Copyright
P.(Paul) Hendricks.

Surveys for grassland birds of the Malta Field Office-BLM, including a seven-year study in north Valley County (Volume 2008) online

. (page 9 of 10)
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tions) that were correctly classified by the model as negative. One minus the Specificity (plotted on the x-axis) is known as the
false positive rate and represents the commission error rate.



Appendix C - 51



Log response of McCown_5_Long5pur to a5pect90m_mtS3clip



TO
S

n











Lofl


es


as|iect9am_mtB3tlip
onseofMcCown s LongspurtonI


d90m


mtS3




























.


































































































































































































































































































































































































II








































1






































II























































.og response of McC


own


s


Long


pur


to statsgoSOm mtS3 c


ip

















































































































































































































































































































































































































109 155 20D 24* 209 333 377 421



510 554 599 643 6B7



Log response of h^


cCown 5 Longspurto


curve


planSOm mtS3























































































































































































































































































































































Log response of McCown_5_Long5pur to elev90m_mtS3clip





Log response of McCown s




mts;





























































































































































































































































































































Log response of McCown_5_Long5pur to tmax90m_mtS3











\

















\^














\














\














\














\
















V














\



tmax90m_mt83



























,

















































































































































































-500 500





lip















































































































Log response of McCown s Longspurto tmin90m mtS3


clip




















'

















































































































Log response


3f McCown s


Longspurto














































































































































































-


-























































































































































Log response ot ft


cCown s Longspurto


soil tmp90


Ti m1S3




















































1,1












/


























1


/


















|09










/




























/




















-07
|06
|05
°04.
= D3

□ 2

□ ,1

□ ,0










/


























1




























/




























1




























1


























1




























1




























I





















































Figure C45. Response curves for individual environmental variables showing how the logistic prediction changes as each environmental variable is varied while all other envi-
ronmental variables are held constant at their average sample values. The value on the y-axis is predicted probability of suitable conditions as given by the logistic formula P(x)
= expfcl *fl(x) + c2 *f2(x) + c3 *f3(x)...) / Z. Note that if any of the environmental variables are correlated, the marginal response curves can be misleading (e.g., two highly
correlated variables with opposite response curves could effectively cancel each other out). Value definitions and/or links to metadata containing these definitions can be found in
the Descriptions of Environmental Input Layers section of the appendix above.



tmin9Dm_mte3clip
tmax90m_mt83
statsgo90m_mt83_clip
soil_tmp90m_mt83H
slope9Dm_mt83clip i
piecip_ann90m_mt83
nlcd90m_mt83
geombmg90mt83clip
elev9Dm_mt83clip
c u ive_p I a n 9 m_mt8 3 f|
aspect90m_mt83clip



0.0



Jackknife of Training gain for IVIcCownsLongspur



Without variable
With only variable
With all variables



0.5



1.0



1.5 2.0

Training cjGin



2.5



3.0



3.5



Figure C46. Jackknife chart showing the relative importance of environmental variables as a function of the change in "gain"
(the log of the number of grid cells minus the average of the negative log probabilities of the sample locations) resulting from the
exclusion or sole inclusion of the environmental variable in the model Variables with the highest training gain resulting from
sole inclusion of those variables (dark blue bars) are the best individual variables at describing suitable habitat for the species.
Jariables with the greatest reduction in training gain resulting from their exclusion (light blue bars) contain information on the
species habitat use that is not present in other variables. The red bar indicates the maximum gain achieved with inclusion of all
variables.



Appendix C - 53



Chestnut-collared Longspur {Calcarius ornatus)



TO

s
X







Figure C47. The hot-to-cold color map indicates the suitability of each grid cell as ajiinction of the environmental variables at that grid cell. Hotter colors indicate areas that
are predicted to have more suitable habitat for the species. Black dots are positive data used to build the model. Gray dots are locations where a survey capable of detecting the
species has been performed. A shaded relief map, BLM Field Office boundaries, and county lines are included for reference.



