years ago Some challenges:
We can’t use NHD Plus, as we’ve remapped all the streams in the park, and NHD Plus hasn’t caught up yet, and won’t for many years. We cannot use current NHD Plus due to gross inaccuracies, but we can use NHD;
In very many, in fact most cases, observations of aquatic species location information does not place the observation location within 30 meters (grid cell of environmental layer) of a NHD reach, some, I struggle to understand how a fish was observed halfway up a mountain near no stream! We’d have to do some pretty extensive QA of the locations.
What I know about Maxent is….that it’s very slow on my computer!
NPS Only GRSM GIS Sites:
Park Map https://grsmgis.nps.gov/MAP/
NPS GIS Portal http://nps.maps.arcgis.com/home/search.html?q=GRSM&t=content&sortField=modified&sortOrder=desc&focus=layers
Looking for some Publicly available GRSM GIS Data?
Open Data http://grsm.nps.opendata.arcgis.com/
ArcGIS Online http://www.arcgis.com/home/search.html?q=GRSM%20and%20orgid%3AfBc8EJBxQRMcHlei&t=content
NPS Data Store https://irma.nps.gov/App/Reference/Search?SearchType=N&collectionId=1336
From: MarkACantrell [mailto:notifications@github.com] Sent: Friday, August 26, 2016 6:51 AM To: nationalparkservice/npmap-species Subject: Re: [nationalparkservice/npmap-species] Mapping of aquatic species (#131)
That might work.
Also, check with Mark Endries mark_endries@fws.gov. He has been working with MaxEnt models for several hundred species across NC, including GRSM. He may have used NHD+ data to predict aquatic species.
Some wholly aquatic species may require a new raster layer of potential habitats for prediction.
Thanks, Mark
Sent from my iPhone
On Aug 26, 2016, at 3:02 AM, John Duggan notifications@github.com wrote:
Perhaps we could add a mask environmental layer that only gets used when looking at aquatic species? We would need a way to know which species are aquatic, though, to make sure that we only use that layer when it's appropriate.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/nationalparkservice/npmap-species/issues/131#issuecomment-242659642
, or mute the thread < https://github.com/notifications/unsubscribe-auth/AUQ4mF8pJjSPh0GMa6BcyW9jHu7mkfX7ks5qjp2bgaJpZM4Jtafw
.
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tpcolson
commented
7 years ago Hi Tomas,
It is my understanding that the NHDPlus lines are the same as the NHD medium resolution. The plus in NHDPlus is the addition of attribute data. Is it the attribute data that you are saying has "gross inaccuracies"? If so I'd be interested in hearing your take on the inaccuracies.
When I did my modelling I simply excluded all occurrences that fell outside of 100 m of a stream. It wasn't a perfect solution, it's likely that there were plenty of occurrences that were incorrect but happened to fall within 100 m of a stream, but I could only do so much.
If you are interested in seeing the methods and results of the modelling work I did we have a webpage up here: https://www.fws.gov/asheville/htmls/Maxent/Maxent.html
Feedback has been very positive on the predictions.
What is it you are all trying to do? I'm interested in collaborating.
Thanks!
Mark
Mark Endries USFWS 160 Zillicoa St Asheville, NC 28801 Office: 828.258.3939 ext. 231 Mobile: 828.215.1740
On Fri, Aug 26, 2016 at 7:08 AM, Thomas Colson thomas_colson@nps.gov wrote:
Some challenges:
We can’t use NHD Plus, as we’ve remapped all the streams in the park, and NHD Plus hasn’t caught up yet, and won’t for many years. We cannot use current NHD Plus due to gross inaccuracies, but we can use NHD;
In very many, in fact most cases, observations of aquatic species location information does not place the observation location within 30 meters (grid cell of environmental layer) of a NHD reach, some, I struggle to understand how a fish was observed halfway up a mountain near no stream! We’d have to do some pretty extensive QA of the locations.
What I know about Maxent is….that it’s very slow on my computer!
NPS Only GRSM GIS Sites:
Park Map https://grsmgis.nps.gov/MAP/
NPS GIS Portal http://nps.maps.arcgis.com/home/search.html?q=GRSM&t=content&sortField=modified&sortOrder=desc&focus=layers
Looking for some Publicly available GRSM GIS Data?
