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* [bug#44033] [PATCH 1/3] gnu: Add r-decon.
@ 2020-10-16 13:13 Aniket Patil
  2020-10-16 13:13 ` [bug#44033] [PATCH 2/3] gnu: Add r-locpol Aniket Patil
                   ` (2 more replies)
  0 siblings, 3 replies; 5+ messages in thread
From: Aniket Patil @ 2020-10-16 13:13 UTC (permalink / raw)
  To: 44033; +Cc: Aniket Patil

* 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"))))
+    (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





^ permalink raw reply	[flat|nested] 5+ messages in thread

* [bug#44033] [PATCH 2/3] gnu: Add r-locpol.
  2020-10-16 13:13 [bug#44033] [PATCH 1/3] gnu: Add r-decon Aniket Patil
@ 2020-10-16 13:13 ` Aniket Patil
  2020-10-16 13:13 ` [bug#44033] [PATCH 3/3] gnu: Add r-lpme Aniket Patil
  2020-10-19 12:09 ` [bug#44033] [PATCH 1/3] gnu: Add r-decon zimoun
  2 siblings, 0 replies; 5+ messages in thread
From: Aniket Patil @ 2020-10-16 13:13 UTC (permalink / raw)
  To: 44033; +Cc: Aniket Patil

* gnu/packages/cran.scm (r-locpol): New variable.
---
 gnu/packages/cran.scm | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 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





^ permalink raw reply	[flat|nested] 5+ messages in thread

* [bug#44033] [PATCH 3/3] gnu: Add r-lpme.
  2020-10-16 13:13 [bug#44033] [PATCH 1/3] gnu: Add r-decon Aniket Patil
  2020-10-16 13:13 ` [bug#44033] [PATCH 2/3] gnu: Add r-locpol Aniket Patil
@ 2020-10-16 13:13 ` Aniket Patil
  2020-10-19 12:09 ` [bug#44033] [PATCH 1/3] gnu: Add r-decon zimoun
  2 siblings, 0 replies; 5+ messages in thread
From: Aniket Patil @ 2020-10-16 13:13 UTC (permalink / raw)
  To: 44033; +Cc: Aniket Patil

* gnu/packages/cran.scm (r-lpme): New variable.
---
 gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 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





^ permalink raw reply	[flat|nested] 5+ messages in thread

* [bug#44033] [PATCH 1/3] gnu: Add r-decon.
  2020-10-16 13:13 [bug#44033] [PATCH 1/3] gnu: Add r-decon Aniket Patil
  2020-10-16 13:13 ` [bug#44033] [PATCH 2/3] gnu: Add r-locpol Aniket Patil
  2020-10-16 13:13 ` [bug#44033] [PATCH 3/3] gnu: Add r-lpme Aniket Patil
@ 2020-10-19 12:09 ` zimoun
  2020-10-19 12:27   ` Aniket Patil
  2 siblings, 1 reply; 5+ messages in thread
From: zimoun @ 2020-10-19 12:09 UTC (permalink / raw)
  To: Aniket Patil; +Cc: 44033

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




^ permalink raw reply	[flat|nested] 5+ messages in thread

* [bug#44033] [PATCH 1/3] gnu: Add r-decon.
  2020-10-19 12:09 ` [bug#44033] [PATCH 1/3] gnu: Add r-decon zimoun
@ 2020-10-19 12:27   ` Aniket Patil
  0 siblings, 0 replies; 5+ messages in thread
From: Aniket Patil @ 2020-10-19 12:27 UTC (permalink / raw)
  To: zimoun; +Cc: 44033

[-- Attachment #1: Type: text/plain, Size: 4715 bytes --]

Sure, I will do that.

On Mon, 19 Oct 2020 at 5:40 PM, zimoun <zimon.toutoune@gmail.com> wrote:

> 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
>

[-- Attachment #2: Type: text/html, Size: 5815 bytes --]

^ permalink raw reply	[flat|nested] 5+ messages in thread

end of thread, other threads:[~2020-10-19 12:47 UTC | newest]

Thread overview: 5+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2020-10-16 13:13 [bug#44033] [PATCH 1/3] gnu: Add r-decon Aniket Patil
2020-10-16 13:13 ` [bug#44033] [PATCH 2/3] gnu: Add r-locpol Aniket Patil
2020-10-16 13:13 ` [bug#44033] [PATCH 3/3] gnu: Add r-lpme Aniket Patil
2020-10-19 12:09 ` [bug#44033] [PATCH 1/3] gnu: Add r-decon zimoun
2020-10-19 12:27   ` Aniket Patil

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