From patchwork Thu Jun 16 15:57:19 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 40049 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 9685027BBEB; Thu, 16 Jun 2022 16:58:16 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 999F027BBE9 for ; Thu, 16 Jun 2022 16:58:15 +0100 (BST) Received: from localhost ([::1]:51608 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1o1rss-0002RV-P4 for patchwork@mira.cbaines.net; Thu, 16 Jun 2022 11:58:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:34472) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o1rsh-0002Q8-Du for guix-patches@gnu.org; Thu, 16 Jun 2022 11:58:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:49051) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1o1rsh-0004zp-5g for guix-patches@gnu.org; Thu, 16 Jun 2022 11:58:03 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1o1rsh-0000jC-4d for guix-patches@gnu.org; Thu, 16 Jun 2022 11:58:03 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56021] [PATCH 1/3] gnu: Add r-nada. References: In-Reply-To: Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 16 Jun 2022 15:58:03 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56021 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <56021@debbugs.gnu.org> Received: via spool by 56021-submit@debbugs.gnu.org id=B56021.16553950702756 (code B ref 56021); Thu, 16 Jun 2022 15:58:03 +0000 Received: (at 56021) by debbugs.gnu.org; 16 Jun 2022 15:57:50 +0000 Received: from localhost ([127.0.0.1]:42946 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1rsU-0000iM-2d for submit@debbugs.gnu.org; Thu, 16 Jun 2022 11:57:50 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:47613) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1rsN-0000hZ-8J for 56021@debbugs.gnu.org; Thu, 16 Jun 2022 11:57:46 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 0B7201602F1 for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:37 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :x-mailer:message-id:date:date:subject:subject:from:from :received:received:received; s=mdc; t=1655395056; x=1657209457; bh=Pw86DTXd5xzY7VH2w9KDPxPsiHX6HuaIqAW5VtVHce4=; b=m9n+qP2uF3vk aVx6Wtnqc7fDI5moDlANWOI7iW/D52Z2A/FPzSDlIQDbcOenUrvsdbKrot8LFvIp 7o5z8WMerN6aXslx4fSSeBPHaAtkyY2h464Hvlf/SHvZcPSSdBOcI4dr8LM/JsFq HemA92fnvni8BBYGYe2fBKQeswQUh3M= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id bjNRsQytbZwk for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:36 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:36 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.9; Thu, 16 Jun 2022 17:57:35 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 16 Jun 2022 17:57:19 +0200 Message-ID: <20220616155721.23547-1-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26958.007 X-TM-AS-Result: No-10--4.704400-5.000000 X-TMASE-MatchedRID: /+von0vPuFH/R1NSMc2qCU7nLUqYrlslFIuBIWrdOePfUZT83lbkEGhf Cbk4OLdme9miqIT5hkfuNT8xdcEnQwE+dA3RWUSvwLYk+NSxc5r4qCLIu0mtIP+aPQT1cxlGqbs +nJ/tFJGGsZX0q3FpiOhAZQXEXXZuLJutez2dKWfi8zVgXoAltuJ5hXsnxp7jC24oEZ6SpSk6XE E7Yhw4Fnu0HBZjeylwSobWRQohS+njgcCxJmpzgqD2LWxmuihunY0d9Ww/8uvNrYsjt5omHfJfu AXJyiQ6a6jGHtmLVl8mmWGFLZYZI98iatREjfpDE8nb9DwdQ4C2jbSab1pg0UjxFpwn53SOfhj5 CZkmSyI= X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.704400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26958.007 X-TM-SNTS-SMTP: FC81E3582F3EF159CBD153215D57204D4554CC824A7F4895F1BBE65CBD7DCFC22002:F X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-nada): New variable. --- gnu/packages/cran.scm | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) base-commit: ef2d908e22f9d4f4a89782766b67d425935ae4eb diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index b326332bf6..28cd2e7fad 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -27881,6 +27881,26 @@ (define-public r-nabor to speed up repeated queries of the same set of target points.") (license license:bsd-3))) +(define-public r-nada + (package + (name "r-nada") + (version "1.6-1.1") + (source (origin + (method url-fetch) + (uri (cran-uri "NADA" version)) + (sha256 + (base32 + "0jp4mqr77cx7q5lff84s6wb0dwjy9mi0jyhbjc5fsx50bdczc3v7")))) + (properties `((upstream-name . "NADA"))) + (build-system r-build-system) + (propagated-inputs (list r-survival)) + (home-page "https://cran.r-project.org/package=NADA") + (synopsis "Nondetects and data analysis