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]

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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'))

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

contour-detectionotolith-classificationotolith-shapeotoliths

2.18 score 3 stars 27 exports 15 dependencies

Last updated 7 months agofrom:7063e7b3cb (on feature/multi_group). Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 16 2024
R-4.5-win-x86_64WARNINGNov 16 2024
R-4.5-linux-x86_64WARNINGNov 16 2024
R-4.4-win-x86_64WARNINGNov 16 2024
R-4.4-mac-x86_64WARNINGNov 16 2024
R-4.4-mac-aarch64WARNINGNov 16 2024
R-4.3-win-x86_64WARNINGNov 16 2024
R-4.3-mac-x86_64WARNINGNov 16 2024
R-4.3-mac-aarch64WARNINGNov 16 2024

Exports:assign_unknownbackwardSelectionbiascorrectcommonMeancrossvalefdefd2coordfcbfflipforwardSelectionfsgen2PCAgetGroupMeansgetGroupProportiongroupMeangroupProportioninterpolateknnleaveoneoutmlcdmlldnormalize_imageprojectionread_imageread_imagesread.genrotate

Dependencies:bootexpmjpeglatticelme4MASSMatrixminqanlmenloptrpngRcppRcppEigentiffTMB

Readme and manuals

Help Manual

Help pageTopics
Convert to otolith_contour_listas.otolith_contour_list
Assign unknown contours by binomial regression on elliptic fourier descriptorsassign_unknown
Calculate Elliptical Fourier Descriptorsefd efd.matrix efd.otolith_contour efd.otolith_contour_list efd.otolith_image
Calculate XY-coordinates from Elliptical Fourier Descriptorsefd2coord
Calculate XY-coordinates from Elliptical Fourier Descriptorsefd2coordOld
Fast Correlation Based Filter for Feature Selection in High-Dimensional Datafcbf
Flip an otolithflip
Fourier Series Basis for Splinesfs
Prepare allele matrix for PCA analysisgen2PCA
Calculate group means for a data frame of covariatesgetGroupMeans getGroupMeans.mlld
Calculate group proportions for a data frame of covariatesgetGroupProportion getGroupProportion.mlld
Get a pixel matrix from an image filegetPixelMatrix
Interpolate otolith coordinates through EFDsinterpolate
k Nearest Neighbourknn
Maximum Likelihood Contour Discriminationmlcd
Maximum likelihood linear discriminationmlld
Normalize an Otolith Imagenormalize_image
Plot otolith contourplot.otolith_contour
Plot otolith contour listplot.otolith_contour_list
Plot otolith imageplot.otolith_image
Signed area of a closed polygonpolygon_area
Print otolith image contourprint.otolith_contour
Print otolith imageprint.otolith_image
LDA-like projectionprojection
Read Otolith Images and Extract Contoursread_image
Extract otolith contours from imagesread_images
Read genepop data filesread.gen
Rotate an otolithrotate
Run shiny example included in the packagerunShinyExample