The R package
IPCAPS is an unsupervised clustering algorithm based on
iterative pruning to capture population structure. This version supports ordinal
data which can be applied directly to SNP data to identify fine-level population
structure and it is built on the iterative pruning Principal Component Analysis
(ipPCA) algorithm by Intarapanich et al. (2009)
and Limpiti et al. (2011). The IPCAPS
involves an iterative process using multiple splits based on multivariate
Gaussian mixture modeling of principal components and Clustering EM estimation
as in Lebret et al. (2015). In each iteration, rough clusters and outliers are
also identified using the function
rubikclust() from the R package
The R package
Here is the list of functions in the R package
Moreover, here is the list of example datasets in the R package
Lastly, here is the list of example data files included in the directory
Install the released version of
IPCAPS from CRAN:
The source codes in this package include the Roxgen's syntax. If there is a
problem for generating the RD files (facing some errors) using RStudio (Build >
Document), try to use
roxygen2::roxygenise() instead of Build > Document
from the menu. Alternatively, install the package
devtools, then enable
RStudio to use the functions from
devtools (check Build > Configure Build
Tools... > use devtools package functions if available) or run
devtools::document() in the console.
When facing error for
testthat, try to update the package
testthat and add
Suggests: testthat in DESCRIPTION file.
Check the submission using
R CMD check --as-cran and a current version of
r-devel, as mandated by the CRAN Repository Policy. (You could do so using the
win-builder service at http://win-builder.r-project.org)
Check downstream dependencies with
Edit ~/.profile, ~/.bash_profile or ~/.bashrc, then add
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