Launches a Shiny app to select clinical codes (see also 'User notes' section below). In general:
Optionally upload a previous codelist.
Click 'Download selected'.
RunCodelistBuilder(
all_lkps_maps = NULL,
options = list(launch.browser = TRUE),
...
)Either a named list of lookup and mapping tables (either
data frames or tbl_dbi objects), or the path to a SQLite database
containing these tables (see also build_all_lkps_maps() and
all_lkps_maps_to_db()). If NULL, will attempt to connect to an SQLite
database named 'all_lkps_maps.db' in the current working directory, or to a
a SQLite database specified by an environmental variable named
'ALL_LKPS_MAPS_DB' (see
here
for how to set environment variables using a .Renviron file). The latter
method will be used in preference.
Named options that should be passed to the runApp call
(these can be any of the following: "port", "launch.browser", "host", "quiet",
"display.mode" and "test.mode"). You can also specify width and
height parameters which provide a hint to the embedding environment
about the ideal height/width for the app.
Additional args passed on to shinyApp
NULL
Essential fields: 'Disease', either 'Code descriptions like...' or at least one of 'Codes starting with...'.
'Download all': downloads all codes under the 'Matching clinical codes' tab, disregarding any selections (i.e. the 'selected' column will appear blank).
'Download selected': downloads all codes under the 'Preview selected codes only' tab.
If uploading a previous codelist selection,
this must be formatted as required by
validate_clinical_codes (see
example_clinical_codes for a valid example).
...this will automatically select any codes matching on 'disease',
'code_type' and 'code' (see update_code_selection function in
utils.R), and on clicking 'Download selected', will copy over any
values in the 'category' column and set the 'selected' column to 'Yes' only
for these rows.
...the full list of uploaded codes can be viewed under the 'Uploaded codelist' tab, which includes a column called 'included_in_matching', indicating whether each uploaded code is present ('Yes') or not present ('No') in the list under 'Matching clinical codes'.
Also, click through the tabs after each step before moving on to the next.
The final list of matching codes is codes matching 'Code descriptions like...' OR 'Codes starting with...'.
CAUTION: make sure there are no inadvertent white spaces (e.g. 'search term', not 'search term ').
if (FALSE) {
# build dummy all_lkps_maps
all_lkps_maps_dummy <- build_all_lkps_maps_dummy()
# launch app
RunCodelistBuilder(all_lkps_maps = all_lkps_maps_dummy)
}