NEWS.md

In PublicHealthEngland/hcaidcs: R functions for the mandatory surveillance of bacteraemia and C. difficile infection

version 0.1.1.9007

bug fixes

Updated mf_lag_trend to remove deprecated function mutate_at from dplyr.

Version 0.1.1.9006

New functions

Two new functions have been added: age_sex_pyramid and graph_age_group. age_sex_pyramid draws age-sex pyramids and graph_age_group produces ordered factors so that axes are plotted in order and the greater that/equal to operator is plotted correctly.

Version 0.1.1.9005

Minor changes and bug fix

Added function graph_species_names which will generate italicised species names for plotting.

Fixed bug in apportion_phc_date. Previously this function only worked for CDI. It is now available for bacteraemias too.

Some minor fixes to function documentation were added too.

Version 0.1.1.9004

Major change

From 01 April 2019, the mandatory surveillance introduced a date of most recent previous discharge for C. difficile infections. This replaced the old set of three questions which asked for yes or no answers around previous trust exposure. Answers to these questions provided the data for the apportioning by prior healthcare. The new function apportion_phc_date performs the apportioning by date and results can be merged with the apportion_phc results.

Minor changes

Added dependcy on cowplot so that annual graphs remain consistently formatted. Mostly this means I've added + theme_cowplot() everywhere. This does not change the input or output of the functions, but for reference this affects the following functions:

• aec_age_sex_plot
• aec_age_trend_rate_pc_change
• aec_age_trend_rate_bar
• aec_ec_source_plot
• aec_subregion_plot
• aec_tto_plot
• mf_fig1_fun

Version 0.1.1.9003

Functions added

• date_to_cmonth Function to convert a date to a calendar month, either as numeric (default), or factor, with levels in calendar year order
• mo_tab_long Function to create long-format monthly tables
• factor_apportioned Creates an ordered factor from apportioned vector
• factor_prior_hc Creates an ordered factor from vector giving prior healthcare status
• factor_apportion_both Creates an ordered factor from output of either normal apportioning or prior trust exposure.

Functions deprecated

• up_or_down has been moved out to the nicethings package.

Minor changes

• ann_tab_long Simplified syntax for this function. This will make it more flexible. Following arguments have been removed: collection_string, org_code, metric_type, output period_var argument added The expectation is that the user will supply the period as an ordered factor and the function will then sort the data by that variable. The same applies to the metric_var argument.

• Functions for comparing wide data tables have been moved out to a separate branch (merge_everything, merge_one, data_compare, highlight, convert_csv2r). The change to reporting long format tables has obviated these functions.

Version 0.1.1.9002

Minor changes

Added tidyr dependency, so that the new function ant_tab_long expands data to include unobserved periods for organisations.

Functions added:

• ann_tab_long Function to create long annual and quarterly tables

Data added

• line_listing Data giving simulated line listing data to be used in examples and function testing

Version 0.1.1.9001

Minor changes

Added two new functions for the preparation of the monthly factsheet and expanded mf_trend_data to add observations and organisms.

Functions added:

• mf_lag_trend preps the data so that lagged values are calculated
• mf_create_text_values creates objects giving changes in counts of cases for use in factsheet

Also minor fix to apportion_prior_hc.

Minor changes

Tweaks to mf_fig1_fun so that the x axis labels are at a 45 degree angle and so that MRSA and MSSA are no longer bold face.

Updated subregions_sp_df to 2018 geography. Previously 2017 geography.

Updated apportion_phc so that if the case is not HOHA and admitted in past three months is No or NA, then the result goes to COCA.

Version 0.1.0

This is the first public release of the HCAIDCS package.

Major changes

• Added functions for PHE colours copied from phecharts package.
• rlang is now an imported package.
• Added functions to produce annual tables in wide format (fixes github issue #3)
• mrsa_source_of_bacteraemia is now deprecated in favour of group_source_bacteraemia
• Added function aec_age_trend_rate_pc_change to produce new age/sex rate trend graphs

Bug fixes

• aec_ec_primary_focus_plot now accepts an arbitrary number of levels of primary focus (issue #22).
• fy_long is now vectorised.
• ordered_m_y has been updated to use tidyeval and now works (fixes github issue #5)
• group_source_bacteraemia now recodes NA to Not reported
• fixed apportion_prior_healthcare so that contradictory information indicating no admission in past 3 months, but admission in past 12 weeks now apportions to COIA.
• Updated documentation on built in data for assignment_data, cdi_prior_hc_data and assignment_data2
• Removed Viridis package dependency as this is no longer used in any function

PublicHealthEngland/hcaidcs documentation built on Jan. 19, 2024, 8:38 a.m.