germinationmetrics - Seed Germination Indices and Curve Fitting
Provides functions to compute various germination indices such as germinability, median germination time, mean germination time, mean germination rate, speed of germination, Timson's index, germination value, coefficient of uniformity of germination, uncertainty of germination process, synchrony of germination etc. from germination count data. Includes functions for fitting cumulative seed germination curves using four-parameter hill function and computation of associated parameters. See the vignette for more, including full list of citations for the methods implemented.
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curve-fittinggerminationgermination-indicesseedseed-germination-curveseed-germination-indices
5.75 score 4 stars 28 scripts 698 downloadsPGRdup - Discover Probable Duplicates in Plant Genetic Resources Collections
Provides functions to aid the identification of probable/possible duplicates in Plant Genetic Resources (PGR) collections using 'passport databases' comprising of information records of each constituent sample. These include methods for cleaning the data, creation of a searchable Key Word in Context (KWIC) index of keywords associated with sample records and the identification of nearly identical records with similar information by fuzzy, phonetic and semantic matching of keywords.
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double-metaphonedouble-metaphone-algorithmnatural-language-processingpgrplant-genetic-resourcesrecord-linkage
5.01 score 1 stars 23 scripts 417 downloadsggmultiglyph - Multivariate Data Visualization using Glyphs
Provides 'ggplot2' geoms for visualizing multivariate data using glyphs. The package implements several established glyph designs described in the information visualization literature, including the review by Borgo et al. (2013) <doi:10.2312/conf/EG2013/stars/039-063>.
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ggplot-extensionggplot2multivariate-datavisualizationcpp
5.00 score 7 stars 22 scripts 273 downloadsrmelting - R Interface to MELTING 5
R interface to the MELTING 5 program (https://www.ebi.ac.uk/biomodels/tools/melting/) to compute melting temperatures of nucleic acid duplexes along with other thermodynamic parameters.
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biomedicalinformaticscheminformaticsbioconductorbioinformaticsmelting-temperatureopenjdk
4.72 score 2 stars 13 scripts 356 downloadsEvaluateCore - Quality Evaluation of Core Collections
Implements various quality evaluation statistics to assess the value of plant germplasm core collections using qualitative and quantitative phenotypic trait data according to Odong et al. (2015) <doi:10.1007/s00122-012-1971-y>.
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core-collectionscore-evaluationgenebankgermplasmpgrplant-genetic-resources
3.98 score 1 stars 24 scripts 527 downloadsDiversityStats - Diversity Indices with Statistical Inference
Provides a comprehensive framework for analyzing diversity from frequency/abundance count data. Implements a wide range of classical and entropy-based diversity indices, including Berger-Parker, Simpson (and related variants), Shannon, Brillouin, McIntosh, Margalef, Menhinick and Smith-Wilson. Supports permutation-based hypothesis tests for comparing groups with respect to diversity (global and pairwise comparisons), as well as confidence interval estimation using multiple bootstrap methods. Includes functionality for generating diversity profiles based on parametric families such as Hill numbers, Rényi entropy, and Tsallis entropy. The methods are applicable to ecological community data (species abundance counts) and genetic or phenotypic class frequency data.
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berger-parkerbootstrap-cibrillouin-indexdiversity-indicesdiversity-measuresdiversity-profilegini-simpsonhill-numbermargalefs-richnessmcintosh-diversitymenhinicks-richnesspermutation-testrenyi-entropyshannon-entropyshannon-weavershannon-wienersimpsons-indexsmith-and-wilson-evennesstsallis-entropy
3.88 score 1 dependents 2 scripts 353 downloadsLEAVcore - Constitution of Core Collections using Length of Encoded Attribute Values
Construct core collections using the information measure Length of Encoded Attribute Values (LEAV) using qualitative and/or quantitative trait data as described by Balakrishnan and Suresh (2001a) <https://indianjournals.com/article/ijpgr-14-1-006> and (2001b) <https://indianjournals.com/article/ijpgr-14-3-005>.
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core-collectionsgenebankgermplasmpgrplant-genetic-resources
3.70 score 250 downloadsrpcss - Constitution of Core Collections by Principal Component Scoring Strategy
Generate a Core Collection with Principal Component Scoring Strategy (PCSS) using qualitative and/or quantitative trait data according to Hamon and Noirot (1990) <https://www.documentation.ird.fr/hor/fdi:36506>, Noirot et al. (1996) <doi:10.2307/2527837> and Noirot et al. (2003) <https://www.documentation.ird.fr/hor/fdi:010031886>.
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core-collectionsgenebankgermplasmpgrplant-genetic-resources
3.54 score 2 scripts 273 downloadsSampleCore - Sampling Strategies for Constructing Core Collections
Implements multiple allocation and selection strategies of sampling to construct core collections primarily from clustered or grouped germplasm collection data. Provides methods for allocating entries to clusters/groups based on group sizes, group-wise distance-based diversity metrics, and group-wise diversity index estimates. Includes procedures for selecting entries within clusters/groups through random sampling, genetic distance-based approaches, and optimized diversity metric–based selection methods. See the package documentation for more, including full list of references for the methods implemented.
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core-collectionsgenebankgermplasmpgrplant-genetic-resources
3.54 score 2 scripts 332 downloads