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Output the individual file with anon_chi
#748
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I've added this as a parameter so you can output CHI if desired, but the default is for anon_chi. For the tests, it swaps back to CHI as there are some tests which specifically us the CHI number.
#746) * rename `hscp` to `hscp2018` * rename `spd` as `slf_pc_lookup` * Add `datazone2011` to coalesce code * Rename `datazone` to `datazone2011` * include `datazone2011_old` in selections * Update R/fill_geographies.R --------- Co-authored-by: James McMahon <[email protected]>
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happy to merge
dabbf57
into
create_individual_file_stable
* Until L594 * Converted until L677 * Until L731 * Update documentation * Remove test ref * Style code * WIP writing functions to fill postcode in line with previous DOB functions * Update documentation * implement quick fix for running 22/23 * Style code * Fix missed comma * Exclude DD code for now - TEMP fix * Correct/rename variables * Style code * Include NSU in `check_year_valid` * Update `check_year_valid_tests` * Update documentation * Update `add_nsu_cohort` to pick up years valid * Style code * remove extra `!` * Exclude `cij_delay` * Style code * improve `max_no_inf()` * Use pmin/max instead of `rowwise` * improve `min_no_inf()` * Use n_distinct(cij_marker) * deal with distinct(ch_chi_cis) * use n_distinct(ooh_case_id) * remove `find_non_duplicates` * Use dplyr::if_else() Co-authored-by: James McMahon <[email protected]> * Fix typo in `ooh_covid_assessment` * Move `ooh_case_id` to aggregate * Use `slfhelper::ltc_vars` * Remove `clean_up_dob` Already done in `correct_demographics` * Update documentation * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/4981058958/attempts/1 Accepted in #654 (comment) Signed-off-by: check-spelling-bot <[email protected]> * Use `start_next_fy_quarter` in place of rowwise * Style code * Use `compute_mid_year_age` * convert code into data.table for improving speed * Update `get_fy_dates`function * remove `date_from_fy`, use `get_fy_dates` * Update documentation * Remove `clean_up_postcode` function Not needed anymore * Remove non duplicates function/move to aggregate * Style code * Update documentation * Add time stamps to `create_individual_file` * Style code * remove `clean_up_postcode` * Deal with ch cis episodes * Style code * add .data$ * Turn ch aggregate into a data table * Style code * use ch_chi_cis * remove `preventable_admissions` from aggregate * exclude `hh_in_fy` for now * Style code * Test - exclude `sc_` vars from aggregate * Style code * Exclude for now * exclude for now * Style code * automate `check_year_valid` * Return dummy file path for NSU not valid * Style code * Fix brackets in aggregate * TEMP - exclude variables * Use `phsmethods::sex_from_chi` * Style code * Add ungroup() * lowercase dob * Remove as.data.table * rewrite aggregate_by_chi with data.table * Style code * minor changes * Use the updated function * to properly import data.table * remove redundant columns dob postcode and gpprac * minor changes to remove redundant postcode gpprac columns * Style code * rename columns with small letters * Style code * newaggregate_ch_episodes * Update documentation * add functions to replace regular expressions to select column/variables * Update documentation * Style code * minor changes * add a missing variable, cij_delay * Style code * add variables cij_delay, preventable_beddays * add missing variables health_net_cost, health_net_costincdnas, and cmh, dd sds columns * Style code * add more variables needed * Style code * Update R/link_delayed_discharge_eps.R * Style code * amend costs * Style code * Revert "amend costs" This reverts commit 8048e68. * Add DN and cij_delay back in * fix the issue * Style code * remove running in chunks * Style code * Update tests to include missing variables * Remove unnecessary comma * fix the bug of preventable_beddays * Update documentation * fix total ae_attendances * fix the bug of preventable_admissions * fix the bug of hbrescode etc * minor fix * minor fix * Style code * Fix some warnings being produced by the tests * Fix failing test * remove running in chunks * Style code * Update the targets config to use `timestamp_positives` as the default reporter * fix the bug of preventable_beddays * Update documentation * fix total ae_attendances * fix the bug of preventable_admissions * fix the bug of hbrescode etc * minor fix * minor fix * Style code * fix home care cost * add ipdc to fix maternity * fix preventable addmission and care home cost * fix preventable_admissions and calculate preventable_beddays here * add monthly_beddays and yearstay to dd * Style code * fix preventable_admissions and