{
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  "Package": "struct",
  "Type": "Package",
  "Title": "Statistics in R Using Class-based Templates",
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  "Authors@R": "c(\nperson(\nc(\"Gavin\",\"Rhys\"),\n\"Lloyd\",\nrole=c(\"aut\",\"cre\"),\nemail=\"g.r.lloyd@bham.ac.uk\"),\nperson(\nc(\"Ralf\",\"Johannes\", \"Maria\"),\n\"Weber\",\nrole=c(\"aut\"),\nemail=\"r.j.weber@bham.ac.uk\")\n)",
  "Description": "Defines and includes a set of class-based templates for\ndeveloping and implementing data processing and analysis\nworkflows, with a strong emphasis on statistics and machine\nlearning. The templates can be used and where needed extended\nto 'wrap' tools and methods from other packages into a common\nstandardised structure to allow for effective and fast\nintegration. Model objects can be combined into sequences, and\nsequences nested in iterators using overloaded operators to\nsimplify and improve readability of the code. Ontology lookup\nhas been integrated and implemented to provide standardised\ndefinitions for methods, inputs and outputs wrapped using the\nclass-based templates.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Collate": "'generics.R' 'ontology_term_class.R' 'struct_class.R'\n'parameter_class.R' 'chart_class.R' 'DatasetExperiment_class.R'\n'entity_class.R' 'enum_class.R' 'output_class.R'\n'model_class.R' 'example_objects.R' 'model_list_class.R'\n'metric_class.R' 'iterator_class.R' 'optimiser_class.R'\n'preprocess_class.R' 'resampler_class.R' 'struct-package.R'\n'struct_templates.R' 'zzz.R'",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:45 UTC",
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  "Author": "Gavin Rhys Lloyd [aut, cre],\nRalf Johannes Maria Weber [aut]",
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    ".struct_class",
    "as_data_frame",
    "as.code",
    "as.DatasetExperiment",
    "as.SummarizedExperiment",
    "calculate",
    "chart",
    "chart_names",
    "chart_plot",
    "citations",
    "DatasetExperiment",
    "entity",
    "enum",
    "evaluate",
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    "example_iterator",
    "example_model",
    "export_xlsx",
    "get_description",
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    "libraries",
    "max_length",
    "max_length<-",
    "metric",
    "model",
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    "model_predict",
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    "model_train",
    "models",
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    "param_value",
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    "result",
    "result_name",
    "result_name<-",
    "run",
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    "seq_in<-",
    "set_obj_method",
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    "struct_template",
    "test_metric",
    "value",
    "value<-"
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    {
      "page": "autocompletion",
      "title": "autocompletion",
      "topics": [
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        ".DollarNames,DatasetExperiment-method",
        ".DollarNames,iterator-method",
        ".DollarNames,metric-method",
        ".DollarNames,model-method",
        ".DollarNames,optimiser-method",
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      "page": "cash-ontology_list-method",
      "title": "Get/set ontology_list slots",
      "topics": [
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      ]
    },
    {
      "page": "cash-ontology_term-method",
      "title": "Get/set ontology term slots",
      "topics": [
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      ]
    },
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      "page": "cash-struct_class-method",
      "title": "Get/set parameter or output values",
      "topics": [
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      ]
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      "title": "Get/set parameter or output values",
      "topics": [
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      ]
    },
    {
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      "title": "convert to data.frame",
      "topics": [
        "as_data_frame"
      ]
    },
    {
      "page": "as.code",
      "title": "Convert to code",
      "topics": [
        "as.code",
        "as.code,iterator-method",
        "as.code,model_seq-method",
        "as.code,struct_class-method"
      ]
    },
    {
      "page": "as.DatasetExperiment",
      "title": "Convert a SummarizedExperiment to DatasetExperiment",
      "topics": [
        "as.DatasetExperiment"
      ]
    },
    {
      "page": "as.DatasetExperiment-SummarizedExperiment-method",
      "title": "Convert a SummarizedExperiment to DatasetExperiment",
