From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from mp0 ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by ms11 with LMTPS id yK72GRV9sl+5KAAA0tVLHw (envelope-from ) for ; Mon, 16 Nov 2020 13:22:29 +0000 Received: from aspmx1.migadu.com ([2001:41d0:2:4a6f::]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits)) by mp0 with LMTPS id 8PUIFhV9sl9fUgAA1q6Kng (envelope-from ) for ; Mon, 16 Nov 2020 13:22:29 +0000 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by aspmx1.migadu.com (Postfix) with ESMTPS id 01C229401BF for ; Mon, 16 Nov 2020 13:22:27 +0000 (UTC) Received: from localhost ([::1]:50166 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1keeSf-00085I-Gc for larch@yhetil.org; Mon, 16 Nov 2020 08:22:25 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:41530) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1keeMU-00038a-DS for guix-patches@gnu.org; Mon, 16 Nov 2020 08:16:03 -0500 Received: from debbugs.gnu.org ([209.51.188.43]:43840) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1keeMU-0004p7-4N for guix-patches@gnu.org; Mon, 16 Nov 2020 08:16:02 -0500 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1keeMT-0003CR-V4 for guix-patches@gnu.org; Mon, 16 Nov 2020 08:16:01 -0500 X-Loop: help-debbugs@gnu.org Subject: [bug#44683] [PATCH] Miscellaneous R packages Resent-From: Lars-Dominik Braun Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Mon, 16 Nov 2020 13:16:01 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: report 44683 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: patch To: 44683@debbugs.gnu.org X-Debbugs-Original-To: guix-patches@gnu.org Received: via spool by submit@debbugs.gnu.org id=B.160553256012290 (code B ref -1); Mon, 16 Nov 2020 13:16:01 +0000 Received: (at submit) by debbugs.gnu.org; 16 Nov 2020 13:16:00 +0000 Received: from localhost ([127.0.0.1]:55386 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1keeMN-0003C4-Fe for submit@debbugs.gnu.org; Mon, 16 Nov 2020 08:16:00 -0500 Received: from lists.gnu.org ([209.51.188.17]:55500) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1keeML-0003Bw-5x for submit@debbugs.gnu.org; Mon, 16 Nov 2020 08:15:54 -0500 Received: from eggs.gnu.org ([2001:470:142:3::10]:41520) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1keeMK-0002wU-RZ for guix-patches@gnu.org; Mon, 16 Nov 2020 08:15:53 -0500 Received: from mail-wm1-x329.google.com ([2a00:1450:4864:20::329]:34501) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1keeMH-0004kF-1Y for guix-patches@gnu.org; Mon, 16 Nov 2020 08:15:52 -0500 Received: by mail-wm1-x329.google.com with SMTP id 23so12011856wmg.1 for ; Mon, 16 Nov 2020 05:15:45 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=leibniz-psychology-org.20150623.gappssmtp.com; s=20150623; h=date:from:to:subject:message-id:mime-version:content-disposition; bh=QoXz0G8NOkgm4EMpnGaKcE4JtCJaCF465Gpfi/Vsimo=; b=OqCygYjoYBSmUGy4dJi+SbSZpzIBCE2OGMx5abTXbuNAAM364Gsn8uRIVIuP/I8fVW gPA3z/GJMz6Y361y/3G9Lg3J+TPsMuBZS4OJGhXQVzSIHdCOWBurJiYeDn9ZHoO+qC1/ WEKVZ8Ul6b/oFh8Nztrfw0ZVAAuiA1F2V7u8/nl7VZ0xG33MHOTvXyAbq6WZh3CcjxGb dGfYHtJQJVkqvBc7YTlGnkeh/9pd4euNMPXtPvZPidoTeE7tdwHpFt1StrHsUNulJkXh 5WWhslqU4oaUMeWj4UvicVmW9fEx5CnEri8hUG4yxgyTVQEfbpZc974nDgtjd7cjy8YG aW2A== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20161025; h=x-gm-message-state:date:from:to:subject:message-id:mime-version :content-disposition; bh=QoXz0G8NOkgm4EMpnGaKcE4JtCJaCF465Gpfi/Vsimo=; b=mFp99ggZ3XnDe1pMcYkuTOUKAFQjWiMw81JlZi+KyM+Vu1fQtGP3TuO11TTZMkSIZ6 uDxjkK2kuBDuIw4jvxu127SO+3/PhjoSTC8RrsXcakJG6iBwRfv0cQugVvm95YtWhG2R f0mLeEzyYMBXN6+6dinaI4KnX7ECHzePj5PA44+Ul2HKTkNh5Ve/DTL19yo2Cj0C1Aj2 