Mountain Quail Habitat Model for NSNF Connectivity - CDFW [ds1046]

SDE Raster Dataset

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Tags
northern Sierra Nevada foohills, Oreortyx pictus, mountain quail, habitat modeling, connectivity modeling, California


Summary

Predicted habitat suitability grid developed using Maxent and reviewed by CDFW staff for use in the northern Sierra Nevada foothills wildlife connectivity project. Scenario7: vegetation, distance to water, and elevation were used to predict habitat suitability. The vegetation data in this scenario was represented by four continuous vegetation datasets (percent conifer, percent grassland, percent hardwood, and percent shrubs). All bioclimatic variables were excluded in order to see the effects of the remaining variables on model outputs.

Description

The Maxent modeling algorithm was used to build the species distribution model at 270 m spatial resolution using species occurrence points and environmental layers as predictors (Phillips et al. 2006). Species occurrence points were primarily obtained from CNDDB (California Natural Diversity Database) and other CDFW sources, GBIF (Global Biodiversity Information Facility), PRBO (Point Blue Conservation Science) and Arctos museum databases. Vegetation, distance to water, elevation, and bioclimatic variables (Franklin et al. 2013) were used as predictor variables.

The models were run at 270 m spatial resolution with five replications using cross-validation as a method of sample evaluation. Cross-validation involved the partitioning of the sample data into n subsets, fitting the models to n-1 subsets, and testing the model on the one subset not used in fitting the model. Initial model runs showed that our models converged around 2,000 iterations and for this reason we ran all models with 2,500 maximum iterations. Maxent was implemented in R using the dismopackage (Hijmans et al. 2011). Model evaluation was carried out using the PresenceAbsencepackage in R ( Freeman and Moisen 2008) . We used AUC as a metric to evaluate model performance. The package also computes threshold values using several accuracy metrics to translate predicted probability maps into binary suitable and unsuitable habitats. We selected the MeanProb, a threshold set based on the mean predicted probability of species occurrences. The output from Maxent are grid datasets in a multiband tifformat with one band for each replication. We averaged the five replicated maps and created a mean grid for each species. The grid was then symbolized to represent low (threshold-50), medium (50-75) and high (75-100) habitat suitability, with pixel values that are below the threshold excluded. Models were reviewed by CDFW species experts; please review the use limitations.

For more information see the project report at [ https://nrm.dfg.ca.gov/FileHandler.ashx?DocumentID=85358].

Credits

Franklin, J, Davis, F. W., Ikegami, M., Syphard, A. D., Flint, L. E., Flint, A. L., Hannah, L. (2013). Modeling plant species distributions under future climates: how fine scale do climate projections need to be? Global Change Biology, 19(2): 473-483 Freeman, E.A. & Moisen, G. (2008) Presence absence: an R package for presence-absence analysis. Journal of Statistical Software, 23, 131. Hijmans, R.J., Phillips S.J., Leathwick, J., and Elith, J. (2011) R package dismo for species distribution modeling. The R Project for Statistical Computing. Phillips, S.J. and Dudik, M. (2008) Modeling species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31, 161-175. National Hydrography Dataset (NHD) http://nhd.usgs.gov/ CDF-FRAP (fveg) http://www.fs.fed.us/r5/rsl/projects/mapping/ http://www.fs.fed.us/pnw/fia/ http://www.frap.cdf.ca.gov/ Northern Sierra Nevada foothills vegetation (BIOS ds566), Central Valley vegetation (BIOS s777) CNDDB http://www.dfg.ca.gov/biogeodata/cnddb/ GBIF http://www.gbif.org/ Arctos http://arctos.database.museum/ PRBO http://www.pointblue.org/

Use limitations

The user accepts sole responsibility for the correct interpretation of this report and the correct use of its accompanying data sets in environmental documents. The northern Sierra Nevada foothills wildlife connectivity project habitat data delineates area likely important to the selected focal species. It is a decision-support tool to be refined by field work and expert knowledge. DO NOT assume that areas predicted as low, medium or high habitat represents the likelihood of the focal species being present or that areas below the predicted threshold are unimportant to wildlife populations or movements.

