NEWS.md

In kridsadakorn/ipcaps2: Iterative Pruning to Capture Population Structure version 2

IPCAPS2 2.3.0

• add new function: heatmap.ipcaps()

IPCAPS2 2.2.2

• Fixed according to the notes from CRAN check: Lines are too long in the examples

IPCAPS2 2.2.1

• Fixed according to the note in CRAN check: PCs is not defined in plot3views.ipcaps

IPCAPS2 2.2.0

• add new function: plot3views.ipcaps

IPCAPS2 2.1.0

• add codes for ipcaps2 to supports kmeans and dbscan

IPCAPS 2.0.0

• parallel version
• add confident scores for multiple clustering for stability
• add more primitive clustering methods
• ipcaps2 supports clara, pam, mixmod, meanshift, apclust, hclust, rubikclust, and mix-mode (mixmod + rubikclust)
• update unit testing

IPCAPS 1.1.8

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

IPCAPS 1.1.7

• 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

• Corrected descripton of export.gorups

IPCAPS 1.1.5

• 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

• 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 and README.Rmd

IPCAPS 1.1.2

• Removed all examples for roxygen2 for all internal functions
• Removed all "library(IPCAPS)" in unit tests and examples
• All example files were changed from simSNP* to IPCAPS_example*
• Added example file in inst/extdata/IPCAPS_example.RData to used in the example of ipcaps()

IPCAPS 1.1.1

• Added unit testing, testthat/test_clusteringmode.R
• Moved the nested functions in pasre.categorical.data and preprocess to parallelization.R
• Added roxygen2 code to pasre.categorical.data, replace.missing, do.glm
• In roxygen part, changed from getwd() to tempdir()
• Fixed errors according to check as cran
• Fixed function, preprocess(): changed filename.label to label.file

IPCAPS 1.1.0

• 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

• 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
.template
postprocess

IPCAPS 1.0.3.0

• Fixed functions, eemoved 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

IPCAPS 1.0.0

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.

kridsadakorn/ipcaps2 documentation built on June 11, 2022, 8:35 p.m.