(address . guix-patches@gnu.org)
CAEM+zmh-qSk95YKJLmgtkg8BS51U0c9noEcQHBg=oJ7O1r8k7A@mail.gmail.com
Dear all,
I am submitting a patch series of r-survminer and its dependencies.
Regards,
Peter
[PATCH] gnu: Add r-survminer and its dependencies
- Done
Details
- 2 participants
- Lo Peter
- Ricardo Wurmus
- Owner
- unassigned
- Submitted by
- Lo Peter
- Severity
- normal
L
P
[PATCH 1/6] gnu: Add r-km-ci.
(address . 42107@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200628092944.19939-1-peterloleungyau@gmail.com
* gnu/packages/cran.scm (r-km-ci): New variable.
---
gnu/packages/cran.scm | 25 +++++++++++++++++++++++++
1 file changed, 25 insertions(+)
Toggle diff (35 lines)
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
P
[PATCH 2/6] gnu: Add r-kmsurv.
(address . 42107@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200628092944.19939-2-peterloleungyau@gmail.com
* gnu/packages/cran.scm (r-kmsurv): New variable.
---
gnu/packages/cran.scm | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
Toggle diff (33 lines)
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
P
[PATCH 3/6] gnu: Add r-survmisc.
(address . 42107@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200628092944.19939-3-peterloleungyau@gmail.com
* gnu/packages/cran.scm (r-survmisc): New variable.
---
gnu/packages/cran.scm | 34 ++++++++++++++++++++++++++++++++++
1 file changed, 34 insertions(+)
Toggle diff (44 lines)
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
P
[PATCH 4/6] gnu: Add r-exactranktests.
(address . 42107@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200628092944.19939-4-peterloleungyau@gmail.com
* gnu/packages/cran.scm (r-exactranktests): New variable.
---
gnu/packages/cran.scm | 23 +++++++++++++++++++++++
1 file changed, 23 insertions(+)
Toggle diff (33 lines)
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
P
[PATCH 5/6] gnu: Add r-maxstat.
(address . 42107@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200628092944.19939-5-peterloleungyau@gmail.com
* gnu/packages/cran.scm (r-maxstat): New variable.
---
gnu/packages/cran.scm | 24 ++++++++++++++++++++++++
1 file changed, 24 insertions(+)
Toggle diff (34 lines)
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
P
[PATCH 6/6] gnu: Add r-survminer.
(address . 42107@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200628092944.19939-6-peterloleungyau@gmail.com
* gnu/packages/cran.scm (r-survminer): New variable.
---
gnu/packages/cran.scm | 41 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 41 insertions(+)
Toggle diff (51 lines)
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
R
Re: [bug#42107] [PATCH] gnu: Add r-survminer and its dependencies
(name . Lo Peter)(address . peterloleungyau@gmail.com)(address . 42107-done@debbugs.gnu.org)
878sdg3cla.fsf@elephly.net
Hi Peter,
Toggle quote (2 lines)
> 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
Closed
?