%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  eDNAjoint
%global packver   0.2
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.2
Release:          1%{?dist}%{?buildtag}
Summary:          Joint Modeling of Traditional and Environmental DNA Survey Data in a Bayesian Framework

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


BuildRequires:    R-devel >= 3.4.0
Requires:         R-core >= 3.4.0
BuildRequires:    R-CRAN-RcppParallel >= 5.0.1
BuildRequires:    R-CRAN-rstantools >= 2.3.1.1
BuildRequires:    R-CRAN-rstan >= 2.26.23
BuildRequires:    R-CRAN-StanHeaders >= 2.26.22
BuildRequires:    R-CRAN-BH >= 1.66.0
BuildRequires:    R-CRAN-RcppEigen >= 0.3.3.3.0
BuildRequires:    R-CRAN-Rcpp >= 0.12.0
BuildRequires:    R-CRAN-bayestestR 
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-lifecycle 
BuildRequires:    R-CRAN-loo 
BuildRequires:    R-CRAN-magrittr 
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-rlist 
BuildRequires:    R-CRAN-tidyr 
BuildRequires:    R-CRAN-scales 
BuildRequires:    R-CRAN-rstantools
Requires:         R-CRAN-RcppParallel >= 5.0.1
Requires:         R-CRAN-rstantools >= 2.3.1.1
Requires:         R-CRAN-rstan >= 2.26.23
Requires:         R-CRAN-Rcpp >= 0.12.0
Requires:         R-CRAN-bayestestR 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-lifecycle 
Requires:         R-CRAN-loo 
Requires:         R-CRAN-magrittr 
Requires:         R-methods 
Requires:         R-CRAN-rlist 
Requires:         R-CRAN-tidyr 
Requires:         R-CRAN-scales 
Requires:         R-CRAN-rstantools

%description
Models integrate environmental DNA (eDNA) detection data and traditional
survey data to jointly estimate species catch rate (see package vignette:
<https://bookdown.org/abigailkeller/eDNAjoint_vignette/>). Models can be
used with count data via traditional survey methods (i.e., trapping,
electrofishing, visual) and replicated eDNA detection/nondetection data
via polymerase chain reaction (i.e., PCR or qPCR) from multiple survey
locations. Estimated parameters include probability of a false positive
eDNA detection, a site-level covariates that scale the sensitivity of eDNA
surveys relative to traditional surveys, and catchability coefficients for
traditional gear types. Models are implemented with a Bayesian framework
(Markov chain Monte Carlo) using the 'Stan' probabilistic programming
language.

%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}