GNU bug report logs - #42107
[PATCH] gnu: Add r-survminer and its dependencies

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Message #5 received at submit <at> debbugs.gnu.org (full text, mbox):

From: Lo Peter <peterloleungyau <at> gmail.com>
To: guix-patches <at> gnu.org
Subject: [PATCH] gnu: Add r-survminer and its dependencies
Date: Sun, 28 Jun 2020 17:28:02 +0800

Dear all,

I am submitting a patch series of r-survminer and its dependencies.

Regards,
Peter

Message #8 received at 42107 <at> debbugs.gnu.org (full text, mbox):

From: Peter Lo <peterloleungyau <at> gmail.com>
To: 42107 <at> debbugs.gnu.org
Cc: Peter Lo <peterloleungyau <at> gmail.com>
Subject: [PATCH 1/6] gnu: Add r-km-ci.
Date: Sun, 28 Jun 2020 17:29:39 +0800

* gnu/packages/cran.scm (r-km-ci): New variable.
---
 gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ab5e57c0e2..b054c62550 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22325,3 +22325,28 @@ across a wide array of bioinformatic R packages.")
 and clustering large sequence datasets using fast alignment-free k-mer
 counting and recursive k-means partitioning.")
     (license license:gpl3)))
+
+(define-public r-km-ci
+  (package
+    (name "r-km-ci")
+    (version "0.5-2")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "km.ci" version))
+        (sha256
+          (base32
+            "1l6kw8jppaa1802yc5pbfwwgac56nhwc9p076ivylhms4w7cdf8v"))))
+    (properties `((upstream-name . "km.ci")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-survival" ,r-survival)))
+    (home-page
+      "https://cran.r-project.org/web/packages/km.ci/")
+    (synopsis
+      "Confidence intervals for the Kaplan-Meier estimator")
+    (description
+      "Computes various confidence intervals for the Kaplan-Meier
+estimator, namely: Petos CI, Rothman CI, CI's based on Greenwoods
+variance, Thomas and Grunkemeier CI and the simultaneous confidence
+bands by Nair and Hall and Wellner.")
+    (license license:gpl2+)))
-- 
2.17.1

Message #11 received at 42107 <at> debbugs.gnu.org (full text, mbox):

From: Peter Lo <peterloleungyau <at> gmail.com>
To: 42107 <at> debbugs.gnu.org
Cc: Peter Lo <peterloleungyau <at> gmail.com>
Subject: [PATCH 2/6] gnu: Add r-kmsurv.
Date: Sun, 28 Jun 2020 17:29:40 +0800

* gnu/packages/cran.scm (r-kmsurv): 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 b054c62550..ceda3c57a3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22350,3 +22350,26 @@ estimator, namely: Petos CI, Rothman CI, CI's based on Greenwoods
 variance, Thomas and Grunkemeier CI and the simultaneous confidence
 bands by Nair and Hall and Wellner.")
     (license license:gpl2+)))
+
+(define-public r-kmsurv
+  (package
+    (name "r-kmsurv")
+    (version "0.1-5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "KMsurv" version))
+        (sha256
+          (base32
+            "0hi5vvk584rl70gbrr75w9hc775xmbxnaig0dd6hlpi4071pnqjm"))))
+    (properties `((upstream-name . "KMsurv")))
+    (build-system r-build-system)
+    (home-page
+      "https://cran.r-project.org/web/packages/KMsurv/")
+    (synopsis
+      "Data sets from Klein and Moeschberger (1997), Survival Analysis")
+    (description
+      "Data sets and functions for Klein and Moeschberger (1997),
+\"Survival Analysis, Techniques for Censored and Truncated Data\",
+Springer.")
+    (license license:gpl3+)))
-- 
2.17.1

Message #14 received at 42107 <at> debbugs.gnu.org (full text, mbox):

From: Peter Lo <peterloleungyau <at> gmail.com>
To: 42107 <at> debbugs.gnu.org
Cc: Peter Lo <peterloleungyau <at> gmail.com>
Subject: [PATCH 3/6] gnu: Add r-survmisc.
Date: Sun, 28 Jun 2020 17:29:41 +0800

* gnu/packages/cran.scm (r-survmisc): 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 ceda3c57a3..6ea06f259f 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22373,3 +22373,37 @@ bands by Nair and Hall and Wellner.")
 \"Survival Analysis, Techniques for Censored and Truncated Data\",
 Springer.")
     (license license:gpl3+)))
+
+(define-public r-survmisc
+  (package
+    (name "r-survmisc")
+    (version "0.5.5")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "survMisc" version))
+        (sha256
+          (base32
+            "00nvvl8gz4477ab24rd0xvfksm8msv8h021b9ld5c9cizc41n2bm"))))
+    (properties `((upstream-name . "survMisc")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-data-table" ,r-data-table)
+        ("r-ggplot2" ,r-ggplot2)
+        ("r-gridextra" ,r-gridextra)
+        ("r-km-ci" ,r-km-ci)
+        ("r-kmsurv" ,r-kmsurv)
+        ("r-knitr" ,r-knitr)
+        ("r-survival" ,r-survival)
+        ("r-xtable" ,r-xtable)
+        ("r-zoo" ,r-zoo)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page
+      "https://cran.r-project.org/web/packages/survMisc/")
+    (synopsis
+      "Miscellaneous Functions for Survival Data")
+    (description
+      "This package provides a collection of functions to help in the
+analysis of right-censored survival data.  These extend the methods
+available in package:survival.")
+    (license license:gpl2)))
-- 
2.17.1

Message #17 received at 42107 <at> debbugs.gnu.org (full text, mbox):

