Adverse event data set included in AdEPro

Description

Adverse event data set included in AdEPro

adeproLogo Function that creates a div container for the AdEPro Logo

Description

creates a div container with AdEPro Logo for the shiny app adepro

Usage

adeproLogo(height = 230, width = 160, align = "right")

Arguments

adepro_slice_plot - function to create pie chart graph

Description

Create pie chart graph for app adepro

Usage

adepro_slice_plot(
  data,
  patients,
  ae_list,
  global_params,
  height,
  width,
  xlines,
  ylines,
  xval,
  title,
  subgroup,
  slider,
  subjidn,
  adepro_colors = c("#e43157", "#377eb8", "#4daf4a", "#984ea3", "#ff7f00", "#ffff33",
    "#a65628", "#f781bf", "#21d4de", "#91d95b", "#b8805f", "#cbbeeb"),
  info = NULL,
  legend_ae = NULL,
  arrow_data = NULL,
  show_arrows = FALSE
)

Arguments

Subject level data set included in AdEPro

Description

Subject level data set included in AdEPro

ae_count - provides adverse event count dataset

Description

Provides data set with one adverse event by day and by treatment groups with variable 'freq', giving a categorization (integer between 0 and 4) of the frequency of the adverse event on a specific day by treatment group.

Usage

ae_count(ae_data, patient)

Arguments

bar_chart - creates barchart of AEs for all patient

Description

Creates bar charts daily and total for all patients separately according to treatment (R Package required: 'dplyr')

Usage

bar_chart(
  ae_data = ae,
  patients = patient,
  day = day_slider,
  variables = vars,
  day_max = day_mx,
  count_max = count_mx,
  treatments = treatments,
  cex.n = 2
)

Arguments

check_data - Consistency checks on the data

Description

Runs consistency checks on the adverse event and patient data

Usage

check_data(ae_data, patients)

Arguments

circle_legend - Function to create legend for displayed subjects

Description

Creates legend object for base R plots

Usage

circle_legend()

circle_legend2 - Creates Legend for Subject elements in AdEPro (version 2)

Description

Drawing legends for symbols in app

Usage

circle_legend2(
  aes,
  colors = c("#e43157", "#377eb8", "#4daf4a", "#984ea3", "#ff7f00", "#ffff33", "#a65628",
    "#f781bf", "#21d4de", "#91d95b", "#b8805f", "#cbbeeb")
)

Arguments

count_event Count the event number for every AE at specified timepoint

Description

Count the event number for every AE at specified timepoint

Usage

count_event(total = tot, day = 1)

Arguments

initQ - generates classification matrix

Description

Creates the classification matrix of adverse events such as treatment-emergent

Usage

initQ(ae_data)

Arguments

launch_adepro - Launches the AdEPro application

Description

Starts the AdEPro application in the client's browser.

Usage

launch_adepro(host = "127.0.0.1", port = NULL, browser = NULL)

Arguments

Details

Further information on how to use this application can be found in the vignette of this package.

Value

A shiny app

Examples

## Not run: 
## Launch application on localhost (127.0.0.1)
## -------------------------------------------
## By default launch_adepro 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_adepro()

## 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_adepro(host="your-hostname", port=8888)


## 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_adepro(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_adepro(browser = "C:/Program Files/Mozilla Firefox/firefox.exe")


## launching the application.

## End(Not run)

Draw Symbols (User Defined) on a Plot

Description

This function draws symbols on a plot. It is similar to the builtin symbols function with the difference that it plots symbols defined by the user rather than a prespecified set of symbols.

Usage

my.symbols(x, y=NULL, symb, inches=1, xsize, ysize,
add=TRUE,
vadj=0.5, hadj=0.5,
symb.plots=FALSE,
xlab=deparse(substitute(x)),
ylab=deparse(substitute(y)), main=NULL,
xlim=NULL, ylim=NULL, linesfun=lines,
..., MoreArgs)

Arguments

Details

The symb argument can be a 2 column matrix or a list with components 'x' and 'y' that defines points on the interval [-1,1] that will be connected with lines to draw the symbol. If you want a closed polygon then be sure to replicate the 1st point as the last point. If any point contains an NA then the line will not be drawn to or from that point. This can be used to create a symbol with disjoint parts that should not be connected. If symb is a function then it should include a '...' argument along with any arguments to define the symbol. Any unmatched arguments that end up in the '...' argument will be replicated to the same length as 'x' (using the rep function) then the values will be passed one at a time to the symb function. If MoreArgs is specified, the elements of it will also be passed to symb without modification. The symb function can either return a matrix or list with the points that will then be passed to the lines function (see above). Or the function can call the plotting functions itself (set symb.plots to TRUE). High level plotting can be done (plot, hist, and other functions), or low level plotting functions (lines, points, etc) can be used; in this case they should add things to a plot with 'x' and 'y' limits of -1 to 1. The size of the symbols can be specified by using inches in which case the symbol will be set inside of squares whose sizes are inches size based on the plotting device. The size can also be set using xsize and/or ysize which use the same units as the x and/or y variables. If only one is specified then the box will be square. If both are specified and they do not match the aspect ratio of the plot then the bounding box will not be square and the symbol will be distorted.

