%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  CFO
%global packver   2.1.0
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          2.1.0
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 
BuildRequires:    R-CRAN-RColorBrewer 
BuildRequires:    R-CRAN-scales 
Requires:         R-CRAN-survival 
Requires:         R-CRAN-dplyr 
Requires:         R-CRAN-ggplot2 
Requires:         R-CRAN-Iso 
Requires:         R-CRAN-pbapply 
Requires:         R-CRAN-RColorBrewer 
Requires:         R-CRAN-scales 

%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>), randomized CFO (rCFO), 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. An interactive web application for CFO is available
at the provided URL.

%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}