[PATCH 1/3] gnu: Add r-decon.

OpenSubmitted by Aniket Patil.
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  • Aniket Patil
  • zimoun
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Aniket Patil wrote 5 days ago
(address . guix-patches@gnu.org)(name . Aniket Patil)(address . aniket112.patil@gmail.com)
20201016131338.62737-1-aniket112.patil@gmail.com
* gnu/packages/cran.scm (r-decon): New variable.--- gnu/packages/cran.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+)
Toggle diff (33 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 59a409f8e9..0370cdd993 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -24596,3 +24596,26 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.") (license license:gpl2)))++(define-public r-decon+ (package+ (name "r-decon")+ (version "1.2-4")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "decon" version))+ (sha256+ (base32+ "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))+ (properties `((upstream-name . "decon")))+ (build-system r-build-system)+ (native-inputs `(("gfortran" ,gfortran)))+ (home-page+ "https://cran.r-project.org/web/packages/decon")+ (synopsis+ "Deconvolution Estimation in Measurement Error Models")+ (description+ "This package contains a collection of functions to deal with nonparametric measurement error problems using deconvolution kernel methods. We focus two measurement error models in the package: (1) an additive measurement error model, where the goal is to estimate the density or distribution function from contaminated data; (2) nonparametric regression model with errors-in-variables. The R functions allow the measurement errors to be either homoscedastic or heteroscedastic. To make the deconvolution estimators computationally more efficient in R, we adapt the \"Fast Fourier Transform\" (FFT) algorithm for density estimation with error-free data to the deconvolution kernel estimation. Several methods for the selection of the data-driven smoothing parameter are also provided in the package. See details in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.")+ (license license:gpl3+)))+-- 2.28.0
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Aniket Patil wrote 5 days ago
[PATCH 2/3] gnu: Add r-locpol.
(address . guix-patches@gnu.org)(name . Aniket Patil)(address . aniket112.patil@gmail.com)
20201016131338.62737-2-aniket112.patil@gmail.com
* gnu/packages/cran.scm (r-locpol): New variable.--- gnu/packages/cran.scm | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+)
Toggle diff (29 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 0370cdd993..1529849211 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -24619,3 +24619,22 @@ absolute GSEA.") "This package contains a collection of functions to deal with nonparametric measurement error problems using deconvolution kernel methods. We focus two measurement error models in the package: (1) an additive measurement error model, where the goal is to estimate the density or distribution function from contaminated data; (2) nonparametric regression model with errors-in-variables. The R functions allow the measurement errors to be either homoscedastic or heteroscedastic. To make the deconvolution estimators computationally more efficient in R, we adapt the \"Fast Fourier Transform\" (FFT) algorithm for density estimation with error-free data to the deconvolution kernel estimation. Several methods for the selection of the data-driven smoothing parameter are also provided in the package. See details in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.") (license license:gpl3+))) +(define-public r-locpol+ (package+ (name "r-locpol")+ (version "0.7-0")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "locpol" version))+ (sha256+ (base32+ "1p915n0l09kbwkly627074jslxl01yssp1rf0c7sygvsw6sgy5lm"))))+ (properties `((upstream-name . "locpol")))+ (build-system r-build-system)+ (home-page+ "https://cran.r-project.org/web/packages/locpol")+ (synopsis "Kernel Local Polynomial Regression")+ (description+ "Computes local polynomial estimators for the regression and also density. It comprises several different utilities to handle kernel estimators.")+ (license license:gpl2+)))-- 2.28.0
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Aniket Patil wrote 5 days ago
[PATCH 3/3] gnu: Add r-lpme.
(address . guix-patches@gnu.org)(name . Aniket Patil)(address . aniket112.patil@gmail.com)
20201016131338.62737-3-aniket112.patil@gmail.com
* gnu/packages/cran.scm (r-lpme): New variable.--- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+)
Toggle diff (37 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 1529849211..27e5db1900 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -24638,3 +24638,30 @@ absolute GSEA.") (description "Computes local polynomial estimators for the regression and also density. It comprises several different utilities to handle kernel estimators.") (license license:gpl2+)))++(define-public r-lpme+ (package+ (name "r-lpme")+ (version "1.1.1")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "lpme" version))+ (sha256+ (base32+ "0si90nkgl8bqk8yvd2igdsrngiwqh8891072pfpzipifnd0f5448"))))+ (properties `((upstream-name . "lpme")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-decon" ,r-decon)+ ("r-flexmix" ,r-flexmix)+ ("r-locpol" ,r-locpol)+ ("r-rcpp" ,r-rcpp)+ ("r-rcpparmadillo" ,r-rcpparmadillo)))+ (home-page+ "https://cran.r-project.org/web/packages/lpme")+ (synopsis+ "Nonparametric Estimation of Measurement Error Models")+ (description+ "Provide nonparametric methods for mean regression model, modal regression and conditional density estimation in the presence/absence of measurement error. Bandwidth selection is also provided for each method.")+ (license license:gpl2+)))-- 2.28.0
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zimoun wrote 2 days ago
Re: [bug#44033] [PATCH 1/3] gnu: Add r-decon.
(name . Aniket Patil)(address . aniket112.patil@gmail.com)(address . 44033@debbugs.gnu.org)
87wnzm76y4.fsf@gmail.com
Dear,
Thank you for this contribution.

