Package 'Pmetrics'

Minimum value.

Maximum value.

Intercept y value in relative coordinates, i.e. 0 (bottom) to 1 (top). The x value is 0.

Slope

Y-intercept of horizontal line, in absolute coordinates

X-intercept of vertical line, in absolute coordinates

Controls characteristics of lines. This argument maps to plotly line attributes. TRUE will plot default lines. FALSE will suppress lines. If a list, can control many line characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > line to see all the ways the line can be formatted. Most common will be:

• color Line color.

• dash Plotting character. See plotly::schema(), traces > scatter > attributes > line > dash > values.

• width Thickness in points.

Example: line = list(color = "red", dash = "longdash", width = 2) . Default is line = list(color = "black", width = 1, dash = "dash").

A PM_data data object

A character vector defining the method to use. Options are

• "jelliffe" or "jel"

• "cockcroft-gault" or "cg"

• "mdrd"

• "ckd-epi" or "ckd"

• "schwartz" For the fuller versions, Only the first 4 letters are required

A character vector with the name of the id column in x. The default is "id".

A character vector with the name of the weight column in x. The default is "wt". Only required for "jelliffe" and "cockcroft-gault" methods. Values must be in kilograms.

A character vector with the name of the height column in x. The default is "ht". Only required for the "schwartz" method. Values must be in meters

A character vector with the name of the column defining sex in x. Male should be 1 and female should be 0. The default is "male".

A character vector with the name of the age column in x. The default is "age". Values must be in years.

A character vector with the name of a column defining black race in x. Male should be 1 and female should be 0. The default is "male".

A character vector with the name of the serum creatinine column in x. Default units are mg/dL, unless SI = TRUE below. The the default name is "scr".

A character vector with the name of the blood urea nitrogen column in x. Default units are mg/dL, unless SI = TRUE below. Default name is "bun". Optional for the Schwartz method.

A character vector with the name of the cystatin C column in x. Units are always mg/L. Default is "cysC". Optional for the Schwartz method.

Boolean value, if true, will expect serum creatinine to be in micromol/L and BUN reported as micromol/L of urea. Default is FALSE.

The plot to which the shape should be added. Default is the last_plot().

A list of attributes that specify a shape. Note that only one shape can be added for each call, but to be consistent with the shapes argument to plotly::layout(), we use the same plural.

The plot to which the shape should be added. Default is the plotly::last_plot().

X value for regression if not the original x value of the plot. Be sure to specify as a formula, e.g. x = ~pred.

Y value for regression if not the original y value of the plot. Be sure to specify as a formula, e.g. y = ~obs.

A secondary data object to use for regression other than the original plot data.

The tegression method, currently either "lm" (the default) for linear regression, or "loess" for loess regression.

Only used for method = "loess". The span parameter to control the degree of smoothing. Default is 0.75.

Controls characteristics of lines. This argument maps to plotly line attributes. TRUE will plot default lines. FALSE will suppress lines. If a list, can control many line characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > line to see all the ways the line can be formatted. Most common will be:

• color Line color.

• dash Plotting character. See plotly::schema(), traces > scatter > attributes > line > dash > values.

• width Thickness in points.

Example: line = list(color = "red", dash = "longdash", width = 2) Default is list(color = "blue", width = 2). The confidence interval will have the same color but at opacity 0.2.

Confidence interval for regressions. Default is 0.95. It can be suppressed by setting to 0.

Add the statistics from linear regression to the plot. Ignored if method = "loess". If missing or FALSE, will be suppressed. Can be set to TRUE which results in default format of list(x= 0.8, y = 0.1, bold = F, font = list(color = "black", family = "Arial", size = 14)). The coordinates are relative to the plot with lower left = (0,0), upper right = (1,1). This argument maps to plotly::add_text(). It is also an option that can be set in setPMoptions to avoid specifying this argument for every plot. The default option is TRUE. If specified as a Pmetrics option, it can be overridden for specific plots by supplying a value.

Initial value for lambda

Vector of coefficients defining assay error polynomial

Estimate if FALSE (default).

A vector to check.

A character string indicating what to return. Can be "test", "vector", or "nonnum". The default is "test".

A character vector of extra values to exclude from the check. The default is c(".", "NA").

Logical. Should the app launch in a browser?

Logical. If TRUE, emits a user-facing CLI summary.

Numeric scalar. Network timeout in seconds used for this check.

The plotly plot to which the click functionality should be added. Default is the plotly::last_plot().

The color to use for traces that are highlighted. Colors for non-highlighted traces will be preserved but dimmed to 20% opacity. Default highlight color is orange().

A correlation matrix.

A vector of standard deviations corresponding to the variables in the correlation matrix.

Optional API response list. Defaults to latestR().

Destination directory. Defaults to the user's Downloads folder.

The plot to which the shape should be added. Default is the plotly::last_plot().

A file path with a suitable file extension (png, jpg, jpeg, webp, svg, or pdf). Unlike save_image, the file argument may include the full path and filename other than in the current working directory.

The width/height of the exported image in pixels, mutliplied by scale.

The scale factor to use when exporting the figure. Default is 1.0. A scale factor larger than 1.0 will increase the image size, and less than 1.0 will decrease the image size. Note that the documentation for save_image says that this argument changes the resolution, but that is not true. The resolution will remain at 72 pixels/inch (28.3 px/cm), which is the default for R. To increase the resolution, export to .pdf or .svg and use an external program, such as Adobe Acrobat, Acrobat Reader, or Mac Preview.

Units for width and height. Default is pixels ("px"). Alternatives are inches ("in") or centimeters ("cm")

Show the exported image in R via base::file.show(). If export format is pdf, it will open the system default pdf viewer. Default is TRUE.

A PM_data object. It can be other data frames but the results will likely not be meaningful.

The number of colors to return from the list.

The option to retrieve. If omitted, all option values will be returned.

Warn if options file doesn't exist. Default TRUE.

Suppress warning messages. Default FALSE.

If type = "lm" (the default) or type = "linear", the covariate value will be linearly interpolated between values when fitting the model to the data. in a model list cov item. To fix covariate values to the value at the last time point, set type = "none".

A suitable data object, i.e. PM_pop, PM_post, PM_op, PM_sim, or some other suitable dataframe with at least time/observation columns referred to by formula.

A formula of the form obs ~ time | group. Default value for group is "id", so when if the data contain an "id" column, the formula can simply be obs ~ time. If the data contain a grouping variable, it can be specified as obs ~ time | group, where group is the name of the grouping variable. This is only required with data that is not of class PM_pop, PM_post, PM_op or PM_sim.

A vector of subject IDs to include in the plot, e.g. c(1:3,5,15)

A vector of subject IDs to exclude in the plot, e.g. c(4,6:14,16:20)

Specify the time to begin AUC calculations. Default is 0.

Specify the time to end AUC calculations so that AUC is calculated from start to end. Default for end is the maximum observation time for each subject. Subjects with insufficient data for a specified interval will have AUC calculated for the available data, not to exceed the specified interval.

