[bug#42119] [PATCH] gnu: Add r-fhtest and its dependencies

[bug#42119] [PATCH] gnu: Add r-fhtest and its dependencies

[Lo Peter]

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

[bug#42119] [PATCH 1/5] gnu: Add r-icens.

[Peter Lo]

* 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

[bug#42119] [PATCH 2/5] gnu: Add r-mlecens.

[Peter Lo]

* 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

[bug#42119] [PATCH 3/5] gnu: Add r-perm.

[Peter Lo]

* 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

[bug#42119] [PATCH 4/5] gnu: Add r-interval.

[Peter Lo]

* 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

[bug#42119] [PATCH 5/5] gnu: Add r-fhtest.

[Peter Lo]

* 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

bug#42119: [PATCH] gnu: Add r-fhtest and its dependencies

[Ricardo Wurmus]

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