File R-BRINDA.spec of Package R-BRINDA
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# Spec file for package BRINDA
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%global packname BRINDA
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 0.1.5
Release: 0
Summary: Computation of BRINDA Adjusted Micronutrient Biomarkers for Inflammation
Group: Development/Libraries/Other
License: CC BY 4.0
URL: http://cran.r-project.org/web/packages/%{packname}
Source: BRINDA_0.1.5.tar.gz
Requires: R-base
Requires: R-berryFunctions
Requires: R-data.table
Requires: R-dplyr
Requires: R-Hmisc
Requires: R-rlang
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# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
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Suggests: R-testthat
%description
Inflammation can affect many micronutrient biomarkers and can thus lead
to incorrect diagnosis of individuals and to over- or under-estimate
the prevalence of deficiency in a population. Biomarkers Reflecting
Inflammation and Nutritional Determinants of Anemia (BRINDA) is a
multi-agency and multi-country partnership designed to improve the
interpretation of nutrient biomarkers in settings of inflammation and
to generate context-specific estimates of risk factors for anemia
(Suchdev (2016) <doi:10.3945/an.115.010215>). In the past few years,
BRINDA published a series of papers to provide guidance on how to
adjust micronutrient biomarkers, retinol binding protein, serum
retinol, serum ferritin by Namaste (2020), soluble transferrin receptor
(sTfR), serum zinc, serum and Red Blood Cell (RBC) folate, and serum
B-12, using inflammation markers, alpha-1-acid glycoprotein (AGP)
and/or C-Reactive Protein (CRP) by Namaste (2020)
<doi:10.1093/ajcn/nqaa141>, Rohner (2017)
<doi:10.3945/ajcn.116.142232>, McDonald (2020)
<doi:10.1093/ajcn/nqz304>, and Young (2020) <doi:10.1093/ajcn/nqz303>.
The BRINDA inflammation adjustment method mainly focuses on Women of
Reproductive Age (WRA) and Preschool-age Children (PSC); however, the
general principle of the BRINDA method might apply to other population
groups. The BRINDA R package is a user-friendly all-in-one R package
that uses a series of functions to implement BRINDA adjustment method,
as described above. The BRINDA R package will first carry out rigorous
checks and provides users guidance to correct data or input errors (if
they occur) prior to inflammation adjustments. After no errors are
detected, the package implements the BRINDA inflammation adjustment for
up to five micronutrient biomarkers, namely retinol-binding-protein,
serum retinol, serum ferritin, sTfR, and serum zinc (when appropriate),
using inflammation indicators of AGP and/or CRP for various population
groups. Of note, adjustment for serum and RBC folate and serum B-12 is
not included in the R package, since evidence shows that no adjustment
is needed for these micronutrient biomarkers in either WRA or PSC
groups (Young (2020) <doi:10.1093/ajcn/nqz303>).
%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
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
