diff --git a/DESCRIPTION b/DESCRIPTION index 44914e3..c3d78c1 100644 --- 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="kingaa@umich.edu"), - 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="kingaa@umich.edu",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 index 214139f..9733627 100644 --- 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 index 7a8fe8d..6e58833 100644 --- 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 index 993b7a6..13cd8f1 100644 --- 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 index d5f16ec..b10f339 100644 --- 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 index a8e6267..86bc096 100644 --- 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 index 93c164e..d0df5c5 100644 --- 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 index ba8a392..ff17140 100644 --- 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 index 3a378a8..22d6f18 100644 --- 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 index c9e55a5..7ed03ba 100644 --- 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 index 5b7f195..fd352ae 100644 --- 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 index 731097e..b781376 100644 --- 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 index 0e4c993..b6da3b7 100644 --- 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 index f08fab1..92b24a2 100644 --- 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 index 1325df3..423b728 100644 --- 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 index d05c44c..9a7b114 100644 --- 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 index 79a0d78..1b30a96 100644 --- 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 index f640150..492ecdc 100644 --- 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 index 38c77af..9f03f57 100644 --- 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 index 817912e..ab43502 100644 --- 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)