preventable_beddays * Style code * include parameter for write to disk/year * Add lookups to indiv file creation pipeline * include parameter for write to disk/year * fix delay discharge beddays and yearstay * Style code * fix preventable issues * Style code * fix the issue of preventable stuff * Style code * Update R/aggregate_by_chi_zihao.R * Update documentation * Fix minor typos * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5443581387/attempts/1 Accepted in #709 (comment) Signed-off-by: check-spelling-bot <[email protected]> * Remove some obsolete comments * Remove some unnecessary brackets * Reformat some code * Use some `dplyr` functions for readability * Style code * Update R/link_delayed_discharge_eps.R * Style code * Remove some code which is no longer needed We now match on these variables after * Work out preventable admissions with similar indicators * Lowercase variable names * Restore `cij_delay` * Restore DN variables * Tidy the code and use integers where possible * Supply `year` as a parameter to `clean_up_ch` * Supply `year` as a parameter to `clean_individual_file` * Only keep required variables to save memory * Rename the parameter so the documentation works * Use `setnames` to change names to lower * Remove unneeded code * Update file path name * Trim the return code * Some fixes * Correctly compute `ooh_cases` * Update documentation * Style code * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5466392495/attempts/1 Accepted in #719 (comment) Signed-off-by: check-spelling-bot <[email protected]> * Add targets for the individual file * Fix missed pipe * Style code * Update some targets to only run once a week * Make the deaths lookup unique * Add `year` back to the individual file * Remove `cost_total_net_inc_dnas` from the indiv file (#737) * Drop `cost_total_net_inc_dnas` * Rename `health_net_costincdnas` to `health_net_cost_inc_dnas` * Join slf lookups onto individual file (#724) * Create function for matching on slf lookups * fix some build warnings * Add `hbrescode` to select list * Pass lookups as parameters/deal with hbrescode * Update R/create_individual_file.R --------- Co-authored-by: James McMahon <[email protected]> * Join sc client variables onto individual file (#740) * New function for matching sc client to indiv file * Style code * [check-spelling] Update metadata Update for https://github.com/Public-Health-Scotland/source-linkage-files/actions/runs/5555048903/attempts/1 Accepted in #740 (comment) Signed-off-by: check-spelling-bot <[email protected]> * Code layout * Style code * Remove redundant sc variables Co-authored-by: James McMahon <[email protected]> * Update comments Co-authored-by: James McMahon <[email protected]> * Update comments Co-authored-by: James McMahon <[email protected]> * Sort order of parameters to pass `data` first * Update documentation * Style code * Update R/create_individual_file.R * Update R/create_individual_file.R * Update R/create_individual_file.R * Style code --------- Signed-off-by: check-spelling-bot <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: James McMahon <[email protected]> Co-authored-by: Moohan <[email protected]> * Update documentation * Output the individual file with `anon_chi` (#748) * Make episode file output with `anon_chi` I've added this as a parameter so you can output CHI if desired, but the default is for anon_chi. For the tests, it swaps back to CHI as there are some tests which specifically us the CHI number. * Output `anon_chi` in the individual file * Style code * Sort variables with issues `hbrescode` (HB2018), `datazone` and `hscp` (#746) * rename `hscp` to `hscp2018` * rename `spd` as `slf_pc_lookup` * Add `datazone2011` to coalesce code * Rename `datazone` to `datazone2011` * include `datazone2011_old` in selections * Update R/fill_geographies.R --------- Co-authored-by: James McMahon <[email protected]> * Fix for anon_chi being NA --------- Co-authored-by: Moohan <[email protected]> Co-authored-by: Jennit07 <[email protected]> --------- Signed-off-by: check-spelling-bot <[email protected]> Co-authored-by: Mandy Norrbo <[email protected]> Co-authored-by: jr-mandy <[email protected]> Co-authored-by: shintoLampgit config --global user.email [email protected] git config --global user.name shintoLamp <[email protected]> Co-authored-by: shintoLamp <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Jennifer Thom <[email protected]> Co-authored-by: Jennit07 <[email protected]> Co-authored-by: Zihao Li <[email protected]> Co-authored-by: lizihao-anu <[email protected]> Co-authored-by: Moohan <[email protected]> Co-authored-by: Zihao Li <[email protected]>
By default it expects the input episode file to have
anon_chi
and it will outputanon_chi
but I've added parameters to deal with other situations if required.