Boxplot function used in app elaborator

Description

Boxplot function used in app elaborator

Usage

elaborator_boxplot(
  elab_data,
  draw_points_logical,
  same_axes_per_treatment_logical,
  boxplot_color,
  boxplot_border_color,
  lines_data,
  number_plots,
  tol_percentage,
  test_results_logical,
  length_visit2_is_one_logical,
  sort_points,
  incProgress,
  outliers_logical,
  col_lines_options,
  custom_visit
)

Arguments

Value

No return value. Boxplots are generated, used in elaborator.

Calculates the index of the color vector in the qualitative trend analysis plot

Description

This function is mostly useful for generating the qualitative trend analysis plots. It returns the index of the color for a percentage which is observed for a specific pattern characterized by decreases/stability/increases from one visit to the next.

Usage

elaborator_calculate_color_index(r)

Arguments

Value

A numeric value between 1 and 11. This value is used as an index for the color legend in the qualitative trends plot in which darker colors reflect more frequent patterns

Returns row of a matrix containing all combinations of elements -1, 0, 1 of a pre-specified length

Description

This function is mostly useful for generating the qualitative trend analysis plots. It returns the (i-1)-th row of a matrix containing all combinations of elements -1, 0 and 1 of a pre-specified length.

Usage

elaborator_calculate_pattern(index, number_combinations)

Arguments

Value

A numeric vector containing a specific combination of elements -1, 0 and 1; this combination is used to calculate pattern for qualitative trend analysis plot.

Pattern number for input patterns defined by decreases, stability and increases

Description

This function is mostly useful for generating the qualitative trend analysis plots. It returns the pattern numbers for input patterns.

Usage

elaborator_calculate_pattern_number(p)

Arguments

Value

A numeric vector giving the pattern numbers for all input patterns.

Returns row of a matrix containing all combinations of elements 0 and 1 of a pre-specified length

Description

This function is mostly useful for generating the reference-value based pattern analysis plots. It returns the (i-1)-th row of a matrix containing all combinations of elements 0 and 1 of a pre-specified length.

Usage

elaborator_calculate_ref_pattern(index, number_combinations)

Arguments

Value

A numeric vector containing a specific combination of elements 0 and 1; this combination is used to calculate pattern for reference-value based pattern analysis plot.

Calculates the distance matrix based on Spearman's correlation coefficient

Description

This function derives the Spearman correlation coefficients for a data matrix and transforms the resulting similarity matrix into a distance/dissimilarity matrix. No difference is made between positive and negative correlations, i.e., correlations of -1 and 1 will be transformed to a distance of 0; correlations of 0 will be transformed to a distance of 1. Missing values in the input data will be handled by casewise deletion.

Usage

elaborator_calculate_spearman_distance(x)

Arguments

Value

A distance matrix of class "dist", which can be used for example for a seriation algorithm

Perform pairwise statistical tests for quantitative trend plots

Description

Perform pairwise statistical tests for quantitative trend plots

Usage

elaborator_calculate_test_for_all_visits(
  elab_data,
  Visit1,
  Visit2,
  sign_test,
  pcutoff
)

Arguments

Value

tibble with test results (estimate/p-values) and color code for quantitative trend graphs

function to change (rdata) or set (csv data) the classes of the required variables in elaborator

Description

function to change (rdata) or set (csv data) the classes of the required variables in elaborator

Usage

elaborator_change_class_required_variables(elab_data, visit, treatment, lab)

Arguments

Value

elab_data with changed classes (and factor levels)

create hover text info in elaborator app zoom panel(s)

Description

create hover text info in elaborator app zoom panel(s)

Usage

elaborator_create_hover_info_text(elab_data, labparameter, treat, select.visit)

Arguments

Value

character string with text about number of visits in every treatment group and labparameter

Returns indices for all elements of a vector x that are contained in another vector y

Description

This function is mostly useful for generating the qualitative trend analysis plots. It returns the indices or all elements of a vector x that are contained in another vector y

Usage

elaborator_derive_equal_values(y, x)

Arguments

Value

A numeric vector with the indices for all elements of a vector x that are contained in another vector y.

Derives p-values and estimates for sign test or t-test

Description

This function is mostly useful for generating the quantitative trend analysis plots. It returns p-values and estimates for the sign test or the t-test used for colorizing the background of the plots.