Omission vs. Predicted Area for Chestnut-collared_Longspur



1.D
D.9
Q.B

□ 7

ra
I 0.5

(J

□ .3
D.2
D.1

a.a






Fraction of background predicted

Omission on training sampies

Omission on test sampies

Predicted omission



10



30 40 50 60
Cumuiative tiiresiioii



70



SO



90



100



Figure C48. An evaluation of omission error rates for training (dark blue line) and test (light blue line) data as a function of the
cumulative threshold and overall predicted area. The red line indicates the overall fraction of the map area fitting each value of
the cumulative threshold. The black line is the predicted omission rate for each cumulative threshold.



Appendix C - 55



Sensitivitpr vs. 1 - Specificity for Chestnut-collared_Longspur



1.D



D.9



O.S



q;0.7



0.6



:eo.4



0.3



0.2



0.1



0.0






Training data (AUC = 0.983)

Test data (AUG =0.976)

Random Prediction (AUC = 0.5)



0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8

1 - Specificity [Fractionai Predicted Area)



0.9



1.0



Figure C49. Receiver Operating Characteristic (ROC) curve evaluating the overall predictive power of the model with the Area
Under the Curve (AUC). The AUC value indicates that when two random locations are chosen the model has that probability
of assigning a higher cumulative threshold value to the location with more suitable habitat. The light blue line indicates how a
neutral or random model would perform (i.e., it only has a 50% probability of assigning a higher cumulative threshold value to
a random location with more suitable habitat than a random location with less suitable habitat). The further toward the top left
of the graph the training (red) and test (blue) data lines are, the better the model is at predicting the presences contained in the
training data. Sensitivity (plotted on the y-axis) is the proportion of positive locations that were correctly classified by the model.
Sensitivity is also known as the true positive rate and can be thought of as the degree of absence of omission errors. Specificity is
the proportion of random locations chosen from the background (these pseudo-absences are used instead of true negative loca-
tions) that were correctly classified by the model as negative. One minus the Specificity (plotted on the x-axis) is known as the
false positive rate and represents the commission error rate.



Appendix C - 56



TO

s

n





Respor


se of Chestnu


-col


are




Longs


urto aspectSOm


mtSSclip




















I






























1

















1










1


1














:








.




1


1









h












M






1


1


1


1


1


1


1


1


1


1


1




L



D.ao









Respo




Of Chestnut-c


ect90m_
ollared


T1183CIIP
Lorqs


pur


to nIcdSOm mtS3






O.S!
DSQ

□.75

□ 7:

0.65

D55

o.sa

D46
40
0.35






































1
































































































































































































































































-


-




-


-




-








-


-




-


-




-




-


-






-




-


-




-








-


-




-


n




-




-


-





Response


of Ch


estnut-CDilared


Lon


jspu


r to 5tatsgo9C


m mt83


clip






































































































































































































.




















1


1






1


1


1




i


1


1


1


i


1


1


1


1


-





Response


of Chestnut-collared Longsp


rto




planSOm


mtS3



































































































































































































































































































































































































Response of Chestnut-collared_Longspur to precip_ann90m_mtS3










Response of Chestnut-co


_Bnn9am_mtB3
lared Longsp


urto tmax90m mt83






















90

■sro85

|d75

™D70
I'D, 65

ooen

^□56
□ 50
45












































\
















\


















\
















\
















\
















\
















\


















\





















Re


ponse


of Chestnut-co


ared Longspurto elevSOm mtSSclip












□.sn














































= "■'"


































~




































































|d5!

Id.so












































/




















/


















■a" '"




/


















_,U.J.




/


















□ 3:




/


















U.J
























°0 7D
i'0 65



Res


ponse of Chestnut-co


lared Lon^


spurtoslopeSOm mtSSclip

























































































































































































slo|5e90m_nitB3cli|i
Response of Chestnut-collared Longspurto tmlnSOm mtS3clip
















OS

,^06

15 0.5
|04
1^3

to.

