demog_table: Make a table of demographics for a set of simulations

In shirewoman2/Consultancy: Standardized tools for using R within the Simcyp Consultancy Team

Make a table of demographics for a set of simulations

Description

demog_table makes a table of the demographics of a set of simulations and, if appliable, observed data. UNDER CONSTRUCTION.

Usage

demog_table(
  demog_dataframe,
  demog_parameters = NA,
  mean_type = "geometric",
  variability_type = "90% CI",
  variability_format = "to",
  break_down_by_sex = TRUE,
  rounding = NA,
  save_table = NA,
  sort_column,
  page_orientation = "landscape",
  fontsize = 11
)

Arguments

demog_dataframe	the output from running extractDemog. Optionally (and we recommend) with added observed demographic data, perhaps from observed overlay XML files.
demog_parameters	Which demographic parameters do you want to include? Options are NA to include all of the parameters in demog_dataframe or a chraacter vector of the columns in demog_dataframe that you want to include. No need to include any columns that are not a demographic parameter because we'll ignore them, e.g., you don't need to tell us to include the columns "File" or "Individual", etc.)
mean_type	What kind of means and CVs or confidence intervals do you want listed in the output table? Options are "arithmetic" or "geometric" (default).
variability_type	What statistic would you like to use for reporting the variability? Options are: "90% CI" (default) 90% confidence interval; this will be geometric or arithmetic based on your choice for mean_type "CV" coefficient of variation; this will be geometric or arithmetic based on your choice for mean_type "SD" arithmetic standard deviation "none" to get no variability stats included in the table
variability_format	formatting used to indicate the variability When the variability is concatenated. Options are "to" (default) to get output like "X to Y", "hyphen" to get output like "X - Y", "brackets" to get output like "[X, Y]", or "parentheses" for the eponymous symbol if you're an American and a bracket if you're British, e.g., "(X, Y)". (Sorry for the ambiguity; this was written by an American who didn't originally realize that there was another name for parentheses.)
break_down_by_sex	TRUE (default) or FALSE for whether to break down the data by sex.
rounding	option for what rounding to perform, if any. Options are: NA or "Consultancy" All output will be rounded according to Simcyp Consultancy Team standards: to three significant figures when the value is < 100 or to the ones place if the value is >= 100. Please see the function round_consultancy, which does the rounding here. "none" No rounding will be performed. "significant X" where "X" is a number Output will be rounded to X significant figures. "signif X" also works fine. "round X" where "X" is a number Output will be rounded to X digits "Word only" Output saved to Word or a csv file will be rounded using the function round_consultancy, but nothing will be rounded in the output R object. This can be useful when you want to have nicely rounded and formatted output in a Word file but you also want to use the results from pksummary_mult to make forest plots, which requires numbers that are not rounded.
save_table	optionally save the output table and, if requested, the QC info, by supplying a file name in quotes here, e.g., "My nicely formatted table.docx" or "My table.csv", depending on whether you'd prefer to have the table saved as a Word or csv file. Do not include any slashes, dollar signs, or periods in the file name. (You can also save the table to a Word file later with the function formatTable_Simcyp.) If you supply only the file extension, e.g., save_table = "docx", the name of the file will be "PK summary table" with that extension. If you supply something other than just "docx" or just "csv" for the file name but you leave off the file extension, we'll assume you want it to be ".csv". All PK info will be included in a single Word or csv file, and, if checkDataSource = TRUE, that will be saved in a single csv file.
sort_column	optionally specify a column to sort by. If none are supplied, the table will not be sorted. If you would like to sort by more than one column, we recommend sorting before using this function, e.g., MyPKTable <- MyPKTable %>% arrange(Study, Dose) to sort by the column "Study" and then by the column "Dose" and then supply "MyPKTable" to formatTable_Simcyp. (This is just an example; your table must include those two columns for that to work.)
page_orientation	set the page orientation for the Word file output to "portrait" (default) or "landscape"
fontsize	the numeric font size for Word output. Default is 11 point. This only applies when you save the table as a Word file.
shading_column	If you would like to alternate the shading of the rows in the output table, supply here the unquoted name of the column to check for when to change the shading; every time that column's value changes, the shading will alternate between white and light gray. For example, if you have a table with PK values for multiple files and you have more than one row per file (an example of this would be the output from the function pksummary_mult), setting shading_column = File will cause the shading of the rows to alternate between white and light gray whenever the file changes. Please see the examples at the bottom of this help file.
merge_shaded_cells	TRUE (default) or FALSE for whether to merge the cells that have the same shade. This only applies when one of the columns in the input data.frame is used for deciding when to alternate shading, that is, shading_column has a value.
merge_columns	a vector of quoted column names or of numeric column positions that should be merged vertically whenever the values are the same. For example, merge_columns = c("File", "Tissue") will cause the cells in the columns "File" and "Tissue" to merge vertically whenever the same value shows up in consecutive rows. Similarly, merge_columns = c(1, 3, 5) will merge vertically the 1st, 3rd, and 5th columns whenever the values are the same. Note: This is different from most other functions in the SimcypConsultancy package, which require unquoted column names. Honestly, we just don't know how code things for you to supply a variable number of unquoted column names for a single argument; we've just hit a coding knowledge limitation here!

Value

a formatted table

Examples

# none yet

shirewoman2/Consultancy documentation built on Feb. 18, 2025, 10 p.m.