Can be either "median" for the predictions based on medians ofpred.type parameter value distributions, or "mean". Default is "median". Only relevant for PMpost or PMpop objects.

Which output equation to plot. Default is 1.

Which block to plot, where blocks are defined by dose reset events (EVID = 4) in the data.

Default is "linear" for AUC trapezoidal calculation. Any other value will result in linear up, log down.

Boolean to add a zero concentration at time 0. Default is FALSE.

PM_data object to analyze.

Boolean switch to use the posterior predictions rather than the observed. concentrations. Default is FALSE. Ignored if an IT2B run is used to supply the raw data file.

A vector of subject IDs to include in the NCA, e.g. c(1:3,5,15)

A vector of subject IDs to exclude in the NCA, e.g. c(4,6:14,16:20). When postPred is TRUE, any subject(s) excluded from the IT2B/NPAG run will be excluded as well.

The number of the input (e.g. drug) to analyze; default 1.

If postPred is TRUE, use predictions based on median or mean of each subject's Bayesian posterior parameter distribution. Default is "median", but could be "mean".

The number of the output equation to analyze; default 1

The number of the observation block within subjects, with each block delimited by EVID=4 in the data file; default 1

The beginning of the time interval to look for doses and observations, e.g. 120. It can be a vector to allow for individual start times per subject, e.g. c(120,120,144,168). If the length of start is less than the number of subjects, the last value will be recycled as needed. If the start time is not 0 (default), then it is assumed that steady state (multiple dose) conditions apply.

Analogous to start, set this equal to the end of the dosing interval. It too can be a vector, with the last value recycled as necessary. Default is Inf, i.e. all data used.

Alternative way to specify time interval for NCA by choosing dose number, e.g. 1 or 3. May be a numeric vector, like start and end, e.g. c(1,1,1,3,1,...) to allow for individualization by subject. The last value will be recycled to ensure length equal to the number of subjects. Default is NA, which means start will be used.

The complement to first, specifying the last dose to end the time interval. If NA, which is the default, then the maximum time per subject will be the upper bound of the time interval.Like first, last can be a vector, with the last value recycled as necessary. Use NA in the vector to signify maximum time for that subject.

Number of observations to use for terminal curve fitting (i.e. to estimate k). Default is 3.

Subject identification

Area under the time-observation curve, using the trapezoidal approximation, from time 0 until the second dose, or if only one dose, until the last observation

Area under the first moment curve

Slope by least-squares linear regression of the final 3 log-transformed observations vs. time. If the final 3 concentrations are not decreasing such that linear regression results in a positive slope, this value and all others that depend on k will be suppressed.

Area under the curve from the time of the last observation to infinity, calculated as ⁠Final obs/k⁠. This value will be suppressed if start != 0.

Area under the first moment curve from the time of the last observation to infinity. This value will be suppressed if start != 0.

Area under the curve from time 0 to infinity, caluculated as auc + auclast

Area under the first moment curve from time 0 to infinity

Mean residence time, calculated as 1/k

Maximum predicted concentration after the first dose

Time to cmax

Clearance, calculated as dose/aucinf

Volume of distribution at steady state, calculated as cl*mrt

Half life of elimination, calculated as ln(2)/k

Dose for each subject

A vector of observations

A vector of standard deviations obtained from repeated measurements at each observation in obs

A Pmetrics data file. From this, the maximum and mininimum observations will be retrieved. This is useful to ensure that calculated standard deviations are not negative at any observation in the dataset. If not specified, the default is the maximum obs.

The output equation in data. Default is 1.

Color of the data points. Default is red.

Relative size of the data points. Default is 3. See par.

Ploting symbol. Default is “+”. See par.

Color of the fitted polynomial lines. Default is blue.

Width of the lines. Default is 2.

Add a reference line at SD 0 to help evaluate that all fitted SDs are >0. Default is true.

Boolean argument to plot legend. Default is TRUE.

Other plotting parameters as in plot.default and par

A data.frame or name of .csv file in working directory whose first two columns are targets and the number of samples for each target. An example can be seen for Staphylococcus aureus susceptibility to vancomycin at EUCAST.

Logical. If TRUE (default), launches the Shiny browser app. If FALSE, returns the model tibble invisibly without launching the app.

Logical. Passed to shiny::runApp() when show = TRUE.

Initial mean.

Initial standard deviation.

A matrix or data frame.

A matrix or data frame.

k An integer.

The confidence level. Default value is 0.05.

Logic value. If it is set to be TRUE the p value of test will be calcuated and reported; if it is set to be false the p value will not be calculated.

Boolean value. If it is set to be TRUE the test result will be reported; if it is set to be FALSE the test result will not be reported.

The name and extension of a NONMEM data (e.g. .csv) file in the working directory, or the full path to a file.

The name and extension of a NONMEM control (e.g. .ctl) file in the working directory, or the full path to a file.

A color name or hex string (e.g. "red", "#FF0000", "#FF0000FF").

The method to use for finding the opposite color. One of "complement", "complement_maxcontrast", or "bw_maxcontrast". Default is "complement".

The degree offset for the hue complement. Default is 180.

The name of an PM_cov data object and loaded with PM_load as a PM_result, e.g. PM_result$cov.

This is a mandatory formula of the form y ~ x, where y and x are the two data parameters to plot.

Controls characteristics of lines. Unlike some other Pmetrics plots, but like plot.PM_op, line is a list of three elements:

• lm If set to TRUE or a list of plotly line attributes, will generate a linear regression of the form y ~ x Line attributes will control the appearance of the regression line and the confidence interval around the line. If set to FALSE, no linear regression will be generated. The default values for the elements of the lm list, all of which can be overriden are:

  • ci Confidence interval around the regression, default 0.95.

  • color Color of the regression line and the confidence area around the line, but at opacity = 0.2. Default is "dodgerblue".

  • width Width of the regression line, default 1.

  • dash See plotly::schema(), traces > scatter > attributes > line > dash > values. Default is "solid". Example: line = list(lm = list(color = "red", dash = "longdash", width = 2))

• loess If set to TRUE or a list of plotly line attributes, will generate a loess regression of the form y ~ x The list elements and default values in the loess list are the same as for lm except the default style is "dash". Example: line = list(lm = FALSE, loess = TRUE)

• ref If set to TRUE or a list of plotly line attributes, will generate a reference line with slope = 1 and intercept = 0. The default values for the elements of the ref list are:

  • color "grey".

  • width 1.

  • dash "dot". Note that there is no ci argument for the ref list. Example: line = list(lm = FALSE, loess = TRUE, ref = list(color = "lightgrey")) If the line argument is missing, it will be set to line = list(lm = FALSE, loess = TRUE, ref = FALSE), i.e. there will be a linear regression with reference line, but no loess regression. If time is chosen as the x variable in the formula, linear, loess and reference lines will be suppressed, although formatting specified in the loess line (except color, see below) will be applied to the lines joining the subject values.

Controls the plotting symbol for observations. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the marker with default characteristics. FALSE will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:

• color Marker color.

• symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values.

• size Character size in points.

• opacity Ranging between 0 (fully transparent) to 1 (fully opaque).

• line A list of additional attributes governing the outline for filled shapes, most commonly color and width.

Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2)) Default is marker = list(color = orange, shape = "circle", size = 10, opacity = 0.5, line = list(color = black, width = 1)).

to use for subjects when time is set as the x parameter. This can be a palette or a vector of colors. For accepted palette names see RColorBrewer::brewer.pal.info. Examples include "BrBG", or "Set2". An example vector could be c("red", "green", "blue"). It is not necessary to specify the same number of colors as groups within color, as colors will be interpolated to generate the correct number. The default is the "Spectral" palette. This will override any color in the marker or line.

Can be either "median" for the predictions based on medians ofpred.type parameter value distributions, or "mean". Default is "median".

A vector of subject IDs to include in the plot, e.g. c(1:3,5,15)

A vector of subject IDs to exclude in the plot, e.g. c(4,6:14,16:20)

Not used for this function.

Boolean operator to plot the y axis in log base 10. This argument maps to the yaxis type value in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > type.

Example: log = T

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

• grid = F

• grid = list(gridcolor = "black", gridwidth = 2)

Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

• xlab = "Time (h)"

• xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))

• xlab = list(text = "Time", font = list(bold = T))

If missing, will default to the name of the x variable in the formula.

Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, and ylab is simply a character label, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

If missing, will default to the name of the y variable in the formula.

Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element. The default for bold is TRUE.

Examples:

• title = "Observed vs. Predicted"

• title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))

Default is to have no title.

Add the statistics from linear regression to the plot. If FALSE, will be suppressed. Default is TRUE which results in default format of list(x= 0.8, y = 0.1, bold = F, font = list(color = "black", family = "Arial", size = 14)). The coordinates are relative to the plot with lower left = (0,0), upper right = (1,1). This argument maps to plotly::add_text().

Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > range.

Example: xlim = c(0,1)

Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > range.

Example: ylim = c(0,100)

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note that log, xlab, ylab, xlim, and ylim are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. See plotly::schema() layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.

Examples:

• NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only

• NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes

.

The name of a PM_cycle object, e.g. NPex$cycle.

Controls characteristics of lines. This argument maps to plotly line attributes. TRUE will plot default lines. FALSE will suppress lines. If a list, can control many line characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > line to see all the ways the line can be formatted. Most common will be:

• color Line color.

• dash Plotting character. See plotly::schema(), traces > scatter > attributes > line > dash > values.

• width Thickness in points.

Example: line = list(color = "red", dash = "longdash", width = 2) Default = list(color = "dodgerblue", width = 2, dash = "solid"). Note The width will apply to all plots, but color and dash will only apply to the first three plots (log-likelihood, AIC, gamma/lambda). Use colors and linetypes below to control the appearance of the line traces for the normalized plots, because each of those traces is mapped to a parameter.

Controls the plotting symbol for observations. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the marker with default characteristics. FALSE will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:

• color Marker color.

• symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values.

• size Character size in points.

• opacity Ranging between 0 (fully transparent) to 1 (fully opaque).

• line A list of additional attributes governing the outline for filled shapes, most commonly color and width.

Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2)) Here, the observation controlled is the value of a given trace at a specific cycle number. Default = list(symbol = "circle", color = "dodgerblue", size = 4). Note the marker color for the normalized parameter value plots will be controlled by the colors parameter below, but size and symbol will apply to all plots.

to use for normalized parameter value line traces. This can be a palette or a vector of colors. For accepted palette names see RColorBrewer::brewer.pal.info. Examples include "BrBG", or "Set2". An example vector could be c("red", "green", "blue"). It is not necessary to specify the same number of colors parameters to be plotted, as colors will be interpolated to generate the correct number. The default when color is not specified is the "Set2" palette.

to use for normalized parameter value line traces. See plotly::schema(), traces > scatter > attributes > line > dash > values. An example vector could be c("solid", "dash", "longdash"). It is not necessary to specify the same number of linetype parameters to be plotted, as they will be recycled to generate the correct number. The default when linetypes is not specified is "solid".

Decimal between 0 and 1 specifying the proportion of "burn-in" cycles to omit from the plots. If missing, the first 20% will be omitted.

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

• grid = F

• grid = list(gridcolor = "black", gridwidth = 2)

Controls the formatting of the x-axis label. The text is fixed by the function and cannot be altered. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

• xlab = list(bold = F, font = list(color = "red", family = "Arial", size = 10))

• xlab = list(font = list(bold = T))

Format for y-axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

Additional R plotting parameters.

A PM_cycle_data object

Additional arguments passed to plot.PM_cycle

The name of an PM_data data object or loaded as a field in a PM_result object

A vector of subject IDs to include in the plot, e.g. c(1:3,5,15)

A vector of subject IDs to exclude in the plot, e.g. c(4,6:14,16:20)

Controls characteristics of lines as for all plotly plots. Here line is a list of two elements:

• join Can either be a boolean or a list. If set to TRUE or a list of plotly line attributes, it will generate line segments joining observations. If set to FALSE, no segments will be generated.

**Note:**The color of the joining line is the same as the marker color for that line. To avoid confusion, the line color cannot be changed. Change the marker color instead. The default values for the other elements of the join list, both of which can be overriden are: - width Width of the segments, default 1. - dash See plotly::schema(), traces > scatter > attributes > line > dash > values. Default is "solid". Example: line = list(join = list(dash = "longdash", width = 2))

• pred Default is FALSE, which means that predictions will not be included in the plot. To include predictions, supply one of the following:

• If plotting data contained in a PM_result, use "pop" or "post" to include population or posterior predictions. ** Example 1: ⁠run1 <- PM_load(1); run1$data$plot(line = list(pred = "post"))⁠

• If plotting data not contained in a PM_result, you may add the name of a population PM_pop or posterior PM_post prediction object in a PM_result object. This might be useful if you want to see how the predictions from one population match the raw data from another. ** Example 2: ⁠dat <- PM_data$new("new.csv"); dat$plot(line = list(pred = run1$post))⁠.

To format the predictions, supply pred as a list, with the prediction object first, followed by named options to control the prediction plot:

• icen Chooses the median or mean of each subject's Bayesian posterior parameter distribution. Default is "median", but could be "mean".

• As for join, the color of the pred line is fixed to the same color as the marker. Other parameters to pass to plotly to control line characteristics that join the predictions are width, and dash. Continuing Example 1 above: pred = list("post", icen = "mean", width = 2). Default formats are the same as for the join argument, since normally one would not plot both lines joining observations and prediction lines, i.e., typical use would be line = list(join = F, pred = "post").

Formats the symbols plotting observations. Controls the plotting symbol for observations. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the marker with default characteristics. FALSE will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:

• color Marker color.

• symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values.

• size Character size in points.

• opacity Ranging between 0 (fully transparent) to 1 (fully opaque).

