Package index • clinsight

Main application

Top-level functions to run the Shiny application

run_app(): Run the Shiny Application

app_ui(): The application User-Interface

app_server(): App Server

Credential management

Functions to manage credentials.

initialize_credentials(): Initialize database

authenticate_server(): Authenticate server

authenticate_ui(): Authenticate UI

Application modules

Modules used in the main Shiny application.

mod_start_page_server(): Start page - Shiny module Server

mod_start_page_ui(): Start page - Shiny module UI

mod_main_sidebar_server(): App sidebar - Shiny module Server

mod_main_sidebar_ui(): App sidebar - Shiny module UI

mod_header_widgets_server(): Header widgets - Shiny module Server

mod_header_widgets_ui(): Header widgets - Shiny module UI

mod_common_forms_server(): Common forms - Shiny module Server

mod_common_forms_ui(): Common forms - Shiny module UI

mod_study_forms_server(): Study forms - Shiny module Server

mod_study_forms_ui(): Study forms - Shiny module UI

mod_db_synch_info_server(): Database Synchronization information - Shiny module Server

mod_db_synch_info_ui(): Database Synchronization information - Shiny module UI

mod_go_to_form_server(): Go to form - Shiny module Server

mod_go_to_form_ui(): Go to form - Shiny module UI

mod_navigate_forms_server(): Navigate forms - Shiny module Server

mod_navigate_forms_ui(): Navigate forms - Shiny module UI

mod_navigate_participants_server(): Navigate participants - Shiny module Server

mod_navigate_participants_ui(): Navigate participants - Shiny module UI

mod_navigate_review_server(): Navigate review tables - Shiny module Server

mod_navigate_review_ui(): Navigate review tables - Shiny module UI

mod_queries_server(): Queries - Shiny module Server

mod_queries_ui(): Queries - Shiny module UI

mod_query_add_server(): Write Query - Shiny module Server

mod_query_add_ui(): Write Query - Shiny module UI

mod_query_follow_up_server(): Add follow-up to a query - Shiny module Server

mod_query_follow_up_ui(): Add follow-up to a query - Shiny module UI

mod_report_server(): Create Report - Shiny module Server

mod_report_ui(): Create Report - Shiny module UI

mod_review_config_server(): Review configuration - Shiny module Server

mod_review_config_ui(): Review configuration - Shiny module UI

mod_review_forms_server(): Review form - Shiny module Server

mod_review_forms_ui(): Review form - Shiny module UI

mod_timeline_server(): Interactive timeline - Shiny module Server

mod_timeline_ui(): Interactive timeline - Shiny module UI

Create wide-form tables

S3 method for creating wide-form study-specific tables.

create_table(): Create table

create_table(<default>): Create wide table

create_table(<adverse_events>): Create Adverse Events table

create_table(<bm_cytology>): Create BM Cytology Table

create_table(<conc_procedures>): Create Concomitant Procedures Table

create_table(<continuous>): Create Table with continuous data.

create_table(<general>): Get general data

create_table(<medical_history>): Create Medical History Table

create_table(<medication>): Create Concomitant Medication Table

Data frame functions

Create data for use in the application.

get_raw_csv_data(): Get raw data from CSV files

merge_meta_with_data(): Merge metadata with raw data

apply_study_specific_fixes(): Apply study-specific fixes

get_appdata(): Get appdata Converts data to a list of data frames in the expected format to be used by the the Shiny application.

get_available_data(): Get available data

get_meta_vars(): Get meta variables

get_review_data(): Get review data

get_static_overview_data(): Create static overview data

get_timeline_data(): Get timeline data

summarize_review_data(): Summarize review data

Database functions

Create, read or append the app database.

get_db_connection(): Connect to database

db_temp_connect(): Connect temporarily to a database.

db_create(): Create app database

db_update(): Update app database

db_save(): Append database table

db_save_review(): Save review in database

db_slice_rows(): Slice database rows

update_review_data(): Update review data

collect_query_data(): Collect query data

db_get_review(): Retrieve review

db_get_query(): Retrieve query from database

Internal dataset

Create or describe internal data.

get_metadata(): Load metadata

metadata: Application Metadata

col_palette: Custom color palette

clinsightful_data: Clinical Trial test data

Figure functions

fig_barplot(): Bar chart

fig_boxplots(): Create custom ggplot() boxplots.

fig_timeline(): Create timeline

fig_timeseries(): time series figure

plotly_figure(): Plotly figure

fix_multiple_choice_vars(): Correct multiple choice variables

custom_plot_theme(): Custom plot theme

get_ggplot_layer_names(): Get ggplot layer names

Report

Create Review reports.

select_report_data(): Select report data

create_report(): Create Report

Helper functions

add_missing_columns(): Add missing columns

adjust_colnames(): Adjust column names

bind_rows_custom(): Custom row bind

check_appdata(): Check data

filter_data(): Filter app data

clean_dates(): Clean dates

collapse_column_vals(): Collapse column values

collapse_fct_levels(): Collapse Factor levels

cols_to_char(): Convert non-numeric columns to character

create_unique_id(): Create Unique ID

datatable_custom(): Custom interactive datatable

date_cols_to_char(): Convert date columns to character

expand_columns(): Expand columns

get_base_value(): Get base value

get_max_time(): Extract latest update time

get_unique_vars(): Get unique vars

get_test_results(): Get package test results

is_date(): Verify date class

order_string(): Order string

remove_boxplot_outliers(): Remove boxplot outliers

simplify_string(): Simplify String

time_stamp(): Time stamp

title_case(): Capitalize words

vector_select(): Select from vector