assignPOP - v1.3.0

Update accuracy.plot to accommodate deprecated aes_string in ggplot2

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Published by alexkychen almost 2 years ago

assignPOP - v1.2.4

• Update membership.plot - add argument 'plot.k' and 'plot.loci' to skip related question prompt.

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Published by alexkychen over 4 years ago

assignPOP -

• Update assign.X - (1)Add argument 'common' to specify whether stopping the analysis when inconsistent features between data sets were found. (2)Add argument 'skipQ' to skip data type checking on non-genetic data. (3)Modify argument 'mplot' to handle membership probability plot output.

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Published by alexkychen over 4 years ago

assignPOP -

• Update read.Genepop and read.Structure - locus has only one allele across samples will be kept. Use reduce.allele to remove single-allele or low variance loci.
• In ver. 1.2.1, errors might be generated when running assign.MC (and other assignment test functions) due to existence of single-allele loci. (fixed in ver. 1.2.2)

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Published by alexkychen over 5 years ago

assignPOP -

• Update read.Genepop to increase file reading speed (~40 times faster)
• Update read.Structure to increase file reading speed (~90 times faster)
• read.Structure now also can handle triploid and tetraploid organisms (see arg. ploidy)
• fix bug in allele.reduce to handle small p threshold across all loci

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Published by alexkychen over 5 years ago

assignPOP -

• Add codes to check model name in assign.MC, assign.kfold, assign.X
• Add text to SVM description
• Fix cbind/stringsAsFactors issues in several places for R 4.0
• Able to inject arugments used in models (e.g., gamma in SVM)

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Published by alexkychen over 5 years ago

assignPOP -

• Fix input non-genetic data (x1) error in assign.X

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Published by alexkychen almost 6 years ago

assignPOP -

• Update following functions to work with R 4.0.0 accuracy.MC, accuracy.kfold, assign.matrix, compile.data, membership.plot
• Add stringsAsFactor=T to read.table and read.csv
• Temporarily turn off testthat due to its current failure to pass test in Debian system

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Published by alexkychen almost 6 years ago

assignPOP - v1.1.7

• add broken-stick method for principal component selection in assign.MC, assign.kfold, and assign.X functions
• update accuracy.MC, accuracy.kfold, assign.matrix to handle missing levels of predicted population in test results
• update assign. and accuracy. functions to handle numeric population names

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Published by alexkychen over 6 years ago

assignPOP - v1.1.6

Fix parallel computing issue in the function assign.kfold.

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Published by alexkychen over 6 years ago

assignPOP -

Update assign.MC & assign.kfold to detect pop size and train.inds/k.fold setting Update accuracy.MC & assign.matrix to handle test individuals not from every pop Slightly modify levels method in accuracy.kfold fix bugs in accuracy.plot for K-fold results fix membership.plot title positioning and set text size to default

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Published by alexkychen almost 8 years ago

assignPOP -

Include testthat for assign.matrix; Fix word break issues in read.Genepop and membership.plot; Update citation

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Published by alexkychen almost 8 years ago

assignPOP -

add assign.matrix function

- R
Published by alexkychen almost 8 years ago

assignPOP - v1.1.3

add unit tests

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Published by alexkychen over 8 years ago

assignPOP - v1.1.2

Add Travis CI badge to README Add website tutorial URL

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Published by alexkychen about 9 years ago