[bug#44345] [PATCH 1/2] gnu: Add r-metafor.

[bug#44345] [PATCH 1/2] gnu: Add r-metafor.

[Aniket Patil]

* gnu/packages/cran.scm (r-metafor): New variable.
---
 gnu/packages/cran.scm | 39 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 39 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 75d9ae7de2..cc4e5f2bba 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24745,3 +24745,42 @@ mutations in each of 96 trinucleotide contexts and identifies
 the weighted combination of published signatures that, when summed, 
 most closely reconstructs the mutational profile.")
     (license license:gpl2+)))
+
+(define-public r-metafor
+  (package
+    (name "r-metafor")
+    (version "2.4-0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "metafor" version))
+        (sha256
+          (base32
+            "1b599fxk7s0brkchmx698fr5k4g1kzkia2rnlvhg349ffs5nfjmn"))))
+    (properties `((upstream-name . "metafor")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrix" ,r-matrix)
+       ("r-nlme" ,r-nlme)))
+    (home-page
+      "https://cran.r-project.org/web/packages/metafor")
+    (synopsis "Meta-Analysis Package for R")
+    (description
+      "This package provides a comprehensive collection of 
+functions for conducting meta-analyses in R.  The package 
+includes functions to calculate various effect sizes or outcome 
+measures, fit fixed-, random-, and mixed-effects models to such 
+data, carry out moderator and meta-regression analyses, and create 
+various types of meta-analytical plots (e.g., forest, funnel, radial, 
+L'Abbe, Baujat, GOSH plots).  For meta-analyses of binomial and 
+person-time data, the package also provides functions that implement 
+specialized methods, including the Mantel-Haenszel method, Peto's 
+method, and a variety of suitable generalized linear (mixed-effects) 
+models (i.e., mixed-effects logistic and Poisson regression models).  
+Finally, the package provides functionality for fitting meta-analytic 
+multivariate/multilevel models that account for non-independent 
+sampling errors and/or true effects (e.g., due to the inclusion of 
+multiple treatment studies, multiple endpoints, or other forms of clustering).  
+Network meta-analyses and meta-analyses accounting for known correlation 
+structures (e.g., due to phylogenetic relatedness) can also be conducted.")
+    (license license:gpl2+)))
-- 
2.28.0

[bug#44346] [PATCH 2/2] gnu: Add r-altmeta.

[Aniket Patil]

* gnu/packages/cran.scm (r-altmeta): New variable.
---
 gnu/packages/cran.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index cc4e5f2bba..b40c5bdb21 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -24784,3 +24784,44 @@ multiple treatment studies, multiple endpoints, or other forms of clustering).
 Network meta-analyses and meta-analyses accounting for known correlation 
 structures (e.g., due to phylogenetic relatedness) can also be conducted.")
     (license license:gpl2+)))
+
+(define-public r-altmeta
+  (package
+    (name "r-altmeta")
+    (version "3.2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "altmeta" version))
+        (sha256
+          (base32
+            "0z252lbsknqp33i0b0xf5r7spr535iq47bv40vgip6nsqhgrl7b0"))))
+    (properties `((upstream-name . "altmeta")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-coda" ,r-coda)
+        ("r-lme4" ,r-lme4)
+        ("r-matrix" ,r-matrix)
+        ("r-metafor" ,r-metafor)
+        ("r-rjags" ,r-rjags)))
+    (home-page
+      "https://cran.r-project.org/web/packages/altmeta")
+    (synopsis "Alternative Meta-Analysis Methods")
+    (description
+      "This package provides alternative statistical methods for 
+meta-analysis, including: - bivariate generalized linear mixed 
+models for synthesizing odds ratios, relative risks, and risk 
+differences (Chu et al., 2012 <doi:10.1177/0962280210393712>) - 
+heterogeneity tests and measures that are robust to outliers 
+(Lin et al., 2017 <doi:10.1111/biom.12543>); - measures, tests, 
+and visualization tools for publication bias or small-study effects 
+(Lin and Chu, 2018 <doi:10.1111/biom.12817>; Lin, 2019 
+<doi:10.1002/jrsm.1340>; Lin, 2020 <doi:10.1177/0962280220910172>; 
+Shi et al., 2020 <doi:10.1002/jrsm.1415>); - meta-analysis of diagnostic 
+tests for synthesizing sensitivities, specificities, etc. 
+(Reitsma et al., 2005 <doi:10.1016/j.jclinepi.2005.02.022>; Chu and Cole, 
+2006 <doi:10.1016/j.jclinepi.2006.06.011>); - meta-analysis methods for 
+synthesizing proportions (Lin and Chu, 2020 
+<doi:10.1097/ede.0000000000001232>); - models for multivariate 
+meta-analysis (Lin and Chu, 2018 <doi:10.1002/jrsm.1293>).")
+    (license license:gpl2+)))
-- 
2.28.0

[bug#44345] [PATCH 1/2] gnu: Add r-metafor.