Open Data http://grsm.nps.opendata.arcgis.com/
ArcGIS Online http://www.arcgis.com/home/search.html?q=GRSM%20and%20orgid%3AfBc8EJBxQRMcHlei&t=content
NPS Data Store https://irma.nps.gov/App/Reference/Search?SearchType=N&collectionId=1336
From: MarkACantrell [mailto:notifications@github.com] Sent: Friday, August 26, 2016 6:51 AM To: nationalparkservice/npmap-species Subject: Re: [nationalparkservice/npmap-species] Mapping of aquatic species (#131)
That might work.
Also, check with Mark Endries mark_endries@fws.gov. He has been working with MaxEnt models for several hundred species across NC, including GRSM. He may have used NHD+ data to predict aquatic species.
Some wholly aquatic species may require a new raster layer of potential habitats for prediction.
Thanks, Mark
Sent from my iPhone
On Aug 26, 2016, at 3:02 AM, John Duggan notifications@github.com wrote:
Perhaps we could add a mask environmental layer that only gets used when looking at aquatic species? We would need a way to know which species are aquatic, though, to make sure that we only use that layer when it's appropriate.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/nationalparkservice/npmap-species/issues/131# issuecomment-242659642, or mute the thread https://github.com/notifications/unsubscribe-auth/ AUQ4mF8pJjSPh0GMa6BcyW9jHu7mkfX7ks5qjp2bgaJpZM4Jtafw .
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nationalparkservice/npmap-species/issues/131#issuecomment-242699755, or mute the thread https://github.com/notifications/unsubscribe-auth/AFlxmM0r-O6hU1yshEvQJ8498i9IY5c8ks5qjsUsgaJpZM4Jtafw .
tpcolson
commented
7 years ago · Download a detailed description of the analysis that generated the shapefile (pdf 1.43 MB) https://www.fws.gov/asheville/pdfs/Aquatic%20Species%20Mapping%20in%20North%20Carolina%20using%20Maxent%20V2.pdf from that page appears to be a dead link.
For the entire application, we’re feeding in every species occurrence/location into a maxent model being run on a super computer at Oak Ridge, and out the other end a dynamic tiled prediction map is generated, per species. On the aquatics sides, gross inaccurate locations could be, a trout observation say, at the very top of a mountain, for which we have no way to QA other than visually check every observation in the database (200,000+). On the NHDPlus, we have since remapped all of the streams in the park, and they are in the NHD, but not the NHDPlus, which was based on old “Blue Line Topo Stream”, which include, for example, a stream flowing UP a ridge, across a mountain, and sideways across a valley. I expect it will be several years before our NHD improvement hits the NHDPlus update cycle….they do it by HUC8 on a 10 year cycle I think. If we can self-generate watershed area and 7Q10 flow-per-reach ourselves, then we could likely do something like you did. Perhaps run an “aquatic species only” version of what we’re doing. Emphasis on this application is fully automatic and hands-free modelling….our intent is for new observations to get consumed by the model and auto-update the distribution maps.
Took a look at your output data, very cool, we’d love to collaborate and reproduce that for all of the HUC 12’s that intersect the park.
NPS Only GRSM GIS Sites:
Park Map https://grsmgis.nps.gov/MAP/
NPS GIS Portal http://nps.maps.arcgis.com/home/search.html?q=GRSM&t=content&sortField=modified&sortOrder=desc&focus=layers
Looking for some Publicly available GRSM GIS Data?
Open Data http://grsm.nps.opendata.arcgis.com/
ArcGIS Online http://www.arcgis.com/home/search.html?q=GRSM%20and%20orgid%3AfBc8EJBxQRMcHlei&t=content
NPS Data Store https://irma.nps.gov/App/Reference/Search?SearchType=N&collectionId=1336
From: Endries, Mark [mailto:mark_endries@fws.gov] Sent: Friday, August 26, 2016 10:35 AM To: Thomas Colson Cc: nationalparkservice/npmap-species; nationalparkservice/npmap-species; Kendra Straub; Tom Remaley Subject: Re: [nationalparkservice/npmap-species] Mapping of aquatic species (#131)
Hi Tomas,
It is my understanding that the NHDPlus lines are the same as the NHD medium resolution. The plus in NHDPlus is the addition of attribute data. Is it the attribute data that you are saying has "gross inaccuracies"? If so I'd be interested in hearing your take on the inaccuracies.