6qu6U+fVWmPJ4+C5vpc4cer5PaCQ/BYzDEWDZvbKH0vXPh9fnxjXxce6JYQGWsXQc0mM s3ESf6BCKMESEEa3D15CH6m7lvW+omRLkLPQ49zLQTDR3HY0RMnAmaltVOi7jxttVj/h e+JA== X-Gm-Message-State: AOAM533AIgns2NCVpz7y+ftTZ/GQYE5aF0p8dNdZqwNThnY1qermivuG sdegrOOAlhE6yBbZZPYIavVdxBcVpekD92P6qgNFv3TpkT3EPC4nU3yeMpzr6hlHd9ih5iJVDnp 3vfOT/WDmXMystVaT+NeRH2lBqsnNoeD+BrQrW7gWxGqZoe814SzMTdOXDhFjpgEf0tEoAW+4aG So8GFYxh5qSQ== X-Google-Smtp-Source: ABdhPJwQd4DSl9naYs1OLZuKpfm6ymmGGERH4hPYcrNSOGH8BAm8hlweElKzRH/hlWa7ftreme1yLw== X-Received: by 2002:a7b:c201:: with SMTP id x1mr15117324wmi.42.1605532543759; Mon, 16 Nov 2020 05:15:43 -0800 (PST) Received: from localhost (dynamic-2a01-0c23-781e-d800-dd9e-4e10-f08b-7920.c23.pool.telefonica.de. [2a01:c23:781e:d800:dd9e:4e10:f08b:7920]) by smtp.gmail.com with ESMTPSA id i10sm22881655wrs.22.2020.11.16.05.15.41 for (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Mon, 16 Nov 2020 05:15:41 -0800 (PST) Date: Mon, 16 Nov 2020 14:15:40 +0100 From: Lars-Dominik Braun Message-ID: <20201116131540.GB4512@zpidnp36> MIME-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha512; protocol="application/pgp-signature"; boundary="KDt/GgjP6HVcx58l" Content-Disposition: inline Received-SPF: none client-ip=2a00:1450:4864:20::329; envelope-from=ldb@leibniz-psychology.org; helo=mail-wm1-x329.google.com X-detected-operating-system: by eggs.gnu.org: No matching host in p0f cache. That's all we know. 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Desc= riptions have been edited slightly. Cheers, Lars --=20 Lars-Dominik Braun Wissenschaftlicher Mitarbeiter/Research Associate www.leibniz-psychology.org ZPID - Leibniz-Institut f=C3=BCr Psychologie / ZPID - Leibniz Institute for Psychology Universit=C3=A4tsring 15 D-54296 Trier - Germany Tel.: +49=E2=80=93651=E2=80=93201-4964 --SkvwRMAIpAhPCcCJ Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="0001-gnu-Add-r-prereg.patch" Content-Transfer-Encoding: quoted-printable =46rom 90f282cc5a9fb369cbb650f847917ccf956e8276 Mon Sep 17 00:00:00 2001 =46rom: Lars-Dominik Braun Date: Mon, 16 Nov 2020 12:56:25 +0100 Subject: [PATCH 1/9] gnu: Add r-prereg. * gnu/packages/cran.scm (r-prereg): 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 64e139c243..eb8ce230d4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24657,3 +24657,26 @@ orthogonal coordinate systems: cartesian, polar, s= pherical, cylindrical, parabolic or user defined by custom scale factors.") (license license:gpl3))) =20 +(define-public r-prereg + (package + (name "r-prereg") + (version "0.4.0") + (source + (origin + (method url-fetch) + (uri (cran-uri "prereg" version)) + (sha256 + (base32 + "1jhlgp7ajq6mx7gn4kf3b7wqzs3v0678pa1r6p4mgvvynic8rnqj")))) + (properties `((upstream-name . "prereg"))) + (build-system r-build-system) + (propagated-inputs + `(("r-rmarkdown" ,r-rmarkdown))) + (home-page "https://github.com/crsh/prereg") + (synopsis + "R Markdown Templates to Preregister Scientific Studies") + (description + "This package provides a collection of templates to author +preregistration documents for scientific studies in PDF format.") + (license license:gpl3))) + --=20 2.25.1 --SkvwRMAIpAhPCcCJ Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="0002-gnu-Add-r-metafor.patch" Content-Transfer-Encoding: quoted-printable =46rom 87219fced97d6359ac43017804347e79b3d2b0d1 Mon Sep 17 00:00:00 2001 =46rom: Lars-Dominik Braun Date: Mon, 16 Nov 2020 12:58:22 +0100 Subject: [PATCH 2/9] gnu: Add r-metafor. * gnu/packages/cran.scm (r-metafor): New variable. --- gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index eb8ce230d4..59f018c123 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24680,3 +24680,40 @@ parabolic or user defined by custom scale factors.