Class that defines the Replace Outputs
ReplaceOutputs.RdThis R6 class allows to, given a template word document and a list of outputs, to add them at the given location in the text. It automates the time-consuming task of adding and formatting tables and figures to a word document. The two main inputs of the class are a template docx file, in this case a clinical trial report and a yaml file that will contain the names of the table/figures to be replaced and pointing to the new ones. The yml file, should have predefined structure and parameters to be set:
type. Indicates if it is a table (TBL) or a figure (FIG)
title. The title or caption of the table/figure in the template docx file
file. The name of the file (csv or image) to be used in the new version of the docx
widths. For tables only, a pre-defined column widths (useful for model parameter table, for example)
occurrence. Int. To be used when captions are duplicated for more than one figure/table. To set the order they appear in the word document.
An example of the yaml structure:
output_1:
type: TBL
title: "Caption of the output 1"
file: output_1.csv
widths: ~
occurrence: ~
output_2:
type: FIG
title: "Caption of the output 2"
file: output_2.png
Active bindings
template_docx_filenameActive binding for setting the path to the template docx
outputs_pathActive binding for setting the path to the folder with the outputs
doc_final_filenameActive binding for setting the path for the updated docx file
yml_filenameActive binding for setting the path to the yaml file
Methods
Method new()
Usage
ReplaceOutputs$new(
template_docx_filename = NA_character_,
outputs_path = NA_character_,
doc_final_filename = NA_character_,
yml_filename = NA_character_
)Arguments
template_docx_filenameString. File name of the template docx to be modified. For example, "/path/to/file/filename.docx"
outputs_pathString. Path to the folder with the outputs (figures and tables-csvs) that will be added to the new version of the docx
doc_final_filenameString. File name of the updated version of the docx file. For example, "/path/to/file/filename_updated.docx"
yml_filenameString. File name of the yaml file that will guide the replacement of the outputs (tables and figures) in the updated docx. For example, "/path/to/file/filename.yml"
Examples
uo <- ReplaceOutputs$new(
template_docx_filename = system.file("use_cases/02_automated_reporting",
"Automated_Reporting_Example.docx",
package="rdocx"),
outputs_path = system.file("use_cases/02_automated_reporting/example_outputs",
package="rdocx"),
doc_final_filename = "./test.docx",
yml_filename = system.file("use_cases/02_automated_reporting",
"example_yml_1.yml",
package="rdocx")
)
Method get_captions_to_yml()
Get captions to yaml Given a docx file, it scans the document to find the Figures and Tables captions and provides a yaml file with all the figures and tables found. It also scans the document for possible "Source:" which has to be after a placeholder figure/table. If source was found, it will be added to "file" param in the yaml file.
Arguments
yml_caption_filenameString. File name of the newly created yaml file that will contain the Figures and Tables of in the provided docx document. For example, "/path/to/file/filename.yml" It will follow the required format for the replacement of the outputs (tables and figures) to update docx.
output_1: type: TBL title: "Caption of the output 1" file: ~ widths: ~ occurrence: ~ output_2: type: FIG title: "Caption of the output 2" file: ~ widths: ~ occurrence: ~
Examples
uo <- ReplaceOutputs$new(
template_docx_filename = system.file("use_cases/02_automated_reporting",
"Automated_Reporting_Example.docx",
package="rdocx"),
outputs_path = system.file("use_cases/02_automated_reporting/example_outputs",
package="rdocx"),
doc_final_filename = "./test.docx"
)
uo$get_captions_to_yml(yml_caption_filename="./test_yml.yml")
Method update_all_outputs()
Update all outputs. It iterates through all the outputs in the yml file, and assigns them in the correct location in the updated docx. If no "file" param given (NA or NULL), it will skip the output.
