File R-ordcrm.spec of Package R-ordcrm
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# Spec file for package ordcrm
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%global packname ordcrm
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 1.0.0
Release: 0
Summary: Likelihood-Based Continual Reassessment Method (CRM) Dose Finding Designs
Group: Development/Libraries/Other
License: GPL (>= 2)
URL: http://cran.r-project.org/web/packages/%{packname}
Source: ordcrm_1.0.0.tar.gz
Requires: R-base
Requires: R-rms
Requires: R-Hmisc
Requires: R-quantreg
Requires: R-ggplot2
Requires: R-SparseM
Requires: R-polspline
Requires: R-multcomp
Requires: R-htmlTable
Requires: R-htmltools
Requires: R-digest
Requires: R-colorspace
Requires: R-knitr
Requires: R-scales
Requires: R-cli
Requires: R-gtable
Requires: R-isoband
Requires: R-lifecycle
Requires: R-rlang
Requires: R-S7
Requires: R-vctrs
Requires: R-withr
Requires: R-gridExtra
Requires: R-data.table
Requires: R-viridis
Requires: R-base64enc
Requires: R-rmarkdown
Requires: R-Formula
Requires: R-stringr
Requires: R-magrittr
Requires: R-checkmate
Requires: R-htmlwidgets
Requires: R-rstudioapi
Requires: R-fastmap
Requires: R-evaluate
Requires: R-highr
Requires: R-xfun
Requires: R-yaml
Requires: R-mvtnorm
Requires: R-TH.data
Requires: R-sandwich
Requires: R-MatrixModels
Requires: R-farver
Requires: R-glue
Requires: R-labeling
Requires: R-R6
Requires: R-RColorBrewer
Requires: R-viridisLite
Requires: R-backports
Requires: R-jsonlite
Requires: R-bslib
Requires: R-fontawesome
Requires: R-jquerylib
Requires: R-tinytex
Requires: R-zoo
Requires: R-stringi
Requires: R-cachem
Requires: R-memoise
Requires: R-mime
Requires: R-sass
Requires: R-fs
Requires: R-rappdirs
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
# # Three others commonly needed
# BuildRequires: tex(ae.sty)
# BuildRequires: tex(fancyvrb.sty)
# BuildRequires: tex(inconsolata.sty)
# BuildRequires: tex(natbib.sty)
# %else
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# %endif
# BuildRequires: texinfo
BuildRequires: fdupes
BuildRequires: R-base
BuildRequires: R-rms
BuildRequires: R-Hmisc
BuildRequires: R-quantreg
BuildRequires: R-ggplot2
BuildRequires: R-SparseM
BuildRequires: R-polspline
BuildRequires: R-multcomp
BuildRequires: R-htmlTable
BuildRequires: R-htmltools
BuildRequires: R-digest
BuildRequires: R-colorspace
BuildRequires: R-knitr
BuildRequires: R-scales
BuildRequires: R-cli
BuildRequires: R-gtable
BuildRequires: R-isoband
BuildRequires: R-lifecycle
BuildRequires: R-rlang
BuildRequires: R-S7
BuildRequires: R-vctrs
BuildRequires: R-withr
BuildRequires: R-gridExtra
BuildRequires: R-data.table
BuildRequires: R-viridis
BuildRequires: R-base64enc
BuildRequires: R-rmarkdown
BuildRequires: R-Formula
BuildRequires: R-stringr
BuildRequires: R-magrittr
BuildRequires: R-checkmate
BuildRequires: R-htmlwidgets
BuildRequires: R-rstudioapi
BuildRequires: R-fastmap
BuildRequires: R-evaluate
BuildRequires: R-highr
BuildRequires: R-xfun
BuildRequires: R-yaml
BuildRequires: R-mvtnorm
BuildRequires: R-TH.data
BuildRequires: R-sandwich
BuildRequires: R-MatrixModels
BuildRequires: R-farver
BuildRequires: R-glue
BuildRequires: R-labeling
BuildRequires: R-R6
BuildRequires: R-RColorBrewer
BuildRequires: R-viridisLite
BuildRequires: R-backports
BuildRequires: R-jsonlite
BuildRequires: R-bslib
BuildRequires: R-fontawesome
BuildRequires: R-jquerylib
BuildRequires: R-tinytex
BuildRequires: R-zoo
BuildRequires: R-stringi
BuildRequires: R-cachem
BuildRequires: R-memoise
BuildRequires: R-mime
BuildRequires: R-sass
BuildRequires: R-fs
BuildRequires: R-rappdirs
%description
Provides the setup and calculations needed to run a likelihood-based
continual reassessment method (CRM) dose finding trial and performs
simulations to assess design performance under various scenarios. 3
dose finding designs are included in this package: ordinal proportional
odds model (POM) CRM, ordinal continuation ratio (CR) model CRM, and
the binary 2-parameter logistic model CRM. These functions allow
customization of design characteristics to vary sample size, cohort
sizes, target dose-limiting toxicity (DLT) rates, discrete or
continuous dose levels, combining ordinal grades 0 and 1 into one
category, and incorporate safety and/or stopping rules. For POM and CR
model designs, ordinal toxicity grades are specified by common
terminology criteria for adverse events (CTCAE) version 4.0. Function
'pseudodata' creates the necessary starting models for these 3 designs,
and function 'nextdose' estimates the next dose to test in a cohort of
patients for a target DLT rate. We also provide the function
'crmsimulations' to assess the performance of these 3 dose finding
designs under various scenarios.
%prep
%setup -q -c -n %{packname}
# the next line is needed, because we build without --clean in between two packages
rm -rf ~/.R
%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
%fdupes -s %{buildroot}%{rlibdir}
#%%check
#%%{_bindir}/R CMD check %%{packname}
%files
%dir %{rlibdir}/%{packname}
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%doc %{rlibdir}/%{packname}/NEWS.md
%{rlibdir}/%{packname}/R
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
