Merge branch 'main' of github.com:waldronlab/taxPPro

.github/workflows/pkgdown.yaml

@@ -14,7 +14,7 @@ name: pkgdown
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
-    container: bioconductor/bioconductor_docker:RELEASE_3_18
+    container: bioconductor/bioconductor_docker:RELEASE_3_19
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: taxPPro
 Type: Package
 Title: Taxonomic and phylogenetic propagation for bugphyzz
-Version: 0.99.2
+Version: 1.0.0
 Authors@R:
     c(
         person(
@@ -21,7 +21,7 @@ VignetteBuilder: knitr
 Depends:
     R (>= 4.3)
 Remotes:
-    waldronlab/bugphyzz@sdgamboa/release18
+    waldronlab/bugphyzz
 Suggests: 
     knitr,
     rmarkdown,
@@ -32,6 +32,7 @@ Suggests:
     ggtree,
     ggpubr,
     reshape2,
+    bugphyzz,
     ggimage
 Imports:
     ape,
@@ -47,7 +48,6 @@ Imports:
     data.tree,
     mclust,
     forcats,
-    bugphyzz,
     phytools,
     tidyr,
     castor

NEWS.md

@@ -0,0 +1,3 @@
+# taxPPro 1.0.0
+
+* This first version was used for the v1.0.0 relase of bugphyzzExports.

README.md

@@ -1,47 +1,17 @@
 # taxPPro - Taxonomic and Phylogenetic Propagation
 
-A provitional package to hold functions for ASR and inheritance
-for bugphyzz
+This package contains functions and data, e.g. taxonomic trees, used for
+performing filtering and propagation of bugphyzz annotations.
 
+The functions in this package are used in the bugphyzzExports script.
+Check the waldronlab/bugphyzzExports repository on GitHun for details.
 
-The package can be installed with:
+## Installaion
 
 ```
 if (!require("BiocManager", quietly = TRUE))
     install.packages("BiocManager")
 
-BiocManager::install('sdgamboa/taxPPro')
+BiocManager::install('waldronlab/taxPPro')
 ```
 
-
-Types of data (spreadsheets)
-
-**Binary data with only TRUE values -- binary-T**
-+ Merge Attribute and Atribute_value.
-+ Don't propagate.
-
-**Binary data with TRUE and FALSE values -- binary-TF**
-+ Merge Attribute and Attribute_value.
-+ Complete binary data with 0s.
-+ Assign 0.5 to unknown tips.
-
-**Multistate-Union with binary data with only TRUE values -- multistate-union-T**
-+ Merge Attribute and Attribute_value.
-+ Don't propagate.
-
-**Multistate-Union with binary data with both TRUE and FALSE values -- multistate-union-TF**
-+ Separate.
-+ Merge Attribute and Attribute_value.
-+ Complete binary data with 0s.
-+ Assign 0.5 to unknown tips.
-
-**Multistate-intersection -- multistate-intersection**
-+ Completey data with 0s.
-+ Assign 1 / n attributes to unknown tips.
-+ Do not export inputed zeros (when data is completed, after binning, and after inheritance).
-
-**Numeric -- numeric**
-+ Convert to range.
-
-**Range -- range**
-+ Convert to categorical.

vignettes/articles/nsti.Rmd

@@ -33,8 +33,9 @@ known_y <- sample(tree$tip.label, 2000)
 ## Get NSTI values
 
 ```{r}
-nsti_x <- getNsti(tree = tree, annotated_tip_labels = known_x)
-nsti_y <- getNsti(tree = tree, annotated_tip_labels = known_y)
+nodes_with_taxid <- grep("^n", tree$node.label, value = TRUE, invert = TRUE)
+nsti_x <- getNsti(tree = tree, annotated_tip_labels = known_x, nodes = nodes_with_taxid)
+nsti_y <- getNsti(tree = tree, annotated_tip_labels = known_y, nodes = nodes_with_taxid)
 ```
 
 ## Plot a couple of histograms