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IPCAPS 1.1.8

Updates

• Updated the package according to R v4.0.2
• Reduce the sizes of example files

IPCAPS 1.1.7

Updates

• Updated the functions to support re-analysis when the result files are moved to another directory; top.discriminator, ipcaps.
• top.discriminator now accepts a percentile for filtering.

IPCAPS 1.1.6

Updates

• Corrected descripton of export.gorups

IPCAPS 1.1.5

Updates

• Added more details in roxygen part of ipcaps-package.R
• Fixed text according to comments from CRAN
• Updated README.md according to the changes above

IPCAPS 1.1.4

Updates

• Added references in the DESCRIPTION file
• Added single quotes for Software’s names in the DESCRRIPTION file

IPCAPS 1.1.3

Fixed Text

• In DESCRIPTION
• In README.Rmd

IPCAPS 1.1.2

Fixed Bugs

• Removed all examples for roxygen2 for all internal functions
• Removed all “library(IPCAPS)” in unit tests and examples

Changes

• All example files were changed from simSNP* to IPCAPS_example*

Added example file

• inst/extdata/IPCAPS_example.RData to used in the example of ipcaps()

IPCAPS 1.1.1

Added unit testing

• testthat/test_clusteringmode.R

Changes

• moved the nested functions in pasre.categorical.data and preprocess to parallelization.R
• add roxygen2 code to pasre.categorical.data, replace.missing, do.glm

Updates

• In roxygen part, changed from getwd() to tempdir()
• fixed errors according to check as cran

Fixed functions

• preprocess(): changed filename.label to label.file

IPCAPS 1.1.0

Updated functions

• In check.stopping(), changed from eigen.fit = max(eigen.fit.vec[1:2]) to eigen.fit = max(eigen.fit.vec). This change may affect clustering result.

IPCAPS 1.0.7

Added data

• data/IPCAPS_example.RData
• inst/extdata/IPCAPS_example.bed
• inst/extdata/IPCAPS_example.bim
• inst/extdata/IPCAPS_example.fam
• inst/extdata/IPCAPS_example.individuals.txt
• inst/extdata/IPCAPS_example_PC10.txt
• inst/extdata/IPCAPS_example_rowVar_colInd.txt

Added R file to describe data files

• R/data.R

Added unit testing

• testthat/test_caleigenfit.R
• testthat/test_checkstopping.R

IPCAPS 1.0.6

Fixed functions

Removed the old RD files and added roxygen script to create manual for these functions:

• save.plots.cluster.html
• save.plots.label.html
• save.plots
• top.discriminator

IPCAPS 1.0.5

Fixed functions

Removed the old RD files and added roxygen script to create manual for these functions:

• preprocess
• process.each.node
• save.eigenplots
• save.html

IPCAPS 1.0.4.0

Fixed functions and objects

Removed the old RD files and added roxygen script to create manual for these functions and objects:

• IPCAPS-package
• ipcaps
• output.template
• postprocess

IPCAPS 1.0.3.0

Fixed functions

Removed the old RD files and added roxygen script to create manual for these functions:

• diff.eigen.fit
• diff.xy
• export.groups
• get.node.info

IPCAPS 1.0.2.0

Fixed functions

Removed the old RD files and added roxygen script to create manual for these functions:

• cal.eigen.fit
• check.stopping
• clustering.mode
• clustering

IPCAPS 1.0.1

Fixed functions

Removed the old RD files and added roxygen script to create manual for these functions:

• cal.pc.linear
• cal.pc.linear
• cal.pc.linear
• cal.pc.linear

IPCAPS 1.0.0.0

Initial functions

• cal.pc.linear A function for linear principal component analysis (PCA)
• fst.each.snp.hudson A function for fixation index (Fst) calculation for all SNPs between two groups.
• fst.hudson A function for average fixation index (Fst) calculation between two groups.
• plot3views A function to create scatter plots in three views.
• read.bed Read the binary PLINK format (BED, BIM, and FAM)
• rubikclust A function for unsupervised clustering to detect rough structures and outliers.
• write.bed Write an list of SNP object to the binary PLINK format (BED, BIM, and FAM)
• xxt A function for calculating matrix multipication between a matrix and its transpose for large data.

Initial R data

• simsnp Synthetic dataset containing single nucleotide polymorphisms (SNP)
• sample_labels Synthetic dataset containing population labels for the dataset simsnp.

Initial example files

• example_SNP.bed Synthetic dataset containing single nucleotide polymorphisms (SNP) in binary format
• example_SNP.bim Simulated SNP information
• example_SNP.fam Simulated sample information

Updates

From the initial idea, some functions were changed their names:

• The name of function cal.PC.linear was changed to cal.pc.linear.
• The name of function plot.3views was changed to plot3views.
• The name of function rubikClust was changed to rubikclust.
• The name of function XXt was changed to xxt.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.