When I did my modelling I simply excluded all occurrences that fell outside of 100 m of a stream. It wasn't a perfect solution, it's likely that there were plenty of occurrences that were incorrect but happened to fall within 100 m of a stream, but I could only do so much.
If you are interested in seeing the methods and results of the modelling work I did we have a webpage up here: https://www.fws.gov/asheville/htmls/Maxent/Maxent.html
Feedback has been very positive on the predictions.
What is it you are all trying to do? I'm interested in collaborating.
Thanks!
Mark
Mark Endries
USFWS
160 Zillicoa St
Asheville, NC 28801
Office: 828.258.3939 ext. 231
Mobile: 828.215.1740
On Fri, Aug 26, 2016 at 7:08 AM, Thomas Colson thomas_colson@nps.gov wrote:
Some challenges:
We can’t use NHD Plus, as we’ve remapped all the streams in the park, and NHD Plus hasn’t caught up yet, and won’t for many years. We cannot use current NHD Plus due to gross inaccuracies, but we can use NHD;
In very many, in fact most cases, observations of aquatic species location information does not place the observation location within 30 meters (grid cell of environmental layer) of a NHD reach, some, I struggle to understand how a fish was observed halfway up a mountain near no stream! We’d have to do some pretty extensive QA of the locations.
What I know about Maxent is….that it’s very slow on my computer!
NPS Only GRSM GIS Sites:
Park Map https://grsmgis.nps.gov/MAP/
NPS GIS Portal http://nps.maps.arcgis.com/home/search.html?q=GRSM&t=content&sortField=modified&sortOrder=desc&focus=layers
Looking for some Publicly available GRSM GIS Data?
Open Data http://grsm.nps.opendata.arcgis.com/
ArcGIS Online http://www.arcgis.com/home/search.html?q=GRSM%20and%20orgid%3AfBc8EJBxQRMcHlei&t=content
NPS Data Store https://irma.nps.gov/App/Reference/Search?SearchType=N&collectionId=1336
From: MarkACantrell [mailto:notifications@github.com] Sent: Friday, August 26, 2016 6:51 AM To: nationalparkservice/npmap-species Subject: Re: [nationalparkservice/npmap-species] Mapping of aquatic species (#131)
That might work.
Also, check with Mark Endries mark_endries@fws.gov. He has been working with MaxEnt models for several hundred species across NC, including GRSM. He may have used NHD+ data to predict aquatic species.
Some wholly aquatic species may require a new raster layer of potential habitats for prediction.
Thanks, Mark
Sent from my iPhone
On Aug 26, 2016, at 3:02 AM, John Duggan notifications@github.com wrote:
Perhaps we could add a mask environmental layer that only gets used when looking at aquatic species? We would need a way to know which species are aquatic, though, to make sure that we only use that layer when it's appropriate.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub < https://github.com/nationalparkservice/npmap-species/issues/131#issuecomment-242659642
, or mute the thread < https://github.com/notifications/unsubscribe-auth/AUQ4mF8pJjSPh0GMa6BcyW9jHu7mkfX7ks5qjp2bgaJpZM4Jtafw
.
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/nationalparkservice/npmap-species/issues/131#issuecomment-242699755, or mute the thread https://github.com/notifications/unsubscribe-auth/AFlxmM0r-O6hU1yshEvQJ8498i9IY5c8ks5qjsUsgaJpZM4Jtafw .
tpcolson
commented
7 years ago need to
determine which species are "aquatic";
QA those obs using HEM tool
I love the mapper, and assume that it uses some Maximum Entropy modeling techniques to predict species occurrences.
Mapping of aquatic species needs a little work to limit aquatic species to aquatic habitats. For example, the predicted occurrences of rockbass or creek chub results in pixels in riparian and other areas. Could the results be constrained to the stream corridor or a stream centerline?