Package: Tplyr 1.2.1

Mike Stackhouse

Tplyr: A Traceability Focused Grammar of Clinical Data Summary

A traceability focused tool created to simplify the data manipulation necessary to create clinical summaries.

Authors:Eli Miller [aut], Mike Stackhouse [aut, cre], Ashley Tarasiewicz [aut], Nathan Kosiba [ctb], Sadchla Mascary [ctb], Andrew Bates [ctb], Shiyu Chen [ctb], Oleksii Mikryukov [ctb], Atorus Research LLC [cph]

Tplyr_1.2.1.tar.gz
Tplyr_1.2.1.zip(r-4.5)Tplyr_1.2.1.zip(r-4.4)Tplyr_1.2.1.zip(r-4.3)
Tplyr_1.2.1.tgz(r-4.4-any)Tplyr_1.2.1.tgz(r-4.3-any)
Tplyr_1.2.1.tar.gz(r-4.5-noble)Tplyr_1.2.1.tar.gz(r-4.4-noble)
Tplyr_1.2.1.tgz(r-4.4-emscripten)Tplyr_1.2.1.tgz(r-4.3-emscripten)
Tplyr.pdf |Tplyr.html✨
Tplyr/json (API)
NEWS

# Install 'Tplyr' in R:
install.packages('Tplyr', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/atorus-research/tplyr/issues

Datasets:

On CRAN:

pharmatables

9.78 score 95 stars 2 packages 137 scripts 618 downloads 95 exports 23 dependencies

Last updated 9 months agofrom:1fa6c4cd42. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 17 2024
R-4.5-winOKNov 17 2024
R-4.5-linuxOKNov 17 2024
R-4.4-winOKNov 17 2024
R-4.4-macOKNov 17 2024
R-4.3-winOKNov 17 2024
R-4.3-macOKNov 17 2024

Exports:%>%add_anti_joinadd_column_headersadd_filtersadd_layeradd_layersadd_missing_subjects_rowadd_risk_diffadd_total_groupadd_total_rowadd_treat_grpsadd_variablesappend_metadataapply_conditional_formatapply_formatsapply_row_masksbuildcollapse_row_labelsf_strget_byget_count_layer_formatsget_data_labelsget_desc_layer_formatsget_layer_templateget_layer_templatesget_meta_resultget_meta_subsetget_metadataget_numeric_dataget_pop_whereget_precision_byget_precision_onget_shift_layer_formatsget_stats_dataget_target_varget_tplyr_regexget_wheregroup_countgroup_descgroup_shiftheader_nheader_n<-keep_levelsnew_layer_templatepop_datapop_data<-pop_treat_varprocess_formattingprocess_metadataprocess_statistic_dataprocess_statistic_formattingprocess_summariesremove_layer_templatereplace_leading_whitespaceset_byset_count_layer_formatsset_custom_summariesset_denom_ignoreset_denom_whereset_denoms_byset_desc_layer_formatsset_distinct_byset_format_stringsset_header_nset_indentationset_limit_data_byset_missing_countset_missing_subjects_row_labelset_nest_countset_numeric_thresholdset_order_count_methodset_ordering_colsset_outer_sort_positionset_pop_dataset_pop_treat_varset_pop_whereset_precision_byset_precision_dataset_precision_onset_result_order_varset_shift_layer_formatsset_stats_as_columnsset_target_varset_total_row_labelset_treat_varset_wherestr_extract_fmt_groupstr_extract_numstr_indent_wraptplyr_layertplyr_metatplyr_tabletreat_grpstreat_varuse_template

Dependencies:assertthatclicpp11dplyrfansiforcatsgenericsgluelifecyclemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselectutf8vctrswithr

Count Layers

Rendered fromcount.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2020-11-20

Creating Custom Tplyr Metadata

Rendered fromcustom-metadata.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2022-10-14

Totals, Missings, and Denominators

Rendered fromdenom.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2020-11-20

Advanced Descriptive Statistic Layer Formatting

Rendered fromdesc_layer_formatting.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2023-01-10

Descriptive Statistic Layers

Rendered fromdesc.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2020-08-31

General String Formatting

Rendered fromgeneral_string_formatting.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2023-01-10

Layer Templates

Rendered fromlayer_templates.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2022-10-14

Tplyr Metadata

Rendered frommetadata.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2022-10-14

Post-Processing

Rendered frompost_processing.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2023-01-10

Shift Layers

Rendered fromshift.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2020-11-20

Tplyr Table Properties

Rendered fromtable.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2020-08-31

Getting Started

Rendered fromTplyr.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2020-08-31

Tplyr Options

Rendered fromoptions.Rmdusingknitr::rmarkdownon Nov 17 2024.

