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Line plot module

mod_lineplot.Rd

Display line plots of raw or summary data over time. Summaries include measures of central tendency (mean, median) and optional deviation and confidence estimators.

Usage

lineplot_UI(id)

lineplot_server(
  id,
  bm_dataset,
  group_dataset,
  summary_fns = list(Mean = lp_mean_summary_fns, Median = lp_median_summary_fns),
  subjid_var = "SUBJID",
  cat_var = "PARCAT",
  par_var = "PARAM",
  visit_vars = c("AVISIT"),
  cdisc_visit_vars = character(0),
  value_vars = c("AVAL", "PCHG"),
  additional_listing_vars = character(0),
  ref_line_vars = character(0),
  on_sbj_click = NULL,
  default_centrality_fn = NULL,
  default_dispersion_fn = NULL,
  default_cat = NULL,
  default_par = NULL,
  default_val = NULL,
  default_visit_var = NULL,
  default_visit_val = NULL,
  default_main_group = NULL,
  default_sub_group = NULL,
  default_transparency = 1,
  default_y_axis_projection = "Linear"
)

mod_lineplot(
  module_id,
  bm_dataset_name,
  group_dataset_name,
  receiver_id = NULL,
  summary_fns = list(Mean = lp_mean_summary_fns, Median = lp_median_summary_fns),
  subjid_var = "SUBJID",
  cat_var = "PARCAT",
  par_var = "PARAM",
  visit_vars = c("AVISIT"),
  cdisc_visit_vars = character(0),
  value_vars = c("AVAL", "PCHG"),
  additional_listing_vars = character(0),
  ref_line_vars = character(0),
  default_centrality_fn = NULL,
  default_dispersion_fn = NULL,
  default_cat = NULL,
  default_par = NULL,
  default_val = NULL,
  default_visit_var = NULL,
  default_visit_val = NULL,
  default_main_group = NULL,
  default_sub_group = NULL,
  default_transparency = 1,
  default_y_axis_projection = "Linear"
)

Arguments

id

Shiny ID [character(1)]

bm_dataset

[data.frame()]

An ADBM-like dataset similar in structure to the one in this example, with one record per subject per parameter per analysis visit.

It should have, at least, the columns specified by the parameters subjid_var, cat_var, par_var, visit_vars and value_vars. The semantics of these columns are as described in the CDISC standard for variables USUBJID, PARCAT, PARAM, AVISIT and AVAL, respectively.

Optional columns specified by ref_line_vars should contain the same numeric value for all records of the same parameter.

group_dataset

[data.frame()]

An ADSL-like dataset similar in structure to the one in this example, with one record per subject.

It should contain, at least, the column specified by the parameter subjid_var.

summary_fns

[list()]

Each element of this named list contains a summary function (e.g. a mean) and a collection of dispersion functions (e.g. standard deviation) defining ranges around the values returned by the summary function.

The structure of each element is then a named list with the following elements:

  • fn: Function that takes a numeric vector as its sole parameter and produces a scalar number.

  • dispersion: Named list of pairs functions that return the top and bottom dispersion ranges. They also take a numeric vector as input and return a single numeric scalar

  • y_prefix: Prefix that will be prepended the Y axis label of the generated plot

For an example, see dv.explorer.parameter::lp_mean_summary_fns.

subjid_var

[character(1)]

Column corresponding to the subject ID

cat_var, par_var, visit_vars

[character(1)]

Columns from bm_dataset that correspond to the parameter category, parameter and visit

cdisc_visit_vars

[character(1)]

Column from bm_dataset that correspond to the parameter visit and is interpreted as a CDISC Visit Days (skipping day 0; jumping from value -1 to value 1 in the X axis)

value_vars

[character(n)]

Columns from bm_dataset that correspond to values of the parameters

additional_listing_vars

[character(n)]

Columns from bm_dataset that will be appended to the single-subject listing

ref_line_vars

[character(n)]

Columns for bm_dataset specifying reference values for parameters

on_sbj_click

[function()]

Function to invoke when a subject is clicked in the single-subject listing

default_cat, default_par, default_visit_var, default_main_group

[character(1)|NULL]

Default values for the selectors

default_visit_val

list([character(n)|numeric(n)])

Named list of default values associated to specific visit_vars, e.g. default_visit_val = list(VISIT = c('VISIT1', 'VISIT2'), AVISITN = c(1, 2))

default_sub_group, default_val, default_centrality_fn, default_dispersion_fn

[character(1)|NULL]

Default values for the selectors

default_transparency

[numeric(1)]

Default values for the selectors

default_y_axis_projection

["Linear"|"Logarithmic"]

Default projection for the Y axis

module_id

Shiny ID [character(1)]

Module identifier

bm_dataset_name, group_dataset_name

[character(1)]

Dataset names

receiver_id

[character(1)]

Shiny ID of the module receiving the selected subject ID in the single subject listing. This ID must be present in the app or be NULL.

Functions

  • lineplot_UI(): UI

  • lineplot_server(): Server