search

DistanceDevelopment / dssd

Distance Sampling Survey Design
1 stars 1 forks source link

Additional reporting in design summary #15

Closed erex closed 5 years ago

erex commented 5 years ago

Laura you asked what else to report. This is what DisWin reports when using simulation to calculate coverage:

Design Class Results:
-------------------------------

DESIGN CLASS: Systematic Random Sampling
SAMPLER CLASS: Line
STRATUM LAYER: Study area
Effort definition by Spacing.
EFFORT UNITS: Kilometer
Deal with boundary regions by using Minus sampling.
COVERAGE PROBABILITY GRID: Simulation calculated
GRID LAYER NAME: Grid
COVERAGE PROBABILITY FIELD NAME: lines
NUMBER OF SIMULATIONS: 1000

STRATUM LAYER COORDINATE SYSTEM: Non-earth
DESIGN COORDINATE SYSTEM: Non-earth
DESIGN UNITS: Meter
RNG SEED VALUE: 111142 (FROM SYSTEM CLOCK)

ON EFFORT TRACKLINE STATISTICS FOR STRATUM 1 :
MINIMUM ON EFFORT TRACKLINE LENGTH: 1978.4556
MAXIMUM ON EFFORT TRACKLINE LENGTH: 1979.7681
MEAN ON EFFORT TRACKLINE LENGTH: 1978.9561
ON EFFORT TRACKLINE LENGTH STANDARD DEVIATION: 0.40997

MINIMUM NUMBER OF SAMPLERS: 80
MAXIMUM  NUMBER OF SAMPLERS: 81
MEAN  NUMBER OF SAMPLERS: 80.3
SAMPLER NUMBER STANDARD DEVIATION: 0.45826

TOTAL TRACKLINE STATISTICS FOR STRATUM 1 :
MINIMUM TOTAL TRACKLINE LENGTH: 2133.2184
MAXIMUM TOTAL TRACKLINE LENGTH: 2154.1588
MEAN TOTAL TRACKLINE LENGTH: 2143.3687
TOTAL TRACKLINE LENGTH STANDARD DEVIATION: 5.77343

MINIMUM ON/TOTAL TRACKLINE LENGTH: 0.919
MAXIMUM ON/TOTAL TRACKLINE LENGTH: 0.928
MEAN ON/TOTAL TRACKLINE LENGTH: 0.9233
ON/TOTAL TRACKLINE LENGTH STANDARD DEVIATION: 0.00244

TOTAL CYCLIC TRACKLINE STATISTICS FOR STRATUM 1 :
MINIMUM TOTAL TRACKLINE LENGTH: 2182.7691
MAXIMUM TOTAL TRACKLINE LENGTH: 2200.7066
MEAN TOTAL TRACKLINE LENGTH: 2191.2997
TOTAL TRACKLINE LENGTH STANDARD DEVIATION: 4.52902

MINIMUM ON/TOTAL TRACKLINE LENGTH: 0.8994
MAXIMUM ON/TOTAL TRACKLINE LENGTH: 0.907
MEAN ON/TOTAL TRACKLINE LENGTH: 0.9031
ON/TOTAL TRACKLINE LENGTH STANDARD DEVIATION: 0.00191

GLOBAL STRATUM
EXPECTED SAMPLER TOTAL: 71
SAMPLER WIDTH: 1 Kilometers
EXPECTED SAMPLER AREA COVERAGE: 4000000000 square Meters
STRATUM AREA: 987500078.743 square Meters
LHMarshall commented 5 years ago

So currently dsuds misses out:

erex commented 5 years ago

What is more important to me when assessing equality of coverage probability is the standard deviation of hit count (or coverage probability) between coverage grid points:

OVERALL COVERAGE PROBABILITY GRID POINT HIT STATISTICS: 
MINIMUM NUMBER OF HITS: 10
MAXIMUM NUMBER OF HITS: 29
MEAN NUMBER OF HITS: 17.746
NUMBER OF HITS STANDARD DEVIATION: 4.245

OVERALL COVERAGE PROBABILITY STATISTICS:
MINIMUM COVERAGE PROBABILITY: 0.1
MAXIMUM COVERAGE PROBABILITY: 0.29
MEAN COVERAGE PROBABILITY: 0.178
COVERAGE PROBABILITY STANDARD DEVIATION: 0.042

The smaller the standard deviation, the closer the design is to equal coverage

erex commented 5 years ago

There ought to be a better statistical measure of evenness--we discussed briefly at last DisDev, but didn't identify a better metric.

erex commented 5 years ago

There is nothing in current output that mentions off-effort. I don't think your current engine measures distances between transect ends. Should do.

Likewise, there are none of the segmented designs (that have off effort intermixed with on effort); there the off effort calculations will be more extensive.

