update

kingaa · Jan 27, 2024 · a72b43c · a72b43c
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,10 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.10.1.4
-Date: 2023-07-10
-Authors@R: c(person(given=c("Aaron","A."),family="King",
-		role=c("aut","cre"),email="[email protected]"),
-	  person(given=c("Qianying"),family="Lin",role=c("aut"))
+Version: 0.10.1.5
+Date: 2024-01-27
+Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]",comment=c(ORCID="0000-0001-6159-3207")),
+	  person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))
 	  )
 Description: Tools for phylodynamic analysis.
 Depends: R(>= 4.2)
@@ -17,7 +16,7 @@ LazyData: true
 Contact: kingaa at umich dot edu
 Encoding: UTF-8
 Roxygen: list(roclets = c("collate", "namespace", "rd"))
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Collate: 
     'package.R'
     'geneal.R'

diff --git a/R/package.R b/R/package.R
@@ -4,12 +4,11 @@
 ##' 
 ##' @name phylopomp
 ##' @aliases phylopomp-package
-##' @docType package
 ##' @author Aaron A. King, Qianying Lin
 ##' @import ggplot2
 ##' @useDynLib phylopomp, .registration = TRUE, .fixes="P_"
 ##'
-NULL
+"_PACKAGE"
 
 ##' @include package.R
 ##' @importFrom foreach registerDoSEQ

diff --git a/README.md b/README.md
@@ -1,16 +1,17 @@
 ## **phylopomp**, an *R* package for POMP inference on genealogies
 
 [![Project Status: WIP - Initial development is in progress, but there
-has not yet been a stable, usable release suitable for the
-public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
+has not yet been a stable, usable release suitable for the public.](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)
 [![Development Release](https://img.shields.io/github/release/kingaa/phylopomp.svg)](https://github.com/kingaa/phylopomp/releases/latest)
 [![](https://www.r-pkg.org/badges/version/phylopomp?color=blue)](https://cran.r-project.org/package=phylopomp)
 [![R-CMD-check](https://github.com/kingaa/phylopomp/actions/workflows/r-cmd-check.yml/badge.svg)](https://github.com/kingaa/phylopomp/actions/workflows/r-cmd-check.yml)
 [![binary-build](https://github.com/kingaa/phylopomp/actions/workflows/binary-build.yml/badge.svg)](https://github.com/kingaa/phylopomp/actions/workflows/binary-build.yml)
 [![test-coverage](https://github.com/kingaa/phylopomp/actions/workflows/test-coverage.yml/badge.svg)](https://github.com/kingaa/phylopomp/actions/workflows/test-coverage.yml)
 [![codecov](https://codecov.io/gh/kingaa/phylopomp/branch/master/graph/badge.svg)](https://codecov.io/gh/kingaa/phylopomp)
-[![manual](https://img.shields.io/badge/manual-HTML-informational)](https://kingaa.github.io/manuals/phylopomp/)
-[![pdf-manual](https://img.shields.io/badge/manual-PDF-informational)](https://kingaa.github.io/manuals/phylopomp/pdf/)
+[![manual](https://img.shields.io/badge/manual-HTML-brown)](https://kingaa.github.io/manuals/phylopomp/)
+[![pdf-manual](https://img.shields.io/badge/manual-PDF-brown)](https://kingaa.github.io/manuals/phylopomp/pdf/)
+[![doxygen](https://img.shields.io/badge/doxygen-HTML-brown)](https://kingaa.github.io/manuals/phylopomp/source/html/index.html)
+
 
 ### Publications
 

diff --git a/src/ball.h b/src/ball.h
@@ -9,7 +9,8 @@
 
 //! BALL COLORS
 
-//! NB: The correctness of the algorithms depends on green being the first color.
+//! NB: The correctness of the algorithms depends on
+//! green being the first color and black being the last.
 typedef enum {green, blue, black} color_t;
 static const char* colores[] = {"green", "blue", "black"};
 static const char* colorsymb[] = {"g", "b", "o"};

diff --git a/src/pocket.h b/src/pocket.h
@@ -15,6 +15,7 @@
 
 //! Without this, order depends on machine state,
 //! defeating reproducibility.
+//! The correctness of the algorithms depends on this order.
 struct ball_order {
   bool operator() (const ball_t* a, const ball_t* b) const {
     return (a->color < b->color) ||

diff --git a/tests/curtail.Rout.save b/tests/curtail.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/diagram.Rout.save b/tests/diagram.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
@@ -18,6 +18,36 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
 Type 'q()' to quit R.
 
