Dear all, I am submitting a patch series of r-survminer and its dependencies. Regards, Peter
* 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
* 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
* 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
* 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
* 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
* 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
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