%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  surveil
%global packver   0.2.2
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.2.2
Release:          1%{?dist}%{?buildtag}
Summary:          Time Series Models for Disease Surveillance

License:          GPL (>= 3)
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 3.5.0
Requires:         R-core >= 3.5.0
BuildRequires:    R-CRAN-RcppParallel >= 5.0.1
BuildRequires:    R-CRAN-tidybayes >= 3.0.0
BuildRequires:    R-CRAN-ggplot2 >= 3.0.0
BuildRequires:    R-CRAN-ggdist >= 3.0.0
BuildRequires:    R-CRAN-rstan >= 2.26.0
BuildRequires:    R-CRAN-StanHeaders >= 2.26.0
BuildRequires:    R-CRAN-rstantools >= 2.1.1
BuildRequires:    R-CRAN-gridExtra >= 2.0
BuildRequires:    R-CRAN-BH >= 1.66.0
BuildRequires:    R-CRAN-tidyr >= 1.1.0
BuildRequires:    R-CRAN-dplyr >= 1.0.7
BuildRequires:    R-CRAN-rlang >= 0.4.0
BuildRequires:    R-CRAN-scales >= 0.4.0
BuildRequires:    R-CRAN-RcppEigen >= 0.3.3.3.0
BuildRequires:    R-CRAN-Rcpp >= 0.12.0
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-rstantools
Requires:         R-CRAN-RcppParallel >= 5.0.1
Requires:         R-CRAN-tidybayes >= 3.0.0
Requires:         R-CRAN-ggplot2 >= 3.0.0
Requires:         R-CRAN-ggdist >= 3.0.0
Requires:         R-CRAN-rstan >= 2.26.0
Requires:         R-CRAN-rstantools >= 2.1.1
Requires:         R-CRAN-gridExtra >= 2.0
Requires:         R-CRAN-tidyr >= 1.1.0
Requires:         R-CRAN-dplyr >= 1.0.7
Requires:         R-CRAN-rlang >= 0.4.0
Requires:         R-CRAN-scales >= 0.4.0
Requires:         R-CRAN-Rcpp >= 0.12.0
Requires:         R-methods 
Requires:         R-CRAN-rstantools

%description
Fits time series models for routine disease surveillance tasks and returns
probability distributions for a variety of quantities of interest,
including age-standardized rates, period and cumulative percent change,
and measures of health inequality. Calculates Theil's index to measure
inequality among multiple groups, and can be extended to measure
inequality across multiple groups nested within geographies. Inference is
completed using Markov chain Monte Carlo via the Stan modeling language.
The models are appropriate for count data such as disease incidence and
mortality data, employing a Poisson or binomial likelihood and the
first-difference (random-walk) prior for unknown risk. Optionally add a
covariance matrix for multiple, correlated time series models. References:
Donegan, Hughes, and Lee (2022) <doi:10.2196/34589>; Stan Development Team
(2021) <https://mc-stan.org>; Theil (1972, ISBN:0-444-10378-3).

%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}