Package index

Functions to setup studies

cctu_initialise() cctu_initialize() cctu_check_dir() rm_output(): initialise objects for using cctu package
library_description(): loads all the packages listed in the DESCRIPTION file
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
plot(<code_tree>): 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

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

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

Functions to create plots

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

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.

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