= ") preregistration documents for scientific studies in PDF format.") (license license:gpl3))) =20 +(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 binomia= l 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 packa= ge +provides functionality for fitting meta-analytic multivariate/multilevel m= odels +that account for non-independent sampling errors and/or true effects (e.g.= , due +to the inclusion of multiple treatment studies, multiple endpoints, or oth= er +forms of clustering). Network meta-analyses and meta-analyses accounting = for +known correlation structures (e.g., due to phylogenetic relatedness) can a= lso +be conducted.") + (license license:gpl2+))) + --=20 2.25.1 --SkvwRMAIpAhPCcCJ Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="0003-gnu-Add-r-ez.patch" Content-Transfer-Encoding: quoted-printable =46rom 0b52713d2c0d9ea38c8d4120ec0a719949064e56 Mon Sep 17 00:00:00 2001 =46rom: Lars-Dominik Braun Date: Mon, 16 Nov 2020 12:58:47 +0100 Subject: [PATCH 3/9] gnu: Add r-ez. * gnu/packages/cran.scm (r-ez): New variable. --- gnu/packages/cran.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 59f018c123..602eec8250 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24717,3 +24717,43 @@ known correlation structures (e.g., due to phyloge= netic relatedness) can also be conducted.") (license license:gpl2+))) =20 +(define-public r-ez + (package + (name "r-ez") + (version "4.4-0") + (source + (origin + (method url-fetch) + (uri (cran-uri "ez" version)) + (sha256 + (base32 + "0a58s94x576dfz7wcbivrr2hmdh5x1vy16zwkqp9fmdzqx38pagq")))) + (properties `((upstream-name . "ez"))) + (build-system r-build-system) + (propagated-inputs + `(("r-car" ,r-car) + ("r-ggplot2" ,r-ggplot2) + ("r-lme4" ,r-lme4) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-mgcv" ,r-mgcv) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr))) + (home-page "https://github.com/mike-lawrence/ez") + (synopsis "Easy Analysis and Visualization of Factorial Experiments") + (description + "Facilitates easy analysis of factorial experiments, including purely +within-Ss designs (a.k.a. \"repeated measures\"), purely between-Ss design= s, +and mixed within-and-between-Ss designs. The functions in this package ai= m to +provide simple, intuitive and consistent specification of data analysis and +visualization. Visualization functions also include design visualization = for +pre-analysis data auditing, and correlation matrix visualization. Finally, +this package includes functions for non-parametric analysis, including +permutation tests and bootstrap resampling. The bootstrap function obtains +predictions either by cell means or by more advanced/powerful mixed effects +models, yielding predictions and confidence intervals that may be easily +visualized at any level of the experiment's design.") + (license license:gpl2+))) + --=20 2.25.1 --SkvwRMAIpAhPCcCJ Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="0004-gnu-Add-r-quantpsyc.patch" Content-Transfer-Encoding: quoted-printable =46rom f7c09f739c894b5e3894eab5f3c832d37cec3ad6 Mon Sep 17 00:00:00 2001 =46rom: Lars-Dominik Braun Date: Mon, 16 Nov 2020 12:59:26 +0100 Subject: [PATCH 4/9] gnu: Add r-quantpsyc. * gnu/packages/cran.scm (r-quantpsyc): New variable. --- gnu/packages/cran.scm | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 602eec8250..4e4c6623e4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24757,3 +24757,25 @@ models, yielding predictions and confidence interv= als that may be easily visualized at any level of the experiment's design.") (license license:gpl2+))) =20 +(define-public r-quantpsyc + (package + (name "r-quantpsyc") + (version "1.5") + (source + (origin + (method url-fetch) + (uri (cran-uri "QuantPsyc" version)) + (sha256 + (base32 + "1i9bh88r8zxndzjqsj14qw64gnvm5a9kvhjhzk3qsrvl3qzjgh93")))) + (properties `((upstream-name . "QuantPsyc"))) + (build-system r-build-system) + (propagated-inputs + `(("r-boot" ,r-boot) ("r-mass" ,r-mass))) + (home-page "https://cran.r-project.org/web/packages/QuantPsyc/") + (synopsis "Quantitative Psychology Tools") + (description + "Contains functions useful for data screening, testing moderation, +mediation and estimating power.") + (license license:gpl2+))) + --=20 2.25.1 --SkvwRMAIpAhPCcCJ Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="0005-gnu-Add-r-visnetwork.patch" Content-Transfer-Encoding: quoted-printable =46rom 00938f70c0e0dcf5303c7eb102e1b7e46813df23 Mon Sep 17 00:00:00 2001 =46rom: Lars-Dominik Braun Date: Mon, 16 Nov 2020 13:00:06 +0100 Subject: [PATCH 5/9] gnu: Add r-visnetwork. * gnu/packages/cran.scm (r-visnetwork): New variable. --- gnu/packages/cran.scm | 26 ++++++++++++++++++++++++++ 1 file changed, 26 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4e4c6623e4..7b6338df0f 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24779,3 +24779,29 @@ visualized at any level of the experiment's design= =2E") mediation and estimating power.") (license license:gpl2+))) =20 +(define-public r-visnetwork + (package + (name "r-visnetwork") + (version "2.0.9") + (source + (origin + (method url-fetch) + (uri (cran-uri "visNetwork" version)) + (sha256 + (base32 + "0854r9znpjd9iy6j5bgrn20vj13dhp606gs3b6iy0rhym71ks2sy")))) + (properties `((upstream-name . "visNetwork"))) + (build-system r-build-system) + (propagated-inputs + `(("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-jsonlite" ,r-jsonlite) + ("r-magrittr" ,r-magrittr))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "http://datastorm-open.github.io/visNetwork/") + (synopsis "Network Visualization using vis.js Library") + (description + "This package provides an R interface to the vis.js JavaScript chart= ing +library. It allows an interactive visualization of networks.") + (license license:expat))) + --=20 2.25.1 --SkvwRMAIpAhPCcCJ Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="0006-gnu-Add-r-diagrammer.patch" Content-Transfer-Encoding: quoted-printable =46rom ecf9923d276b2a5e2889c1bab049fe6ffbf01957 Mon Sep 17 00:00:00 2001 =46rom: Lars-Dominik Braun Date: Mon, 16 Nov 2020 13:01:13 +0100 Subject: [PATCH 6/9] gnu: Add r-diagrammer. * gnu/packages/cran.scm (r-diagrammer): New variable. --- gnu/packages/cran.scm | 45 +++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 45 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 7b6338df0f..e567cc8c2b 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24805,3 +24805,48 @@ mediation and estimating power.") library. It allows an interactive visualization of networks.") (license license:expat))) =20 +(define-public r-diagrammer + (package + (name "r-diagrammer") + (version "1.0.6.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "DiagrammeR" version)) + (sha256 + (base32 + "0gb7ccdrh7jlyqafdk8zs465ygczxxd25s05whn914in1994qkmy")))) + (properties `((upstream-name . "DiagrammeR"))) + (build-system r-build-system) + (propagated-inputs + `(("r-downloader" ,r-downloader) + ("r-dplyr" ,r-dplyr) + ("r-glue" ,r-glue) + ("r-htmltools" ,r-htmltools) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-igraph" ,r-igraph) + ("r-influencer" ,r-influencer) + ("r-magrittr" ,r-magrittr) + ("r-purrr" ,r-purrr) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-readr" ,r-readr) + ("r-rlang" ,r-rlang) + ("r-rstudioapi" ,r-rstudioapi) + ("r-scales" ,r-scales) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-viridis" ,r-viridis) + ("r-visnetwork" ,r-visnetwork))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/rich-iannone/DiagrammeR") + (synopsis "Graph/Network Visualization") + (description + "Build graph/network structures using functions for stepwise addition +and deletion of nodes and edges. Work with data available in tables for b= ulk +addition of nodes, edges, and associated metadata. Use graph selections a= nd +traversals to apply changes to specific nodes or edges. A wide selection = of +graph algorithms allow for the analysis of graphs. Visualize the graphs a= nd +take advantage of any aesthetic properties assigned to nodes and edges.") + (license license:expat))) + --=20 2.25.1 --SkvwRMAIpAhPCcCJ Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="0007-gnu-Add-r-lavaanplot.patch" Content-Transfer-Encoding: quoted-printable =46rom 6bf8cfb004441ae75e2ca93075ae7a1d0a9799aa Mon Sep 17 00:00:00 2001 =46rom: Lars-Dominik Braun Date: Mon, 16 Nov 2020 13:01:50 +0100 Subject: [PATCH 7/9] gnu: Add r-lavaanplot. * gnu/packages/cran.scm (r-lavaanplot): New variable. --- gnu/packages/cran.scm | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index e567cc8c2b..4a7c1535f4 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24850,3 +24850,31 @@ graph algorithms allow for the analysis of graphs.= Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.") (license license:expat))) =20 +(define-public r-lavaanplot + (package + (name "r-lavaanplot") + (version "0.5.1") + (source + (origin + (method url-fetch) + (uri (cran-uri "lavaanPlot" version)) + (sha256 + (base32 + "01bx1snd3zhc8dmq0f407qhw2d00f6d38qpr791qc1mq5kr3d8qj")))) + (properties `((upstream-name . "lavaanPlot"))) + (build-system r-build-system) + (propagated-inputs + `(("r-diagrammer" ,r-diagrammer) + ("r-lavaan" ,r-lavaan) + ("r-stringr" ,r-stringr))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/alishinski/lavaanPlot") + (synopsis "Path Diagrams for Lavaan Models via DiagrammeR") + (description + "Plots path diagrams from models in lavaan using the plotting +functionality from the DiagrammeR package. DiagrammeR provides nice path +diagrams via Graphviz, and these functions make it easy to generate these +diagrams from a lavaan path model without having to write the DOT language +graph specification.") + (license license:gpl2+))) + --=20 2.25.1 --SkvwRMAIpAhPCcCJ Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="0008-gnu-Add-r-clubsandwich.patch" Content-Transfer-Encoding: quoted-printable =46rom 3312c0c3754f62222dfe67733f8610aa6e7d687a Mon Sep 17 00:00:00 2001 =46rom: Lars-Dominik Braun Date: Mon, 16 Nov 2020 13:02:28 +0100 Subject: [PATCH 8/9] gnu: Add r-clubsandwich. * gnu/packages/cran.scm (r-clubsandwich): New variable. --- gnu/packages/cran.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 4a7c1535f4..0caff23582 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24878,3 +24878,36 @@ diagrams from a lavaan path model without having t= o write the DOT language graph specification.") (license license:gpl2+))) =20 +(define-public r-clubsandwich + (package + (name "r-clubsandwich") + (version "0.3.2") + (source + (origin + (method url-fetch) + (uri (cran-uri "clubSandwich" version)) + (sha256 + (base32 + "1q4kidxcarlazh9zaav6vdc7ixb3hdg3zh5kr6mwkm087gi05nw5")))) + (properties `((upstream-name . "clubSandwich"))) + (build-system r-build-system) + (propagated-inputs + `(("r-sandwich" ,r-sandwich))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/jepusto/clubSandwich") + (synopsis "Cluster-Robust (Sandwich) Variance Estimators with Small-Sa= mple +Corrections") + (description + "Provides several cluster-robust variance estimators (i.e., sandwich +estimators) for ordinary and weighted least squares linear regression mode= ls, +including the bias-reduced linearization estimator introduced by +@url{http://www.statcan.gc.ca/pub/12-001-x/2002002/article/9058-eng.pdf, B= ell +and McCaffrey (2002)} and developed further by +@url{DOI:10.1080/07350015.2016.1247004, Pustejovsky and Tipton (2017)}. T= he +package includes functions for estimating the variance- covariance matrix = and +for testing single- and multiple- contrast hypotheses based on Wald test +statistics. Tests of single regression coefficients use Satterthwaite or +saddle-point corrections. Tests of multiple- contrast hypotheses use an +approximation to Hotelling's T-squared distribution.") + (license license:gpl3))) + --=20 2.25.1 --SkvwRMAIpAhPCcCJ Content-Type: text/x-diff; charset=us-ascii Content-Disposition: attachment; filename="0009-gnu-Add-r-puniform.patch" Content-Transfer-Encoding: quoted-printable =46rom dd2095db08802c6481903466b58866b2e987eb60 Mon Sep 17 00:00:00 2001 =46rom: Lars-Dominik Braun Date: Mon, 16 Nov 2020 13:03:16 +0100 Subject: [PATCH 9/9] gnu: Add r-puniform. * gnu/packages/cran.scm (r-puniform): New variable. --- gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 0caff23582..caf8cfbfc1 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -24911,3 +24911,37 @@ saddle-point corrections. Tests of multiple- cont= rast hypotheses use an approximation to Hotelling's T-squared distribution.") (license license:gpl3))) =20 +(define-public r-puniform + (package + (name "r-puniform") + (version "0.2.3") + (source + (origin + (method url-fetch) + (uri (cran-uri "puniform" version)) + (sha256 + (base32 + "1y47y6s76pjvp10m8rvdh7y1iidjw96a4wrr920w0js3rn4fi1fz")))) + (properties `((upstream-name . "puniform"))) + (build-system r-build-system) + (propagated-inputs + `(("r-adgoftest" ,r-adgoftest) + ("r-metafor" ,r-metafor) + ("r-rcpp" ,r-rcpp) + ("r-rcpparmadillo" ,r-rcpparmadillo))) + (home-page + "https://cran.r-project.org/web/packages/puniform") + (synopsis + "Meta-Analysis Methods Correcting for Publication Bias") + (description + "This package provides meta-analysis methods that correct for publica= tion +bias and outcome reporting bias. Four methods and a visual tool are curre= ntly +included in the package. The p-uniform method as described in +@url{doi:10.1037/met0000025, van Assen and and van Aert and Wicherts (2015= )}, +the p-uniform* method as described in @url{doi:10.31222/osf.io/zqjr9, van = Aert +and van Assen (2019)}, the hybrid method as described in +@url{doi:10.3758/s13428-017-0967-6, van Aert and van Assen (2017)} and the +Snapshot Bayesian Hybrid Meta-Analysis Method as described in +@url{doi:10.1371/journal.pone.0175302, van Aert and van Assen (2018)}.") + (license license:gpl2+))) + --=20 2.25.1 --SkvwRMAIpAhPCcCJ-- --KDt/GgjP6HVcx58l Content-Type: application/pgp-signature; name="signature.asc" -----BEGIN PGP SIGNATURE----- iQGzBAABCgAdFiEEyk+M9DfXR4/aBV/UQhN3ARo3hEYFAl+ye3kACgkQQhN3ARo3 hEbUoQwAp8mpeA311sTdeFEd6BDbqoXEoXj9G3S8fUTOEarvcEt+wEJly4AP/GXG Kbqu7Et0aNCYRdPHpMdzvgaovImLZGoWGqHZVaEynKzXoXFZYjSXHLsCTChwQcl7 vGseeKf1nCmq1N4C1BRB5ZaCVpbUko76rOncsv4VFvP5tZmWTp4e6GQBWZuXH7qE Lc5GwNP0rVF5HFBJaGsHg5zjU6LCdWIL+qwrwEMSoroPmEA36iGbBgljVzgjBOMM 5xWiP3dPN0rSUzwubg6PPAKkdImR+PtOZK6/sF6RULpWwBOhmoW6URXtOOx1l+Q/ jG3IzMOsTR7+H4c7bMibmlvT9VppQr5yJyIaem4UbkbIUwIjgUAN0+/cuHH8QmtI 6tCW9U9F0wcCoPmhDmQzMWAfF/QlhJHpgoxgqHoJwDmfrzNQDB3AFrVtmKc3fWKU WPonNcYIeipilRwmn5w+nZYOO1/TRyhvNybAvBIs+0JfZ6DxACEvwTgtAJ5tGvxk xGHpUFV4 =du0z -----END PGP SIGNATURE----- --KDt/GgjP6HVcx58l--