• line A list of additional attributes governing the outline for filled shapes, most commonly color and width.

Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2)) . When a group and/or multiple outeq are specified, the ⁠$color⁠ element should be a palette or a vector of colors. For accepted palette names see RColorBrewer::brewer.pal.info. Examples include "BrBG", or "Set2". An example vector could be c("red", "green", "blue"). It is not necessary to specify the same number of colors as groups within group, as colors will be interpolated to generate the correct number. The default when group is specified is the "Set1" palette. When there are groups, the ⁠$color⁠ element for join or pred lines will be set to the same as marker$color.

Character vector naming one column in x to group by, e.g. "id" or a covariate like "gender"

A character vector of names to label the groups if legend = TRUE. This vector must be the same length as the number of groups within group. If missing, the vector will be generated from the unique values in group. Example: c("Male", "Female") if group = "gender" and "gender" is a covariate in the data.

Multiplication factor for y axis, e.g. to convert mg/L to ng/mL

Which output equation to plot. Default is 1. Default is 1, but can be multiple if present in the data, e.g. 1:2 or c(1, 3). In the case of multiple outputs, group_colors will be used to color the lines and markers.

Character vector of names to label the outputs if legend = TRUE. These can be combined with group_names. The number must match the number of outputs in outeq. If missing, the default is "Output 1", "Output 2", etc.

Which block to plot, where blocks are defined by dose reset events (EVID = 4) in the data. Default is 1, but can be multiple if present in the data, as for outeq.

Boolean operator to use time after dose rather than time after start. Default is FALSE.

Operator to overlay all time concentration profiles in a single plot. The default is TRUE. If FALSE, will trellisplot subjects one at a time. Can also be specified as a vector with number of rows and columns, e.g. c(3, 2) for 3 rows and 2 columns of subject splots to include in each trellis.

Controls display of legend. This argument maps to the plotly layout showlegend and legend arguments. It is either a boolean operator (most common) or a list of parameters to be supplied to plotly. See plotly::schema() > layout > layoutAttributes > legend and showlegend for more details on the available options for formatting. If legend is supplied as a list, the plotly layout > layoutAttributes > showlegend value will be set to TRUE automatically.

Examples:

• legend = T

• legend = list(orientation = "h", font = list(color = "blue"))

Default is FALSE unless groups are specified with colorabove.

Boolean operator to plot the y axis in log base 10. This argument maps to the yaxis type value in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > type.

Example: log = T

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

• grid = F

• grid = list(gridcolor = "black", gridwidth = 2)

Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

• xlab = "Time (h)"

• xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))

• xlab = list(text = "Time", font = list(bold = T))

Default is "Time".

Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, and ylab is simply a character label, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

Default is "Output".

Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element. The default for bold is TRUE.

Examples:

• title = "Observed vs. Predicted"

• title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))

Default is to have no title.

Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > range.

Example: xlim = c(0,1)

Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > range.

Example: ylim = c(0,100)

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note that log, xlab, ylab, xlim, and ylim are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. See plotly::schema() layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.

Examples:

• NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only

• NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes

.

A data frame in the format of the standard_data field of a PM_data object

Additional arguments passed to plot.PM_data

The name of an PM_final data object as a field in a PM_result R6 object, e.g PM_result$final.

An optional formula of the form y ~ x, where y and x are two model parameters to plot in a 3-dimensional bivariate plot. See details.

Controls characteristics of lines. This argument maps to plotly line attributes. TRUE will plot default lines. FALSE will suppress lines. If a list, can control many line characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > line to see all the ways the line can be formatted. Most common will be:

• color Line color.

• dash Plotting character. See plotly::schema(), traces > scatter > attributes > line > dash > values.

• width Thickness in points.

Example: line = list(color = "red", dash = "longdash", width = 2) The line argument is used to format:

• the density line drawn over an NPAG PM_final object. Default is FALSE, which means no density line will be drawn. Use TRUE to draw the default line, which is black, solid, and of width 1, or specify as a list to control these elements, e.g. line = list(color = "red", width = 2, dash = "dash")

• the drop lines from point to lower surface when a formula is specified to generate a bivariate plot from an NPAG PM_final object. In this case, default is line = TRUE. The default format is black, dashed, and of width 1.

• the lines drawing the normal distribution of parameter values from an IT2B PM_Final object. Again, here the default is line = TRUE, and the format is black, solid, of width 1. See density. Ignored for IT2B output.

See details for which objects the marker argument controls. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the marker with default characteristics. FALSE will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:

• color Fill color for NPAG bars, marker color for bivariate NPAG plots. Ignored for IT2B plots.

• symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values. Only relevant for bivariate NPAG plots.

• size Character size in points. Only relevant for bivariate NPAG plots.

• opacity Bar fill color for univariate NPAG plots or marker opacity for bivariate NPAG plots. Ignored for IT2B plots. Ranges between 0 (fully transparent) to 1 (fully opaque).

• line A list of additional attributes governing the outline for bars in univariate NPAG plots or markers in bivariate NPAG plots. Ignored for IT2B plots.

  • color Outline color. Default is "black".

  • width Outline width. Default is 1. Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2))

Standardize the normal parameter distribution plots from IT2B to the same scale x-axis. Ignored for NPAG output.

Ignored for this plot.

Boolean operator to plot the y axis in log base 10. This argument maps to the yaxis type value in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > type.

Example: log = T

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

• grid = F

• grid = list(gridcolor = "black", gridwidth = 2)

Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

• xlab = "Time (h)"

• xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))

• xlab = list(text = "Time", font = list(bold = T))

Default is the name of the plotted x-variable. Formatting can be controlled, but the text is recommended to not be changed.

Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, and ylab is simply a character label, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

Default is "Probability" for univariate plots, and the name of the plotted y-variable for bivariate plots. Formatting can be controlled, but the text is recommended to not be changed.

Only for bivariate plots. Default is "Probability". Can be a list to control formatting or default text, as for xlab and zlab.

Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element. The default for bold is TRUE.

Examples:

• title = "Observed vs. Predicted"

• title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))

Default is to have no title on plots.

Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > range.

Example: xlim = c(0,1)

Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > range.

Example: ylim = c(0,100)

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note that log, xlab, ylab, xlim, and ylim are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. See plotly::schema() layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.

Examples:

• NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only

• NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes

.

A 'PM_final_data“ object

Additional arguments passed to plot.PM_final

The name of an PM_model object.

Controls the characteristics of the compartments (nodes). It can be boolean or a list. TRUE will plot the compartments with default characteristics. FALSE will suppress compartment plotting. If a list, can control some marker characteristics, including overriding defaults. These include:

• color Marker color (default: dodgerblue).

• opacity Ranging between 0 (fully transparent) to 1 (fully opaque). Default is 0.5.

• size Relative size of boxes, ranging from 0 to 1. Default is 0.25.

• line A list of additional attributes governing the outline for filled shapes, most commonly color (default: black) and width (default: 0.5).

