[PATCH] gnu: Add r-fhtest and its dependencies

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Lo Peter wrote 7 days ago
(address . guix-patches@gnu.org)
CAEM+zmjKA6w9w3vp39LpMgaCaQrUsJVWkAbN-0cah+7yBdMtnA@mail.gmail.com
Dear all,
I am submitting a patch series for r-fhtest and its dependencies.Note that one of its dependency r-kmsurv is not included here, becauseI previously submitted its patch in patch 2 of bug#42107.
Regards,Peter
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Peter Lo wrote 7 days ago
[PATCH 1/5] gnu: Add r-icens.
(address . 42119@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200629080340.13200-1-peterloleungyau@gmail.com
* gnu/packages/bioconductor.scm (r-icens): New variable.--- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+)
Toggle diff (33 lines)diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scmindex 002f4a0edb..763c219d9e 100644--- a/gnu/packages/bioconductor.scm+++ b/gnu/packages/bioconductor.scm@@ -8117,3 +8117,26 @@ dimensional mass cytometry data.") Tool) analysis automatic by constructing a HTTP POST request according to user's input and automatically retrieving results from GREAT web server.") (license license:expat)))++(define-public r-icens+ (package+ (name "r-icens")+ (version "1.60.0")+ (source+ (origin+ (method url-fetch)+ (uri (bioconductor-uri "Icens" version))+ (sha256+ (base32+ "0fh7wgkrw20f61p06i87nccnbig9wv4m0jcg7cx1rw7g2ndnabgp"))))+ (properties `((upstream-name . "Icens")))+ (build-system r-build-system)+ (propagated-inputs `(("r-survival" ,r-survival)))+ (home-page+ "https://bioconductor.org/packages/release/bioc/html/Icens.html")+ (synopsis+ "NPMLE for Censored and Truncated Data")+ (description+ "Many functions for computing the NPMLE for censored and+truncated data.")+ (license license:artistic2.0)))-- 2.17.1
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Peter Lo wrote 7 days ago
[PATCH 2/5] gnu: Add r-mlecens.
(address . 42119@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200629080340.13200-2-peterloleungyau@gmail.com
* gnu/packages/cran.scm (r-mlecens): New variable.--- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+)
Toggle diff (39 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex ab5e57c0e2..8be110a9bd 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -22325,3 +22325,32 @@ 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-mlecens+ (package+ (name "r-mlecens")+ (version "0.1-4")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "MLEcens" version))+ (sha256+ (base32+ "0zlmrcjraypscgs2v0w4s4hm7qccsmaz4hjsgqpn0058vx622945"))))+ (properties `((upstream-name . "MLEcens")))+ (build-system r-build-system)+ (home-page "http://stat.ethz.ch/~maathuis/")+ (synopsis+ "Computation of the MLE for bivariate (interval) censored data")+ (description+ "This package contains functions to compute the nonparametric+maximum likelihood estimator (MLE) for the bivariate distribution+of (X,Y), when realizations of (X,Y) cannot be observed directly. To+be more precise, we consider the situation where we observe a set of+rectangles that are known to contain the unobservable realizations+of (X,Y). We compute the MLE based on such a set of rectangles. The+methods can also be used for univariate censored data (see data set+@code{cosmesis}), and for censored data with competing risks (see data+set @code{menopause}). We also provide functions to visualize the+observed data and the MLE.")+ (license license:gpl2+)))-- 2.17.1
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Peter Lo wrote 7 days ago
[PATCH 3/5] gnu: Add r-perm.
(address . 42119@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200629080340.13200-3-peterloleungyau@gmail.com
* gnu/packages/cran.scm (r-perm): New variable.--- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+)
Toggle diff (31 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex 8be110a9bd..fe1a8e0b46 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -22354,3 +22354,24 @@ methods can also be used for univariate censored data (see data set set @code{menopause}). We also provide functions to visualize the observed data and the MLE.") (license license:gpl2+)))++(define-public r-perm+ (package+ (name "r-perm")+ (version "1.0-0.0")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "perm" version))+ (sha256+ (base32+ "0075awl66ynv10vypg63fcxk33qzvxddrp8mi4w08ysvimcyxijk"))))+ (properties `((upstream-name . "perm")))+ (build-system r-build-system)+ (home-page+ "https://cran.r-project.org/web/packages/perm/")+ (synopsis+ "Exact or Asymptotic permutation tests")+ (description+ "Perform Exact or Asymptotic permutation tests")+ (license (list license:gpl2+ license:gpl3+))))-- 2.17.1
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Peter Lo wrote 7 days ago
[PATCH 4/5] gnu: Add r-interval.
(address . 42119@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200629080340.13200-4-peterloleungyau@gmail.com
* gnu/packages/cran.scm (r-interval): New variable.--- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+)
Toggle diff (37 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex fe1a8e0b46..d3cd199130 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -22375,3 +22375,30 @@ observed data and the MLE.") (description "Perform Exact or Asymptotic permutation tests") (license (list license:gpl2+ license:gpl3+))))++(define-public r-interval+ (package+ (name "r-interval")+ (version "1.1-0.1")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "interval" version))+ (sha256+ (base32+ "1lln9jkli28i4wivwzqrsxvv2n15560f7msjy5gssrm45vxrxms8"))))+ (properties `((upstream-name . "interval")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-icens" ,r-icens)+ ("r-mlecens" ,r-mlecens)+ ("r-perm" ,r-perm)+ ("r-survival" ,r-survival)))+ (home-page+ "https://cran.r-project.org/web/packages/interval/")+ (synopsis+ "Weighted Logrank Tests and NPMLE for interval censored data")+ (description+ "This package provides functions to fit nonparametric survival+curves, plot them, and perform logrank or Wilcoxon type tests.")+ (license license:gpl2+)))-- 2.17.1
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Peter Lo wrote 7 days ago
[PATCH 5/5] gnu: Add r-fhtest.
(address . 42119@debbugs.gnu.org)(name . Peter Lo)(address . peterloleungyau@gmail.com)
20200629080340.13200-5-peterloleungyau@gmail.com
* gnu/packages/cran.scm (r-fhtest): New variable.--- gnu/packages/cran.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+)
Toggle diff (41 lines)diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scmindex d3cd199130..3d02139f87 100644--- a/gnu/packages/cran.scm+++ b/gnu/packages/cran.scm@@ -22402,3 +22402,34 @@ observed data and the MLE.") "This package provides functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests.") (license license:gpl2+)))++(define-public r-fhtest+ (package+ (name "r-fhtest")+ (version "1.4")+ (source+ (origin+ (method url-fetch)+ (uri (cran-uri "FHtest" version))+ (sha256+ (base32+ "1wsn0j9ydpp9nfswiqg21p09kgkvaq8fh0y0h8syqgizah7i8vs2"))))+ (properties `((upstream-name . "FHtest")))+ (build-system r-build-system)+ (propagated-inputs+ `(("r-interval" ,r-interval)+ ("r-kmsurv" ,r-kmsurv)+ ("r-mass" ,r-mass)+ ("r-perm" ,r-perm)+ ("r-survival" ,r-survival)))+ (home-page+ "https://cran.r-project.org/web/packages/FHtest/")+ (synopsis+ "Tests for Survival Data Based on the Fleming-Harrington Class")+ (description+ "This package provides functions to compare two or more survival+curves with: a) The Fleming-Harrington test for right-censored data+based on permutations and on counting processes. b) An extension of+the Fleming-Harrington test for interval-censored data based on a+permutation distribution and on a score vector distribution.")+ (license license:gpl2+)))-- 2.17.1
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