The file gnu/packages/cran.scm has changed between so your patches donot apply anymore. Could you rebase on the top? Please.
(Note that using “git format-patch --base=<hash>” where <hash> is thehash on which your patch is applying simplifies the process. IMHO.)

On Fri, 16 Oct 2020 at 18:43, Aniket Patil <aniket112.patil@gmail.com> wrote:
Toggle quote (26 lines)> * gnu/packages/cran.scm (r-decon): New variable.> ---> gnu/packages/cran.scm | 23 +++++++++++++++++++++++> 1 file changed, 23 insertions(+)>> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm> index 59a409f8e9..0370cdd993 100644> --- a/gnu/packages/cran.scm> +++ b/gnu/packages/cran.scm> @@ -24596,3 +24596,26 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering.> Without filtering, users can perform (original) two-tailed or one-tailed> absolute GSEA.")> (license license:gpl2)))> +> +(define-public r-decon> + (package> + (name "r-decon")> + (version "1.2-4")> + (source> + (origin> + (method url-fetch)> + (uri (cran-uri "decon" version))> + (sha256> + (base32> + "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
The indentation does not seem correct. It should be:
(sha256 (base32 "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))
Toggle quote (4 lines)> + (properties `((upstream-name . "decon")))> + (build-system r-build-system)> + (native-inputs `(("gfortran" ,gfortran)))
Usually, we use:
(native-inputs `(("gfortran" ,gfortran)))
instead on the in-line.
Toggle quote (5 lines)> + (home-page> + "https://cran.r-project.org/web/packages/decon")> + (synopsis> + "Deconvolution Estimation in Measurement Error Models")
Usually, the synopsis is on the same line:
(synopsis "Deconvolution Estimation in Measurement Error Models")

Toggle quote (5 lines)> + (description> + "This package contains a collection of functions to deal with nonparametric measurement error problems using deconvolution kernel methods. We focus two measurement error models in the package: (1) an additive measurement error model, where the goal is to estimate the density or distribution function from contaminated data; (2) nonparametric regression model with errors-in-variables. The R functions allow the measurement errors to be either homoscedastic or heteroscedastic. To make the deconvolution estimators computationally more efficient in R, we adapt the \"Fast Fourier Transform\" (FFT) algorithm for density estimation with error-free data to the deconvolution kernel estimation. Several methods for the selection of the data-driven smoothing parameter are also provided in the package. See details in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.")> + (license license:gpl3+)))> +
The lines should not be longer than 80 characters. Something like.
(description "This package contains a collection of functions to deal with nonparametric measurement error problems using deconvolution kernel methods. We focus two measurement error models in the package: (1) an additive measurement error model, where the goal is to estimate the density or distribution function from contaminated data; (2) nonparametric regression model with errors-in-variables. The R functions allow the measurement errors to be either homoscedastic or heteroscedastic. To make the deconvolution estimators computationally more efficient in R, we adapt the \"Fast Fourier Transform\" (FFT) algorithm for density estimation with error-free data to the deconvolution kernel estimation. Several methods for the selection of the data-driven smoothing parameter are also provided in the package. See details in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in measurement error models: The R package decon. Journal of Statistical Software, 39(10), 1-24.")

To help you to spot, you can apply the linter with:
./pre-inst-env guix lint r-deconv
and then address the warnings, if any.

