Merge branch 'develop'

.travis.yml

@@ -7,5 +7,8 @@ env:
   - NOT_CRAN=true
 r_packages:
   - covr
+before_install:
+  - sudo apt-get -qq update
+  - sudo apt-get install -y libmagick++-dev
 after_success:
   - Rscript -e 'library(covr); codecov(quiet = FALSE)'

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PhylogeneticEM
 Title: Automatic Shift Detection using a Phylogenetic EM
-Version: 1.2.1
+Version: 1.3.0
 Authors@R: c(
     person("Paul", "Bastide", email = "[email protected]", role = c("aut", "cre")),
     person("Mahendra", "Mariadassou", role = "ctb"))
@@ -11,29 +11,28 @@ Description:
     available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and
     Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.
 Depends:
-    ape (>= 3.5),
+    ape (>= 5.3),
     Matrix (>= 1.2.3),
-    R (>= 3.2.1),
+    R (>= 3.6.0),
 Imports:
     capushe (>= 1.1.1),
     foreach (>= 1.4.3),
     gglasso (>= 1.4),
     glmnet (>= 2.0.5),
-    graphics (>= 3.2.1),
-    grDevices (>= 3.2.1),
-    LINselect (>= 0.0.2),
+    graphics (>= 3.6.0),
+    grDevices (>= 3.6.0),
+    LINselect (>= 1.1.1),
     MASS (>= 7.3.45),
-    methods (>= 3.2.1),
+    methods (>= 3.6.0),
     plyr (>= 1.8.4),
-    Rcpp (>= 0.12.6),
+    Rcpp (>= 1.0.2),
     robustbase (>= 0.92.6),
-    stats (>= 3.2.1),
-    utils (>= 3.2.1)
+    stats (>= 3.6.0),
+    utils (>= 3.6.0)
 Suggests:
     combinat (>= 0.0.8),
     doParallel (>= 1.0.10),
     phytools (>= 0.5.38),
-    Rphylopars (>= 0.2.9),
     testthat (>= 1.0.2),
     TreeSim (>= 2.2),
     knitr,
@@ -44,7 +43,7 @@ LinkingTo:
 License: GPL (>= 2) | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 URL: https://github.com/pbastide/PhylogeneticEM
 BugReports: https://github.com/pbastide/PhylogeneticEM/issues
 VignetteBuilder: knitr

NEWS.md

@@ -1,3 +1,17 @@
+# PhylogeneticEM 1.3.0
+* Bug fix:
+  * Bug fix in plot function for univariate result.
+  * Tree does not need to be ultrametric for a BM
+  * Change `tol` to `tol_EM` in `estimateEM` for actual binding
+  * Bug fixes in plot function for displying traits.
+* New Option:
+  * Add option "name_trait" to plot function for ancestral state reconstruction.
+* API Change
+  * For a univariate trait, the BM re-scaling is now applied by default.
+* Deprecation Fix:
+  * Update `ape`, and replace `is.binary.tree` by `is.binary`.
+  * Remove dependency to Rphylopars (no longer on CRAN).
+
 # PhylogeneticEM 1.2.1
 * CRAN maintenance
   * Added references in Description

R/generic_functions.R

@@ -402,12 +402,12 @@ test.root.state.BM <- function(root.state, ...) {
     warning("The BM does not have a stationary state. root.state$stationary.root is set to NULL")
     root.state$stationary.root <- NULL
   }
-  if (root.state$random && !is.na(root.state$value.root)) {
+  if (root.state$random && !anyNA(root.state$value.root)) {
     warning("As root state is supposed random, its value is not defined and set to NA")
     root.state$value.root <- NA
     root.state$var.root <- as(root.state$var.root, "dpoMatrix")
   }
-  if (!root.state$random && (!is.na(root.state$exp.root) || !is.na(root.state$exp.root))) {
+  if (!root.state$random && (!anyNA(root.state$exp.root) || !anyNA(root.state$exp.root))) {
     warning("As root state is supposed fixed, its expectation and variance are not defined and set to NA")
     root.state$exp.root <- NA
     root.state$var.root <- NA
@@ -416,12 +416,12 @@ test.root.state.BM <- function(root.state, ...) {
 }
 
 test.root.state.OU <- function(root.state, process, variance, selection.strength, optimal.value, ...) {
-  if (root.state$random && !is.na(root.state$value.root)) {
+  if (root.state$random && !anyNA(root.state$value.root)) {
     warning("As root state is supposed random, its value is not defined and set to NA")
     root.state$value.root <- NA
     root.state$var.root <- as(root.state$var.root, "dpoMatrix")
   }
-  if (!root.state$random && (!is.na(root.state$exp.root) || !is.na(root.state$exp.root))) {
+  if (!root.state$random && (!anyNA(root.state$exp.root) || !anyNA(root.state$exp.root))) {
     warning("As root state is supposed fixed, its expectation and variance are not defined and set to NA")
     root.state$exp.root <- NA
     root.state$var.root <- NA
@@ -497,7 +497,7 @@ compute_stationary_variance <- function(variance, selection.strength){
     kro_sum_A_inv <- solve(kro_sum_A)
     root_var_vec <- kro_sum_A_inv %*% variance_vec
     gamma <- matrix(root_var_vec, dim(variance))
-    if (!isSymmetric(gamma)) stop("Error in computation of stationary variance: matrix computed was not symmetric.")
+    if (!isSymmetric(gamma, tol = (.Machine$double.eps)^(0.7))) stop("Error in computation of stationary variance: matrix computed was not symmetric.")
     gamma <- forceSymmetric(gamma)
     return(as(gamma, "dpoMatrix"))
   }
@@ -874,13 +874,13 @@ merge_params_independent <- function(params_split){
     } else {
       params$shifts$values <- matrix(0, p, 0)
     }
-    if (!is.na(params$root.state$value.root)){
+    if (!anyNA(params$root.state$value.root)){
       params$root.state$value.root <- sapply(params_split, function(z) return(z$root.state$value.root))
     }
-    if (!is.na(params$root.state$exp.root)){
+    if (!anyNA(params$root.state$exp.root)){
       params$root.state$exp.root <- sapply(params_split, function(z) return(z$root.state$exp.root))
     }
-    if (!is.na(as.vector(params$root.state$var.root))){
+    if (!anyNA(as.vector(params$root.state$var.root))){
       params$root.state$var.root <- diag(sapply(params_split, function(z) return(as.vector(z$root.state$var.root))))
     }
     if (!is.null(params$optimal.value)){