Arguments
truerange_areas
The list of areas (as 0-based
numbers) in this geographic range/state.
numareas
The function needs to know the total
number of areas in the analysis.
detects_df
A column/vector of detection counts, as
produced from a column of the output from
read_detections. controls_df
A column/vector of detection counts,
as produced from a column of the output from
read_controls. dp
The detection probability. This is the
per-sample probability that you will detect the OTU in
question. In other words, the model assumes that each
specimen from the taphonomic control group has a chance
of being a representative of the OTU you are looking for.
The default is 1, which assumes perfect detection, i.e.
the assumption being made in all historical biogeography
analyses that do not take into account detection
probability. A value of 1 will only work when the
taphonomic control count equals the detection count; any
other data would have likelihood=0.
fdp
The false detection probability. This is
probability of falsely concluding a detection occurred,
when in fact the specimen was of something else. The
default is 0, which assumes zero error rate, i.e. the
assumption being made in all historical biogeography
analyses that do not take into account detection
probability. This option is being included for
completeness, but it may not be wise to try to infer both
dp and fdp at once due to identifiability
issues (and estimation of fdp may take a very large
amount of data).
mean_frequency
This is the proportion of samples
from the taphonomic control group that will truly be from
this OTU, GIVEN that the OTU is present. This could be
estimated, but a decent first guess is (total # samples
of OTU of interest / total # of samples in the taphonomic
control group where the OTU is known to be present). All
that is really needed is some reasonable value, such that
more sampling without detection lowers the likelihood of
the data on the hypothesis of true presence, and vice
versa. This value can only be 1 when the number of
detections = the number of taphonomic control detections,
for every OTU and area. This is the implicit assumption
in e.g. standard historical biogeography analyses in
LAGRANGE or BioGeoBEARS.