Man pages for RJ333/phyloseq2ML
Connects Phyloseq To Ranger And Keras
| add_sample_data | Select sample data variables and add them to the count... |
| add_unique_lineages | Add columns with unique lineages to phyloseq 'tax_table()' |
| augment | Replicate observations with added noise. |
| augment_and_noise | Replicate observations with added noise. |
| build_the_model | Build and compile keras sequential models with 2 hidden... |
| categoric_to_factor | Reverse keras::to_categorical |
| categorize | Categorize continuous values into classes. |
| categorize_response_variable | Categorize continuous response variable columns. |
| classification_metrics | calculate measures for classification performance |
| create_community_table_subsets | Create subsets of phyloseq objects based on ASV/OTU counts... |
| create_taxonomy_lookup | Creates a dictionary list to translate taxonomic ranks. |
| dummify_input_tables | Turn response column levels into dummy variables. |
| extract_parameters | Extract parameters from named input list. |
| extract_response_variable | Extract response variable columns from phyloseq sample data... |
| filter_subsets | Remove ASV/OTU/etc from a phyloseq object based on relative... |
| initialize_results | This function sets up a parameter data frame. |
| inputtables_to_keras | Separate independent variables from response column for... |
| is.dummy | Tests if a vector is a dummy column |
| is.wholenumber | Tests if a numeric vector is completely consisting of... |
| keras_classification | Run keras tensorflow classification. |
| keras_regression | Run keras tensorflow regression |
| merge_input_response | Merge all community tables with each response variable. |
| otu_table_to_df | Turn subsets of phyloseq objects into relative abundance... |
| pipe | Pipe operator |
| prediction_accuracy | Calculate accuracy percentage for ranger predicted_rfs |
| ranger_classification | Run ranger with parameters of data.frame rows. |
| ranger_regression | Run ranger regression with parameters of data.frame rows. |
| scaling | Apply scaling to numeric columns in test and train sets. |
| split_data | Split data frames according to a ratio into training and test... |
| standardize_phyloseq_headers | Change naming style of the taxa in the phyloseq object. |
| store_classification | Store results from ranger classification training and... |
| store_classification_results | Store results from keras tf classification training and... |
| store_regression | Store results from ranger regression training and prediction. |
| store_regression_results | Store results from keras tf regression training and... |
| TNT_communities | Microbial communities in ammunition contaminated sediments. |
| to_relative_abundance | Turn otu_table() of phyloseq objects to relative abundance |
| translate_ID | Translate unique IDs such as ASV/OTUs to specified tax rank. |