      "topics": [
        "as.DatasetExperiment,SummarizedExperiment-method"
      ]
    },
    {
      "page": "as.SummarizedExperiment",
      "title": "Convert a DatasetExperiment to a SummarizedExperiment",
      "topics": [
        "as.SummarizedExperiment"
      ]
    },
    {
      "page": "as.SummarizedExperiment-DatasetExperiment-method",
      "title": "Convert a DatasetExperiment to SummarizedExperiment",
      "topics": [
        "as.SummarizedExperiment,DatasetExperiment-method"
      ]
    },
    {
      "page": "metric",
      "title": "Calculate metric",
      "topics": [
        "calculate",
        "calculate,metric-method",
        "max_length<-",
        "metric",
        "value",
        "value,metric-method",
        "value<-",
        "value<-,metric-method"
      ]
    },
    {
      "page": "chart",
      "title": "Constructor for struct chart objects",
      "topics": [
        "chart"
      ]
    },
    {
      "page": "chart_names",
      "title": "chart names",
      "topics": [
        "chart_names",
        "chart_names,struct_class-method"
      ]
    },
    {
      "page": "chart_plot",
      "title": "chart_plot",
      "topics": [
        "chart_plot",
        "chart_plot,chart,ANY-method"
      ]
    },
    {
      "page": "citations",
      "title": "Citations for an object",
      "topics": [
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        "citations,struct_class-method"
      ]
    },
    {
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      "title": "DatasetExperiment class",
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        "$<-,DatasetExperiment-method",
        "DatasetExperiment"
      ]
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    {
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      "title": "Enum objects",
      "topics": [
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        "value<-,enum-method"
      ]
    },
    {
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      "title": "example chart object",
      "topics": [
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        "example_chart"
      ]
    },
    {
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      "title": "Example iterator",
      "topics": [
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        "example_iterator-class",
        "run,example_iterator,DatasetExperiment,metric-method"
      ]
    },
    {
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      "title": "Example model",
      "topics": [
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        "model_predict,example_model,DatasetExperiment-method",
        "model_train,example_model,DatasetExperiment-method"
      ]
    },
    {
      "page": "export_data",
      "title": "write a dataset object to file",
      "topics": [
        "export_xlsx",
        "export_xlsx,DatasetExperiment-method"
      ]
    },
    {
      "page": "get_description",
      "title": "Get struct object help description",
      "topics": [
        "get_description"
      ]
    },
    {
      "page": "iris_DatasetExperiment",
      "title": "Fisher's Iris data",
      "topics": [
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      ]
    },
    {
      "page": "is_output",
      "title": "Verify output",
      "topics": [
        "is_output",
        "is_output,struct_class-method"
      ]
    },
    {
      "page": "is_param",
      "title": "Verify parameter",
      "topics": [
        "is_param",
        "is_param,struct_class-method"
      ]
    },
    {
      "page": "libraries",
      "title": "Libraries for an object",
      "topics": [
        "libraries",
        "libraries,struct_class-method"
      ]
    },
    {
      "page": "entity",
      "title": "get the max value vector length for an entity",
      "topics": [
        "entity",
        "max_length",
        "max_length,entity-method",
        "max_length<-,entity-method",
        "value,entity-method",
        "value<-,entity-method"
      ]
    },
    {
      "page": "model",
      "title": "model class",
      "topics": [
        "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"
      ]
    },
    {
      "page": "model_apply",
      "title": "Apply a model",
      "topics": [
        "model_apply"
      ]
    },
    {
      "page": "predict",
      "title": "Model prediction",
      "topics": [
        "model_predict"
      ]
    },
    {
      "page": "model_reverse",
      "title": "Reverse preprocessing",
      "topics": [
        "model_reverse"
      ]
    },
    {
      "page": "model_seq",
      "title": "model_seq class",
      "topics": [
        "+,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"
      ]
    },
    {
      "page": "train",
      "title": "Train a model",
      "topics": [
        "model_train"
      ]
    },
    {
      "page": "models",