 > library(phylopomp)
+Registered S3 methods overwritten by 'treeio':
+  method              from    
+  MRCA.phylo          tidytree
+  MRCA.treedata       tidytree
+  Nnode.treedata      tidytree
+  Ntip.treedata       tidytree
+  ancestor.phylo      tidytree
+  ancestor.treedata   tidytree
+  child.phylo         tidytree
+  child.treedata      tidytree
+  full_join.phylo     tidytree
+  full_join.treedata  tidytree
+  groupClade.phylo    tidytree
+  groupClade.treedata tidytree
+  groupOTU.phylo      tidytree
+  groupOTU.treedata   tidytree
+  inner_join.phylo    tidytree
+  inner_join.treedata tidytree
+  is.rooted.treedata  tidytree
+  nodeid.phylo        tidytree
+  nodeid.treedata     tidytree
+  nodelab.phylo       tidytree
+  nodelab.treedata    tidytree
+  offspring.phylo     tidytree
+  offspring.treedata  tidytree
+  parent.phylo        tidytree
+  parent.treedata     tidytree
+  root.treedata       tidytree
+  rootnode.phylo      tidytree
+  sibling.phylo       tidytree
 
 Attaching package: 'phylopomp'
 

diff --git a/tests/lbdp1.Rout.save b/tests/lbdp1.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/lbdp2.Rout.save b/tests/lbdp2.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/lbdp3.Rout.save b/tests/lbdp3.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/lineages.Rout.save b/tests/lineages.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/moran1.Rout.save b/tests/moran1.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/parse.Rout.save b/tests/parse.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/plot.Rout.save b/tests/plot.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
@@ -20,6 +20,36 @@ Type 'q()' to quit R.
 > png(filename="plot-%02d.png",res=100)
 > 
 > library(phylopomp)
+Registered S3 methods overwritten by 'treeio':
+  method              from    
+  MRCA.phylo          tidytree
+  MRCA.treedata       tidytree
+  Nnode.treedata      tidytree
+  Ntip.treedata       tidytree
+  ancestor.phylo      tidytree
+  ancestor.treedata   tidytree
+  child.phylo         tidytree
+  child.treedata      tidytree
+  full_join.phylo     tidytree
+  full_join.treedata  tidytree
+  groupClade.phylo    tidytree
+  groupClade.treedata tidytree
+  groupOTU.phylo      tidytree
+  groupOTU.treedata   tidytree
+  inner_join.phylo    tidytree
+  inner_join.treedata tidytree
+  is.rooted.treedata  tidytree
+  nodeid.phylo        tidytree
+  nodeid.treedata     tidytree
+  nodelab.phylo       tidytree
+  nodelab.treedata    tidytree
+  offspring.phylo     tidytree
+  offspring.treedata  tidytree
+  parent.phylo        tidytree
+  parent.treedata     tidytree
+  root.treedata       tidytree
+  rootnode.phylo      tidytree
+  sibling.phylo       tidytree
 
 Attaching package: 'phylopomp'
 

diff --git a/tests/seir1.Rout.save b/tests/seir1.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/seir2.Rout.save b/tests/seir2.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/si2r.Rout.save b/tests/si2r.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/siir1.Rout.save b/tests/siir1.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 

diff --git a/tests/simulate.Rout.save b/tests/simulate.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)
 
@@ -18,6 +18,36 @@ Type 'demo()' for some demos, 'help()' for on-line help, or
 Type 'q()' to quit R.
 
 > library(phylopomp)
+Registered S3 methods overwritten by 'treeio':
+  method              from    
+  MRCA.phylo          tidytree
+  MRCA.treedata       tidytree
+  Nnode.treedata      tidytree
+  Ntip.treedata       tidytree
+  ancestor.phylo      tidytree
+  ancestor.treedata   tidytree
+  child.phylo         tidytree
+  child.treedata      tidytree
+  full_join.phylo     tidytree
+  full_join.treedata  tidytree
+  groupClade.phylo    tidytree
+  groupClade.treedata tidytree
+  groupOTU.phylo      tidytree
+  groupOTU.treedata   tidytree
+  inner_join.phylo    tidytree
+  inner_join.treedata tidytree
+  is.rooted.treedata  tidytree
+  nodeid.phylo        tidytree
+  nodeid.treedata     tidytree
+  nodelab.phylo       tidytree
+  nodelab.treedata    tidytree
+  offspring.phylo     tidytree
+  offspring.treedata  tidytree
+  parent.phylo        tidytree
+  parent.treedata     tidytree
+  root.treedata       tidytree
+  rootnode.phylo      tidytree
+  sibling.phylo       tidytree
 
 Attaching package: 'phylopomp'
 

diff --git a/tests/sir1.Rout.save b/tests/sir1.Rout.save
@@ -1,5 +1,5 @@
 
-R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
+R version 4.3.2 (2023-10-31) -- "Eye Holes"
 Copyright (C) 2023 The R Foundation for Statistical Computing
 Platform: x86_64-pc-linux-gnu (64-bit)