LHMarshall commented 5 years ago

put in sd for now and we'll duscuss more at some point

LHMarshall commented 5 years ago

Trackline / Cyclic trackline included for systematic parallel lines

design <- make.design(region, transect.type = "line",
                      design = "systematic",
                      samplers = 20,
                      effort.allocation = c(0.5,0.5),
                      edge.protocol = c("minus"),
                      design.angle = 0,
                      truncation = 150,
                      coverage.grid = cover)

transects <- generate.transects(design)
transects

   Strata A:
   __________
Design:  systematically spaced parallel transects
Spacing:  NA
Line length: 28825.98
Trackline length: 39582.16
Cyclic trackline length: 48409.61
Number of samplers:  10
Design angle:  0
Edge protocol:  minus
Covered area:  8501028
Strata coverage:  30.89 %
Strata area:  27518840

   Strata B:
   __________
Design:  systematically spaced parallel transects
Spacing:  NA
Line length: 38591.75
Trackline length: 50941.35
Cyclic trackline length: 59942.77
Number of samplers:  10
Design angle:  0
Edge protocol:  minus
Covered area:  11321442
Strata coverage:  32.62 %
Strata area:  34704914

   Study Area Totals:
   _________________
Line length: 67417.73
Trackline length: 90523.51
Cyclic trackline length: 108352.4
Number of samplers:  20
Effort allocation:  50%, 50 %
Covered area:  19822470
Average coverage:  31.86 %

Screenshot 2019-06-20 at 15 40 32

LHMarshall commented 5 years ago 
> design <- make.design(region, transect.type = "line",
+                       design = "random",
+                       samplers = 20,
+                       effort.allocation = c(0.5,0.5),
+                       edge.protocol = c("minus"),
+                       design.angle = 0,
+                       truncation = 150,
+                       coverage.grid = cover)
> 
> transects <- generate.transects(design)
> transects

   Strata A:
   __________
Design:  randomly located transects
Line length: 28726.44
Trackline length: 39380.47
Cyclic trackline length: 48550.33
Number of samplers:  10
Design angle:  0
Edge protocol:  minus
Covered area:  8403125
Strata coverage:  30.54 %
Strata area:  27518840

   Strata B:
   __________
Design:  randomly located transects
Line length: 32311.45
Trackline length: 44907.81
Cyclic trackline length: 53534.9
Number of samplers:  10
Design angle:  0
Edge protocol:  minus
Covered area:  9543906
Strata coverage:  27.5 %
Strata area:  34704914

   Study Area Totals:
   _________________
Line length: 61037.9
Trackline length: 84288.28
Cyclic trackline length: 102085.2
Number of samplers:  20
Effort allocation:  50%, 50 %
Covered area:  17947031
Average coverage:  28.84 %

Screenshot 2019-06-20 at 17 21 07

LHMarshall commented 5 years ago 
> design <- make.design(region, transect.type = "line",
+                       design = "eszigzag",
+                       samplers = 20,
+                       effort.allocation = c(0.5,0.5),
+                       edge.protocol = c("minus"),
+                       design.angle = 0,
+                       truncation = 150,
+                       bounding.shape = "convex.hull",
+                       coverage.grid = cover)
> 
> transects <- generate.transects(design)
> transects

   Strata A:
   __________
Design:  equal spaced zigzag
Spacing:  NA
Line length: 29630.62
Trackline length: 32668.14
Cyclic trackline length: 41673.85
Number of samplers:  11
Design angle:  0
Edge protocol:  minus
Covered area:  8680453
Strata coverage:  31.54 %
Strata area:  27518840

   Strata B:
   __________
Design:  equal spaced zigzag
Spacing:  NA
Line length: 37719.87
Trackline length: 41217.74
Cyclic trackline length: 49777.73
Number of samplers:  10
Design angle:  0
Edge protocol:  minus
Covered area:  11112577
Strata coverage:  32.02 %
Strata area:  34704914

   Study Area Totals:
   _________________
Line length: 67350.48
Trackline length: 73885.88
Cyclic trackline length: 91451.58
Number of samplers:  21
Effort allocation:  50%, 50 %
Covered area:  19793029
Average coverage:  31.81 %

Screenshot 2019-06-20 at 17 34 37

LHMarshall commented 5 years ago 
> design <- make.design(region, transect.type = "line",
+                       design = "eszigzagcom",
+                       samplers = 20,
+                       effort.allocation = c(0.5,0.5),
+                       edge.protocol = c("minus"),
+                       design.angle = 0,
+                       truncation = 150,
+                       bounding.shape = "convex.hull",
+                       coverage.grid = cover)
> transects <- generate.transects(design)
> transects

