Package index • cctu

Functions to setup studies

cctu_initialise() cctu_initialize() cctu_check_dir() rm_output(): initialise objects for using cctu package

attach_pop() detach_pop(): Functions that attach and detach environments based on which populations are used for a given table number

clean_up(): removes all the objects in the environment, apart from those listed in reserved and detaches the environment used to create tables or figures corresponding to the number

data_table_summary(): Provides a summary with date stamps of external data files.

order_dewey(): sorts inputs that look like Dewey decimal numbering

get_meta_table() set_meta_table(): Functions to handle meta_table

get_code_tree() reset_code_tree(): track which files of code are called by which oher files

print(<code_tree>): Print methods for code_tree object

plot(<code_tree>): Print/plot the code tree.

create_popn_envir(): create environments contain a set of data frames filtered for each population

rm_envir(): A function to remove all attached objects from the search path with any exceptions specified

run_batch(): Runs a script in batch mode directly from within R.

source(): A modified version of the source() function to capture in a data.frame what file was called and from which file

read_data(): Automatic reading in data from a meta-table of external data sets.

meta_table_example: Example of a meta_table data frame

Macro utility functions

Functions manipulating MACRO data

apply_macro_dict(): Apply DLU/CLU file to the data frame

extract_form(): Extract data by form from MACRO dataset

merge_data(): Merge vertically split data

set_dlu() get_dlu(): Set/get DLU data

tidy_dlu(): Tidy DLU form

dump_missing_report() get_missing_report() reset_missing_report(): Save/Get/Reset missingness report

Formating/conversion function

Functions to format digits, convert characters.

format_percent(): Format number to percent

format_pval(): Format p-value

signif_pad() round_pad(): Round numbers with 0-padding.

p_format(): formats p values with rounding and <0.001

to_factor() to_character() to_numeric() to_logical(): Convert vector but keep value/value labels.

propercase(): Function to convert text to proper case

Summry data

Functions to create summary statistics

cttab(): Generate an table of descriptive statistics.

print(<cttab>): Print

rbind(<cttab>): Combine descriptive statistics table by rows

render_cat(): Render categorical values for table output.

render_numeric(): Render continuous values for table output.

num_stat() cat_stat(): Compute some basic descriptive statistics.

sumby(): Produces summary statistics on a variable broken down by arm, display a graphical equivalent.

sumfig(): Produce ggplot to represent summary statistics graphically, either boxplot or barchart

regression_table(): Produce a table summarising a regression model for a study report

Plotting

Functions to create plots

geom_stepribbon(): Step ribbon plots.

km_ggplot(): Create a Kaplan-Meier plot using ggplot2

plot(<km_ggplot>): plot methods for km_ggplot object

print(<km_ggplot>): print methods for km_ggplot object

Writing outputs

Functions to write tables, figures and report

write_docx(): Produces the final Docx file

write_ggplot(): Function to save ggplot figures.

write_manual(): Function to write to meta-table and clean up without creating a table,text, or figure. For manual use

write_plot(): Function to save plot figures

write_table(): Function to write a table into xml format in the correct directory, and edit TableofTables

write_text(): Function to write a text into xml format in the correct directory, and edit TableofTables

create_word_xml(): Produces the final xml file

Variable and value labels

Functions for labels

val_lab() `val_lab<-`() has.labels() unval(): Set or get value labels

var_lab() `var_lab<-`() has.label() drop_lab(): Set or get variable label

unlab(): Drop variable label and value labels

copy_lab(): Copy variable label and value labels

lab2val(): Replace vector/matrix/data.frame values with corresponding value labels.

Miscellaneous

all_is_numeric(): Check if All Elements in Character Vector are Numeric

clean_names() clean_string(): Tidies up names of a data frame within certain rules

detect_invalid_utf8() remove_invalid_utf8(): Functions to detect and delete non-UTF8 characters, which the XML output will not like

is_empty(): Check whether string, list or vector is empty

rbind_space(): Function to bind tables/matrices with a blank row between them

remove_blank_rows_cols(): Function to remove blank rows/columns from a df