Skip to content

Commit

Permalink
changing version to v1.0.0
Browse files Browse the repository at this point in the history
  • Loading branch information
sdgamboa committed Apr 15, 2024
1 parent 86035bd commit 2afc189
Show file tree
Hide file tree
Showing 2 changed files with 7 additions and 37 deletions.
2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
@@ -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(
Expand Down
42 changes: 6 additions & 36 deletions README.md
Original file line number Diff line number Diff line change
@@ -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.

0 comments on commit 2afc189

Please sign in to comment.