File R-SuRF.vs.spec of Package R-SuRF.vs
# Automatically generated by CRAN2OBS
#
# Spec file for package SuRF.vs
# This file is auto-generated using information in the package source,
# esp. Description and Summary. Improvements in that area should be
# discussed with upstream.
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%global packname SuRF.vs
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 1.1.0.1
Release: 0
Summary: Subsampling Ranking Forward Selection (SuRF)
Group: Development/Libraries/Other
License: GPL-3
URL: http://cran.r-project.org/web/packages/%{packname}
Source: SuRF.vs_1.1.0.1.tar.gz
Requires: R-base
Requires: R-glmnet
Requires: R-dplyr
Requires: R-cli
Requires: R-generics
Requires: R-glue
Requires: R-lifecycle
Requires: R-magrittr
Requires: R-pillar
Requires: R-R6
Requires: R-rlang
Requires: R-tibble
Requires: R-tidyselect
Requires: R-vctrs
Requires: R-foreach
Requires: R-shape
Requires: R-Rcpp
Requires: R-RcppEigen
Requires: R-iterators
Requires: R-utf8
Requires: R-pkgconfig
Requires: R-withr
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
# # Three others commonly needed
# BuildRequires: tex(ae.sty)
# BuildRequires: tex(fancyvrb.sty)
# BuildRequires: tex(inconsolata.sty)
# BuildRequires: tex(natbib.sty)
# %else
# BuildRequires: texlive
# %endif
# BuildRequires: texinfo
BuildRequires: fdupes
BuildRequires: R-base
BuildRequires: R-glmnet
BuildRequires: R-dplyr
BuildRequires: R-cli
BuildRequires: R-generics
BuildRequires: R-glue
BuildRequires: R-lifecycle
BuildRequires: R-magrittr
BuildRequires: R-pillar
BuildRequires: R-R6
BuildRequires: R-rlang
BuildRequires: R-tibble
BuildRequires: R-tidyselect
BuildRequires: R-vctrs
BuildRequires: R-foreach
BuildRequires: R-shape
BuildRequires: R-Rcpp-devel
BuildRequires: R-RcppEigen-devel
BuildRequires: R-iterators
BuildRequires: R-utf8
BuildRequires: R-pkgconfig
BuildRequires: R-withr
Suggests: R-foreach
Suggests: R-doParallel
Suggests: R-knitr
%description
Performs variable selection based on subsampling, ranking forward
selection. Details of the method are published in Lihui Liu, Hong Gu,
Johan Van Limbergen, Toby Kenney (2020) SuRF: A new method for sparse
variable selection, with application in microbiome data analysis
Statistics in Medicine 40 897-919 <doi:10.1002/sim.8809>. Xo is the
matrix of predictor variables. y is the response variable. Currently
only binary responses using logistic regression are supported. X is a
matrix of additional predictors which should be scaled to have sum 1
prior to analysis. fold is the number of folds for cross-validation.
Alpha is the parameter for the elastic net method used in the
subsampling procedure: the default value of 1 corresponds to LASSO.
prop is the proportion of variables to remove in the each subsample.
weights indicates whether observations should be weighted by class
size. When the class sizes are unbalanced, weighting observations can
improve results. B is the number of subsamples to use for ranking the
variables. C is the number of permutations to use for estimating the
critical value of the null distribution. If the 'doParallel' package is
installed, the function can be run in parallel by setting ncores to the
number of threads to use. If the default value of 1 is used, or if the
'doParallel' package is not installed, the function does not run in
parallel. display.progress indicates whether the function should
display messages indicating its progress. family is a family variable
for the glm() fitting. Note that the 'glmnet' package does not permit
the use of nonstandard link functions, so will always use the default
link function. However, the glm() fitting will use the specified link.
The default is binomial with logistic regression, because this is a
common use case. pval is the p-value for inclusion of a variable in the
model. Under the null case, the number of false positives will be
geometrically distributed with this as probability of success, so if
this parameter is set to p, the expected number of false positives
should be p/(1-p).
%prep
%setup -q -c -n %{packname}
# the next line is needed, because we build without --clean in between two packages
rm -rf ~/.R
%build
%install
mkdir -p %{buildroot}%{rlibdir}
%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
rm -f %{buildroot}%{rlibdir}/R.css
%fdupes -s %{buildroot}%{rlibdir}
#%%check
#%%{_bindir}/R CMD check %%{packname}
%files
%dir %{rlibdir}/%{packname}
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
