Package: struct 1.19.0
Gavin Rhys Lloyd
struct: Statistics in R Using Class-based Templates
Defines and includes a set of class-based templates for developing and implementing data processing and analysis workflows, with a strong emphasis on statistics and machine learning. The templates can be used and where needed extended to 'wrap' tools and methods from other packages into a common standardised structure to allow for effective and fast integration. Model objects can be combined into sequences, and sequences nested in iterators using overloaded operators to simplify and improve readability of the code. Ontology lookup has been integrated and implemented to provide standardised definitions for methods, inputs and outputs wrapped using the class-based templates.
Authors:
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struct.pdf |struct.html✨
struct/json (API)
NEWS
| # Install 'struct' in R: |
| install.packages('struct', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:struct-1.19.0(bioc 3.21)struct-1.18.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:fd866cf155. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | NOTE | Dec 19 2024 |
| R-4.5-linux | NOTE | Dec 19 2024 |
| R-4.4-win | NOTE | Dec 19 2024 |
| R-4.4-mac | NOTE | Dec 19 2024 |
| R-4.3-win | OK | Dec 19 2024 |
| R-4.3-mac | OK | Dec 19 2024 |
Exports:.DollarNames.struct_classas_data_frameas.codeas.DatasetExperimentas.SummarizedExperimentcalculatechartchart_nameschart_plotcitationsDatasetExperimententityentity_statoenumenum_statoevaluateexample_chartexample_iteratorexample_modelexport_xlsxget_descriptioniris_DatasetExperimentis_outputis_paramiteratorlibrariesmax_lengthmax_length<-metricmodelmodel_applymodel_predictmodel_reversemodel_seqmodel_trainmodelsmodels<-new_structontologyontology_listontology_termoptimiseroutput_idsoutput_listoutput_list<-output_nameoutput_objoutput_obj<-output_valueoutput_value<-param_idsparam_listparam_list<-param_nameparam_objparam_obj<-param_valueparam_value<-predictedpredicted_namepredicted_name<-preprocessresamplerresultresult_nameresult_name<-runseq_inseq_in<-set_obj_methodset_obj_showset_struct_objstatostato_definitionstato_idstato_namestato_summarystruct_classstruct_templatetest_metricvaluevalue<-
Dependencies:abindaskpassBiobaseBiocGenericsclicrayoncurlDelayedArrayevaluategenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehighrhttrhttr2IRangesjsonliteknitrlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeontologyIndexopensslR6rappdirsrlangrolsS4ArraysS4VectorsSparseArraySummarizedExperimentsysUCSC.utilsvctrswithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| autocompletion | .DollarNames,chart-method .DollarNames,DatasetExperiment-method .DollarNames,iterator-method .DollarNames,metric-method .DollarNames,model-method .DollarNames,optimiser-method .DollarNames,preprocess-method .DollarNames,resampler-method .DollarNames,struct_class-method .DollarNames.chart .DollarNames.DatasetExperiment .DollarNames.iterator .DollarNames.metric .DollarNames.model .DollarNames.optimiser .DollarNames.preprocess .DollarNames.resampler .DollarNames.struct_class |
| Get/set ontology_list slots | $,ontology_list-method |
| Get/set ontology term slots | $,ontology_term-method |
| Get/set parameter or output values | $,struct_class-method |
| Get/set parameter or output values | $<-,struct_class-method |
| convert to data.frame | as_data_frame |
| Convert to code | as.code as.code,iterator-method as.code,model_seq-method as.code,struct_class-method |
| Convert a SummarizedExperiment to DatasetExperiment | as.DatasetExperiment |
| Convert a SummarizedExperiment to DatasetExperiment | as.DatasetExperiment,SummarizedExperiment-method |
| Convert a DatasetExperiment to a SummarizedExperiment | as.SummarizedExperiment |
| Convert a DatasetExperiment to SummarizedExperiment | as.SummarizedExperiment,DatasetExperiment-method |
| catenate ontology_lists | c,ontology_list-method |
| Calculate metric | calculate calculate,metric-method max_length<- metric value value,metric-method value<- value<-,metric-method |
| Constructor for struct chart objects | chart |
| chart names | chart_names chart_names,struct_class-method |
| chart_plot | chart_plot chart_plot,chart,ANY-method |
| Citations for an object | citations citations,struct_class-method |
| DatasetExperiment class | $,DatasetExperiment-method $<-,DatasetExperiment-method DatasetExperiment |
| entity_stato class | entity_stato |
| Enum objects | enum value<-,enum-method |
| enum_stato class | enum_stato |