Examples
uo <- ReplaceOutputs$new(
template_docx_filename = system.file("use_cases/02_automated_reporting",
"Automated_Reporting_Example.docx",
package="rdocx"),
outputs_path = system.file("use_cases/02_automated_reporting/example_outputs",
package="rdocx"),
doc_final_filename = "./test.docx",
yml_filename = system.file("use_cases/02_automated_reporting",
"example_yml_1.yml",
package="rdocx")
)
uo$update_all_outputs()Examples
## ------------------------------------------------
## Method `ReplaceOutputs$new`
## ------------------------------------------------
uo <- ReplaceOutputs$new(
template_docx_filename = system.file("use_cases/02_automated_reporting",
"Automated_Reporting_Example.docx",
package="rdocx"),
outputs_path = system.file("use_cases/02_automated_reporting/example_outputs",
package="rdocx"),
doc_final_filename = "./test.docx",
yml_filename = system.file("use_cases/02_automated_reporting",
"example_yml_1.yml",
package="rdocx")
)
## ------------------------------------------------
## Method `ReplaceOutputs$get_captions_to_yml`
## ------------------------------------------------
uo <- ReplaceOutputs$new(
template_docx_filename = system.file("use_cases/02_automated_reporting",
"Automated_Reporting_Example.docx",
package="rdocx"),
outputs_path = system.file("use_cases/02_automated_reporting/example_outputs",
package="rdocx"),
doc_final_filename = "./test.docx"
)
uo$get_captions_to_yml(yml_caption_filename="./test_yml.yml")
## ------------------------------------------------
## Method `ReplaceOutputs$update_all_outputs`
## ------------------------------------------------
uo <- ReplaceOutputs$new(
template_docx_filename = system.file("use_cases/02_automated_reporting",
"Automated_Reporting_Example.docx",
package="rdocx"),
outputs_path = system.file("use_cases/02_automated_reporting/example_outputs",
package="rdocx"),
doc_final_filename = "./test.docx",
yml_filename = system.file("use_cases/02_automated_reporting",
"example_yml_1.yml",
package="rdocx")
)
uo$update_all_outputs()
#> INFO [15:20:46.836] Word template filename: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/Automated_Reporting_Example.docx
#> INFO [15:20:46.867] Outputs path: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_outputs
#> INFO [15:20:46.874] Yml filename: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_yml_1.yml
#> INFO [15:20:46.875] Final doc filename: ./test.docx
#> INFO [15:20:46.876] Date and time: 2024-11-19 15:20:46.8759 UTC
#> INFO [15:20:46.877] DaVinci user: runner
#> INFO [15:20:46.878] ****************************************************************
#> INFO [15:20:46.919] Output: FIG Data Point Distribution in Sample Set A
#> INFO [15:20:47.160] Figure updated with: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_outputs/Figure_2_1_Data_Point_Distribution.png
#> INFO [15:20:47.161] Output: FIG Comparative Analysis of Categories X and Y
#> INFO [15:20:47.358] Figure updated with: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_outputs/Figure_2_2_Comparative_Analysis.png
#> INFO [15:20:47.359] Output: FIG Comparative Analysis of Categories X and Y
#> INFO [15:20:47.559] Figure updated with: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_outputs/Figure_2_3_Comparative_Analysis.png
#> INFO [15:20:47.560] Output: FIG Trend Analysis Over Time (Yearly Data)
#> INFO [15:20:47.755] Figure updated with: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_outputs/Figure_2_4_Trend_Analysis.png
#> INFO [15:20:47.756] Output: FIG Trend Analysis Over Time (Yearly Data)
#> INFO [15:20:47.951] Figure updated with: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_outputs/Figure_2_5_Trend_Analysis.png
#> INFO [15:20:47.952] Output: FIG Trend Analysis Over Time (Monthly Data)
#> INFO [15:20:48.146] Figure updated with: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_outputs/Figure_3_1_Trend_Analysis.png
#> INFO [15:20:48.147] Output: TBL Summary of Sample Statistics
#> INFO [15:20:48.247] Table updated with: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_outputs/Table_2_1_Sample_Statistics.csv
#> INFO [15:20:48.248] Output: TBL Breakdown of Category X by Subcategory
#> INFO [15:20:48.338] Table updated with: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_outputs/Table_2_2_Breakdown_of_Category_X.csv
#> INFO [15:20:48.339] Output: TBL Yearly Performance Metrics
#> INFO [15:20:48.453] Table updated with: /home/runner/work/_temp/Library/rdocx/use_cases/02_automated_reporting/example_outputs/Table_3_1_Yearly_Performance_Metrics.csv
#> INFO [15:20:48.612] Docx saved!! File located at: ./test.docx
#> INFO [15:20:48.613] ****************************************************************
#> INFO [15:20:48.614] Information about this R session
#> INFO [15:20:48.615] [1] "/home/runner/work/_temp/Library" "/opt/R/4.4.2/lib/R/site-library"
#> INFO [15:20:48.615] [3] "/opt/R/4.4.2/lib/R/library"
#> INFO [15:20:48.616] ****************************************************************
#> INFO [15:20:48.629] R version 4.4.2 (2024-10-31)
#> INFO [15:20:48.629] Platform: x86_64-pc-linux-gnu
#> INFO [15:20:48.629] Running under: Ubuntu 22.04.5 LTS
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