Description Usage Arguments Details Value See Also
search the images/ semi-landmarks configuration(s) of new, unknown specimens against the configurations saved in the project.
1 2 |
project |
path to a project ( |
query |
path(s) to otolith images/ path(s) of folder
containing the otolith images/ |
show |
integer. how many search results to be shown (in order of ranking). Note that if number of specimens in database searched against is less than show, the result shown will be less than the given number |
saveresult |
logical. whether to save the result |
showplot |
logical. whether to show plot of query and their matches |
savename |
character. optional. the file name, if
|
The search is based on the Procrustes (Riemannian) distance
between the query and the database. the lower the distance
(rdist
) between the query and the project's
configuration, the higher their ranking in the search
result. Perfect match will have 0 distance (for non-sliding
landmark method).
To shorten the time of searching, the query is first
searched against the meanshape configurations of each
species present in the project. For each species in the
project, maximum distance between individuals and the
species's meanshape was already calculated (by
sprdist
, wrapped within rGPA
).
First the search will determine if the query to each
species's meanshape distance is within this range, if say,
the query is within the range of 2 species' range, then
searching will be continued with the individuals of these 2
species only. Otherwise, searching will be continued with
the individuals of the top 5 closest species only.
The search has taken the semi-landmarks configuration arrangements into consideration already, hence the user doesn't need to know the side/ direction of the query.
Note: sliding semi-landmark is currently not
supported due to the difficulty to achieve short searching
time and correct configuration guessing at the same time.
Therefore the gpa
object saved in the project should
be built with fixed semi-landmarks. However, this does not
affect otopred
, thus if sliding is preferred,
otopred
will still give good predictions.
The search result. if saveresult=TRUE
, the result is
written into a .txt
file. The results include:
rdist
: distance between the query
and the match
label
: label of the match from
the database
species
: species of the match
inside
: whether the rdist
is within the
range of that species in the database
orient
:
type of configuration that match
Similar: otopred
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