File R-psfmi.spec of Package R-psfmi
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# Spec file for package psfmi
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%global packname psfmi
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 1.4.0
Release: 0
Summary: Prediction Model Pooling, Selection and Performance Evaluation Across Multiply Imputed Datasets
Group: Development/Libraries/Other
License: GPL (>= 2)
URL: http://cran.r-project.org/web/packages/%{packname}
Source: psfmi_1.4.0.tar.gz
Requires: R-base
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Requires: R-lme4
Requires: R-car
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Requires: R-gtable
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Requires: R-reformulas
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Requires: R-broom
Requires: R-glmnet
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Requires: R-pkgconfig
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Requires: R-rmarkdown
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# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
# # Three others commonly needed
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BuildRequires: R-rms
BuildRequires: R-magrittr
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Suggests: R-covr
%description
Pooling, backward and forward selection of linear, logistic and Cox
regression models in multiply imputed datasets. Backward and forward
selection can be done from the pooled model using Rubin's Rules (RR),
the D1, D2, D3, D4 and the median p-values method. This is also
possible for Mixed models. The models can contain continuous,
dichotomous, categorical and restricted cubic spline predictors and
interaction terms between all these type of predictors. The stability
of the models can be evaluated using (cluster) bootstrapping. The
package further contains functions to pool model performance measures
as ROC/AUC, Reclassification, R-squared, scaled Brier score, H&L test
and calibration plots for logistic regression models. Internal
validation can be done across multiply imputed datasets with
cross-validation or bootstrapping. The adjusted intercept after
shrinkage of pooled regression coefficients can be obtained. Backward
and forward selection as part of internal validation is possible. A
function to externally validate logistic prediction models in multiple
imputed datasets is available and a function to compare models. For Cox
models a strata variable can be included. Eekhout (2017)
<doi:10.1186/s12874-017-0404-7>. Wiel (2009)
<doi:10.1093/biostatistics/kxp011>. Marshall (2009)
<doi:10.1186/1471-2288-9-57>.
%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
%{rlibdir}/%{packname}/data
%{rlibdir}/%{packname}/doc
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
