File R-PoolTestR.spec of Package R-PoolTestR

# Automatically generated by CRAN2OBS
# 
# Spec file for package PoolTestR 
# This file is auto-generated using information in the package source, 
# esp. Description and Summary. Improvements in that area should be 
# discussed with upstream. 
# 
# Copyright (c) 2025 SUSE LINUX GmbH, Nuernberg, Germany. 
# 
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# remain the property of their copyright owners, unless otherwise agreed 
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# file, is the same license as for the pristine package itself (unless the 
# license for the pristine package is not an Open Source License, in which 
# case the license is the MIT License). An "Open Source License" is a 
# license that conforms to the Open Source Definition (Version 1.9) 
# published by the Open Source Initiative. 
#  
# Please submit bugfixes or comments via http://bugs.opensuse.org/ 
# 
 
%global packname  PoolTestR 
%global rlibdir   %{_libdir}/R/library 
 
Name:           R-%{packname} 
Version:        0.2.0 
Release:        0 
Summary:        Prevalence and Regression for Pool-Tested (Group-Tested) Data 
Group:          Development/Libraries/Other 
License:        GPL (>= 3) 
URL:            http://cran.r-project.org/web/packages/%{packname} 
Source:         PoolTestR_0.2.0.tar.gz 
Requires:       R-base 
Requires:	R-brms
Requires:	R-dplyr
Requires:	R-lme4
Requires:	R-progress
Requires:	R-Rcpp
Requires:	R-RcppParallel
Requires:	R-rlang
Requires:	R-rstan
Requires:	R-rstantools
Requires:	R-stringr
Requires:	R-tibble
Requires:	R-BH
Requires:	R-RcppEigen
Requires:	R-StanHeaders
Requires:	R-ggplot2
Requires:	R-loo
Requires:	R-posterior
Requires:	R-bayesplot
Requires:	R-bridgesampling
Requires:	R-glue
Requires:	R-future
Requires:	R-future.apply
Requires:	R-matrixStats
Requires:	R-nleqslv
Requires:	R-coda
Requires:	R-abind
Requires:	R-backports
Requires:	R-cli
Requires:	R-generics
Requires:	R-lifecycle
Requires:	R-magrittr
Requires:	R-pillar
Requires:	R-R6
Requires:	R-tidyselect
Requires:	R-vctrs
Requires:	R-minqa
Requires:	R-nloptr
Requires:	R-reformulas
Requires:	R-crayon
Requires:	R-hms
Requires:	R-prettyunits
Requires:	R-inline
Requires:	R-gridExtra
Requires:	R-pkgbuild
Requires:	R-QuickJSR
Requires:	R-desc
Requires:	R-stringi
Requires:	R-pkgconfig
Requires:	R-ggridges
Requires:	R-reshape2
Requires:	R-tidyr
Requires:	R-mvtnorm
Requires:	R-Brobdingnag
Requires:	R-scales
Requires:	R-digest
Requires:	R-globals
Requires:	R-listenv
Requires:	R-parallelly
Requires:	R-gtable
Requires:	R-isoband
Requires:	R-S7
Requires:	R-withr
Requires:	R-checkmate
Requires:	R-utf8
Requires:	R-callr
Requires:	R-processx
Requires:	R-tensorA
Requires:	R-distributional
Requires:	R-Rdpack
Requires:	R-numDeriv
Requires:	R-ps
Requires:	R-rbibutils
Requires:	R-plyr
Requires:	R-farver
Requires:	R-labeling
Requires:	R-RColorBrewer
Requires:	R-viridisLite
Requires:	R-purrr
Requires:	R-cpp11
 
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse} 
# # Three others commonly needed 
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# BuildRequires:  tex(inconsolata.sty) 
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# BuildRequires:  texlive 
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BuildRequires:  gcc gcc-c++ gcc-fortran
 
Suggests:	R-covr
%description 
An easy-to-use tool for working with presence/absence tests on 'pooled' 
or 'grouped' samples. The primary application is for estimating 
prevalence of a marker in a population based on the results of tests on 
pooled specimens.  This sampling method is often employed in 
surveillance of rare conditions in humans or animals (e.g. molecular 
xenomonitoring). The package was initially conceived as an R-based 
alternative to the molecular xenomonitoring software, 'PoolScreen' 
<https://sites.uab.edu/statgenetics/software/>. However, it goes 
further, allowing for estimates of prevalence to be adjusted for 
hierarchical sampling frames, and perform flexible mixed-effect 
regression analyses (McLure et al. Environmental Modelling and 
Software.  <DOI:10.1016/j.envsoft.2021.105158>). The package is 
currently in early stages, however more features are planned or in the 
works: e.g. adjustments for imperfect test specificity/sensitivity, 
functions for helping with optimal experimental design, and functions 
for spatial modelling. 
 
%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} 
%{rlibdir}/%{packname}/CITATION
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%doc %{rlibdir}/%{packname}/NEWS.md
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%{rlibdir}/%{packname}/include
%{rlibdir}/%{packname}/libs
%{rlibdir}/%{packname}/stan
 
%changelog