Example: marker = list(color = "red", opacity = 0.8, line = list(color = "black", width = 1))

Controls characteristics of arrows (edges). TRUE will plot default lines. FALSE will suppress lines. If a list, can control some line characteristics, including overriding defaults. These include:

• color Line color (default: black)

• width Thickness in points (default: 1).

Example: line = list(color = "red", width = 2)

A data frame or tibble containing two columns named from and to to add additional connecting arrows to the plot indicating transfer between compartments. For each row, the from column contains the compartment number of the arrow origin, and the to column contains the compartment number of the arrow destination. Use 0 to indicate a destination to the external sink. e.g., explicit = data.frame(from = 3, to = 0)

Similar to explicit, used to add dashed connecting arrows to the plot indicating implicit transfer between compartments. For each row, the from column contains the compartment number of the arrow origin, and the to column contains the compartment number of the arrow destination. Use 0 to indicate a destination to the external sink. e.g., implicit = data.frame(from = 2, to = 4)

If TRUE, will print the object and return it. If FALSE, will only return the object.

Not used.

The name of a PM_op data object and loaded with PM_load as a field in a PM_result, e.g. PM_result$op.

Controls characteristics of lines. Unlike some other Pmetrics plots, for plot.PM_op, line is a list of three elements:

• lm If set to TRUE (default) or a list of plotly line attributes, will generate a linear regression of the form obs ~ pred. Line attributes will control the appearance of the regression line and the confidence interval around the line. If set to FALSE, no linear regression will be generated. The default values for the elements of the lm list, all of which can be overriden are:

  • ci Confidence interval around the regression, default 0.95.

  • color Color of the regression line and the confidence area around the line, but at opacity = 0.2. Default is "dodgerblue".

  • width Width of the regression line, default 1.

  • dash See plotly::schema(), traces > scatter > attributes > line > dash > values. Default is "solid". Example: line = list(lm = list(color = "red", dash = "longdash", width = 2))

• loess If set to TRUE (default is FALSE) or a list of plotly line attributes, will generate a loess regression of the form obs ~ pred. The list elements and default values in the loess list are the same as for lm except the default style is "dash". Example: line = list(lm = FALSE, loess = TRUE)

• ref If set to TRUE (default) or a list of plotly line attributes, will generate a reference line with slope = 1 and intercept = 0. The default values for the elements of the ref list are:

  • color "grey".

  • width 1.

  • dash "dot". Note that there is no ci argument for the ref list. Example: line = list(lm = FALSE, loess = TRUE, ref = list(color = "lightgrey")) If the line argument is missing, it will be set to line = list(lm = TRUE, loess = FALSE, ref = TRUE), i.e. there will be a linear regression with reference line, but no loess regression. However, if resid = T, the default will become line = list(lm = FALSE, loess = TRUE, ref = TRUE), i.e., loess regression with reference line, but no linear regression.

Controls the plotting symbol for observations. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the marker with default characteristics. FALSE will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:

• color Marker color.

• symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values.

• size Character size in points.

• opacity Ranging between 0 (fully transparent) to 1 (fully opaque).

• line A list of additional attributes governing the outline for filled shapes, most commonly color and width.

Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2)) Default is marker = list(color = orange, shape = "circle", size = 10, opacity = 0.5, line = list(color = black, width = 1)). The color of any BLQ points is set to a color 90 degrees different on the color wheel from the color of the other points using opposite_color to ensure good contrast. The symbol for BLQ points is fixed to "triangle-down", and the opacity is fixed to 1. Size is the same as for other points.

Boolean operator to generate a plot of weighted prediction error vs. time, a plot of weighted prediction error vs. prediction. Prediction error is pred - obs. By default a loess regression will indicate deviation from zero prediction error.

Can be either "median" for the predictions based on medians ofpred.type parameter value distributions, or "mean". Default is "median".

Either 'post' for a posterior object or 'pop' for a population object. Default is 'post'.

Which output equation to plot. Default is 1.

Which block to plot, where blocks are defined by dose reset events (EVID = 4) in the data. Default is missing, which results in all blocks included.

A vector of subject IDs to include in the plot, e.g. c(1:3,5,15)

A vector of subject IDs to exclude in the plot, e.g. c(4,6:14,16:20)

Multiplication factor for y axis, e.g. to convert mg/L to ng/mL

Ignored for this plot.

Boolean operator to plot the y axis in log base 10. This argument maps to the yaxis type value in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > type.

Example: log = T

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

• grid = F

• grid = list(gridcolor = "black", gridwidth = 2)

Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

• xlab = "Time (h)"

• xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))

• xlab = list(text = "Time", font = list(bold = T))

If missing, will default to "Predicted" for plots when resid = F and either "Time" or "Predicted" for residual plots.

Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, and ylab is simply a character label, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

If missing, will default to "Observed" for plots when resid = F and either "Individual weighted residuals" or "Population weighted residuals" for residual plots, depending on the value of pred.type.

Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element. The default for bold is TRUE.

Examples:

• title = "Observed vs. Predicted"

• title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))

Default is to have no title.

Add the statistics from linear regression to the plot. If FALSE, will be suppressed. Default is TRUE which results in default format of list(x= 0.8, y = 0.1, font = list(color = "black", family = "Arial", size = 14, bold = FALSE)). The coordinates are relative to the plot with lower left = (0,0), upper right = (1,1). This argument maps to plotly::add_text().

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > range.

Example: xlim = c(0,1)

Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > range.

Example: ylim = c(0,100)

Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note that log, xlab, ylab, xlim, and ylim are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. See plotly::schema() layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.

Examples:

• NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only

• NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes

.

A 'PM_op_data“ object

Additional arguments passed to plot.PM_op

A PM_opt object

Passed to plot.PM_sim with default as list(probs = NA).

Format the vertical lines for optimal times. Default is dashed red line. r template("line")'

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

Other parameters to pass to plot.PM_sim.

Default is NA. See plot.PM_sim for details.

The name of a PM_pop object, e.g. NPex$pop. in a PM_result object

A vector of subject IDs to include in the plot, e.g. c(1:3,5,15)

A vector of subject IDs to exclude in the plot, e.g. c(4,6:14,16:20)

Controls characteristics of lines as for all plotly plots. It can either be a boolean or a list. If set to TRUE or a list of plotly line attributes, it will generate line segments joining observations. If set to FALSE, no segments will be generated. Line colors are fixed to match marker colors for group displays and cannot be overridden. Other customizable line properties are: - width Width of the segments, default 1. - dash See plotly::schema(), traces > scatter > attributes > line > dash > values. Default is "solid". - join Set to TRUE (default) to join markers with lines, or FALSE for markers only. Example: line = list(width = 2, dash = "longdash", join = FALSE)

Formats the symbols plotting observations. Controls the plotting symbol for observations. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the marker with default characteristics. FALSE will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:

• color Marker color.

• symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values.

• size Character size in points.

• opacity Ranging between 0 (fully transparent) to 1 (fully opaque).

• line A list of additional attributes governing the outline for filled shapes, most commonly color and width.

Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2))

Marker colors control group display colors. When multiple output equations are displayed (via outeq), marker$color can be a palette name from RColorBrewer::brewer.pal.info or a vector of colors. Line colors are automatically matched to marker colors.

A character vector of names to label the output equations if legend = TRUE. Must be at least as long as the maximum value in outeq. Example: c("Conc A", "Conc B") if outeq = c(1, 2).

Multiplication factor for y axis, e.g. to convert mg/L to ng/mL

Can be "median" for predictions based on the median of the parameter value distributions, or "mean". Default is "median". Only a single value is accepted; outeq is the sole grouping dimension.

Which output equation to plot. Default is 1. Default is 1, but can be multiple if present in the data, e.g. 1:2 or c(1, 3).

Which block to plot, where blocks are defined by dose reset events (EVID = 4) in the data. Default is 1, but can be multiple if present in the data, as for outeq.

Operator to overlay all time prediction profiles in a single plot. The default is TRUE. If FALSE, will trellisplot subjects one at a time. Can also be specified as a vector with number of rows and columns, e.g. c(3, 2) for 3 rows and 2 columns of subject splots to include in each trellis.

Not used for this plot.

Boolean operator to plot the y axis in log base 10. This argument maps to the yaxis type value in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > type.

Example: log = T

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

• grid = F

• grid = list(gridcolor = "black", gridwidth = 2)

Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

• xlab = "Time (h)"

• xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))

• xlab = list(text = "Time", font = list(bold = T))

Default is "Time".

Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, and ylab is simply a character label, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

Default is "Output".

Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element. The default for bold is TRUE.

Examples:

• title = "Observed vs. Predicted"

• title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))

Default is to have no title.

Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > range.

Example: xlim = c(0,1)

Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > range.

Example: ylim = c(0,100)

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note that log, xlab, ylab, xlim, and ylim are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. See plotly::schema() layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.

Examples:

• NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only

• NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes

.

The name of a PM_post object, e.g. NPex$post. in a PM_result object

A vector of subject IDs to include in the plot, e.g. c(1:3,5,15)

A vector of subject IDs to exclude in the plot, e.g. c(4,6:14,16:20)

Controls characteristics of lines as for all plotly plots. It can either be a boolean or a list. If set to TRUE or a list of plotly line attributes, it will generate line segments joining observations. If set to FALSE, no segments will be generated. Line colors are fixed to match marker colors for group displays and cannot be overridden. Other customizable line properties are: - width Width of the segments, default 1. - dash See plotly::schema(), traces > scatter > attributes > line > dash > values. Default is "solid". - join Set to TRUE (default) to join markers with lines, or FALSE for markers only. Example: line = list(width = 2, dash = "longdash", join = FALSE)

Formats the symbols plotting observations. Controls the plotting symbol for observations. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the marker with default characteristics. FALSE will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:

• color Marker color.

• symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values.

• size Character size in points.

• opacity Ranging between 0 (fully transparent) to 1 (fully opaque).

• line A list of additional attributes governing the outline for filled shapes, most commonly color and width.

Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2))

Marker colors control group display colors. When multiple output equations are displayed (via outeq), marker$color can be a palette name from RColorBrewer::brewer.pal.info or a vector of colors. Line colors are automatically matched to marker colors.

A character vector of names to label the output equations if legend = TRUE. Must be at least as long as the maximum value in outeq. Example: c("Conc A", "Conc B") if outeq = c(1, 2).

Multiplication factor for y axis, e.g. to convert mg/L to ng/mL

Can be "median" for predictions based on the median of the parameter value distributions, or "mean". Default is "median". Only a single value is accepted; outeq is the sole grouping dimension.

Which output equation to plot. Default is 1. Default is 1, but can be multiple if present in the data, e.g. 1:2 or c(1, 3).

Which block to plot, where blocks are defined by dose reset events (EVID = 4) in the data. Default is 1, but can be multiple if present in the data, as for outeq.

Operator to overlay all time prediction profiles in a single plot. The default is TRUE. If FALSE, will trellisplot subjects one at a time. Can also be specified as a vector with number of rows and columns, e.g. c(3, 2) for 3 rows and 2 columns of subject splots to include in each trellis.

Not used for this plot.

Boolean operator to plot the y axis in log base 10. This argument maps to the yaxis type value in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > type.

Example: log = T

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

• grid = F

• grid = list(gridcolor = "black", gridwidth = 2)

Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

• xlab = "Time (h)"

• xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))

• xlab = list(text = "Time", font = list(bold = T))

Default is "Time".

Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, and ylab is simply a character label, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

Default is "Output".

Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element. The default for bold is TRUE.

Examples:

• title = "Observed vs. Predicted"

• title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))

Default is to have no title.

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > range.

Example: xlim = c(0,1)

Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > range.

Example: ylim = c(0,100)

Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note that log, xlab, ylab, xlim, and ylim are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. See plotly::schema() layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.

Examples:

• NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only

• NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes

.

The name of an PM_pta data object

Which object in the PM_pta result list to plot. By default "intersect" if an intersection is present due to creation of the object with multiple target types, or 1 if no intersection is present, which means only 1 target type was selected. If "intersect" is present in the object, the default can be overridden with a number to plot one of the individual PTAs, e.g. at = 2 to plot the second PTA rather than the intersection of all the PTAs.

A vector of subject IDs to include in the plot, e.g. c(1:3,5,15)

A vector of subject IDs to exclude in the plot, e.g. c(4,6:14,16:20)

Character vector controlling type of plot. Default is "pta", which plots proportion with success on the y-axis and target on the x-axis. The other choice is "pdi", which plots the median pdi (pharmacodynamic index), e.g. AUC/MIC, on the y-axis, and target on the x-axis.

Multiplication factor for y axis, e.g. to convert mg/L to ng/mL

Which output equation to plot. Default is 1.

Controls characteristics of lines. This argument maps to the plotly line object. It can be boolean or a list. TRUE will plot the line with default characteristics for each simulated regimen. FALSE will suppress line plotting. If a list, it functions a little differently than other Pmetrics plotly functions. Rather than controlling individual line characteristics, for this plot, the line argument should be a list of the options for group based plotting, where each group corresponds to a simulated regimen. The possible elements of the line list should be exactly named:

• color Maps to the plot_ly colors argument to override default colors applied to the lines for each regimen. This can be a named palette, which can be obtained with RColorBrewer::display.brewer.all() or a vector of hexadecimal color names. One way to ensure reliable color palettes is to use the ColorBrewer site. Choosing the number of data classes to correspond to regimens, and qualitative data results in a distinct palette. Easiest importing into R is to copy/paste the Export of JavaScript on the ColorBrewer website. The default is "Set1". Palettes with fewer colors than regimens will be recycled. A color can also be a character vector of color names, recycled as needed. For example, a print-friendly choice is line = list(color = "black").

• width Maps to the plot_ly width argument to override default widths applied to the lines for each regimen. All lines will have the same width. The default value is 2.

