Just to augment what Steve said regarding unsuitable habitat (just
focussing on that one issue):
As Steve said, it's fine to omit sampling the parts of your transect
lines that go through unsuitable habitat, where you do not expect any
butterflies. Then, when it comes to the analysis, you have a few
options, all of which should lead to the same estimates of abundance.
The first is to tell the software you surveyed the entire lines, and
that the size of the study area is the whole area within which you
placed the lines (both suitable and unsuitable habitat). Assuming you
laid your lines out at random (systematic random is fine), this will
yield an estimate of the average density of butterflies in the whole
area (both suitable and unsuitable habitat). Multiplying density by
study area size gives an abundance of butterflies in the whole area.
The second is to tell the software you only surveyed the parts of the
lines in suitable habitat. For example let's say that the entire lines
are of length L but that length L_u was found to be unsuitable, leaving
L_s suitable. So for survey effort, you'd enter just the suitable line
length per transect, which would total L_s. Then you get a density of
butterflies in *suitable* habitat. So, to get the correct abundance,
you need to tell the software what the area is of suitable habitat in
your study area. You may not know this, but assuming the proportion of
suitable habitat on your transect lines is an unbiased estimate of the
proportion of suitable habitat in the study area, then you can take the
study area size and multiply that by L_s / L. As I expect you can see,
you've reduced the line length by L_s / L and then reduced the study
area size by L_s / L, so the two balance out and you get the same
estimate of abundance as the first method above.
One difference, however, is that the variance estimate will be
different. As you know, we use the line-to-line variation in detection
rate as part of variance estimation, and in the first case part of the
variation in detection rate will be due to variation in the proportion
of unsuitable habitat. So likely the first method will give you a
higher variance than the second. On the other hand, using the second
method, we have estimated the proportion of unsuitable habitat in the
study area but not accounted for uncertainty in this estimation process
in our overall variance. It would be possible to account for this, by
taking the proportion of unsuitable habitat by line, then taking a (line
length weighted) mean and a weighted variance, and entering these as
multipliers. But that seems a hassle to me, so overall I favour the
first of the two approaches I outline above.
However, if you know what proportion of your study area is suitable
habitat (e.g., from aerial photos) then the second method could be used
but with a true value for the suitable area size within the study area
rather than an estimate.
Feel free to pitch in, anyone, if you disagree with the above!
Cheers to all, Len
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Len Thomas (he/him)
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Centre for Research into Ecological and Environmental Modelling
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