| example chart object | chart_plot,example_chart,example_model-method example_chart |
| Example iterator | example_iterator example_iterator-class run,example_iterator,DatasetExperiment,metric-method |
| Example model | example_model model_predict,example_model,DatasetExperiment-method model_train,example_model,DatasetExperiment-method |
| write a dataset object to file | export_xlsx export_xlsx,DatasetExperiment-method |
| Get struct object help description | get_description |
| Fisher's Iris data | iris_DatasetExperiment |
| Verify output | is_output is_output,struct_class-method |
| Verify parameter | is_param is_param,struct_class-method |
| Libraries for an object | libraries libraries,struct_class-method |
| get the max value vector length for an entity | entity max_length max_length,entity-method max_length<-,entity-method value,entity-method value<-,entity-method |
| model class | model model_apply,model,DatasetExperiment-method model_predict,model,DatasetExperiment-method model_reverse,model,DatasetExperiment-method model_train,model,DatasetExperiment-method predicted,model-method predicted_name,model-method predicted_name<-,model,character-method seq_in,model-method seq_in<-,model,character-method |
| Apply a model | model_apply |
| Model prediction | model_predict |
| Reverse preprocessing | model_reverse |
| model_seq class | +,model,model-method +,model,model_seq-method +,model_seq,model-method length,model_seq-method models,model_seq-method models<-,model_seq,list-method model_apply,model_seq,DatasetExperiment-method model_predict,model_seq,DatasetExperiment-method model_seq model_train,model_seq,DatasetExperiment-method predicted,model_seq-method [,model_seq,ANY,ANY,ANY-method [<-,model_seq,ANY,ANY,ANY-method |
| Train a model | model_train |
| Get/set models of a model_seq | models models<- |
| Generate a 'struct' object from a Class | new_struct |
| Ontology for an object | length,ontology_list-method ontology ontology,struct_class-method ontology_list ontology_term [,ontology_list,ANY,ANY,ANY-method [<-,ontology_list,ANY,ANY,ANY-method |
| optimiser class | optimiser |
| Output identifiers | output_ids output_ids,struct_class-method |
| output list | output_list output_list,struct_class-method output_list<- output_list<-,struct_class,list-method |
| output name | output_name output_name,struct_class,character-method |
| Output objects | output_obj output_obj,struct_class,character-method output_obj<- output_obj<-,struct_class,character-method |
| output values | output_value output_value,struct_class,character-method output_value<- output_value<-,struct_class,character-method |
| Parameter identifiers | param_ids param_ids,struct_class-method |
| Parameter list | param_list param_list,struct_class-method param_list<- param_list<-,struct_class,list-method |
| Parameter name | param_name param_name,struct_class,character-method |
| Parameter objects | param_obj param_obj,struct_class,character-method param_obj<- param_obj<-,struct_class,character-method |
| Parameter values | param_value param_value,struct_class,character-method param_value<- param_value<-,struct_class,character-method |
| Prediction output | predicted |
| Predicted output name | predicted_name predicted_name<- |
| preprocessing class | model_reverse,preprocess,DatasetExperiment-method preprocess |
| resampler class | resampler |
| Iterator result | result |
| get/set output name as prediction output for a model | result_name result_name<- |
| Run iterator | *,iterator,model_OR_iterator-method evaluate evaluate,iterator,metric-method iterator models,iterator-method models<-,iterator,model_OR_iterator-method result,iterator-method result_name,iterator-method result_name<-,iterator,character-method run run,iterator,DatasetExperiment,metric-method [,iterator,ANY,ANY,ANY-method [<-,iterator,ANY,ANY,ANY-method |
| Sequence input | seq_in seq_in<- |
| update method for a struct object | set_obj_method |
| a helper function to update the show method for a struct object | set_obj_show |
| define a new struct object | set_struct_obj |
| get the stato_id for an object | stato stato_definition stato_definition,stato-method stato_id stato_id,stato-method stato_name stato_name,stato-method stato_summary stato_summary,stato-method |
| Constructor for struct_class objects | struct_class |
| 'struct_class' object definition | .struct_class struct_class-class |
| StRUCT templates | struct_template |
| Example metric | calculate,test_metric-method test_metric test_metric-class |