for environmental data") + (description + "This package contains methods described by Dennis Helsel in his book +@emph{Nondetects and Data Analysis: Statistics for Censored Environmental Data}.") + (license license:gpl2+))) + (define-public r-naturalsort (package (name "r-naturalsort") From patchwork Thu Jun 16 15:57:20 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 40050 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id CFA5A27BBE9; Thu, 16 Jun 2022 16:58:16 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id BB7B427BBEA for ; Thu, 16 Jun 2022 16:58:15 +0100 (BST) Received: from localhost ([::1]:51674 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1o1rss-0002UU-RM for patchwork@mira.cbaines.net; Thu, 16 Jun 2022 11:58:14 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:34464) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o1rsg-0002Pr-L4 for guix-patches@gnu.org; Thu, 16 Jun 2022 11:58:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:49049) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1o1rsg-0004zU-CV for guix-patches@gnu.org; Thu, 16 Jun 2022 11:58:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1o1rsg-0000iy-BV for guix-patches@gnu.org; Thu, 16 Jun 2022 11:58:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56021] [PATCH 2/3] gnu: Add r-zcompositions. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 16 Jun 2022 15:58:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56021 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <56021@debbugs.gnu.org> Received: via spool by 56021-submit@debbugs.gnu.org id=B56021.16553950662736 (code B ref 56021); Thu, 16 Jun 2022 15:58:02 +0000 Received: (at 56021) by debbugs.gnu.org; 16 Jun 2022 15:57:46 +0000 Received: from localhost ([127.0.0.1]:42942 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1rsQ-0000hx-AR for submit@debbugs.gnu.org; Thu, 16 Jun 2022 11:57:46 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:59007) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1rsN-0000hc-8m for 56021@debbugs.gnu.org; Thu, 16 Jun 2022 11:57:45 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id CE8511602FD for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:37 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received:received:received; s=mdc; t= 1655395057; x=1657209458; bh=BvftzInu5hDYcaR81+RjCREzBuFoRzW3Xn0 nDyf+24w=; b=qoV+IovVlKJR1XtYGdwvO0YX9W7fPsIFANCIKwxFmxR4DYIJTJp jOxHWdkeR1RHDF1voZXsmS+L8TgRu5p7GnRsRfMxM2aajfK004l2y0Iwlx7sOTTZ lk5uR1QsnV2s7350dRfIFmW7mLIOB1xMRk7+vm7hGvl0FDcqeNGiDq+U= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id zkSzD8QrEAZP for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:37 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:37 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.9; Thu, 16 Jun 2022 17:57:35 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 16 Jun 2022 17:57:20 +0200 Message-ID: <20220616155721.23547-2-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20220616155721.23547-1-madalinionel.patrascu@mdc-berlin.de> References: <20220616155721.23547-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26958.007 X-TM-AS-Result: No-10--4.214400-5.000000 X-TMASE-MatchedRID: 4RK2gbhxGJP/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6pyd7XCgr5tcSwak5eNXy+6Y5ZGw7wyeHPNh MoIUJiCIZjraH8rGmfVQgiThZnRmDjh6UpEWMa1LgyusN8bViiBDkv2q7d+VDlwV2iaAfSWcURS Scn+QSXt0H8LFZNFG7doMssNsUwYVGoOsFd1OizS5YZOEMBUBsgyXgFJqS2qvWhgZjALNnHs+g+ Ga4BAcMC3UIZvv8PwNS9gbaHiYkmsZ/upop1w2NCNXjWCKcB47HpeHdXLjLb473WzsXAufzELZr sYgA6obyh3JNelCjdRkfAFx3Dn4y X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--4.214400-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26958.007 X-TM-SNTS-SMTP: C0445BFDDCBD4CA1AAF56E50644471B8E7576035BCFB0DB0EBB3ADD3B42D2CA22002:F X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/cran.scm (r-zcompositions): New variable. --- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 28cd2e7fad..945cb5bdce 100644 --- a/gnu/packages/cran.scm +++ b/gnu/packages/cran.scm @@ -836,6 +836,37 @@ (define-public r-dlm known as Dynamic Linear Models.") (license license:gpl2+))) +(define-public r-zcompositions + (package + (name "r-zcompositions") + (version "1.4.0-1") + (source (origin + (method url-fetch) + (uri (cran-uri "zCompositions" version)) + (sha256 + (base32 + "1rrhja9iaq123r2gqw1bzrn1ri0s3z4wzq8p0sfcr1yb6pv13vik")))) + (properties `((upstream-name . "zCompositions"))) + (build-system r-build-system) + (propagated-inputs + (list r-mass + r-nada + r-truncnorm)) + (home-page "https://github.com/Japal/zCompositions") + (synopsis + "Treatment of zeros, left-censored and missing values in compositional data") + (description + "This package @code{zCompositions} is an @code{R} package for the imputation +of left-censored data under a compositional approach. The implemented methods +consider aspects of relevance for a compositional approach such as scale +invariance, subcompositional coherence or preserving the multivariate relative +structure of the data. Based on solid statistical frameworks, it comprises the +ability to deal with single and varying censoring thresholds, consistent treatment +of closed and non-closed data, exploratory tools, multiple imputation, @dfn{MCMC} +(Markov Chain Monte Carlo), robust and non-parametric alternatives, and recent +proposals for count data.") + (license license:gpl2+))) + (define-public r-zoo (package (name "r-zoo") From patchwork Thu Jun 16 15:57:21 2022 Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit X-Patchwork-Submitter: =?utf-8?b?TcSDZMSDbGluIElvbmVsIFBhdHJhyJljdQ==?= X-Patchwork-Id: 40048 Return-Path: X-Original-To: patchwork@mira.cbaines.net Delivered-To: patchwork@mira.cbaines.net Received: by mira.cbaines.net (Postfix, from userid 113) id 2BEB727BBEA; Thu, 16 Jun 2022 16:58:15 +0100 (BST) X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on mira.cbaines.net X-Spam-Level: X-Spam-Status: No, score=-3.7 required=5.0 tests=BAYES_00,DKIM_INVALID, DKIM_SIGNED,MAILING_LIST_MULTI,RCVD_IN_MSPIKE_H2,SPF_HELO_PASS, URIBL_BLOCKED autolearn=unavailable autolearn_force=no version=3.4.6 Received: from lists.gnu.org (lists.gnu.org [209.51.188.17]) by mira.cbaines.net (Postfix) with ESMTPS id 72BEA27BBE9 for ; Thu, 16 Jun 2022 16:58:14 +0100 (BST) Received: from localhost ([::1]:51584 helo=lists1p.gnu.org) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1o1rsr-0002QW-JH for patchwork@mira.cbaines.net; Thu, 16 Jun 2022 11:58:13 -0400 Received: from eggs.gnu.org ([2001:470:142:3::10]:34466) by lists.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_256_GCM_SHA384:256) (Exim 4.90_1) (envelope-from ) id 1o1rsh-0002Q0-0i for guix-patches@gnu.org; Thu, 16 Jun 2022 11:58:03 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:49050) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1o1rsg-0004za-Ov for guix-patches@gnu.org; Thu, 16 Jun 2022 11:58:02 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1o1rsg-0000j5-OL for guix-patches@gnu.org; Thu, 16 Jun 2022 11:58:02 -0400 X-Loop: help-debbugs@gnu.org Subject: [bug#56021] [PATCH 3/3] gnu: Add r-aldex2. Resent-From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Original-Sender: "Debbugs-submit" Resent-CC: guix-patches@gnu.org Resent-Date: Thu, 16 Jun 2022 15:58:02 +0000 Resent-Message-ID: Resent-Sender: help-debbugs@gnu.org X-GNU-PR-Message: followup 56021 X-GNU-PR-Package: guix-patches X-GNU-PR-Keywords: To: <56021@debbugs.gnu.org> Received: via spool by 56021-submit@debbugs.gnu.org id=B56021.16553950672742 (code B ref 56021); Thu, 16 Jun 2022 15:58:02 +0000 Received: (at 56021) by debbugs.gnu.org; 16 Jun 2022 15:57:47 +0000 Received: from localhost ([127.0.0.1]:42944 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1rsQ-0000i5-Nf for submit@debbugs.gnu.org; Thu, 16 Jun 2022 11:57:47 -0400 Received: from b2062.mx.srv.dfn.de ([194.95.234.172]:50129) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1o1rsO-0000hf-0M for 56021@debbugs.gnu.org; Thu, 16 Jun 2022 11:57:45 -0400 Received: from localhost (localhost [127.0.0.1]) by b2062.mx.srv.dfn.de (Postfix) with ESMTP id 8E660160304 for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:38 +0200 (CEST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=mdc-berlin.de; h= content-type:content-type:content-transfer-encoding:mime-version :references:in-reply-to:x-mailer:message-id:date:date:subject :subject:from:from:received:received:received; s=mdc; t= 1655395057; x=1657209458; bh=GZFt1MbwOPSpPLHyHaawaKjcLCYO5JVrlyL G90SjITA=; b=PfUVJ09q/EzVXLTTFhBwqBnp38eWY8XROVgYHmVuNdMtOtJXsDg ZcwalEzYa7MH84JRVpCmesG8Qgr78yIbQUniXU/kecr3+oHYyDHmQxfwUPxvMZYN 7A5LsZw2mQzqhkxr1ztWjh2VF7zm+q7Rqufnzl1ZjuMQfVGSSXYZLXkQ= Received: