From 2afc189480410979b4a250622cffa55c12a2d3cd Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Mon, 15 Apr 2024 16:26:03 -0400 Subject: [PATCH 1/8] changing version to v1.0.0 --- DESCRIPTION | 2 +- README.md | 42 ++++++------------------------------------ 2 files changed, 7 insertions(+), 37 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 02320b6..d36b526 100644 --- a/DESCRIPTION +++ b/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( diff --git a/README.md b/README.md index 72aafb7..8f2b79e 100644 --- a/README.md +++ b/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. From acd155149ad8284e5b4a8fe0396b4dfe65272e85 Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Mon, 15 Apr 2024 16:29:03 -0400 Subject: [PATCH 2/8] Add News.md with info about version used for bugphyzzExports --- NEWS.md | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 NEWS.md diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..d3a8b8e --- /dev/null +++ b/NEWS.md @@ -0,0 +1,3 @@ +# taxPPro 1.0.0 + +* This first version was used for the v1.0.0 relase of bugphyzzExports. From 7e28949dec71d2f3c78295f00296ccb2510d6c3a Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Mon, 15 Apr 2024 16:45:38 -0400 Subject: [PATCH 3/8] fix bug in vignette --- vignettes/articles/nsti.Rmd | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/vignettes/articles/nsti.Rmd b/vignettes/articles/nsti.Rmd index 0a1e466..ee669eb 100644 --- a/vignettes/articles/nsti.Rmd +++ b/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 From d734d427504a2ed17c3eda0762afaef7a0f3fc46 Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Fri, 19 Apr 2024 16:01:27 -0400 Subject: [PATCH 4/8] update DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d36b526..7d6d4fe 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -21,7 +21,7 @@ VignetteBuilder: knitr Depends: R (>= 4.3) Remotes: - waldronlab/bugphyzz@sdgamboa/release18 + waldronlab/bugphyzz@sdgamboa-bpscores Suggests: knitr, rmarkdown, From b047d9ace6393d0a42b8922e8084e579bb0cbdc9 Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Mon, 6 May 2024 14:13:32 -0400 Subject: [PATCH 5/8] Change bugphyzz version in DESCRIPTION --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7d6d4fe..9b7e8b4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -21,7 +21,7 @@ VignetteBuilder: knitr Depends: R (>= 4.3) Remotes: - waldronlab/bugphyzz@sdgamboa-bpscores + waldronlab/bugphyzz Suggests: knitr, rmarkdown, From 008026c9ad3456c5cd0b462ae3c585f5492e6076 Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Mon, 6 May 2024 14:23:30 -0400 Subject: [PATCH 6/8] remove docker tag for bioc (set to latest) --- .github/workflows/pkgdown.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index dfa8831..3adc103 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.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 env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} From a83f1ed4a0d5f538476fbbd99459fc4cd3b7df9e Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Mon, 6 May 2024 14:34:07 -0400 Subject: [PATCH 7/8] update docker tag to RELEASE_3_19 --- .github/workflows/pkgdown.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 3adc103..64d04a0 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -14,7 +14,7 @@ name: pkgdown jobs: pkgdown: runs-on: ubuntu-latest - container: bioconductor/bioconductor_docker + container: bioconductor/bioconductor_docker:RELEASE_3_19 env: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} From b0460fea862c585c5c79b0998e37fd61d3e7a601 Mon Sep 17 00:00:00 2001 From: sdgamboa Date: Thu, 9 May 2024 11:27:25 -0400 Subject: [PATCH 8/8] change bugphyzz from 'Depends' to 'Suggests' --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9b7e8b4..b794f38 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -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