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@thomas-neitmann thomas-neitmann released this 06 Sep 07:21
· 2004 commits to main since this release
v0.8.0
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Learn about vigilant mode.

New Features

  • get_summary_records() creates summary records e.g. derive analysis value (AVAL) from multiple records, only keeping the derived observations (#525)

  • derive_param_framingham() adds a Parameter for Framingham Heart Study Cardiovascular Disease 10-Year Risk Score (#977)

  • compute_qual_imputation() imputes values when qualifier exists in character result (#976)

  • derive_vars_merged_lookup() maps lookup tables (#940)

  • filter_confirmation() filters out confirmed observations
    (#1292) including supporting functions count_vals(), min_cond(), and
    max_cond().

  • derive_var_confirmation_flag() derives a flag which
    depends on other observations of the input dataset (#1293)

  • derive_var_atoxgr() derives lab toxicity/severity grade ATOXGR
    from ATOXGRL and ATOXGRH. ATOXGRL holds toxicity/severity grade for low lab values,
    and ATOXGRH holds toxicity/severity grade for high lab values.

  • derive_var_atoxgr_dir() derives lab toxicity/severity grade for low
    lab values (ATOXGRL) or for high lab values (ATOXGRH). The grading is created from
    metadata.

  • New metadata data set called atoxgr_criteria_ctcv4 which holds criteria for lab grading
    based on Common Terminology Criteria for Adverse Events (CTCAE) v4.0

Updates of Existing Functions

  • list_tte_source_objects() gains a package parameter and is now exported (#1212)

  • list_all_templates() and use_ad_template() gain a package parameter which
    can be used to indicate in which package to look for templates (#1205)

  • Randomization Date RANDDT variable added to ADSL template and vignette (#1126)

  • Renamed derive_derived_param() to derive_param_computed() and added a
    deprecation notice (#1229)

  • derive_vars_duration() updated to not display units when there is missing duration (#1207)

  • value_var parameter added to derive_vars_atc() (#1120)

  • format_eoxxstt_default() - Updated the default value of EOSSTT for screen failure patients (#885)

  • The imputation functions (derive_vars_dtm(), derive_vars_dt(),
    convert_dtc_to_dtm(), convert_dtc_to_dt()) have been enhanced to address
    users feedback (#1300):

    • Partial dates with missing components in the middle like
      "2003-12-15T-:15:18", "2003-12-15T13:-:19", "2020-07--T00:00" are
      handled now.

    • The control of the level of imputation has been refined by adding the
      highest_imputation argument. For example, highest_imputation = "D"
      requests imputation for day and time but not for year and month.

      (For the date_imputation and the time_imputation argument NULL is no
      longer a permitted value.)

    • It is now possible to impute completely missing dates by specifying
      highest_imputation = "Y" and the min_dates or max_dates argument.

  • order parameter added to dthcaus_source() which allows an additional
    character vector to be used for sorting the dataset, derive_vars_dthcaus()
    updated to process additional parameter (#1125).

  • create_single_dose_dataset() Fixed bug where ASTDTM and AENDTM were not updated when start_date = ASTDT and end_date = AENDT. The function has been amended to now require start_datetime and end_datetime parameters in addition to start_date and end_date.The keep_source_vars has been added to specify the variables to be retained from the source dataset (#1224)

Breaking Changes

  • Moved all developer-facing functions and vignettes to {admiraldev}. {admiraldev} is now a dependency of {admiral} (#1231)

  • All ADaM datasets but admiral_adsl have been removed from the package (#1234)

  • derive_var_agegr_ema() and derive_var_agegr_fda() have been deprecated (#1333)

  • Imputation related arguments have been deprecated for all functions except the
    imputation functions themselves (#1299). I.e., if a derivation like last known alive
    date is based on dates, DTC variables have to be converted to numeric date or
    datetime variables in a preprocessing step. For examples see the ADSL
    vignette    .

    The following arguments were deprecated:

    • date_imputation, time_imputation, and preserve in date_source()

    The following arguments no longer accept DTC variables:

    • date in date_source(), dthcaus_source(), censor_source(), and
      event_source()
    • dose_date and analysis_date in derive_vars_last_dose(),
      derive_var_last_dose_amt(), derive_var_last_dose_date(),
      derive_var_last_dose_grp()

    The following functions were deprecated:

    • derive_vars_merged_dt()
    • derive_vars_merged_dtm()

  • For the date_imputation and the time_imputation argument of the imputation
    functions (derive_vars_dtm(), derive_vars_dt(), convert_dtc_to_dtm(),
    convert_dtc_to_dt()) NULL is no longer a permitted value. The level of
    imputation can be controlled by the highest_imputation argument now.

  • The following functions, which were deprecated in previous {admiral} versions,
    have been removed:

    • derive_var_disposition_dt()
    • derive_var_lstalvdt()
    • lstalvdt_source()
    • derive_var_trtedtm()
    • derive_var_trtsdtm()

  • The following functions and parameters, which were deprecated in previous
    {admiral} versions, are now defunct and will output an ERROR if used:

    • derive_var_ady()
    • derive_var_aendy()
    • derive_var_astdy()
    • derive_var_atirel()
    • filter parameter in derive_var_extreme_flag() and derive_var_worst_flag()

Documentation

  • New ADMH template script can be accessed using admiral::use_ad_template("admh") (#502)

  • New vignette "Higher Order Functions" (#1047)

  • New vignette "Lab Grading" (#1369)

  • Fixed derive_var_disposition_status() argument to render correctly (#1268)

  • Added link to pharmaverse YouTube channel to README

Various

  • Restructured Reference page and updated all functions to use family tag
    in roxygen headers for finding similar functions. (#1105)

  • Rename "Articles" page on website to "User Guides" and moved developer vignettes to {admiraldev} website (#1356)

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