Last update: 2024-02-21
Started: 2020-08-31

Readme and manuals

Help Manual

Help pageTopics
Add an anti-join onto a tplyr_meta objectadd_anti_join
Attach column headers to a Tplyr outputadd_column_headers
Attach a layer to a 'tplyr_table' objectadd_layer add_layers
Add a missing subject row into a count summary.add_missing_subjects_row
Add risk difference to a count layeradd_risk_diff
Add a Total row into a count summary.add_total_row
Combine existing treatment groups for summaryadd_total_group add_treat_grps treat_grps
Add variables to a tplyr_meta objectadd_filters add_variables
Append the Tplyr table metadata dataframeappend_metadata
Conditional reformatting of a pre-populated string of numbersapply_conditional_format
Apply Format Strings outside of a Tplyr tableapply_formats
Replace repeating row label variables with blanks in preparation for display.apply_row_masks
Trigger the execution of the 'tplyr_table'build
Collapse row labels into a single columncollapse_row_labels
Create a 'f_str' objectf_str
Set or return by layer bindingget_by set_by
Get Data Labelsget_data_labels
Get or set the default format strings for descriptive statistics layersget_count_layer_formats get_desc_layer_formats get_shift_layer_formats set_count_layer_formats set_desc_layer_formats set_shift_layer_formats
Extract the result metadata of a Tplyr tableget_meta_result
Extract the subset of data based on result metadataget_meta_subset get_meta_subset.data.frame get_meta_subset.tplyr_table
Get the metadata dataframe from a tplyr_tableget_metadata
Retrieve the numeric data from a tplyr objectsget_numeric_data
Set or return precision_by layer bindingget_precision_by set_precision_by
Set or return precision_on layer bindingget_precision_on set_precision_on
Get statistics dataget_stats_data
Set or return treat_var bindingget_target_var set_target_var
Retrieve one of Tplyr's regular expressionsget_tplyr_regex
Set or return where binding for layer or tableget_pop_where get_where get_where.tplyr_layer get_where.tplyr_table set_pop_where set_where set_where.tplyr_layer set_where.tplyr_table
Create a 'count', 'desc', or 'shift' layer for discrete count based summaries, descriptive statistics summaries, or shift count summariesgroup_count group_desc group_shift
Return or set header_n bindingheader_n header_n<- set_header_n
Select levels to keep in a count layerkeep_levels
Create, view, extract, remove, and use Tplyr layer templatesget_layer_template get_layer_templates new_layer_template remove_layer_template use_template
Return or set population data bindingspop_data pop_data<- set_pop_data
Return or set pop_treat_var bindingpop_treat_var set_pop_treat_var
Reformat strings with leading whitespace for HTMLreplace_leading_whitespace
Set custom summaries to be performed within a descriptive statistics layerset_custom_summaries
Set values the denominator calculation will ignoreset_denom_ignore
Set Logic for denominator subsettingset_denom_where
Set variables used in pct denominator calculationset_denoms_by
Set counts to be distinct by some grouping variable.set_distinct_by
Set the format strings and associated summaries to be performed in a layerset_format_strings set_format_strings.count_layer set_format_strings.desc_layer
Set the option to prefix the row_labels in the inner count_layerset_indentation
Set variables to limit reported data values only to those that exist rather than fully completing all possible levelsset_limit_data_by
Set the display for missing stringsset_missing_count
Set the label for the missing subjects rowset_missing_subjects_row_label
Set the option to nest count layersset_nest_count
Set a numeric cutoffset_numeric_threshold
Set the ordering logic for the count layerset_ordering_cols set_order_count_method set_result_order_var
Set the value of a outer nested count layer to Inf or -Infset_outer_sort_position
Set precision dataset_precision_data
Set descriptive statistics as columnsset_stats_as_columns
Set the label for the total rowset_total_row_label
Extract format group strings or numbersstr_extract_fmt_group str_extract_num
Wrap strings to a specific width with hyphenation while preserving indentationstr_indent_wrap
A grammar of summary data for clinical reportsTplyr-package Tplyr
ADAE Datatplyr_adae
ADAS Datatplyr_adas
ADLB Datatplyr_adlb
ADPE Datatplyr_adpe
ADSL Datatplyr_adsl
Create a 'tplyr_layer' objecttplyr_layer
Tplyr Metadata Objecttplyr_meta
Create a Tplyr table objecttplyr_table
Return or set the treatment variable bindingset_treat_var treat_var