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# taxPPro - Taxonomic and Phylogenetic Propagation | ||
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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. | ||
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The functions in this package are used in the bugphyzzExports script. | ||
Check the waldronlab/bugphyzzExports repository on GitHun for details. | ||
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The package can be installed with: | ||
## Installaion | ||
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``` | ||
if (!require("BiocManager", quietly = TRUE)) | ||
install.packages("BiocManager") | ||
BiocManager::install('sdgamboa/taxPPro') | ||
BiocManager::install('waldronlab/taxPPro') | ||
``` | ||
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Types of data (spreadsheets) | ||
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**Binary data with only TRUE values -- binary-T** | ||
+ Merge Attribute and Atribute_value. | ||
+ Don't propagate. | ||
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**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. | ||
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**Multistate-Union with binary data with only TRUE values -- multistate-union-T** | ||
+ Merge Attribute and Attribute_value. | ||
+ Don't propagate. | ||
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**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. | ||
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**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). | ||
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**Numeric -- numeric** | ||
+ Convert to range. | ||
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**Range -- range** | ||
+ Convert to categorical. |