Could you send a v2?
All the best,simon
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Aniket Patil wrote 2 days ago
(name . zimoun)(address . zimon.toutoune@gmail.com)(address . 44033@debbugs.gnu.org)
CAF-xJguThfaHPUMQHhywQ5Aa4qFrJNFDFYLMY7Ta1HiaTNqyng@mail.gmail.com
Sure, I will do that.
On Mon, 19 Oct 2020 at 5:40 PM, zimoun <zimon.toutoune@gmail.com> wrote:
Toggle quote (120 lines)> Dear,>> Thank you for this contribution.>>> The file gnu/packages/cran.scm has changed between so your patches do> not apply anymore. Could you rebase on the top? Please.>> (Note that using “git format-patch --base=<hash>” where <hash> is the> hash on which your patch is applying simplifies the process. IMHO.)>>> On Fri, 16 Oct 2020 at 18:43, Aniket Patil <aniket112.patil@gmail.com>> wrote:> > * gnu/packages/cran.scm (r-decon): New variable.> > ---> > gnu/packages/cran.scm | 23 +++++++++++++++++++++++> > 1 file changed, 23 insertions(+)> >> > diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm> > index 59a409f8e9..0370cdd993 100644> > --- a/gnu/packages/cran.scm> > +++ b/gnu/packages/cran.scm> > @@ -24596,3 +24596,26 @@ enrichment analysis (GSEA) calculation with or> without the absolute filtering.> > Without filtering, users can perform (original) two-tailed or> one-tailed> > absolute GSEA.")> > (license license:gpl2)))> > +> > +(define-public r-decon> > + (package> > + (name "r-decon")> > + (version "1.2-4")> > + (source> > + (origin> > + (method url-fetch)> > + (uri (cran-uri "decon" version))> > + (sha256> > + (base32> > + "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))>> The indentation does not seem correct. It should be:>> (sha256> (base32> "1v4l0xq29rm8mks354g40g9jxn0didzlxg3g7z08m0gvj29zdj7s"))))>> > + (properties `((upstream-name . "decon")))> > + (build-system r-build-system)> > + (native-inputs `(("gfortran" ,gfortran)))>> Usually, we use:>> (native-inputs> `(("gfortran" ,gfortran)))>> instead on the in-line.>> > + (home-page> > + "https://cran.r-project.org/web/packages/decon")> > + (synopsis> > + "Deconvolution Estimation in Measurement Error Models")>> Usually, the synopsis is on the same line:>> (synopsis "Deconvolution Estimation in Measurement Error Models")>>> > + (description> > + "This package contains a collection of functions to deal with> nonparametric measurement error problems using deconvolution kernel> methods. We focus two measurement error models in the package: (1) an> additive measurement error model, where the goal is to estimate the density> or distribution function from contaminated data; (2) nonparametric> regression model with errors-in-variables. The R functions allow the> measurement errors to be either homoscedastic or heteroscedastic. To make> the deconvolution estimators computationally more efficient in R, we adapt> the \"Fast Fourier Transform\" (FFT) algorithm for density estimation with> error-free data to the deconvolution kernel estimation. Several methods> for the selection of the data-driven smoothing parameter are also provided> in the package. See details in: Wang, X.F. and Wang, B. (2011).> Deconvolution estimation in measurement error models: The R package decon.> Journal of Statistical Software, 39(10), 1-24.")> > + (license license:gpl3+)))> > +>> The lines should not be longer than 80 characters. Something like.>> (description> "This package contains a collection of functions to deal with> nonparametric measurement error problems using deconvolution> kernel methods. We focus two measurement error models in the> package: (1) an additive measurement error model, where the goal> is to estimate the density or distribution function from> contaminated data; (2) nonparametric regression model with> errors-in-variables. The R functions allow the measurement errors> to be either homoscedastic or heteroscedastic. To make the> deconvolution estimators computationally more efficient in R, we> adapt the \"Fast Fourier Transform\" (FFT) algorithm for density> estimation with error-free data to the deconvolution kernel> estimation. Several methods for the selection of the data-driven> smoothing parameter are also provided in the package. See details> in: Wang, X.F. and Wang, B. (2011). Deconvolution estimation in> measurement error models: The R package decon. Journal of> Statistical Software, 39(10), 1-24.")>>> To help you to spot, you can apply the linter with:>> ./pre-inst-env guix lint r-deconv>> and then address the warnings, if any.>>> Could you send a v2?>> All the best,> simon>
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