Extent

West -122.597118 East -119.536199
North 40.993118 South 36.779502

Scale Range
Maximum (zoomed in) 1:5,000
Minimum (zoomed out) 1:150,000,000

ArcGIS Metadata

Topics and Keywords

Themes or categories of the resource biota, environment, geoscientificInformation, location


* Content type Downloadable Data
Export to FGDC CSDGM XML format as Resource Description No

Place keywords northern Sierra Nevada foothills, California

Theme keywords Oreortyx pictus, Mountain Quail, habitat modeling, connectivity modeling

Citation

Title Mountain Quail Habitat Model for NSNF Connectivity - CDFW [ds1046]
Publication date 2014-06-1700:00:00


Presentation formats * digital table


Citation Contacts

Responsible party
Individual's name Melanie Gogol-Prokurat
Organization's name California Department of Fish and Wildlife, Data and Technology Division, Biogeographic Data Branch
Contact's position Conservation Analysis Unit Coordinator
Contact's role point of contact


Contact information
Phone
Voice (916) 324-9265

Address
Type physical
City Sacramento
Administrative area CA
Country US
e-mail address Melanie.Gogol-Prokurat@Wildlife.ca.gov



Resource Details

Dataset languages * English(UNITED STATES)
Dataset character set utf8 - 8 bit UCS Transfer Format


Status completed
Spatial representation type * grid


* Processing environment Microsoft Windows 7 Version 6.1 (Build 7601) Service Pack 1; Esri ArcGIS 10.2.0.3348


Credits
Franklin, J, Davis, F. W., Ikegami, M., Syphard, A. D., Flint, L. E., Flint, A. L., Hannah, L. (2013). Modeling plant species distributions under future climates: how fine scale do climate projections need to be? Global Change Biology, 19(2): 473-483 Freeman, E.A. & Moisen, G. (2008) Presence absence: an R package for presence-absence analysis. Journal of Statistical Software, 23, 131. Hijmans, R.J., Phillips S.J., Leathwick, J., and Elith, J. (2011) R package dismo for species distribution modeling. The R Project for Statistical Computing. Phillips, S.J. and Dudik, M. (2008) Modeling species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography, 31, 161-175. National Hydrography Dataset (NHD) http://nhd.usgs.gov/ CDF-FRAP (fveg) http://www.fs.fed.us/r5/rsl/projects/mapping/ http://www.fs.fed.us/pnw/fia/ http://www.frap.cdf.ca.gov/ Northern Sierra Nevada foothills vegetation (BIOS ds566), Central Valley vegetation (BIOS s777) CNDDB http://www.dfg.ca.gov/biogeodata/cnddb/ GBIF http://www.gbif.org/ Arctos http://arctos.database.museum/ PRBO http://www.pointblue.org/
ArcGIS item properties
* Name Mountain Quail Habitat Model for NSNF Connectivity CDFW [ds1046]
* Location Server=; :; Database=; User=; Version=
* Access protocol ArcSDE Connection

Extents

Extent
Geographic extent
Bounding rectangle
Extent type Extent used for searching
* West longitude -122.597118
* East longitude -119.536199
* North latitude 40.993118
* South latitude 36.779502
* Extent contains the resource Yes

Extent in the item's coordinate system
* West longitude -13647448.799721
* East longitude -13306708.799721
* South latitude 4408416.613912
* North latitude 5011326.613912
* Extent contains the resource Yes

Resource Maintenance

Resource maintenance
Update frequency not planned


Resource Constraints

Constraints
Limitations of use

The user accepts sole responsibility for the correct interpretation of this report and the correct use of its accompanying data sets in environmental documents. The northern Sierra Nevada foothills wildlife connectivity project habitat data delineates area likely important to the selected focal species. It is a decision-support tool to be refined by field work and expert knowledge. DO NOT assume that areas predicted as low, medium or high habitat represents the likelihood of the focal species being present or that areas below the predicted threshold are unimportant to wildlife populations or movements.


