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

27 exports 3 stars 0.49 score 15 dependencies

Last updated 5 months agofrom:7063e7b3cb (on feature/multi_group). Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 17 2024
R-4.5-win-x86_64	WARNING	Sep 17 2024
R-4.5-linux-x86_64	WARNING	Sep 17 2024
R-4.4-win-x86_64	WARNING	Sep 17 2024
R-4.4-mac-x86_64	WARNING	Sep 17 2024
R-4.4-mac-aarch64	WARNING	Sep 17 2024
R-4.3-win-x86_64	WARNING	Sep 17 2024
R-4.3-mac-x86_64	WARNING	Sep 17 2024
R-4.3-mac-aarch64	WARNING	Sep 17 2024

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 Rcpp RcppEigen 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