Usage

elaborator_derive_test_values(
  data = data,
  signtest = TRUE,
  Visit1 = c("Randomization"),
  Visit2 = c("End of Treatment"),
  lab_column
)

Arguments

Value

A list with p-values and estimates of the selected statistical test. The p-values and estimates will be used to colorize the background of the quantitative trend analysis plots.

• p.value - p.value of statistical test.

• estimate - estimate of statistical test.

Draws a curved line from start to end point

Description

This function is mostly useful for generating the reference-value based pattern analysis plots. It draws a curved line from a start to an end point.

Usage

elaborator_draw_curved_line(x1, y1, x2, y2, ...)

Arguments

Value

No return value; this function is called to draw curved lines of the reference-value based pattern plot.

Draws a circle with specified size, coordinates and color in a plot window

Description

This function is mostly useful for generating the reference-value based pattern analysis plots. It draws a circle with specified size, coordinates and color in a plot window.

Usage

elaborator_draw_dots(
  x,
  y,
  height,
  dot_col,
  pattern_Matrix,
  number_column,
  dot_Radius,
  dot_radius,
  fontsize,
  empty_color = "#A9A9A9",
  upper_color = "#2fb39f",
  lower_color = "#f78300"
)

Arguments

Value

No return value; this function is called to draw the circles for the reference-value based pattern analysis plot.

Generates tree diagram according to the reference-value based pattern analysis

Description

Generate tree diagram showing the number of patients with normal/abnormal values at each visit of a study according to the reference-value based pattern analysis.

Usage

elaborator_draw_ref_pattern(
  pattern_Matrix,
  fontsize,
  number_columns,
  background_color = "#E2F3F2"
)

Arguments

Value

No return value; this function is called to draw a tree diagram according to the reference-value based pattern analysis.

Color scheme preview

Description

This function is mostly useful for changing the color scheme of the qualitative trend analysis plots.

Usage

elaborator_draw_scheme_preview(x)

Arguments

Value

No return value; this function is used to generate plots with the selected color scheme for the qualitative trend analysis.

Transform data and fill them with missing values in app elaborator

Description

Transform data and fill them with missing values in app elaborator

Usage

elaborator_fill_with_missings(elab_data)

Arguments

Value

Transformed data frame

loading function for elaborator data, also performs checks for required variables

Description

loading function for elaborator data, also performs checks for required variables

Usage

elaborator_load_and_check(
  data_switch = "*.RData file",
  rdata_file_path = NULL,
  csv_file_path = NULL,
  loaded_file = NULL,
  separator = NULL,
  quote = NULL,
  decimal = NULL
)

Arguments

Value

list with data and error message

Performs binomial test for changes of a laboratory parameter between two visits

Description

This function is mostly useful for generating the quantitative trend analysis plots. It returns the output of a binomial test result used for colorizing the background of the plots.

Usage

elaborator_perform_binomial_test(
  data,
  treatment,
  lab_parameter,
  Visit1 = "Randomization",
  Visit2 = "End of Treatment",
  lab_column
)

Arguments

Value

A list of class "htest", with the results of the binomial test.

Performs t-test for changes of a laboratory parameter between two visits

Description

This function is mostly useful for generating the quantitative trend analysis plots. It returns the output of a t-test result used for colorizing the background of the plots.

Usage

elaborator_perform_ttest(
  data,
  treatment,
  lab_parameter,
  Visit1 = "Randomization",
  Visit2 = "End of Treatment",
  lab_column
)

Arguments

Value

A list of class "htest" with the results of the t-test.

Generates the qualitative trends analysis plots in the shiny app elaborator

Description

Generates diagrams showing the frequency of specific patterns of decreased, stable and increased values between adjacent visits of a study separately by treatment group and laboratory parameter according to the qualitative trend analysis.

Usage

elaborator_plot_qual_trends(
  dat1,
  Variab,
  fontsize = 1,
  method = "InQuRa",
  color_palette = c("#ffffff", "#ffffcc", "#ffeda0", "#fed976", "#feb24c", "#fd8d3c",
    "#fc4e2a", "#e31a1c", "#bd0026", "#800026", "#000000"),
  Summa = Summa
)

Arguments

Value

No return value. Generates plots for the qualitative trend analysis.

