Merge pull request #45 from LotharukpongJS/master

Removed `taxonomy()` function to deprecation of `taxize()`.
drostlab · Sep 30, 2024 · dca16b6 · dca16b6
2 parents 435da0f + 5e5a50e
commit dca16b6
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: myTAI
 Type: Package
 Title: Evolutionary Transcriptomics
-Version: 1.0.1.9000
+Version: 1.0.2.9000
 Date: 2023-07-08
 Authors@R: c(person("Hajk-Georg", "Drost",
                 role = c("aut", "cre"),
@@ -56,7 +56,6 @@ Suggests:
     devtools (>= 1.6.1),
     testthat (>= 0.9.1),
     mgcv,
-    taxize (>= 0.6.0),
     Seurat,
     decor,
     RcppThread

diff --git a/NAMESPACE b/NAMESPACE
@@ -62,7 +62,6 @@ export(rcpp_tei_parallel)
 export(reversehourglassScore)
 export(rhScore)
 export(taxid)
-export(taxonomy)
 export(tf)
 export(tfPS)
 export(tfStability)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,13 @@
+myTAI 1.0.2.9000
+===========
+## New Functions
+- New function `tfPS()` : Perform transformation of phylostratum values, analogous to `PS()` which transforms expression levels. Currently, `tfPS()` supports quantile rank transformation.
+- New function `PairwiseTest()` : Statistically evaluate the pairwise difference in the phylotranscriptomic pattern between two contrasts based on \code{\link{TAI}} or \code{\link{TDI}} computations.
+- New function `pairScore()` : Compute pairwise difference in TAI (or TDI) score.
+
+## Bug and Issue Fixes
+- Removed `taxonomy()` and references to it due to the deprecation of `taxize()`. This is needed for CRAN submission.
+
 myTAI 1.0.1.9000
 ===========
 ## New Functions

diff --git a/R/taxonomy.R b/R/taxonomy.R
diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -8,6 +8,5 @@ articles:
   Intermediate: Intermediate.html
   Introduction: Introduction.html
   Phylostratigraphy: Phylostratigraphy.html
-  Taxonomy: Taxonomy.html
 last_built: 2024-05-24T09:34Z
 
diff --git a/docs/reference/index.html b/docs/reference/index.html
diff --git a/docs/search.json b/docs/search.json