[zimoun]

Hi Aniket,

On Sat, 31 Oct 2020 at 20:38, Aniket Patil <aniket112.patil@gmail.com> wrote:
> * gnu/packages/cran.scm (r-metafor): New variable.
> ---
>  gnu/packages/cran.scm | 39 +++++++++++++++++++++++++++++++++++++++
>  1 file changed, 39 insertions(+)
>
> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
> index 75d9ae7de2..cc4e5f2bba 100644
> --- a/gnu/packages/cran.scm
> +++ b/gnu/packages/cran.scm

Idem than bug#44311.  <http://issues.guix.gnu.org/issue/44311>

Repeat here to easy the reading. :-)

The patch does not apply because the file gnu/packages/cran.scm changed
in the meantime.  I am sorry that we have not been enough reactive.

However, when creating the patch, you had used the option ’--base’;
which really helps because I would be able to apply it and rebase
myself.

Currently, I do not know how to do without copy/pasting by hand, so
loosing your authorship.  Could you rebase on the top of master?

If you cannot, no worry.  Just let me know.


All the best,
simon

[bug#44345] [PATCH 1/2] gnu: Add r-metafor.

[Ricardo Wurmus]

Hi Simon,

>
> On Sat, 31 Oct 2020 at 20:38, Aniket Patil <aniket112.patil@gmail.com> wrote:
>> * gnu/packages/cran.scm (r-metafor): New variable.
>> ---
>>  gnu/packages/cran.scm | 39 +++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 39 insertions(+)
>>
>> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
>> index 75d9ae7de2..cc4e5f2bba 100644
>> --- a/gnu/packages/cran.scm
>> +++ b/gnu/packages/cran.scm
>
> Idem than bug#44311.  <http://issues.guix.gnu.org/issue/44311>
>
> Repeat here to easy the reading. :-)
>
> The patch does not apply because the file gnu/packages/cran.scm changed
> in the meantime.  I am sorry that we have not been enough reactive.

You can still apply the patch with “git am -C0” to ignore all context.
Sometimes with patches that add packages this works.

-- 
Ricardo

bug#44345: [PATCH 1/2] gnu: Add r-metafor.

[Ricardo Wurmus]

zimoun <zimon.toutoune@gmail.com> writes:

> Hi Aniket,
>
> On Sat, 31 Oct 2020 at 20:38, Aniket Patil <aniket112.patil@gmail.com> wrote:
>> * gnu/packages/cran.scm (r-metafor): New variable.
>> ---
>>  gnu/packages/cran.scm | 39 +++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 39 insertions(+)
>>
>> diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
>> index 75d9ae7de2..cc4e5f2bba 100644
>> --- a/gnu/packages/cran.scm
>> +++ b/gnu/packages/cran.scm
>
> Idem than bug#44311.  <http://issues.guix.gnu.org/issue/44311>
>
> Repeat here to easy the reading. :-)
>
> The patch does not apply because the file gnu/packages/cran.scm changed
> in the meantime.  I am sorry that we have not been enough reactive.

I applied the two patches with commit
6d1160db8e16ee0da5b38c5297cf22cd6dd230d6.

I used “git am -C0” to ignore mismatched context.  I also updated the
descriptions and re-indented the definitions.

-- 
Ricardo

[bug#44345] [PATCH 1/2] gnu: Add r-metafor.

[zimoun]

Hi Ricardo,

On Tue, 22 Dec 2020 at 23:32, Ricardo Wurmus <rekado@elephly.net> wrote:

> I applied the two patches with commit
> 6d1160db8e16ee0da5b38c5297cf22cd6dd230d6.
>
> I used “git am -C0” to ignore mismatched context.  I also updated the
> descriptions and re-indented the definitions.

Thanks for both, the tip and the patch application.

Cheers,
simon