Generates boxplots for each treatment group and laboratory parameter

Description

Generate boxplots showing the distribution of laboratory values at each visits of a study separately by treatment group and laboratory parameter according to the quantitative trend analysis.

Usage

elaborator_plot_quant_trends(
  elab_data,
  signtest = TRUE,
  Visit1,
  Visit2,
  sameaxes,
  cols = NULL,
  labelvis = NULL,
  labcolumn,
  sortpoints = FALSE,
  pcutoff = 0.01,
  infotest = NULL,
  sortinput,
  bordercol = NULL,
  add_points = TRUE,
  connect_lines,
  lin_data = NULL,
  outliers,
  tolerated_percentage = 100,
  color_lines_options,
  custom_visits = NULL
)

Arguments

Value

No return value. Generates plots for the quantitative trends analysis.

Generates the reference-value based pattern analysis plots in the shiny app elaborator

Description

Generates diagrams showing the frequency of normal and abnormal values at each visit of a study separately by treatment group and laboratory parameter according to the reference-value based pattern analysis.

Usage

elaborator_plot_ref_pattern(
  data,
  criterion,
  fontsize = 0.6,
  sorting_vector = as.character(unique(data[, "LBTESTCD"])),
  abnormal_value_factor = 1
)

Arguments

Value

No return value, called to plot the reference-based value pattern.

Transform data in form for cluster analysis in app elaborator

Description

Transform data in form for cluster analysis in app elaborator

Usage

elaborator_prepare_clustering_matrix(elab_data, first_variable, last_variable)

Arguments

Value

Transformed data frame

Transform data by removing visits with too many missing values in app elaborator

Description

Transform data by removing visits with too many missing values in app elaborator

Usage

elaborator_remove_visits_due_tolerated_missings(elab_data, tolerated_value)

Arguments

Value

Transformed data frame

Server part of the elaborator application

Description

Server part of the elaborator application

Usage

elaborator_server(input, output, session)

Arguments

Value

No return value. Server part of the app, used in launch_elaborator-function.

Calculates the transparent version of a given color

Description

Calculates the transparent version of a given color

Usage

elaborator_transform_transparent(some_color, alpha = 100)

Arguments

Value

A character string representing a color hexcode with added transparency.

User Interface of the elaborator application

Description

User Interface of the elaborator application

Usage

elaborator_ui()

Value

No return value. User interface part of the app, used in launch_elaborator-function.

Launches the elaborator application

Description

Starts the elaborator application in the client's browser.

Usage

launch_elaborator(
  elaborator_data = NULL,
  host = "0.0.0.0",
  port = NULL,
  browser = NULL
)

Arguments

Value

A shiny app

Examples

if(interactive()){
## Launch application on localhost (127.0.0.1)
## -------------------------------------------
## By default launch_elaborator starts the application on localhost
## and a randomly selected port (e.g. 9876), in which case you can connect
## to the running application by navigating your browser to
## http://localhost:9876.
launch_elaborator()

## Launch application on a different host
## --------------------------------------
## You can also run the application on a different host
## by specifying a hostname and port. Just make sure to
## use an open port on your machine. Here "open" means
## that the port should not be used by another service
## and the port is opened by your firewall.
launch_elaborator(host="your-hostname", port = 8888, browser = NULL)


## Make the application available to your coworkers
## ------------------------------------------------
## within your local area network even without a
## dedicated Shiny server. The value set through the
## host argument says to accept any connection (not just from localhost).
## Then take note of your local IP (if you are under linux,
## you can see it through ifconfig). Say your IP is 192.168.1.70.
## Your colleagues can use your app by inserting in the address
## bar of their browser 192.168.1.70:8888, i.e. your IP followed
## by : and the port number you selected.
launch_elaborator(host="0.0.0.0", port=8888)

## Launch application on a different browser
## ----------------------------------------
## To run the shiny app on a different browser than your standard browser
## use the "browser" argument to set the path to the respective .exe file.
launch_elaborator(browser = "C:/Program Files/Mozilla Firefox/firefox.exe")
}

Demo data documentation for elaborator app

Description

Demo data documentation for elaborator app