      "title": "Get/set models of a model_seq",
      "topics": [
        "models",
        "models<-"
      ]
    },
    {
      "page": "new_struct",
      "title": "Generate a 'struct' object from a Class",
      "topics": [
        "new_struct"
      ]
    },
    {
      "page": "ontology",
      "title": "Ontology for an object",
      "topics": [
        "length,ontology_list-method",
        "ontology",
        "ontology,model_seq-method",
        "ontology,struct_class-method",
        "ontology_list",
        "ontology_term",
        "[,ontology_list,ANY,ANY,ANY-method",
        "[<-,ontology_list,ANY,ANY,ANY-method",
        "[[,ontology_list,ANY,ANY-method"
      ]
    },
    {
      "page": "ontology_online",
      "title": "Enable or disable Ontology Lookup Service (OLS) requests",
      "topics": [
        "ontology_online"
      ]
    },
    {
      "page": "optimiser",
      "title": "optimiser class",
      "topics": [
        "optimiser"
      ]
    },
    {
      "page": "output_ids",
      "title": "Output identifiers",
      "topics": [
        "output_ids",
        "output_ids,struct_class-method"
      ]
    },
    {
      "page": "output_list",
      "title": "output list",
      "topics": [
        "output_list",
        "output_list,struct_class-method",
        "output_list<-",
        "output_list<-,struct_class,list-method"
      ]
    },
    {
      "page": "output_name",
      "title": "output name",
      "topics": [
        "output_name",
        "output_name,struct_class,character-method"
      ]
    },
    {
      "page": "output_obj",
      "title": "Output objects",
      "topics": [
        "output_obj",
        "output_obj,struct_class,character-method",
        "output_obj<-",
        "output_obj<-,struct_class,character-method"
      ]
    },
    {
      "page": "output_value",
      "title": "output values",
      "topics": [
        "output_value",
        "output_value,struct_class,character-method",
        "output_value<-",
        "output_value<-,struct_class,character-method"
      ]
    },
    {
      "page": "param_ids",
      "title": "Parameter identifiers",
      "topics": [
        "param_ids",
        "param_ids,struct_class-method"
      ]
    },
    {
      "page": "param_list",
      "title": "Parameter list",
      "topics": [
        "param_list",
        "param_list,struct_class-method",
        "param_list<-",
        "param_list<-,struct_class,list-method"
      ]
    },
    {
      "page": "param_name",
      "title": "Parameter name",
      "topics": [
        "param_name",
        "param_name,struct_class,character-method"
      ]
    },
    {
      "page": "param_obj",
      "title": "Parameter objects",
      "topics": [
        "param_obj",
        "param_obj,struct_class,character-method",
        "param_obj<-",
        "param_obj<-,struct_class,character-method"
      ]
    },
    {
      "page": "param_value",
      "title": "Parameter values",
      "topics": [
        "param_value",
        "param_value,struct_class,character-method",
        "param_value<-",
        "param_value<-,struct_class,character-method"
      ]
    },
    {
      "page": "predicted",
      "title": "Prediction output",
      "topics": [
        "predicted"
      ]
    },
    {
      "page": "predicted_name",
      "title": "Predicted output name",
      "topics": [
        "predicted_name",
        "predicted_name<-"
      ]
    },
    {
      "page": "preprocessing",
      "title": "preprocessing class",
      "topics": [
        "model_reverse,preprocess,DatasetExperiment-method",
        "preprocess"
      ]
    },
    {
      "page": "resampler",
      "title": "resampler class",
      "topics": [
        "resampler"
      ]
    },
    {
      "page": "result",
      "title": "Iterator result",
      "topics": [
        "result"
      ]
    },
    {
      "page": "result_name",
      "title": "get/set output name as prediction output for a model",
      "topics": [
        "result_name",
        "result_name<-"
      ]
    },
    {
      "page": "iterator",
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      "filename": "struct_templates_and_helper_functions.html",
      "title": "Introduction to STRUCT - STatistics in R using Class-based Templates",
      "author": "Gavin R Lloyd, Ralf J Weber",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "Getting started",
        "struct helper functions",
        "Creating a new struct object",
        "Changing the default methods",
        "Changing the default show output",
        "Class-based templates and struct objects",
        "DatasetExperiment objects",
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        "chart objects",
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      "modified": "2026-04-13 16:24:06",
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