From: Peter Lo <peterloleungyau <at> gmail.com>
To: 42107 <at> debbugs.gnu.org
Cc: Peter Lo <peterloleungyau <at> gmail.com>
Subject: [PATCH 4/6] gnu: Add r-exactranktests.
Date: Sun, 28 Jun 2020 17:29:42 +0800

* gnu/packages/cran.scm (r-exactranktests): 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 6ea06f259f..3077b1e132 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22407,3 +22407,26 @@ Springer.")
 analysis of right-censored survival data.  These extend the methods
 available in package:survival.")
     (license license:gpl2)))
+
+(define-public r-exactranktests
+  (package
+    (name "r-exactranktests")
+    (version "0.8-31")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "exactRankTests" version))
+        (sha256
+          (base32
+            "1154dkcid3njhamdp87qs9bnx7l8bdqkcjsds9q9f2xmizs9x8gw"))))
+    (properties
+      `((upstream-name . "exactRankTests")))
+    (build-system r-build-system)
+    (home-page
+      "https://cran.r-project.org/web/packages/exactRankTests/")
+    (synopsis
+      "Exact Distributions for Rank and Permutation Tests")
+    (description
+      "Computes exact conditional p-values and quantiles using an
+implementation of the Shift-Algorithm by Streitberg & Roehmel.")
+    (license license:gpl2+)))
-- 
2.17.1

Message #20 received at 42107 <at> debbugs.gnu.org (full text, mbox):

From: Peter Lo <peterloleungyau <at> gmail.com>
To: 42107 <at> debbugs.gnu.org
Cc: Peter Lo <peterloleungyau <at> gmail.com>
Subject: [PATCH 5/6] gnu: Add r-maxstat.
Date: Sun, 28 Jun 2020 17:29:43 +0800

* gnu/packages/cran.scm (r-maxstat): New variable.
---
 gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 3077b1e132..f51e69689b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22430,3 +22430,27 @@ available in package:survival.")
       "Computes exact conditional p-values and quantiles using an
 implementation of the Shift-Algorithm by Streitberg & Roehmel.")
     (license license:gpl2+)))
+
+(define-public r-maxstat
+  (package
+    (name "r-maxstat")
+    (version "0.7-25")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "maxstat" version))
+        (sha256
+          (base32
+            "114z1rwxwvk05ijjhdppzm148n1h192fp0w12ky10zkrhf6kphbg"))))
+    (properties `((upstream-name . "maxstat")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-exactranktests" ,r-exactranktests)
+        ("r-mvtnorm" ,r-mvtnorm)))
+    (home-page
+      "https://cran.r-project.org/web/packages/maxstat/")
+    (synopsis "Maximally Selected Rank Statistics")
+    (description
+      "Maximally selected rank statistics with several p-value
+approximations.")
+    (license license:gpl2+)))
-- 
2.17.1

Message #23 received at 42107 <at> debbugs.gnu.org (full text, mbox):

From: Peter Lo <peterloleungyau <at> gmail.com>
To: 42107 <at> debbugs.gnu.org
Cc: Peter Lo <peterloleungyau <at> gmail.com>
Subject: [PATCH 6/6] gnu: Add r-survminer.
Date: Sun, 28 Jun 2020 17:29:44 +0800

* gnu/packages/cran.scm (r-survminer): 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 f51e69689b..4b28f25954 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22454,3 +22454,44 @@ implementation of the Shift-Algorithm by Streitberg & Roehmel.")
       "Maximally selected rank statistics with several p-value
 approximations.")
     (license license:gpl2+)))
+
+(define-public r-survminer
+  (package
+    (name "r-survminer")
+    (version "0.4.7")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "survminer" version))
+        (sha256
+          (base32
+            "1pdj3gs4aii8gn8wf4smbwmjymbzwkjwr3kxf90dxyy6i66mqq3v"))))
+    (properties `((upstream-name . "survminer")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-broom" ,r-broom)
+        ("r-dplyr" ,r-dplyr)
+        ("r-ggplot2" ,r-ggplot2)
+        ("r-ggpubr" ,r-ggpubr)
+        ("r-gridextra" ,r-gridextra)
+        ("r-magrittr" ,r-magrittr)
+        ("r-maxstat" ,r-maxstat)
+        ("r-purrr" ,r-purrr)
+        ("r-rlang" ,r-rlang)
+        ("r-scales" ,r-scales)
+        ("r-survival" ,r-survival)
+        ("r-survmisc" ,r-survmisc)
+        ("r-tibble" ,r-tibble)
+        ("r-tidyr" ,r-tidyr)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page
+      "http://www.sthda.com/english/rpkgs/survminer/")
+    (synopsis
+      "Drawing Survival Curves using 'ggplot2'")
+    (description
+      "Contains the function @code{ggsurvplot()} for drawing easily
+beautiful and 'ready-to-publish' survival curves with the 'number at
+risk' table and 'censoring count plot'.  Other functions are also
+available to plot adjusted curves for `Cox` model and to visually
+examine 'Cox' model assumptions.")
+    (license license:gpl2)))
-- 
2.17.1

Message #28 received at 42107-done <at> debbugs.gnu.org (full text, mbox):

From: Ricardo Wurmus <rekado <at> elephly.net>
To: Lo Peter <peterloleungyau <at> gmail.com>
Cc: 42107-done <at> debbugs.gnu.org
Subject: Re: [bug#42107] [PATCH] gnu: Add r-survminer and its dependencies
Date: Fri, 11 Sep 2020 11:08:17 +0200

Hi Peter,

> I am submitting a patch series of r-survminer and its dependencies.

Thank you!

I have re-indented the package definitions and updated their
descriptions to match our guidelines.  After making sure that the
packages all build fine I pushed the patches to the “master” branch with
commit 04e6851aa8.

-- 
Ricardo

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