   Strata A:
   __________
Design:  complementaty equal spaced zigzags
Spacing:  NA
Line length: 31695.33
Trackline length: 38778.28
Cyclic trackline length: 40727.27
Number of samplers:  10
Design angle:  0
Edge protocol:  minus
Covered area:  9193582
Strata coverage:  33.41 %
Strata area:  27518840

   Strata B:
   __________
Design:  complementaty equal spaced zigzags
Spacing:  NA
Line length: 41120.95
Trackline length: 47763.65
Cyclic trackline length: 49712.3
Number of samplers:  11
Design angle:  0
Edge protocol:  minus
Covered area:  12054842
Strata coverage:  34.74 %
Strata area:  34704914

   Study Area Totals:
   _________________
Line length: 72816.28
Trackline length: 86541.94
Cyclic trackline length: 90439.58
Number of samplers:  21
Effort allocation:  50%, 50 %
Covered area:  21248423
Average coverage:  34.15 %

Screenshot 2019-06-20 at 17 36 49

LHMarshall commented 5 years ago

New Line transect output including sd's and coverage score summary

    Strata A:
   __________
Design:  complementaty equal spaced zigzags
Spacing:  NA
Number of samplers:  20  (shared across strata)
Line Length: NA
Design angle:  0
Edge protocol:  minus

   Strata B:
   __________
Design:  complementaty equal spaced zigzags
Spacing:  NA
Number of samplers:  20  (shared across strata)
Line Length: NA
Design angle:  0
Edge protocol:  minus

Effort allocation across strata:  50 %, 50 %

    Number of samplers:

           A    B Total
Minimum 10.0 10.0  20.0
Mean    11.2 11.1  22.3
Median  11.0 11.0  22.0
Maximum 12.0 12.0  24.0
sd       0.9  0.7   1.1

    Covered area:

                A          B      Total
Minimum 8711116.4 11051026.1 19989475.4
Mean    9421923.4 11538800.4 20960723.8
Median  9515967.1 11632902.1 20976247.1
Maximum 9973202.9 12067236.2 22008694.7
sd       427001.4   344726.2   514117.9

    % of region covered:

           A    B Total
Minimum 0.32 0.32  0.32
Mean    0.34 0.33  0.34
Median  0.35 0.34  0.34
Maximum 0.36 0.35  0.35
sd        NA   NA    NA

    Line length:

               A        B    Total
Minimum 29667.95 37855.09 68516.91
Mean    32158.61 39409.61 71568.22
Median  32557.30 39527.02 71803.25
Maximum 33854.80 41201.39 75014.11
sd       1440.55  1053.19  1662.12

    Trackline length:

               A        B    Total
Minimum 36093.43 44290.35 81959.60
Mean    37963.03 46469.44 84432.47
Median  38222.67 46360.63 84477.80
Maximum 39432.53 48015.82 86735.62
sd        856.81   938.55  1252.80

    Cyclic trackline length:

               A        B    Total
Minimum 36583.89 45967.55 83801.50
Mean    39601.24 48222.38 87823.62
Median  40112.12 48188.77 87735.88
Maximum 41793.49 49949.45 91742.94
sd       1458.31  1006.98  1919.16

    Coverage Score Summary:

Minimum coverage score:  0.06
Maximum coverage score:  0.9
Mean coverage score:  0.3373747
Coverage score sd:  0.1091773
erex commented 5 years ago

that's helpful. Why is the sd for covered area percentage NA?

LHMarshall commented 5 years ago

oops didn't mean to add that as I wasn't sure about calculations but have now added the calculations.

Also added strata areas and number of coverage reps

erex commented 5 years ago

Laura

Do I understand correctly:

LHMarshall commented 5 years ago

Yes that is correct... I was going to do diagrams!

I think the definition of "first" transect is unnecessary as because it is a cyclic track you can start and then finish at any location on that cyclic trackline and you will have travelled the same distance. I'm hesitant to say westernmost as depends on the orientation of the transects and how they were spun round on the design axis when they were generated!

LHMarshall commented 5 years ago

Note though that between transect effort is as the crow flies and may not relate well to reality as there may be islands or coastline complexities to travel round for shipboard surveys for example.

LHMarshall commented 5 years ago

Trackline indicated by red arrows, cyclic trackline is the red arrows plus the light blue arrow

Random Parallel Lines

RandomLines

Systematic Parallel Lines

SystematicLines

Equal Spaced Zigzag

ZigzagDesign

Equal Spaced Zigzag with Complementary Lines ComZigzag

LHMarshall commented 5 years ago

These diagrams have now been included in the Getting Started in dssd vignette

LHMarshall commented 5 years ago

Now explicitly states that region and effort units are the same