Calculate Risk Statistics for treatment pairs from pre-processed Adverse Events data

Usage

risk_stat(
  datain,
  a_subset = NA_character_,
  summary_by = "Patients",
  eventvar,
  ctrlgrp,
  trtgrp,
  statistics = "Risk Ratio",
  alpha = 0.05,
  cutoff_where = NA,
  sort_opt = "Ascending",
  sort_var = "Count",
  g_sort_by_ht = "N",
  riskdiff_pct = "N",
  sigdec = 1,
  pctsyn = "Y",
  hoveryn = "Y"
)

Arguments

datain: Input data from mentry() output to get counts for each category
a_subset: Analysis Subset condition specific to categorical analysis.
summary_by: Measure to construct the summary by. Values: 'Patients' or 'Events'.
eventvar: Event Variable to review by. Example: 'AEDECOD', 'AEBODSYS'.
ctrlgrp: Treatment Control value.
trtgrp: Treatment(s) to create pairs. Only 1 value for Volcano/table, can be multiple for forest_plot().
statistics: Statistic to be calculated. Values: 'Risk Ratio' or 'Risk Difference'.
alpha: Alpha value to determine confidence interval for risk calculation. Default: 0.05
cutoff_where: Filter condition for incidence/pct. Consider only terms with eg: "FREQ > 5" or "PCT <3". Must contain FREQ or PCT (count or percent)
sort_opt: How to sort terms, only for table/forest plot. Values: 'Ascending','Descending','Alphabetical'.
sort_var: Metric to sort by. Values: 'Count','Percent','RiskValue'.
g_sort_by_ht: For Forest Plot only - include sorting by high term/BYVAR1? Values: "Y"/"N". In the output, terms will be sorted by group first, then term. To be used along with ht_dispyn = Y in ae_forest_plot()
riskdiff_pct: To display risk and CI as % if statistic = risk difference (Y/N)
sigdec: Number of decimal places for % displayed in output
pctsyn: Display Percentage Sign in table or not. Values: "Y"/"N"
hoveryn: Include hover information (for graphs) Y/N

Value

A dataset containing risk statistic calculations for given treatment pair(s).

Examples

## Pre-processed AE data
data("ae_pre_process")

ae_entry <- mentry(
  datain = ae_pre_process$data,
  subset = NA,
  byvar = "AEBODSYS",
  trtvar = "TRTA",
  trtsort = "TRTAN",
  subgrpvar = NA,
  trttotalyn = "N",
  add_grpmiss = "N",
  sgtotalyn = "N",
  pop_fil = "SAFFL"
)

risk_stat(
  datain = ae_entry,
  a_subset = ae_pre_process$a_subset,
  summary_by = "Patients",
  eventvar = "AEDECOD",
  ctrlgrp = "Placebo",
  trtgrp = "Xanomeline High Dose",
  statistics = "Risk Ratio",
  alpha = 0.05,
  cutoff_where = "PCT > 2",
  sort_opt = "Ascending",
  sort_var = "Count"
)
#> mcatstat success
#> # A tibble: 80 × 30
#>    BYVAR1   TRTVAR DPTVAR DPTVAL CVALUE DENOMN  FREQ DPTVALN BYVAR1N   PCT CPCT 
#>    <chr>    <ord>  <chr>  <chr>  <chr>   <dbl> <dbl>   <dbl>   <dbl> <dbl> <chr>
#>  1 CARDIAC… Place… AEDEC… ATRIA… 1 ( 1…     69     1      30       1  1.45 " 1.…
#>  2 GENERAL… Place… AEDEC… APPLI… 1 ( 1…     69     1      25       6  1.45 " 1.…
#>  3 GENERAL… Place… AEDEC… FATIG… 1 ( 1…     69     1     110       6  1.45 " 1.…
#>  4 INJURY,… Place… AEDEC… CONTU… 1 ( 1…     69     1      71      10  1.45 " 1.…
#>  5 INJURY,… Place… AEDEC… HIP F… 1 ( 1…     69     1     129      10  1.45 " 1.…
#>  6 MUSCULO… Place… AEDEC… BACK … 1 ( 1…     69     1      35      13  1.45 " 1.…
#>  7 CARDIAC… Xanom… AEDEC… ATRIA… 3 ( 3…     79     3      30       1  3.80 " 3.…
#>  8 GENERAL… Xanom… AEDEC… APPLI… 6 ( 7…     79     6      25       6  7.59 " 7.…
#>  9 GENERAL… Xanom… AEDEC… FATIG… 5 ( 6…     79     5     110       6  6.33 " 6.…
#> 10 INJURY,… Xanom… AEDEC… CONTU… 2 ( 2…     79     2      71      10  2.53 " 2.…
#> # ℹ 70 more rows
#> # ℹ 19 more variables: XVAR <chr>, DPTVARN <dbl>, CN <chr>, CUTFL <chr>,
#> #   CTRL_N <int>, CTRL_PCT <dbl>, PVALUE <dbl>, RISK <dbl>, RISKCIL <dbl>,
#> #   RISKCIU <dbl>, ADJPVALUE <dbl>, RISK_CI <chr>, TRTPAIR <chr>, CTRL <chr>,
#> #   ACTIVE <chr>, TOTAL_N <dbl>, HOVER_PCT <chr>, HOVER_RISK <chr>,
#> #   HOVER_TEXT <chr>