File R-phase12designs.spec of Package R-phase12designs
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# Spec file for package phase12designs
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%global packname phase12designs
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 0.3.1
Release: 0
Summary: Comprehensive Tools for Running Model-Assisted Phase I/II Trial Simulations
Group: Development/Libraries/Other
License: MIT + file LICENSE
URL: http://cran.r-project.org/web/packages/%{packname}
Source: phase12designs_0.3.1.tar.gz
Requires: R-base
Requires: R-trialr
Requires: R-Iso
Requires: R-Rcpp
Requires: R-rstan
Requires: R-rstantools
Requires: R-rlang
Requires: R-dplyr
Requires: R-purrr
Requires: R-magrittr
Requires: R-stringr
Requires: R-ggplot2
Requires: R-gtools
Requires: R-coda
Requires: R-tidybayes
Requires: R-tibble
Requires: R-binom
Requires: R-StanHeaders
Requires: R-BH
Requires: R-RcppEigen
Requires: R-RcppParallel
Requires: R-cli
Requires: R-generics
Requires: R-glue
Requires: R-lifecycle
Requires: R-pillar
Requires: R-R6
Requires: R-tidyselect
Requires: R-vctrs
Requires: R-gtable
Requires: R-isoband
Requires: R-S7
Requires: R-scales
Requires: R-withr
Requires: R-inline
Requires: R-gridExtra
Requires: R-loo
Requires: R-pkgbuild
Requires: R-QuickJSR
Requires: R-desc
Requires: R-stringi
Requires: R-pkgconfig
Requires: R-ggdist
Requires: R-tidyr
Requires: R-arrayhelpers
Requires: R-posterior
Requires: R-svUnit
Requires: R-distributional
Requires: R-numDeriv
Requires: R-quadprog
Requires: R-checkmate
Requires: R-matrixStats
Requires: R-utf8
Requires: R-callr
Requires: R-processx
Requires: R-abind
Requires: R-tensorA
Requires: R-farver
Requires: R-labeling
Requires: R-RColorBrewer
Requires: R-viridisLite
Requires: R-cpp11
Requires: R-backports
Requires: R-ps
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
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# %else
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# BuildRequires: texinfo
BuildRequires: fdupes
BuildRequires: R-base
BuildRequires: R-trialr
BuildRequires: R-Iso
BuildRequires: R-Rcpp-devel
BuildRequires: R-rstan-devel
BuildRequires: R-rstantools
BuildRequires: R-rlang
BuildRequires: R-dplyr
BuildRequires: R-purrr
BuildRequires: R-magrittr
BuildRequires: R-stringr
BuildRequires: R-ggplot2
BuildRequires: R-gtools
BuildRequires: R-coda
BuildRequires: R-tidybayes
BuildRequires: R-tibble
BuildRequires: R-binom
BuildRequires: R-StanHeaders-devel
BuildRequires: R-BH-devel
BuildRequires: R-RcppEigen-devel
BuildRequires: R-RcppParallel-devel
BuildRequires: R-cli
BuildRequires: R-generics
BuildRequires: R-glue
BuildRequires: R-lifecycle
BuildRequires: R-pillar
BuildRequires: R-R6
BuildRequires: R-tidyselect
BuildRequires: R-vctrs
BuildRequires: R-gtable
BuildRequires: R-isoband
BuildRequires: R-S7
BuildRequires: R-scales
BuildRequires: R-withr
BuildRequires: R-inline
BuildRequires: R-gridExtra
BuildRequires: R-loo
BuildRequires: R-pkgbuild
BuildRequires: R-QuickJSR-devel
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BuildRequires: R-tidyr
BuildRequires: R-arrayhelpers
BuildRequires: R-posterior
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BuildRequires: R-numDeriv
BuildRequires: R-quadprog
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BuildRequires: R-utf8
BuildRequires: R-callr
BuildRequires: R-processx
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BuildRequires: R-tensorA
BuildRequires: R-farver
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BuildRequires: R-RColorBrewer
BuildRequires: R-viridisLite
BuildRequires: R-cpp11-devel
BuildRequires: R-backports
BuildRequires: R-ps
Suggests: R-knitr
Suggests: R-rmarkdown
%description
Provides a comprehensive set of tools to simulate, evaluate, and
compare model-assisted designs for early-phase (Phase I/II) clinical
trials, including: - BOIN12 (Bayesian optimal interval phase 1/11 trial
design; Lin et al. (2020) <doi:10.1200/PO.20.00257>), - BOIN-ET
(Takeda, K., Taguri, M., & Morita, S. (2018) <doi:10.1002/pst.1864>), -
EffTox (Thall, P. F., & Cook, J. D. (2004)
<doi:10.1111/j.0006-341X.2004.00218.x>), - Ji3+3 (Joint i3+3 design;
Lin, X., & Ji, Y. (2020) <doi:10.1080/10543406.2020.1818250>), - PRINTE
(probability intervals of toxicity and efficacy design; Lin, X., & Ji,
Y. (2021) <doi:10.1177/0962280220977009>), - STEIN (simple toxicity and
efficacy interval design; Lin, R., & Yin, G. (2017)
<doi:10.1002/sim.7428>), - TEPI (toxicity and efficacy probability
interval design; Li, D. H., Whitmore, J. B., Guo, W., & Ji, Y. (2017)
<doi:10.1158/1078-0432.CCR-16-1125>), - uTPI (utility-based toxicity
Probability interval design; Shi, H., Lin, R., & Lin, X. (2024)
<doi:10.1002/sim.8922>). Includes flexible simulation parameters that
allow researchers to efficiently compute operating characteristics
under various fixed and random trial scenarios and export the results.
%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
%license %{rlibdir}/%{packname}/LICENSE
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