from b2062.mx.srv.dfn.de ([127.0.0.1]) by localhost (mgw4-tub.srv.dfn.de [127.0.0.1]) (amavisd-new, port 20134) with ESMTP id wf9LdgFI3d0x for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:37 +0200 (CEST) Received: from SW-IT-P-EX4.mdc-berlin.net (mgw4.mdc-berlin.de [141.80.113.62]) by b2062.mx.srv.dfn.de (Postfix) with ESMTPS for <56021@debbugs.gnu.org>; Thu, 16 Jun 2022 17:57:37 +0200 (CEST) Received: from Guix-Ubuntu18.04 (141.80.113.106) by SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) with Microsoft SMTP Server (version=TLS1_2, cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.1.2507.9; Thu, 16 Jun 2022 17:57:35 +0200 From: =?utf-8?b?TcSDZMSDbGlu?= Ionel =?utf-8?b?UGF0cmHImWN1?= Date: Thu, 16 Jun 2022 17:57:21 +0200 Message-ID: <20220616155721.23547-3-madalinionel.patrascu@mdc-berlin.de> X-Mailer: git-send-email 2.36.1 In-Reply-To: <20220616155721.23547-1-madalinionel.patrascu@mdc-berlin.de> References: <20220616155721.23547-1-madalinionel.patrascu@mdc-berlin.de> MIME-Version: 1.0 X-Originating-IP: [141.80.113.106] X-ClientProxiedBy: SW-IT-P-EX3.mdc-berlin.net (141.80.113.61) To SW-IT-P-EX4.mdc-berlin.net (141.80.113.62) X-TM-AS-Product-Ver: SMEX-14.0.0.3092-9.0.1002-26958.007 X-TM-AS-Result: No-10--0.286500-5.000000 X-TMASE-MatchedRID: SzbEz7SZt2v/R1NSMc2qCU7nLUqYrlslFIuBIWrdOeOjEIt+uIPPOAbo TDS3zulAcjTcMkuJPYkZijt1cgK90C/33TWoSUH6194/5X9VfCxSHjB5Y+o5ZEyi1T9AUgUbsUh +OkaOhpfN57BJxyhEO3wBfyL06jKAmv0Xhs8HK808o3fwIs8rQQwMqNovfwOoaGL2D7wHkbXizy 75l6H5qX0tCKdnhB589yM15V5aWpj6C0ePs7A07ba607moR85RKzQhmWmrAKFISmIp7fCMIURQi Zjlai/4Yoani0CN60UElhXQWrfGQLdTLbLmr7KW7krrHdP6mXxDNMCPzHf5Y95nfdZUf8KIdAnz xkc/wOO+Yl/q6i1mnv1mO1iYLJDqT4cbBIKMuHq+68HqACCvKA== X-TM-AS-User-Approved-Sender: Yes X-TM-AS-User-Blocked-Sender: No X-TMASE-Result: 10--0.286500-5.000000 X-TMASE-Version: SMEX-14.0.0.3092-9.0.1002-26958.007 X-TM-SNTS-SMTP: 1388152BD02AA69B6028D12098BE6B695F2BEB632E64CD7B466FD7E57173F6D52002:F X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list X-BeenThere: guix-patches@gnu.org List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+patchwork=mira.cbaines.net@gnu.org Sender: "Guix-patches" X-getmail-retrieved-from-mailbox: Patches * gnu/packages/bioconductor.scm (r-aldex2): New variable. --- gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++ 1 file changed, 42 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 1e87b190c2..3abd57359d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1987,6 +1987,48 @@ (define-public r-agimicrorna objects are used so that other packages could be used as well.") (license license:gpl3))) +(define-public r-aldex2 + (package + (name "r-aldex2") + (version "1.28.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ALDEx2" version)) + (sha256 + (base32 + "0xppx52sllbz4pli174422i4kkf37v0yl844088nbj3j9r6pfbj9")))) + (properties `((upstream-name . "ALDEx2"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocparallel + r-genomicranges + r-iranges + r-multtest + r-rfast + r-s4vectors + r-summarizedexperiment + r-zcompositions)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/ggloor/ALDEx_bioc") + (synopsis + "Analysis Of differential abundance taking sample variation into account") + (description + "This package provides a differential abundance analysis for the comparison +of two or more conditions. Useful for analyzing data from standard RNA-seq or +meta-RNA-seq assays as well as selected and unselected values from in-vitro +sequence selections. Uses a Dirichlet-multinomial model to infer abundance from +counts, optimized for three or more experimental replicates. The method infers +biological and sampling variation to calculate the expected false discovery +rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test +(via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear +model (via aldex.glm), or a correlation test (via aldex.corr). All tests report +p-values and Benjamini-Hochberg corrected p-values. ALDEx2 also calculates +expected standardized effect sizes for paired or unpaired study designs.") + ;; The code for the function "rdirichlet" which is from the "R" package + ;; "mc2d_0.1-14.tar.gz", which is denoted as GPL>=2, and where the tar-ball + ;; LICENSE specifies GPL-3. + (license (list license:agpl3+ license:gpl2+ license:gpl3)))) + (define-public r-aneufinder (package (name "r-aneufinder")