Package: otoclass 0.8.0

otoclass: Otolith Classification and Proportion Estimation

Methods for classification and analysis of otoliths along with methods for estimating species proportions in samples.

Authors:Christoffer Moesgaard Albertsen [aut, cre]

otoclass_0.8.0.tar.gz
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otoclass.pdf |otoclass.html✨
otoclass/json (API)

# Install 'otoclass' in R:

install.packages('otoclass', repos = c('https://calbertsen.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/calbertsen/otoclass/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

contour-detection otolith-classification otolith-shape otoliths cpp

2.18 score 3 stars 27 exports 18 dependencies

Last updated 11 months agofrom:7063e7b3cb (on feature/multi_group). Checks:1 OK, 11 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 16 2025
R-4.5-win-x86_64	WARNING	Mar 16 2025
R-4.5-mac-x86_64	WARNING	Mar 16 2025
R-4.5-mac-aarch64	WARNING	Mar 16 2025
R-4.5-linux-x86_64	WARNING	Mar 16 2025
R-4.4-win-x86_64	WARNING	Mar 16 2025
R-4.4-mac-x86_64	WARNING	Mar 16 2025
R-4.4-mac-aarch64	WARNING	Mar 16 2025
R-4.4-linux-x86_64	WARNING	Mar 16 2025
R-4.3-win-x86_64	WARNING	Mar 16 2025
R-4.3-mac-x86_64	WARNING	Mar 16 2025
R-4.3-mac-aarch64	WARNING	Mar 16 2025

Exports:assign_unknown backwardSelection biascorrect commonMean crossval efd efd2coord fcbf flip forwardSelection fs gen2PCA getGroupMeans getGroupProportion groupMean groupProportion interpolate knn leaveoneout mlcd mlld normalize_image projection read_image read_images read.gen rotate

Dependencies:boot expm jpeg lattice lme4 MASS Matrix minqa nlme nloptr png rbibutils Rcpp RcppEigen Rdpack reformulas tiff TMB

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Convert to otolith_contour_list	as.otolith_contour_list
Assign unknown contours by binomial regression on elliptic fourier descriptors	assign_unknown
Calculate Elliptical Fourier Descriptors	efd efd.matrix efd.otolith_contour efd.otolith_contour_list efd.otolith_image
Calculate XY-coordinates from Elliptical Fourier Descriptors	efd2coord
Calculate XY-coordinates from Elliptical Fourier Descriptors	efd2coordOld
Fast Correlation Based Filter for Feature Selection in High-Dimensional Data	fcbf
Flip an otolith	flip
Fourier Series Basis for Splines	fs
Prepare allele matrix for PCA analysis	gen2PCA
Calculate group means for a data frame of covariates	getGroupMeans getGroupMeans.mlld
Calculate group proportions for a data frame of covariates	getGroupProportion getGroupProportion.mlld
Get a pixel matrix from an image file	getPixelMatrix
Interpolate otolith coordinates through EFDs	interpolate
k Nearest Neighbour	knn
Maximum Likelihood Contour Discrimination	mlcd
Maximum likelihood linear discrimination	mlld
Normalize an Otolith Image	normalize_image
Plot otolith contour	plot.otolith_contour
Plot otolith contour list	plot.otolith_contour_list
Plot otolith image	plot.otolith_image
Signed area of a closed polygon	polygon_area
Print otolith image contour	print.otolith_contour
Print otolith image	print.otolith_image
LDA-like projection	projection
Read Otolith Images and Extract Contours	read_image
Extract otolith contours from images	read_images
Read genepop data files	read.gen
Rotate an otolith	rotate
Run shiny example included in the package	runShinyExample