0,1
0,0




~-^






N














\














\
















\














\














\














\,














\

























Response of Chestnut


collared


Lor


gspurto


geombm


g90mt83Glip












































































































































































































































































-


















































J































































Longspurto


soil tmp9Dm


mtS3





































































































































































































1 ■


1 I


■ I








■ I


■ I


1 I


1 ■


1 ■


1



il_tmpE)am_mt83



31 67 108 153 199 344 388 333 378 432 466 510 555 599 643 687

sta1sgo90m_mtB3_(lip



tm85f90m_m183



tmin90m_mt83(lip



Figure C50. Response curves for individual environmental variables showing how the logistic prediction changes as each environmental variable is varied while all other envi-
ronmental variables are held constant at their average sample values. The value on the y-axis is predicted probability of suitable conditions as given by the logistic formula P(x)
= exp(cl "^ fl(x) + c2 "^ f2(x) + c3 "^ f3(x) ...) / Z. Note that if any of the environmental variables are correlated, the marginal response curves can be misleading (e.g., two highly
correlated variables with opposite response curves could effectively cancel each other out). Value definitions and/or links to metadata containing these definitions can be found in
the Descriptions of Environmental Input Layers section of the appendix above.



Jackknife of regularized training gain for Cliestnut-collaredLong

n 1 1 1 1



c u ive_p I a n 9 m_mt8 3

elev90m_mt83clip

geornbmg90mt83clip

nlcd90m_mt83

piecip_ann90m_mt83

slope90m_mt83clip

soil_tmp90m_mt83

statsgo90rn_mt83_clip

tmax90m_mt83

tmin9Dm_mt83clip



spur

Without variable
With only variable
With all variables



Q.Q 0.5 1.0 1.5

regularized training gain



2.0



2.6



Figure C51. Jackknife chart showing the relative importance of environmental variables as a function of the change in "gain "
(the log of the number of grid cells minus the average of the negative log probabilities of the sample locations) resulting from the
exclusion or sole inclusion of the environmental variable in the model Variables with the highest training gain resulting from
sole inclusion of those variables (dark blue bars) are the best individual variables at describing suitable habitat for the species.
Jariables with the greatest reduction in training gain resulting from their exclusion (light blue bars) contain information on the
species habitat use that is not present in other variables. The red bar indicates the maximum gain achieved with inclusion of all
variables.



Appendix C - 58



Bobolink {Dolichonyx oryzivorus)



TO

s
X







Figure C52. The hot-to-cold color map indicates the suitability of each grid cell as a function of the environmental variables at that grid cell. Hotter colors indicate areas that
are predicted to have more suitable habitat for the species. Black dots are positive data used to build the model Gray dots are locations where a survey capable of detecting the
species has been performed. A shaded relief map, BLM Field Office boundaries, and county lines are included for reference.



Omission vs. Predicted Area for Bobolink



1.D
D.9

□ .3

□ 7

ra
I 0.5

(J

□ .3

□ .2

□ .1

Q.a





















^
















4


A
















A


J
















/(■


r


/














A


J


J














^


f


r-r


/










y


y


^


r^


fl








Y




/




/












L


y




r^














_^




^

















Fraction of background predicted

Omission on training sampies

Omission on test sampies

Predicted omission



10



30 40 50 60
Cumuiative tiiresiioii



70



SO



90



100



Figure C53. An evaluation of omission error rates for training (dark blue line) and test (light blue line) data as a function of the
cumulative threshold and overall predicted area. The red line indicates the overall fraction of the map area fitting each value of
the cumulative threshold. The black line is the predicted omission rate for each cumulative threshold.



Appendix C - 60









Sensitivity vs. Specificity


for Bobolink






i.a

D.9

o.s

I0.7

£=



E


;go.4

I0.3

□.2

□.1

Q.D




























{






/


_/


^








/








m


r


—/










/








i


J












/










r'












/






















/






















/






















/






















/






















/






















/













































Training data (AUC = 0.995)

Test data (AUG =0.901)

Random Prediction (AUC = 0.5)



0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8

Specificity (1 - Fractionai Predicted Area)



0.9



1.0



Figure C54. Receiver Operating Characteristic (ROC) curve evaluating the overall predictive power of the model with the Area
Under the Curve (AUC). The AUC value indicates that when two random locations are chosen the model has that probability
of assigning a higher cumulative threshold value to the location with more suitable habitat The light blue line indicates how a
neutral or random model would perform (i.e., it only has a 50% probability of assigning a higher cumulative threshold value to
a random location with more suitable habitat than a random location with less suitable habitat). The further toward the top left
of the graph the training (red) and test (blue) data lines are, the better the model is at predicting the presences contained in the
training data. Sensitivity (plotted on the y-axis) is the proportion of positive locations that were correctly classified by the model.
Sensitivity is also known as the true positive rate and can be thought of as the degree of absence of omission errors. Specificity is
the proportion of random locations chosen from the background (these pseudo-absences are used instead of true negative loca-
tions) that were correctly classified by the model as negative. One minus the Specificity (plotted on the x-axis) is known as the
false positive rate and represents the commission error rate.



