rtables (version 0.3.8)

analyze: Generate Rows Analyzing Variables Across Columns

Description

Adding /analyzed variables/ to our table layout defines the primary tabulation to be performed. We do this by adding calls to analyze and/or analyze_colvars into our layout pipeline. As with adding further splitting, the tabulation will occur at the current/next level of nesting by default.

Usage

analyze(
  lyt,
  vars,
  afun = simple_analysis,
  var_labels = vars,
  table_names = vars,
  format = NULL,
  nested = TRUE,
  inclNAs = FALSE,
  extra_args = list(),
  show_labels = c("default", "visible", "hidden"),
  indent_mod = 0L
)

Arguments

lyt

layout object pre-data used for tabulation

vars

character vector. Multiple variable names.

afun

function. Analysis function, must take x or df as its first parameter. Can optionally take other parameters which will be populated by the tabulation framework. See Details in analyze.

var_labels

character. Variable labels for 1 or more variables

table_names

character. Names for the tables representing each atomic analysis. Defaults to var.

format

FormatSpec. Format associated with this split. Formats can be declared via strings ("xx.x") or function. In cases such as analyze calls, they can character vectors or lists of functions.

nested

boolean, Add this as a new top-level split (defining a new subtable directly under root). Defaults to FALSE

inclNAs

boolean. Should observations with NA in the var variable(s) be included when performing this analysis. Defaults to FALSE

extra_args

list. Extra arguments to be passed to the tabulation function. Element position in thte list corresponds to the children of this split. Named elements in the child-specific lists are ignored if they do not match a formal argument of the ttabulation function.

show_labels

character(1). Should the variable labels for corresponding to the variable(s) in vars be visible in the resulting table.

indent_mod

numeric. Modifier for the default indent position for the structure created by this function(subtable, content table, or row) and all of that structure's children. Defaults to 0, which corresponds to the unmodified default behavior.

Value

A PreDataTableLayouts object suitable for passing to further layouting functions, and to build_table.

Details

When non-NULL format is used to specify formats for all generated rows, and can be a character vector, a function, or a list of functions. It will be repped out to the number of rows once this is known during the tabulation process, but will be overridden by formats specified within rcell calls in afun.

The analysis function (afun) should take as its first parameter either x or df. Which of these the function accepts changes the behavior when tabulation is performed.

• If afun's first parameter is x, it will receive the corresponding subset vector of data from the relevant column (from var here) of the raw data being used to build the table.

• If afun's first parameter is df, it will receive the corresponding subset data.frame (i.e. all columns) of the raw data being tabulated

In addition to differentiation on the first argument, the analysis function can optionally accept a number of other parameters which, if and only if present in the formals will be passed to the function by the tabulation machinery. These are as follows:

.N_col

column-wise N (column count) for the full column being tabulated within

.N_total

overall N (all observation count, defined as sum of column counts) for the tabulation

.N_row

row-wise N (row group count) for the group of observations being analyzed (ie with no column-based subsetting)

.df_row

data.frame for observations in the row group being analyzed (ie with no column-based subsetting)

.var

variable that is analyzed

.ref_group

data.frame or vector of subset corresponding to the ref_group column including subsetting defined by row-splitting. Optional and only required/meaningful if a ref_group column has been defined

.ref_full

data.frame or vector of subset corresponding to the ref_group column without subsetting defined by row-splitting. Optional and only required/meaningful if a ref_group column has been defined

.in_ref_col

boolean indicates if calculation is done for cells withing the reference column

Examples

# NOT RUN {
l <- basic_table() %>%
    split_cols_by("ARM") %>%
    analyze("AGE", afun = list_wrap_x(summary) , format = "xx.xx")
l
build_table(l, DM)


l <- basic_table() %>%
    split_cols_by("Species") %>%
    analyze(head(names(iris), -1), afun = function(x) {
        list(
            "mean / sd" = rcell(c(mean(x), sd(x)), format = "xx.xx (xx.xx)"),
            "range" = rcell(diff(range(x)), format = "xx.xx")
        )
    })
l
build_table(l, iris)

# }