This function generates descriptive statistics for a sample of data, including cases and non-cases, and saves the results to an Excel file.
Usage
descriptive(
pids_cases,
RG = NULL,
drug = NULL,
save_in_excel = TRUE,
file_name = "Descriptives.xlsx",
vars = c("sex", "Submission", "Reporter", "age_range", "Outcome", "country",
"continent", "age_in_years", "wt_in_kgs", "Reactions", "Indications", "Substances",
"year", "role_cod", "time_to_onset"),
list_pids = list(),
method = "independence_test",
temp_demo = Demo,
temp_drug = Drug,
temp_reac = Reac,
temp_indi = Indi,
temp_outc = Outc,
temp_ther = Ther
)Arguments
- pids_cases
A vector of primary IDs for cases.
- RG
A vector of primary IDs: reference group. Default is NULL.
- drug
A vector of drug names. Default is NULL.
- save_in_excel
Whether to save the outcome in an excel. Defaults to TRUE
- file_name
The name of the Excel file to save the results. Default is "Descriptives.xlsx". It only works if save_in_excel is TRUE.
- vars
A character vector of variable names to include in the analysis.
- list_pids
A list of vectors with primary IDs for custom groups whose distribution should be described. Default is an empty list.
- method
The method for Chi-square test analysis, either "independence_test" or "goodness_of_fit". Default is "independence_test". It applies only for comparisons between cases and non-cases.
- temp_demo
Demo dataset. Defaults to Demo. Can be se to sample_Demo for testing
- temp_drug
Drug dataset. Can be set to sample_Drug for testing
- temp_reac
Reac dataset. Can be set to sample_Reac for testing
- temp_indi
Indi dataset. Can be set to sample_Indi for testing
- temp_outc
Outc dataset. Can be set to sample_Outc for testing
- temp_ther
Ther dataset. Can be set to sample_Ther for testing
Value
The function generates descriptive statistics as a gt_table and potentially saves them to an Excel file.
Examples
pids_cases <- unique(sample_Demo[sex == "M"]$primaryid)
RG <- unique(sample_Demo[sex == "M"]$primaryid)
# Generate descriptive statistics for cases
descriptive(
pids_cases = pids_cases, save_in_excel = FALSE,
temp_demo = sample_Demo, temp_drug = sample_Drug,
temp_reac = sample_Reac, temp_indi = sample_Indi,
temp_outc = sample_Outc, temp_ther = sample_Ther
)
#> Warning: Variables role_cod and time_to_onset not considered. If you want to include them please provide the drug investigated
#> # A tibble: 113 × 3
#> `**Characteristic**` N_cases `%_cases`
#> <chr> <chr> <chr>
#> 1 N 355 ""
#> 2 sex NA NA
#> 3 Male 355 "100.00"
#> 4 Submission NA NA
#> 5 Direct 24 "6.76"
#> 6 Expedited 181 "50.99"
#> 7 Periodic 150 "42.25"
#> 8 Reporter NA NA
#> 9 Consumer 163 "48.37"
#> 10 Healthcare practitioner 20 "5.93"
#> # ℹ 103 more rows
# Generate descriptive statistics for cases and non-cases
descriptive(
pids_cases = pids_cases, RG = RG, save_in_excel = FALSE,
temp_demo = sample_Demo, temp_drug = sample_Drug,
temp_reac = sample_Reac, temp_indi = sample_Indi,
temp_outc = sample_Outc, temp_ther = sample_Ther
)
#> Warning: Variables role_cod and time_to_onset not considered. If you want to include them please provide the drug investigated
#> Warning: NAs introduced by coercion
#> Warning: number of columns of result, 6, is not a multiple of vector length 7 of arg 1
#> # A tibble: 113 × 6
#> `**Characteristic**` N_cases `%_cases` N_controls `%_controls` `**q-value**`
#> <chr> <chr> <chr> <chr> <chr> <chr>
#> 1 N 355 "" NA "" ""
#> 2 __sex__ NA NA NA NA NA
#> 3 Male 355 "100.00" NA NA NA
#> 4 __Submission__ NA NA NA NA NA
#> 5 Direct 24 "6.76" NA NA NA
#> 6 Expedited 181 "50.99" NA NA NA
#> 7 Periodic 150 "42.25" NA NA NA
#> 8 __Reporter__ NA NA NA NA NA
#> 9 Consumer 163 "48.37" NA NA NA
#> 10 Healthcare practitio… 20 "5.93" NA NA NA
#> # ℹ 103 more rows