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bootstrap table updates #66

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bootstrap table updates #66

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graceannobrien
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@graceannobrien graceannobrien commented Aug 5, 2024

This PR does the following:

  1. Update addErrLogDV description in parameter key (Update param key description #65)
  • param-key
  1. Remove unnecessary messages
  • loadParamEstimates
  • define_boot_table (remove show_col_types = FALSE)
  1. Add .cleanup_cols argument to format functions. Check for backwards compatibility
  • select_cols will still work, but we will use .cleanup_cols in examples moving forward.
  • format_param_table
  • format_boot_table
  1. Allow user to specify bootstrap percentiles (define_boot_table column assumptions #64). Check for backwards compatibility
  • getBootPercentiles: allow user to input .ci = 90, 95, "IQR" or percentiles = c(list of percentiles <1)
    - if .ci provided or number of percentiles = 3, then names = lower_perc_X, value_perc_Y, upper_perc_Z
    - if number of percentiles > 3, then names = percX, etc.
  • backTrans-log and backTrans-logit: updated to work with new "perc" names
  • formatValuesBoot: update to work with new "perc" names.
    - if .ci provided or number of percentiles = 3, then calculate CI (upper- lower) and name columns "boot_perc_(upper-lower)" and "boot_value_Y"
    - if number of percentiles > 3, then keep names = percX, etc.
  • define_boot_table: drop 95CI-specific code, use getBootPercentiles
  1. Remove nonboot_estimates argument in define_boot_table. Check for backwards compatibility
  • define_boot_table: user will get warning if provide non-boot argument
  • Workflow is that user will join on non-boot estimates right before make_boot_pmtable
  1. Make bootstrap table function (make_pmtable bootstrap tables #54) Not finished
  • make_boot_pmtable: new function to generate parameter table with non-boot estimates and bootstrap percentiles
  • make_pmtable: drop description that works with format_boot_table output. It still does, but you would want to use make_boot_pmtable once it's available

Functions to QC:
Misc:

  • param-key
  • loadParamEstimates

Non-boot:

  • format_param_table

Bootstrap-related: These all need more tests for different percentile cases

  • define_boot_table
  • getBootPercentiles (internal, used in define_boot_table)
  • backTrans-log (internal, used in define_boot_table)
  • backTrans-logit (internal, used in define_boot_table)
  • format_boot_table
  • formatBootValues (internal, used in format_boot_table)

Make bootstrap table: Not finished

  • make_pmtable
  • make_boot_pmtable

@graceannobrien graceannobrien linked an issue Aug 5, 2024 that may be closed by this pull request
@graceannobrien graceannobrien linked an issue Aug 20, 2024 that may be closed by this pull request
barrettk added a commit that referenced this pull request Oct 23, 2024
 - Also improve documentation formatting/examples
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define_boot_table column assumptions Update param key description
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