• dash Maps to the plot_ly linetypes argument to override default styles applied to the lines for each regimen. If numeric, will map to lty par values. It can also be a character vector of dash names as listed in plot_ly. Example: line = list(color = "Blues", width = 1, dash = 2), whicb will result in dotted lines (dash = 2) all with width 1 but in different shades of blue.

Controls the plotting symbol. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the profiles with default characteristics for each simulated regimen. FALSE will suppress line plotting. If a list, it functions a little differently than other Pmetrics plotly functions. Rather than controlling individual marker characteristics, for this plot, the marker argument should be a list of the options for group based plotting, where each group corresponds to a simulated regimen. The possible elements of the marker list should be exactly named:

• color Default marker color is the same as the line color. If line color is specified, marker color does not need to also be specified. Even if line plotting is suppressed with line = F, the default color value of "Set1" will be applied to markers, unless specified, e.g. marker = list(color = "Blues").

• symbol Maps to the plot_ly symbols argument to override default symbols applied to the markers for each regimen. If only one value is supplied for this, it will be recycled for each regimen, i.e. all will have the same symbol. See plotly::schema(), traces > scatter > attributes > marker > symbol > values for options.

• size Maps to the plot_ly size argument to override default size applied to the markers for each regimen. All markers will have the same size. The default value is 12.

Confidence interval around curves on type = "pdi" plot, on scale of 0 to 1. Default is 0.9.

Controls display of legend. This argument maps to the plotly layout showlegend and legend arguments. It is either a boolean operator (most common) or a list of parameters to be supplied to plotly. See plotly::schema() > layout > layoutAttributes > legend and showlegend for more details on the available options for formatting. If legend is supplied as a list, the plotly layout > layoutAttributes > showlegend value will be set to TRUE automatically.

Examples:

• legend = T

• legend = list(orientation = "h", font = list(color = "blue"))

Default will be the labeled regimen names as an argument when creating a PM_pta object, or if missing, "Regimen 1, Regimen 2,...Regimen n", where n is the number of regimens in the PM_pta object.

Boolean operator to plot the x axis in log base 10. This argument maps to the xaxis type value in the layout object in plotly. Many other Pmetrics plots map this argument to the y axis, but for PTA plots, the x axis is the more common axis to log transform. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > type. Example: log = T

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

• grid = F

• grid = list(gridcolor = "black", gridwidth = 2)

Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

• xlab = "Time (h)"

• xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))

• xlab = list(text = "Time", font = list(bold = T))

Default is "Target" when targets are discrete, and "Regimen" when targets are sampled.

Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, and ylab is simply a character label, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

Default is "Proportion with success" for plot type = "pta" and "Pharmacodynamic Index" for plot type = "pdi".

Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element. The default for bold is TRUE.

Examples:

• title = "Observed vs. Predicted"

• title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))

Default is to have no title.

Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > range.

Example: xlim = c(0,1)

Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > range.

Example: ylim = c(0,100)

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note that log, xlab, ylab, xlim, and ylim are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. See plotly::schema() layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.

Examples:

• NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only

• NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes

.

The name of an PM_sim data object generated by PM_sim

A vector of subject IDs to include in the plot, e.g. c(1:3,5,15) .

A vector of subject IDs to exclude in the plot, e.g. c(4,6:14,16:20) .

Multiplication factor for y axis, e.g. to convert mg/L to ng/mL

Width of confidence interval bands around simulated quantiles, from 0 to 1. If 0, or nsim<100, will not plot. Default is 0.95, i.e. 95th percentile with tails of 2.5 percent above and below excluded.

Width of binning interval for simulated concentrations, in time units, e.g. hours. A binSize of 0.5 will pull all simulated concentrations +/- 0.5 hours into the same time. This is useful for plotting PMsim objects made during make_valid. The default is 0, i.e. no binning. If an obs object is provided, it will be binned similarly.

Which output equation to plot. Default is 1.

Controls the appearance of lines. It can be specified in several ways.

• Default is TRUE which results in simulated profiles summarized as quantiles, with default values of 0.05, 0.25, 0.5, 0.75, and 0.95. The default format will be applied, which is solid black lines of width 1. Numerical predictive checking will be calculated if observations are also included (see obs below).

• FALSE results in no lines plotted and the plot will be blank.

• NA Quantile summaries will be suppressed, but lines joining simulated outputs will be plotted in default format as above. In other words, all profiles will be plotted, not just the quantiles. Numerical predictive checking will be suppressed.

• List of quantiles and formats to plot with the following elements:

  • probs Vector of quantiles to include. If missing, will be set to defaults above, i.e., ⁠c(0.05, 0.5, and 0.95)⁠ Example: line = list(probs = c(0.25, 0.5, 0.75)).

  • color Vector of color names whose order corresponds to probs. If shorter than probs, will be recycled. Default is "dodgerblue", but if median is present (prob = 0.5), that line will be "red". Examples: line = list(color = "red") or line = list(color = c("red", "blue")).

  • fill Fill color between quantile lines. Can be specified in several ways:

    • FALSE (the default) will not fill between lines.

    • TRUE will fill between lines with a default color of "dodgerblue", opacity 0.2.

    • A list with the following elements:

      • color Fill color name. Default is "dodgerblue", e.g., fill = list(color = "red").

      • opacity Fill opacity. Default is 0.2 e.g., fill = list(opacity = 0.3).

      • probs Vector of paired quantiles to fill between. Default is the minimum and maximum quantile specified in probs, or fill = list(probs = c(0.05, 0.95)) if not specified. Including probs in fill which are not in probs above will result in an error.

  • width Vector of widths in pixels, as for color. Default is 1. Example: line = list(width = 2).

  • dash Vector of dash types, as for color. Default is "solid". See plotly::schema(), traces > scatter > attributes > line > dash > values. Example: line = list(dash = "dashdot").

Controls the plotting symbol for observations. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the marker with default characteristics. FALSE will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:

• color Marker color.

• symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values.

• size Character size in points.

• opacity Ranging between 0 (fully transparent) to 1 (fully opaque).

• line A list of additional attributes governing the outline for filled shapes, most commonly color and width.

Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2)) Formatting will only be applied to observations if included via the obs argument.

The name of a PM_result data object or the PM_op field in the PM_result object, all generated by PM_load. For example, if run1 <- PM_load(1) and sim1 is a PM_sim object, then sim1$plot(obs = run1) or sim1$plot(obs = run1$op). If specified, the observations will be overlaid upon the simulation plot enabling a visual predictive check. In this case, a list object will be returned with two items: $npc containing the quantiles and probability that the observations are below each quantile (binomial test); and $simsum, the times of each observation and the value of the simulated quantile with upper and lower confidence intervals at that time. Additionally, the number of observations beyond the 5th and 95th percentiles will be reported and the binomial test P-value if this number is different than the expected 10% value.

If TRUE, suppresses the message about simulation report generation, defaults to FALSE.

Controls display of legend. This argument maps to the plotly layout showlegend and legend arguments. It is either a boolean operator (most common) or a list of parameters to be supplied to plotly. See plotly::schema() > layout > layoutAttributes > legend and showlegend for more details on the available options for formatting. If legend is supplied as a list, the plotly layout > layoutAttributes > showlegend value will be set to TRUE automatically.

