update CITATION file and author list

.Rbuildignore

@@ -34,6 +34,7 @@ Makefile
 rules.mk
 scripts
 lib
+tools
 library
 check
 www

DESCRIPTION

@@ -2,9 +2,9 @@ Package: ouch
 Type: Package
 Title: Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses
 Version: 2.19-0
-Date: 2022-04-24
-Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]"),
-	  person(given=c("Marguerite","A."),family="Butler",role=c("ctb")))
+Date: 2023-04-24
+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("Marguerite","A."),family="Butler",role=c("ctb")))
 Maintainer: Aaron A. King <[email protected]>
 Description: Fit and compare Ornstein-Uhlenbeck models for evolution along a phylogenetic tree.
 Depends: R(>= 3.6)

Makefile

@@ -1,3 +1,4 @@
+REPODIR = ../www
 INCLUDES=
 HEADERS=
 

NAMESPACE

@@ -1,6 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(as.data.frame,brown)
+S3method(as.data.frame,browntree)
 S3method(as.data.frame,hansentree)
 S3method(as.data.frame,ouchtree)
 export(ape2ouch)

R/as_data_frame.R

@@ -14,7 +14,7 @@ as.data.frame.ouchtree <- function (x, ...) as(x,"data.frame")
 
 #' @rdname as_data_frame
 #' @export
-as.data.frame.brown <- function (x, ...) as(x,"data.frame")
+as.data.frame.browntree <- function (x, ...) as(x,"data.frame")
 
 #' @rdname as_data_frame
 #' @export

examples/anolis.R

@@ -1,4 +1,5 @@
 ## Analysis of sexual size dimorphism data
+\donttest{ ## Save time for CRAN
 tree <- with(anolis.ssd,ouchtree(node,ancestor,time/max(time),species))
 plot(tree,node.names=TRUE)
 
@@ -13,4 +14,4 @@ plot(h2)
 h3 <- hansen(anolis.ssd['log.SSD'],tree,anolis.ssd['OU.7'],sqrt.alpha=1,sigma=1)
 h3
 plot(h3)
-
+}

examples/bimac.R

@@ -1,4 +1,5 @@
 ## Analysis of Anolis bimaculatus data
+\donttest{ ## save time for CRAN
 tree <- with(bimac,ouchtree(node,ancestor,time/max(time),spcode))
 plot(tree,node.names=TRUE)
 
@@ -28,4 +29,4 @@ hsim <- update(h5,data=simdat[[1]])
 summary(hsim)
 bsim <- update(h1,data=simdat[[1]])
 summary(bsim)
-
+}

examples/geospiza.R

@@ -1,4 +1,5 @@
 ### Darwin's finches.
+\donttest{ ## Save time for CRAN
 ### The data were taken from package 'geiger' due to the latter being orphaned.
 if (requireNamespace("ape")) {
 
@@ -38,3 +39,4 @@ if (requireNamespace("ape")) {
   plot(h1)
 
 }
+}

inst/CITATION

@@ -6,9 +6,9 @@ c(
   bibentry(
     header=paste("To cite the",sQuote("ouch"),"package in publications, use:"),
     bibtype="Article",
-    author=personList(
-      as.person("Marguerite A. Butler"),
-      as.person("Aaron A. King")
+    author=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("Marguerite","A."),family="Butler",role=c("ctb"))
     ),
     title="Phylogenetic comparative analysis: a modeling approach for adaptive evolution",
     journal="American Naturalist",
@@ -27,9 +27,9 @@ c(
     header="Additionally, consider citing the package itself:",
     bibtype="Manual",
     title="ouch: Ornstein-Uhlenbeck models for phylogenetic comparative hypotheses",
-    author=personList(
-      as.person("Aaron A. King"),
-      as.person("Marguerite A. Butler")
+    author=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("Marguerite","A."),family="Butler",role=c("ctb"))
     ),
     year=year,
     note=note1,

