File R-NST.spec of Package R-NST
# Automatically generated by CRAN2OBS
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# Spec file for package NST
# This file is auto-generated using information in the package source,
# esp. Description and Summary. Improvements in that area should be
# discussed with upstream.
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%global packname NST
%global rlibdir %{_libdir}/R/library
Name: R-%{packname}
Version: 3.1.10
Release: 0
Summary: Normalized Stochasticity Ratio
Group: Development/Libraries/Other
License: GPL-2
URL: http://cran.r-project.org/web/packages/%{packname}
Source: NST_3.1.10.tar.gz
Requires: R-base
Requires: R-vegan
Requires: R-permute
Requires: R-ape
Requires: R-bigmemory
Requires: R-iCAMP
Requires: R-DirichletReg
Requires: R-Rcpp
Requires: R-digest
Requires: R-bigmemory.sri
Requires: R-uuid
Requires: R-BH
Requires: R-Formula
Requires: R-maxLik
Requires: R-nortest
Requires: R-minpack.lm
Requires: R-Hmisc
Requires: R-data.table
Requires: R-ggplot2
Requires: R-gtable
Requires: R-gridExtra
Requires: R-htmlTable
Requires: R-viridisLite
Requires: R-htmltools
Requires: R-base64enc
Requires: R-colorspace
Requires: R-rmarkdown
Requires: R-knitr
Requires: R-miscTools
Requires: R-sandwich
Requires: R-generics
Requires: R-cli
Requires: R-isoband
Requires: R-lifecycle
Requires: R-rlang
Requires: R-S7
Requires: R-scales
Requires: R-vctrs
Requires: R-withr
Requires: R-glue
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-bslib
Requires: R-fontawesome
Requires: R-jquerylib
Requires: R-jsonlite
Requires: R-tinytex
Requires: R-zoo
Requires: R-cachem
Requires: R-memoise
Requires: R-mime
Requires: R-sass
Requires: R-backports
Requires: R-farver
Requires: R-labeling
Requires: R-R6
Requires: R-RColorBrewer
Requires: R-stringi
Requires: R-fs
Requires: R-rappdirs
# %%if 0%%{?sle_version} > 120400 || 0%%{?is_opensuse}
# # Three others commonly needed
# BuildRequires: tex(ae.sty)
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# %else
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# BuildRequires: texinfo
BuildRequires: fdupes
BuildRequires: R-base
BuildRequires: R-vegan
BuildRequires: R-permute
BuildRequires: R-ape
BuildRequires: R-bigmemory
BuildRequires: R-iCAMP
BuildRequires: R-DirichletReg
BuildRequires: R-Rcpp-devel
BuildRequires: R-digest
BuildRequires: R-bigmemory.sri
BuildRequires: R-uuid
BuildRequires: R-BH-devel
BuildRequires: R-Formula
BuildRequires: R-maxLik
BuildRequires: R-nortest
BuildRequires: R-minpack.lm
BuildRequires: R-Hmisc
BuildRequires: R-data.table
BuildRequires: R-ggplot2
BuildRequires: R-gtable
BuildRequires: R-gridExtra
BuildRequires: R-htmlTable
BuildRequires: R-viridisLite
BuildRequires: R-htmltools
BuildRequires: R-base64enc
BuildRequires: R-colorspace
BuildRequires: R-rmarkdown
BuildRequires: R-knitr
BuildRequires: R-miscTools
BuildRequires: R-sandwich
BuildRequires: R-generics
BuildRequires: R-cli
BuildRequires: R-isoband
BuildRequires: R-lifecycle
BuildRequires: R-rlang
BuildRequires: R-S7
BuildRequires: R-scales
BuildRequires: R-vctrs
BuildRequires: R-withr
BuildRequires: R-glue
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-bslib
BuildRequires: R-fontawesome
BuildRequires: R-jquerylib
BuildRequires: R-jsonlite
BuildRequires: R-tinytex
BuildRequires: R-zoo
BuildRequires: R-cachem
BuildRequires: R-memoise
BuildRequires: R-mime
BuildRequires: R-sass
BuildRequires: R-backports
BuildRequires: R-farver
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BuildRequires: R-stringi
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BuildRequires: R-rappdirs
%description
To estimate ecological stochasticity in community assembly.
Understanding the community assembly mechanisms controlling
biodiversity patterns is a central issue in ecology. Although it is
generally accepted that both deterministic and stochastic processes
play important roles in community assembly, quantifying their relative
importance is challenging. The new index, normalized stochasticity
ratio (NST), is to estimate ecological stochasticity, i.e. relative
importance of stochastic processes, in community assembly. With
functions in this package, NST can be calculated based on different
similarity metrics and/or different null model algorithms, as well as
some previous indexes, e.g. previous Stochasticity Ratio (ST), Standard
Effect Size (SES), modified Raup-Crick metrics (RC). Functions for
permutational test and bootstrapping analysis are also included.
Previous ST is published by Zhou et al (2014)
<doi:10.1073/pnas.1324044111>. NST is modified from ST by considering
two alternative situations and normalizing the index to range from 0 to
1 (Ning et al 2019) <doi:10.1073/pnas.1904623116>. A modified version,
MST, is a special case of NST, used in some recent or upcoming
publications, e.g. Liang et al (2020)
<doi:10.1016/j.soilbio.2020.108023>. SES is calculated as described in
Kraft et al (2011) <doi:10.1126/science.1208584>. RC is calculated as
reported by Chase et al (2011) <doi:10.1890/ES10-00117.1> and Stegen et
al (2013) <doi:10.1038/ismej.2013.93>. Version 3 added NST based on
phylogenetic beta diversity, used by Ning et al (2020)
<doi:10.1038/s41467-020-18560-z>.
%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}
%{rlibdir}/%{packname}/CITATION
%doc %{rlibdir}/%{packname}/DESCRIPTION
%{rlibdir}/%{packname}/INDEX
%{rlibdir}/%{packname}/Meta
%{rlibdir}/%{packname}/NAMESPACE
%{rlibdir}/%{packname}/R
%{rlibdir}/%{packname}/data
%doc %{rlibdir}/%{packname}/help
%doc %{rlibdir}/%{packname}/html
%changelog