Examples:

• legend = T

• legend = list(orientation = "h", font = list(color = "blue"))

Default is FALSE

Boolean operator to plot the y axis in log base 10. This argument maps to the yaxis type value in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > type.

Example: log = T Default is TRUE.

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

• grid = F

• grid = list(gridcolor = "black", gridwidth = 2)

Default is FALSE

Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

• xlab = "Time (h)"

• xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))

• xlab = list(text = "Time", font = list(bold = T))

Default is "Time".

Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, and ylab is simply a character label, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

Default is "Output".

Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element. The default for bold is TRUE.

Examples:

• title = "Observed vs. Predicted"

• title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))

Default is to have no title.

Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > range.

Example: xlim = c(0,1)

Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > range.

Example: ylim = c(0,100)

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note that log, xlab, ylab, xlim, and ylim are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. See plotly::schema() layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.

Examples:

• NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only

• NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes

.

The name of an PM_valid data object, which is usually called by the ⁠$validate⁠ method for PM_result objects.

Default is "vpc" for a visual predictive check, but could be "pcvpc" for a prediction-corrected visual predictive check, or "npde" for a normalized prediction distribution error analysis/plot. Choosing npde will call npde::plot.NpdeObject. To modify this plot, supply argmuents as a named list: npde = (...). Available arguments are in the user manual for the npde package.

Boolean operator to use time after dose rather than time after start. Default is FALSE.

Which output equation to plot. Default is 1.

A list of three elements ⁠$upper⁠, ⁠$mid⁠, and ⁠$lower⁠, each of which controls characteristics of corresponding quantiles. The arguments to each of these list elements map to several plotly attributes. Each can be a boolean value or a list. TRUE will plot default characteristics. FALSE will suppress quantile plots. The elements of the list for each argument are as follows:

• value The quantile value. Default for lower is 0.025, mid is 0.5, and upper is 0.975.

• color The color for both the 95%CI region around simulated quantile vs. time, and the color of the line for the observation quantile vs. time. Default for lower and upper is "dodgerblue" and for mid it is "red".

• dash The style of the obervation quantile line. See plotly::schema(), traces > scatter > attributes > line > dash > values. Default for lower and upper is "dash" and for mid it is "solid".

• width Default is 1 for lower, mid, and upper.

• opacity The opacity of the 95%CI region around simulated quantile vs. time. Default is 0.4 for lower, mid and upper, but can range between 0 (fully transparent) to 1 (fully opaque). Example: line = list(upper = list(value = 0.9, color = "red", dash = "longdash", opacity = 0.5, width = 2))

Controls the plotting symbol for observations. This argument maps to the plotly marker object. It can be boolean or a list. TRUE will plot the marker with default characteristics. FALSE will suppress marker plotting. If a list, can control many marker characteristics, including overriding defaults. Use the plotly plotly::schema() command in the console and navigate to traces > scatter > attributes > marker to see all the ways the marker can be formatted. Most common will be:

• color Marker color.

• symbol Plotting character. See plotly::schema(), traces > scatter > attributes > marker > symbol > values.

• size Character size in points.

• opacity Ranging between 0 (fully transparent) to 1 (fully opaque).

• line A list of additional attributes governing the outline for filled shapes, most commonly color and width.

Example: marker = list(color = "red", symbol = "triangle", opacity = 0.8, line = list(color = "black", width = 2))

Controls display of legend. This argument maps to the plotly layout showlegend and legend arguments. It is either a boolean operator (most common) or a list of parameters to be supplied to plotly. See plotly::schema() > layout > layoutAttributes > legend and showlegend for more details on the available options for formatting. If legend is supplied as a list, the plotly layout > layoutAttributes > showlegend value will be set to TRUE automatically.

Examples:

• legend = T

• legend = list(orientation = "h", font = list(color = "blue"))

Default is FALSE

Boolean operator to plot the y axis in log base 10. This argument maps to the yaxis type value in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > type.

Example: log = T

Controls grid display. This argument maps to the xaxis and yaxis layout objects in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis or yaxis > gridcolor or gridwidth. It is a Boolean operator. If FALSE, no grid is plotted. If TRUE, the default color grey and width 1 will be plotted at major tick marks. If a list, color and width can be customized.

Examples:

• grid = F

• grid = list(gridcolor = "black", gridwidth = 2)

Value for x axis label. This argument maps to the the xaxis title element of the layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the axis, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > title to see the ways to customize this axis label. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element, either on its own or within the font list. The default for bold is TRUE.

Examples:

• xlab = "Time (h)"

• xlab = list(text = "Time", bold = F, font = list(color = "red", family = "Arial", size = 10))

• xlab = list(text = "Time", font = list(bold = T))

Default is "Time" or "Time after dose" if tad = TRUE.

Value for y axis label. This argument maps to the the yaxis title element of the layout object in plotly. See xlab for details. If xlab is specified as a list with formatting, and ylab is simply a character label, then the formatting for the xlab will be applied to the ylab. To format ylab independently, specify a formatting list as for xlab.

Default is "Output".

Plot title. This argument maps to the the title layout object in plotly. It can simply be a character vector of length 1 that specifies the name of the plot title, or it can be a list for greater control. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > title to see other ways to customize the title using lists as additional arguments. In addition to the plotly attributes, a custom Pmetrics attribute bold may be included as a list element. The default for bold is TRUE.

Examples:

• title = "Observed vs. Predicted"

• title = list(text = "Raw Data", font = list(color = "red", family = "Arial", size = 10, bold = T))

Default is to have no title.

Limits of the x axis as a vector. This argument maps to the the xaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > xaxis > range.

Example: xlim = c(0,1)

Limits of the y axis as a vector. This argument maps to the the yaxis range in the layout object in plotly. Use the plotly plotly::schema() command in the console and navigate to layout > layoutAttributes > yaxis > range.

Example: ylim = c(0,100)

If TRUE, will print the plotly object and return it. If FALSE, will only return the plotly object.

If type is not "npde", the following apply. Other attributes which can be passed to the layout > xaxis/yaxis in a plotly plot to further control formatting. Note that log, xlab, ylab, xlim, and ylim are all controlled by the layout object, but are provided throughout Pmetrics plotly function arguments as shortcuts that map to layout elements. Therefore, the dots argument should be used to specify other aspects of the x axis, y axis, or both. See plotly::schema() layout > layoutAttributes > xaxis/yaxis for options. To add to single axis, name it as a list. If attributes are specified without an enclosing xaxis or yaxis list, they will be applied to both axes.

Examples:

• NPex$data$plot(xaxis = list(tickcolor = "black", tickfont = list(family = "Arial", size = 14, color = "black"))) #applies to x axis only

• NPex$data$plot(linecolor = "red", ticks = "inside") #applies to both axes

. . However, if type is "npde", to modify the appearance of the plot, supply a list of options, npde = list(...). See the documentation for the type argument above.