Spatial Reference

ArcGIS coordinate system
* Type Projected
* Geographic coordinate reference GCS_WGS_1984
* Projection WGS_1984_Web_Mercator_Auxiliary_Sphere
* Coordinate reference details
Projected coordinate system
Well-known identifier 102100
X origin -20037700
Y origin -30241100
XY scale 148923141.92838538
Z origin -100000
Z scale 10000
M origin -100000
M scale 10000
XY tolerance 0.001
Z tolerance 0.001
M tolerance 0.001
High precision true
Latest well-known identifier 3857
Well-known text PROJCS["WGS_1984_Web_Mercator_Auxiliary_Sphere",GEOGCS["GCS_WGS_1984",DATUM["D_WGS_1984",SPHEROID["WGS_1984",6378137.0,298.257223563]],PRIMEM["Greenwich",0.0],UNIT["Degree",0.0174532925199433]],PROJECTION["Mercator_Auxiliary_Sphere"],PARAMETER["False_Easting",0.0],PARAMETER["False_Northing",0.0],PARAMETER["Central_Meridian",0.0],PARAMETER["Standard_Parallel_1",0.0],PARAMETER["Auxiliary_Sphere_Type",0.0],UNIT["Meter",1.0],AUTHORITY["EPSG",3857]]

Reference system identifier
* Value 3857
* Codespace EPSG
* Version 8.1.1


Spatial Data Properties

Georectified Grid
* Number of dimensions 2


Axis dimensions properties
Dimension type column (x-axis)
* Dimension size 954
* Resolution 270.000000Meter

Axis dimensions properties
Dimension type row (y-axis)
* Dimension size 1723
* Resolution 270.000000Meter

* Cell geometry area
* Point in pixel center


* Transformation parameters are available Yes


* Check points are available No


Corner points
* Point -218705.840000 -134473.310000
* Point -218705.840000 330736.690000
* Point 38874.160000 330736.690000
* Point 38874.160000 -134473.310000

* Center point -89915.840000 98131.690000




ArcGIS Raster Properties
General Information
* Pixel depth 32
* Compression type RLE
* Number of bands 1
* Raster format GRID
* Source type continuous
* Pixel type floating point
* No data value -3.4028235e+038
* Has colormap No
* Has pyramids No




Spatial Data Content

Image Description
* Type of information physical measurement


Band information
* Description moqu_ex_tm
* Maximum value 100.000000
* Minimum value 33.762035
* Number of bits per value 32


Geoprocessing history

Process
Process name Project Raster
Date 2014-10-1509:08:13
Tool location c:\program files (x86)\arcgis\desktop10.2\ArcToolbox\Toolboxes\Data Management Tools.tbx\ProjectRaster
Command issued
Include in lineage when exporting metadata No


Distribution

Distribution format
* Name SDE Raster Dataset


Transfer options
Online source
Location http://bios.dfg.ca.gov
Function performed information

Online source
Location ftp://ftp.dfg.ca.gov/BDB/GIS/BIOS/Public_Datasets/1000_1099/ds1046.zip
Function performed download

Metadata Details

Metadata language English(UNITED STATES)
Metadata character set utf8 - 8 bit UCS Transfer Format


Scope of the data described by the metadata dataset
Scope name * dataset


* Last update 2015-01-13


ArcGIS metadata properties
Metadata format ArcGIS1.0
Metadata style FGDC CSDGM Metadata
Standard or profile used to edit metadata ISO19139


Created in ArcGIS for the item 2014-06-1613:04:16
Last modified in ArcGIS for the item 2015-01-1311:38:04


Automatic updates
Have been performed Yes
Last update 2015-01-1311:37:47

Item location history
Item copied or moved 2014-06-1613:04:16
From E:\SDM_results\thld_applied\times\moqu_s7
To \\WBD41RDPL1\K\Final_BIOS\SDM\moqu_s7


Metadata Contacts

Metadata contact
Individual's name Melanie Gogol-Prokurat
Organization's name California Department of Fish and Wildlife, Data and Technology Division, Biogeographic Data Branch
Contact's position Conservation Analysis Unit Coordinator
Contact's role point of contact


Contact information
Phone
Voice (916) 324-9265

Address
Type physical
City Sacramento
Administrative area CA
Country US
e-mail address Melanie.Gogol-Prokurat@Wildlife.ca.gov



Metadata Maintenance

Maintenance
Update frequency not planned


Thumbnail and Enclosures