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, because I previously submitted its patch in patch 2 of bug#42107. Regards, Peter
* gnu/packages/bioconductor.scm (r-icens): New variable. --- gnu/packages/bioconductor.scm | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 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
* gnu/packages/cran.scm (r-mlecens): New variable. --- gnu/packages/cran.scm | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 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
* gnu/packages/cran.scm (r-perm): New variable. --- gnu/packages/cran.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 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
* gnu/packages/cran.scm (r-interval): New variable. --- gnu/packages/cran.scm | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm index 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
* gnu/packages/cran.scm (r-fhtest): 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 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
Hi Peter,
> I am submitting a patch series for r-fhtest and its dependencies.
> Note that one of its dependency r-kmsurv is not included here, because
> I previously submitted its patch in patch 2 of bug#42107.
Thank you for this patch set. I moved r-fhtest and r-interval to (gnu
packages bioconductor) because they (untypically for CRAN packages)
depend on Bioconductor things.
I heavily edited the description and synopses and pushed everything to
the “master” branch with commit 7e88ee9f02.
--
Ricardo