%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  hdbayes
%global packver   0.2.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.2.0
Release:          1%{?dist}%{?buildtag}
Summary:          Bayesian Analysis of Generalized Linear Models with Historical Data

License:          MIT + file LICENSE
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 4.2.0
Requires:         R-core >= 4.2.0
BuildRequires:    R-CRAN-instantiate >= 0.1.0
BuildRequires:    R-CRAN-callr 
BuildRequires:    R-CRAN-fs 
BuildRequires:    R-CRAN-formula.tools 
BuildRequires:    R-stats 
BuildRequires:    R-CRAN-posterior 
BuildRequires:    R-CRAN-enrichwith 
BuildRequires:    R-CRAN-bridgesampling 
BuildRequires:    R-CRAN-mvtnorm 
BuildRequires:    R-CRAN-loo 
Requires:         R-CRAN-instantiate >= 0.1.0
Requires:         R-CRAN-callr 
Requires:         R-CRAN-fs 
Requires:         R-CRAN-formula.tools 
Requires:         R-stats 
Requires:         R-CRAN-posterior 
Requires:         R-CRAN-enrichwith 
Requires:         R-CRAN-bridgesampling 
Requires:         R-CRAN-mvtnorm 
Requires:         R-CRAN-loo 

%description
User-friendly functions for leveraging (multiple) historical data set(s)
in Bayesian analysis of generalized linear models (GLMs) and survival
models, along with support for Bayesian model averaging (BMA). The package
provides functions for sampling from posterior distributions under various
informative priors, including the prior induced by the Bayesian
hierarchical model, power prior by Ibrahim and Chen (2000)
<doi:10.1214/ss/1009212673>, normalized power prior by Duan et al. (2006)
<doi:10.1002/env.752>, normalized asymptotic power prior by Ibrahim et al.
(2015) <doi:10.1002/sim.6728>, commensurate prior by Hobbs et al. (2011)
<doi:10.1111/j.1541-0420.2011.01564.x>, robust meta-analytic-predictive
prior by Schmidli et al. (2014) <doi:10.1111/biom.12242>, latent
exchangeability prior by Alt et al. (2024) <doi:10.1093/biomtc/ujae083>,
and a normal (or half-normal) prior. The package also includes functions
for computing model averaging weights, such as BMA, pseudo-BMA, pseudo-BMA
with the Bayesian bootstrap, and stacking (Yao et al., 2018
<doi:10.1214/17-BA1091>), as well as for generating posterior samples from
the ensemble distributions to reflect model uncertainty. In addition to
GLMs, the package supports survival models including: (1) accelerated
failure time (AFT) models, (2) piecewise exponential (PWE) models, i.e.,
proportional hazards models with piecewise constant baseline hazards, and
(3) mixture cure rate models that assume a common probability of cure
across subjects, paired with a PWE model for the non-cured population.
Functions for computing marginal log-likelihoods under each implemented
prior are also included. The package compiles all the 'CmdStan' models
once during installation using the 'instantiate' package.

%prep
%setup -q -c -n %{packname}

# fix end of executable files
find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \;
# prevent binary stripping
[ -d %{packname}/src ] && find %{packname}/src -type f -exec \
  sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true
[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \
  sed -i 's@-g0@@g' {} \; || true
# don't allow local prefix in executable scripts
find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \;

%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
# remove buildroot from installed files
find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \;

%files
%{rlibdir}/%{packname}