Release 3.12 (#31)

* fix for #18 (#19)

- incorrect use of `$assay` replaced with `$data` for DatasetExperiment objects
- specify SummarizedExperiment package as source of `rowData` and `colData` functions

* fix for #20 (#21)

data now gets passed through as intended when model_seq is being used. Allows seq_in to be used at the nth step in a sequence

* fix for #20 (#23)

data now gets passed through as intended when model_seq is being used. Allows seq_in to be used at the nth step in a sequence

* Issue 22 seq in (#24)

* add seq_in generics

* add seq_in methods

- added methods for models to get.set seq_in
- added checks for valid input/output names to seq_in and predicted_name methods

* update documentation

* use correct input param id

* update documentation

- use of input_1 instead of value_1 fixed in examples
- corrected rdname for seq_in

* add as.code method (#25)

* add as.code method

produces a string of text that can be used to recreate the model/sequence/iterator

* use correct input parameter names

cmd check fails if examples dont run

* Issue 27 citations (#29)

* add citations and libraries methods for #27

- these methods scan over all inherited objects and generate a complte ist of citations/libraries
- a citations slot has been added to struct_class

* use bibtex for citations

The citations slot is now a list of bibentry objects to provide a more formalised method for storing citations and make them easer to use with bibliography packages etc.

* update imports for utils package

* fix various cmd and bioc check issues

- add importFrom utils citation to namespace
- replace incorrect use of "error" with "stop"
- use first index of class() output in messages

* Update NEWS

* version bump

* fix typo in documentation

Author: grlloyd

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: struct
 Type: Package
 Title: Statistics in R Using Class-based Templates
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: c(
     person(
         c("Gavin","Rhys"),
@@ -49,7 +49,7 @@ Collate:
     'resampler_class.R'
     'struct.R'
     'struct_templates.R'
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 Depends: R (>= 4.0)
 Suggests: 
  testthat,

NAMESPACE

@@ -8,11 +8,13 @@ export("param_value<-")
 export(DatasetExperiment)
 export(as.DatasetExperiment)
 export(as.SummarizedExperiment)
+export(as.code)
 export(as_data_frame)
 export(calculate)
 export(chart)
 export(chart_names)
 export(chart_plot)
+export(citations)
 export(entity)
 export(entity_stato)
 export(enum)
@@ -24,6 +26,7 @@ export(iris_DatasetExperiment)
 export(is_output)
 export(is_param)
 export(iterator)
+export(libraries)
 export(max_length)
 export(metric)
 export(model)
@@ -52,6 +55,7 @@ export(resampler)
 export(result)
 export(result_name)
 export(run)
+export(seq_in)
 export(set_obj_method)
 export(set_obj_show)
 export(set_struct_obj)
@@ -81,17 +85,21 @@ exportMethods("param_obj<-")
 exportMethods("param_value<-")
 exportMethods("predicted_name<-")
 exportMethods("result_name<-")
+exportMethods("seq_in<-")
 exportMethods("value<-")
 exportMethods(as.DatasetExperiment)
 exportMethods(as.SummarizedExperiment)
+exportMethods(as.code)
 exportMethods(calculate)
 exportMethods(chart_names)
 exportMethods(chart_plot)
+exportMethods(citations)
 exportMethods(evaluate)
 exportMethods(export_xlsx)
 exportMethods(is_output)
 exportMethods(is_param)
 exportMethods(length)
+exportMethods(libraries)
 exportMethods(max_length)
 exportMethods(model_apply)
 exportMethods(model_predict)
@@ -113,6 +121,7 @@ exportMethods(predicted_name)
 exportMethods(result)
 exportMethods(result_name)
 exportMethods(run)
+exportMethods(seq_in)
 exportMethods(stato_definition)
 exportMethods(stato_id)
 exportMethods(stato_name)
@@ -126,4 +135,8 @@ importFrom(graphics,plot)
 importFrom(knitr,purl)
 importFrom(ontologyIndex,get_ontology)
 importFrom(stats,runif)
+importFrom(utils,as.person)
+importFrom(utils,bibentry)
+importFrom(utils,capture.output)
+importFrom(utils,citation)
 importFrom(utils,file.edit)

NEWS

@@ -1,3 +1,13 @@
+Changes in 1.1.1
++ added citations slot to struct classes
++ added corresponding citations method
++ added method to get/set seq_in slot
++ as.SummarizedExepriment now works correctly
++ using seq_in now works for sequences with more than 2 steps
+
+Changes in 1.0.0
++ Biconductor 3.11 release
+
 Changes in 0.99.10
 + update vignettes
 + update documentation