%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  CFO
%global packver   2.0.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          2.0.0
Release:          1%{?dist}%{?buildtag}
Summary:          CFO-Type Designs in Phase I/II Clinical Trials

License:          GPL-2
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel
Requires:         R-core
BuildArch:        noarch
BuildRequires:    R-CRAN-survival 
BuildRequires:    R-CRAN-dplyr 
BuildRequires:    R-CRAN-ggplot2 
BuildRequires:    R-CRAN-Iso 
BuildRequires:    R-CRAN-pbapply 
Requires:         R-CRAN-survival 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-Iso 
Requires:         R-CRAN-pbapply 

%description
In phase I clinical trials, the primary objective is to ascertain the
maximum tolerated dose (MTD) corresponding to a specified target toxicity
rate. The subsequent phase II trials are designed to examine the potential
efficacy of the drug based on the MTD obtained from the phase I trials,
with the aim of identifying the optimal biological dose (OBD). The 'CFO'
package facilitates the implementation of dose-finding trials by utilizing
calibration-free odds type (CFO-type) designs. Specifically, it
encompasses the calibration-free odds (CFO) (Jin and Yin (2022)
<doi:10.1177/09622802221079353>), two-dimensional CFO (2dCFO) (Wang et al.
(2023) <doi:10.3389/fonc.2023.1294258>), time-to-event CFO (TITE-CFO) (Jin
and Yin (2023) <doi:10.1002/pst.2304>), fractional CFO (fCFO),
accumulative CFO (aCFO), TITE-aCFO, and f-aCFO designs (Fang and Yin
(2024) <doi: 10.1002/sim.10127>). It supports phase I/II trials for the
CFO design and only phase I trials for the other CFO-type designs. The
‘CFO' package accommodates diverse CFO-type designs, allowing users to
tailor the approach based on factors such as dose information inclusion,
handling of late-onset toxicity, and the nature of the target drug
(single-drug or drug-combination). The functionalities embedded in 'CFO'
package include the determination of the dose level for the next cohort,
the selection of the MTD for a real trial, and the execution of single or
multiple simulations to obtain operating characteristics. Moreover, these
functions are equipped with early stopping and dose elimination rules to
address safety considerations. Users have the flexibility to choose
different distributions, thresholds, and cohort sizes among others for
their specific needs. The output of the 'CFO' package can be summary
statistics as well as various plots for better visualization.

%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}