tools/check.env

@@ -0,0 +1,87 @@
+_R_CHECK_ALL_NON_ISO_C_=false
+_R_CHECK_ALWAYS_LOG_VIGNETTE_OUTPUT_=false
+_R_CHECK_ASCII_CODE_=true
+_R_CHECK_ASCII_DATA_=true
+_R_CHECK_AUTOCONF_=true
+_R_CHECK_BASHISMS_=true
+_R_CHECK_BOGUS_RETURN_=true
+_R_CHECK_BUILD_VIGNETTES_SEPARATELY_=true
+_R_CHECK_CLEAN_VIGN_TEST_=true
+_R_CHECK_CODE_ASSIGN_TO_GLOBALENV_=true
+_R_CHECK_CODE_ATTACH_=true
+_R_CHECK_CODE_CLASS_IS_STRING_=true
+_R_CHECK_CODE_DATA_INTO_GLOBALENV_=true
+_R_CHECK_CODE_USAGE_VIA_NAMESPACES_=true
+_R_CHECK_CODE_USAGE_WITH_ONLY_BASE_ATTACHED_=true
+_R_CHECK_CODOC_S4_METHODS_=true
+_R_CHECK_COMPACT_DATA_=true
+_R_CHECK_COMPILATION_FLAGS_=true
+_R_CHECK_CONNECTIONS_LEFT_OPEN_=true
+_R_CHECK_CRAN_INCOMING_=true
+_R_CHECK_DATALIST_=true
+_R_CHECK_DEPRECATED_DEFUNCT_=true
+_R_CHECK_DONTTEST_EXAMPLES_=false
+_R_CHECK_DOT_FIRSTLIB_=true
+_R_CHECK_DOT_INTERNAL_=true
+_R_CHECK_EXAMPLE_TIMING_THRESHOLD_=5
+_R_CHECK_EXCESSIVE_IMPORTS_=20
+_R_CHECK_EXECUTABLES_=true
+_R_CHECK_EXECUTABLES_EXCLUSIONS_=false
+_R_CHECK_EXIT_ON_FIRST_ERROR_=false
+_R_CHECK_FF_CALLS_=true
+_R_CHECK_FF_DUP_=true
+_R_CHECK_FORCE_SUGGESTS_=false
+_R_CHECK_FUTURE_FILE_TIMESTAMPS_=true
+_R_CHECK_GCT_N_=0
+_R_CHECK_INSTALL_DEPENDS_=true
+_R_CHECK_LENGTH_1_CONDITION_ =package:_R_CHECK_PACKAGE_NAME_
+_R_CHECK_LENGTH_1_LOGIC2_=package:_R_CHECK_PACKAGE_NAME_,abort,verbose
+_R_CHECK_LICENSE_=true
+_R_CHECK_LIMIT_CORES_=true
+_R_CHECK_MATRIX_DATA_=true
+_R_CHECK_NATIVE_ROUTINE_REGISTRATION_=true
+_R_CHECK_NO_RECOMMENDED_=true
+_R_CHECK_NO_STOP_ON_TEST_ERROR_=true
+_R_CHECK_ORPHANED_=true
+_R_CHECK_OVERWRITE_REGISTERED_S3_METHODS_=true
+_R_CHECK_PACKAGES_USED_IN_TESTS_USE_SUBDIRS_=true
+_R_CHECK_PKG_SIZES_=true
+_R_CHECK_PKG_SIZES_THRESHOLD_=5
+_R_CHECK_PRAGMAS_=true
+_R_CHECK_RD_CHECKRD_MINLEVEL_=-1
+_R_CHECK_RD_CONTENTS_=true
+_R_CHECK_RD_EXAMPLES_T_AND_F_=false
+_R_CHECK_RD_LINE_WIDTHS_=true
+_R_CHECK_RD_STYLE_=true
+_R_CHECK_RD_VALIDATE_RD2HTML_=true
+_R_CHECK_RD_XREFS_=true
+_R_CHECK_REPLACING_IMPORTS_=true
+_R_CHECK_R_DEPENDS_="warn"
+_R_CHECK_R_ON_PATH_=true
+_R_CHECK_S3_METHODS_NOT_REGISTERED_=true
+_R_CHECK_SERIALIZATION_=true
+_R_CHECK_SHLIB_OPENMP_FLAGS_=true
+_R_CHECK_SKIP_ARCH_=none
+_R_CHECK_SRC_MINUS_W_IMPLICIT_=true
+_R_CHECK_SRC_MINUS_W_UNUSED_=true
+_R_CHECK_SUBDIRS_NOCASE_=true
+_R_CHECK_SUBDIRS_STRICT_=default
+_R_CHECK_SUGGESTS_ONLY_=true
+_R_CHECK_SYSTEM_CLOCK_=false
+_R_CHECK_TESTS_NLINES_=13
+_R_CHECK_THINGS_IN_CHECK_DIR_=true
+_R_CHECK_THINGS_IN_OTHER_DIRS_=false
+_R_CHECK_THINGS_IN_TEMP_DIR_=true
+_R_CHECK_TIMINGS_=10
+_R_CHECK_TOPLEVEL_FILES_=true
+_R_CHECK_UNSAFE_CALLS_=true
+_R_CHECK_USE_CODETOOLS_=true
+_R_CHECK_USE_INSTALL_LOG_=true
+_R_CHECK_VC_DIRS_=true
+_R_CHECK_VIGNETTES_NLINES_=10
+_R_CHECK_VIGNETTES_SKIP_RUN_MAYBE_=true
+_R_CHECK_WALL_FORTRAN_=true
+_R_CHECK_XREFS_MIND_SUSPECT_ANCHORS_=false
+_R_CHECK_XREFS_PKGS_ARE_DECLARED_=false
+_R_CHECK_XREFS_USE_ALIASES_FROM_CRAN_=false
+_R_CHECK_CODETOOLS_PROFILE_="suppressLocalUnused=FALSE,suppressPartialMatchArgs=FALSE,suppressParamUnused=TRUE,suppressUndefined=FALSE"