Package: struct 1.25.0

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:Gavin Rhys Lloyd [aut, cre], Ralf Johannes Maria Weber [aut]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
struct/json (API)

# Install 'struct' in R:

install.packages('struct', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:struct-1.25.0(bioc 3.24)struct-1.24.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

workflowstep

6.11 score 3 packages 90 scripts 501 downloads 4 mentions 77 exports 37 dependencies

Last updated from:1d098a078e. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	248
linux-devel-x86_64	OK	298
source / vignettes	OK	255
linux-release-x86_64	OK	299
macos-release-arm64	OK	147
macos-oldrel-arm64	OK	169
windows-devel	OK	261
windows-release	OK	214
windows-oldrel	OK	219
wasm-release	OK	135

Exports:.DollarNames .struct_class as_data_frame as.code as.DatasetExperiment as.SummarizedExperiment calculate chart chart_names chart_plot citations DatasetExperiment entity enum evaluate example_chart example_iterator example_model export_xlsx get_description iris_DatasetExperiment is_output is_param iterator libraries max_length max_length<-metric model model_apply model_predict model_reverse model_seq model_train models models<-new_struct ontology ontology_list ontology_online ontology_term optimiser output_ids output_list output_list<-output_name output_obj output_obj<-output_value output_value<-param_ids param_list param_list<-param_name param_obj param_obj<-param_value param_value<-predicted predicted_name predicted_name<-preprocess resampler result result_name result_name<-run seq_in seq_in<-set_obj_method set_obj_show set_struct_obj struct_class struct_template test_metric value value<-

Dependencies:abind askpass Biobase BiocGenerics cli curl DelayedArray evaluate generics GenomicRanges glue highr httr2 IRanges jsonlite knitr lattice lifecycle magrittr Matrix MatrixGenerics matrixStats openssl R6 rappdirs rlang S4Arrays S4Vectors Seqinfo SparseArray SummarizedExperiment sys vctrs withr xfun XVector yaml

Introduction to STRUCT - STatistics in R using Class-based Templates

Rendered fromstruct_templates_and_helper_functions.Rmdusingknitr::rmarkdown

Last update: 2026-04-13
Started: 2020-04-23

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
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
Enum objects	enum value<-,enum-method
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,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
Enable or disable Ontology Lookup Service (OLS) requests	ontology_online
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
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

Package: struct 1.25.0

struct: Statistics in R Using Class-based Templates

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