Appendix C - 61



TO

s

n



On









Log res


ponse of Bobolink to asp


sctSOm mt83cllp






[14


1





































1


















1


















II











. II




1


D.1
D.2
D.3
□ 4









I


' 11








i




1




1








s




|l




|l


















































u a





















B2 83 B4 B5 91







Lpg response of Bobolink to curve


pl<in90m mtS3






1









































































































































































































































































































Log response of Bobolink to elev90m_mtS3clip











Log resp


sspect90m_mtB3clip
onse of Bobolink to nIcdSOm


mt83




































1




































































































































































































































































































































































II












III




II




















1


















II




















1


































T


1



















Log


cuive_plan9am_mta3
response of Bobolink to precip an


n90m


mtS3


































D.DB

^ [1[12
§-□□2
-'-□□6












































































































































































































































LIU.




























10



































Log respon


se


of Bob


□ 1


nkto statsgoSOm


mtS3 clip






























































































































































































































































































1




1


















! 1


1 ! 1





















Log response of Bobolink to trniiK9Dm


mt83


















;

























































































































































































































































/"




L_^


















































































































/




















/
























Log response of Bobolink to


slopeSOm


mtSSclip






-DS


























































■3.5
■4




























































,














\





























slope9[]m_m103clip
Log response of Bobolink to tmin90m


nrit83clip














































































\











































Log response


of Bobo


ink to geomb


mg90mtS3clip








































































































































































































































































































1





































































Log response of E


obolinktosoil tmp90m mtS3























































































































































































































































































































































544 5B7 S31 674



in90m_m1S3cli|i



Figure C55. Response curves for individual environmental variables showing how the logistic prediction changes as each environmental variable is varied while all other envi-
ronmental variables are held constant at their average sample values. The value on the y-axis is predicted probability of suitable conditions as given by the logistic formula P(x)
= expfcl * fl(x) + c2 *f2(x) + c3 *f3(x)...) / Z. Note that if any of the environmental variables are correlated, the marginal response curves can be misleading (e.g., two highly
correlated variables with opposite response curves could effectively cancel each other out). Value definitions and/or links to metadata containing these definitions can be found in
the Descriptions of Environmental Input Layers section of the appendix above.



tmin9Dm_mte3clip

tmax90m_mt83

statsgo90m_mt83_clip

soil_tmp90m_mt83

slope9Dm_mt83clip

piecip_ann90m_mt83

nlcd90m_mt83

geombmg90mt83clip

elev9Dm_mt83clip

c u ive_p I a n 9 m_mt8 3

aspect90m_mt83clip



Jackknife of Training gain for Bobolink






^^ 1 1


^^^^^^"






^^^^^H






' n 1


^^^^





i ^^^^^^




1 :




^^^


.




1 1 1 1 1 1 1 1



Q.O



Without variable
With only variable
With all variables



0.5



1.0



1.5 2.0

Training gain



2.5



3.0



3.5



Figure C56. Jackknife chart showing the relative importance of environmental variables as a function of the change in "gain"
(the log of the number of grid cells minus the average of the negative log probabilities of the sample locations) resulting from the
exclusion or sole inclusion of the environmental variable in the model Variables with the highest training gain resulting from
sole inclusion of those variables (dark blue bars) are the best individual variables at describing suitable habitat for the species.
Jariables with the greatest reduction in training gain resulting from their exclusion (light blue bars) contain information on the


1 2 3 4 5 6 7 9

Online LibraryP.(Paul) HendricksSurveys for grassland birds of the Malta Field Office-BLM, including a seven-year study in north Valley County (Volume 2008) → online text (page 9 of 10)