Value

This function is run for its side effect of plotting, it returns an invisible NULL.

Note

Since the '...' argument is passed to both lines and symb, the symb function should have a '...' argument so that it will ignore any additional arguments. Arguments such as 'type' can be passed through the '...' argument if you want the symbol made of something other than lines. Plotting coordinates and sizes are based on the size of the device at the time the function is called. If you resize the device after plotting, all bets are off. Currently missing values in x or y are not handled well. It is best if remove all missing values first.

Author(s)

Greg Snow

order_patient - Arranges patients by sequencing technique

Description

Arranges patients by sequencing technique (R Package required: 'dplyr', 'reshape2, 'seriation')

Usage

order_patient(
  ae_data = ae_data,
  patients = patient_d,
  variables = input$varSeq,
  method_dist = "euclidean",
  method_seriate = input$methSeq
)

Arguments

pie_legend - Function to create legend for displayed adverse events

Description

Creates legend object for base R plots

Usage

pie_legend(
  aes,
  colors = c("#e43157", "#377eb8", "#4daf4a", "#984ea3", "#ff7f00", "#ffff33", "#a65628",
    "#f781bf", "#21d4de", "#91d95b", "#b8805f", "#cbbeeb")
)

Arguments

pie_legend2 - Creates Legend for adverse events slices in AdEPro (version 2)

Description

Drawing legends for adverse event symbols in app

Usage

pie_legend2(
  tmp,
  aes,
  colors = c("#e43157", "#377eb8", "#4daf4a", "#984ea3", "#ff7f00", "#ffff33", "#a65628",
    "#f781bf", "#21d4de", "#91d95b", "#b8805f", "#cbbeeb"),
  legend_click = NULL,
  info
)

Arguments

prepare_data - read SAS or CSV raw data and prepare the data sets

Description

Creates a list with two data sets 'pat_data' and 'ae_data' in format which is used in the AdEPro Application

Usage

prepare_data(
  dat,
  SUBJIDN = "SUBJIDN",
  TRT01A = "TRT01A",
  SAFFN = "SAFFN",
  LVDT = "LVDT",
  DTHDT = "DTHDT",
  TRTSDT = "TRTSDT",
  AEDECOD = "AEDECOD",
  AESTDY = "AESTDY",
  AETRTEMN = "AETRTEMN",
  AEENDY = "AEENDY",
  AESEVN = "AESEVN",
  AESERN = "AESERN",
  AERELN = "AERELN",
  AERELPRN = "AERELPRN",
  AEACNN = "AEACNN",
  optional_vars = NULL,
  adsl_data = NULL
)

Arguments

preproc_ae - Preprocessing adverse event data

Description

Preprocesses adverse event dataset

Usage

preproc_ae(ae_data)

Arguments

preproc_patients - Preprocessing Patient Data

Description

Preprocesses patient dataset

Usage

preproc_patients(patients, height)

Arguments

Server part of the AdEPro application

Description

Server part of the AdEPro application

Usage

server(input, output, session)

Value

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

set_global_params - sets all global parameters

Description

Function that sets all global parameters

Usage

set_global_params(
  ae_data,
  patients,
  title = NULL,
  height = NULL,
  treatment = NULL
)

Arguments

set_group_lines - determines coordinates for the separating lines

Description

Calculates coordinates for separating lines between the treatment groups

Usage

set_group_lines(patients, height, treatment)

Arguments

set_vector_layout - creates vector layout

Description

creates vector layout for circles considering number of rows and treatment groups

Usage

set_vector_layout(patients, height)

Arguments

set_width - calculates width (number of columns with circles)

Description

Calculates vector with 1's with its length as the number of circles on the vertical axis

Usage

set_width(patients, height)

Arguments

tone - Function that plays two different sounds for adverse events

Description

Plays two different sounds (after one another) for treatment group comparison for a specific adverse event

Usage

tone(no1 = 0, no2 = 0, d = 0.7)

Arguments

User Interface of the AdEPro application

Description

User Interface of the AdEPro application

Usage

ui

Format

An object of class shiny.tag.list (inherits from list) of length 4.

Value

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