[bug#42103] [PATCH] gnu: Add r-flexsurv and dependency

[bug#42103] [PATCH] gnu: Add r-flexsurv and dependency

[Lo Peter]

Dear all,

I am submitting a patch series of r-flexsurv and its dependency.

Regards,
Peter

[bug#42103] [PATCH 1/2] gnu: Add r-muhaz.

[Peter Lo]

* gnu/packages/cran.scm (r-muhaz): 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 ab5e57c0e2..b6cc9b48c3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22325,3 +22325,26 @@ 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-muhaz
+  (package
+    (name "r-muhaz")
+    (version "1.2.6.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "muhaz" version))
+        (sha256
+          (base32
+            "08qh43zx6h3yby44q2vxphfvmfdmqxpgyp0734yn341sy9n8pkkk"))))
+    (properties `((upstream-name . "muhaz")))
+    (build-system r-build-system)
+    (propagated-inputs `(("r-survival" ,r-survival)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page
+      "https://cran.r-project.org/web/packages/muhaz")
+    (synopsis
+      "Hazard Function Estimation in Survival Analysis")
+    (description
+      "Produces a smooth estimate of the hazard function for censored data.")
+    (license (list license:gpl2+ license:gpl3+))))
-- 
2.17.1

[bug#42103] [PATCH 2/2] gnu: Add r-flexsurv.

[Peter Lo]

* gnu/packages/cran.scm (r-flexsurv): New variable.
---
 gnu/packages/cran.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index b6cc9b48c3..0ddd0d29d2 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22348,3 +22348,40 @@ counting and recursive k-means partitioning.")
     (description
       "Produces a smooth estimate of the hazard function for censored data.")
     (license (list license:gpl2+ license:gpl3+))))
+
+(define-public r-flexsurv
+  (package
+    (name "r-flexsurv")
+    (version "1.1.1")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (cran-uri "flexsurv" version))
+        (sha256
+          (base32
+            "0x7p1rv51pplfyyzcg63ssb8z56mig7y0363hkr0219w3cvyq9nr"))))
+    (properties `((upstream-name . "flexsurv")))
+    (build-system r-build-system)
+    (propagated-inputs
+      `(("r-desolve" ,r-desolve)
+        ("r-mstate" ,r-mstate)
+        ("r-muhaz" ,r-muhaz)
+        ("r-mvtnorm" ,r-mvtnorm)
+        ("r-quadprog" ,r-quadprog)
+        ("r-rcpp" ,r-rcpp)
+        ("r-survival" ,r-survival)
+        ("r-tibble" ,r-tibble)
+        ("r-tidyr" ,r-tidyr)))
+    (native-inputs `(("r-knitr" ,r-knitr)))
+    (home-page
+      "https://github.com/chjackson/flexsurv-dev")
+    (synopsis
+      "Flexible Parametric Survival and Multi-State Models")
+    (description
+      "Flexible parametric models for time-to-event data, including
+the Royston-Parmar spline model, generalized gamma and generalized F
+distributions.  Any user-defined parametric distribution can be
+fitted, given at least an R function defining the probability density
+or hazard.  There are also tools for fitting and predicting from fully
+parametric multi-state models.")
+    (license license:gpl2+)))
-- 
2.17.1

bug#42103: [PATCH] gnu: Add r-flexsurv and dependency

[Ricardo Wurmus]

Hi Peter,

> I am submitting a patch series of r-flexsurv and its dependency.

I changed synopsis and description of both package definitions and
pushed them to the master branch with commit 9e4ef763ea.

Sorry for the delay!

-- 
Ricardo