Package 'coveffectsplot'

Correlated Covariates data

Description

A example dataset used to illustrate multivariate joint covariate effects.

Usage

covdatasim

Format

A dataset with 2000 rows and 5 variables

ID

Subject ID

AGE

Age in years

WT

Weight in kg

Sex

0=male; 1=female

ALB

Albumin in g/dL

Source

simulated based on a real dataset

---

Horizontal key drawing functions from ggstance in case it is deprecated

Description

Horizontal key drawing functions from ggstance in case it is deprecated

Usage

draw_key_hpath(data, params, size)

draw_key_pointrangeh(data, params, size)

Arguments

data	A single row data frame containing the scaled aesthetics to display in this key
params	A list of additional parameters supplied to the geom.
size	Width and height of key in mm.

Value

A grid grob.

---

Expand covariate values choices and reference values varying one at a time

Description

Expand covariate values choices and reference values varying one at a time

Usage

expand_modelframe(rv, covcol = "covname", ...)

Arguments

rv	a data.frame with columns names of covariate(s) and values equal reference
covcol	column name for the covariate being varied
...	Arguments to be passed to methods

Value

A data.frame with combination of covariates

Examples

reference.values <- data.frame(WT = 85, ALB = 45, SEX = 0)   
covcomb <- expand_modelframe(
  WT  = c(56, 72, 98, 128), # P05, P25, P75, P95 # ref is P50
ALB = c(40, 50),          # P05, P95 # ref is P50
  SEX = c(1),               # Reference is for SEX=0 (female)
  rv = reference.values)
covcomb

---

Forest plot

Description

Produce forest plots to visualize covariate effects

Usage

forest_plot(
  data,
  facet_formula = "covname~paramname",
  xlabel = "",
  ylabel = "",
  x_facet_text_size = 13,
  y_facet_text_size = 13,
  x_facet_text_angle = 0,
  y_facet_text_angle = 0,
  x_facet_text_vjust = 0.5,
  y_facet_text_vjust = 0.5,
  x_facet_text_hjust = 0.5,
  y_facet_text_hjust = 0.5,
  x_facet_text_col = "black",
  y_facet_text_col = "black",
  xy_facet_text_bold = TRUE,
  x_label_text_size = 16,
  y_label_text_size = 16,
  legend_title_size = 12,
  break_ylabel = FALSE,
  y_label_text_width = 25,
  table_text_size = 7,
  table_text_colour_overwrite = FALSE,
  table_text_colour = "none",
  base_size = 22,
  theme_benrich = FALSE,
  table_title = "",
  table_title_size = 15,
  ref_legend_text = "",
  area_legend_text = "",
  interval_legend_text = "",
  interval_legend_title = "",
  shape_legend_title = "",
  legend_order = c("pointinterval", "ref", "area", "shape"),
  combine_area_ref_legend = TRUE,
  combine_interval_shape_legend = FALSE,
  legend_position = "top",
  show_ref_area = TRUE,
  ref_area = c(0.8, 1.25),
  ref_area_col = "#BEBEBE50",
  show_ref_value = TRUE,
  ref_value = 1,
  ref_value_col = "black",
  ref_value_size = 1,
  ref_value_linetype = "dashed",
  ref_value_by_panel = FALSE,
  ref_value_by_panel_data = NULL,
  interval_col = "blue",
  interval_size = 1,
  interval_fatten = 4,
  interval_linewidth = 1,
  interval_shape = "circle small",
  bsv_col = "red",
  bsv_shape = "circle small",
  bsv_text_id = c("BSV", "bsv", "IIV", "Bsv"),
  interval_bsv_text = "",
  strip_col = "#E5E5E5",
  paramname_shape = FALSE,
  paramname_color = FALSE,
  legend_shape_reverse = FALSE,
  legend_color_reverse = FALSE,
  facet_switch = c("both", "y", "x", "none"),
  facet_scales = c("fixed", "free_y", "free_x", "free"),
  facet_space = c("fixed", "free_x", "free_y", "free"),
  facet_labeller = "label_value",
  label_wrap_width = 55,
  facet_labeller_multiline = FALSE,
  strip_placement = c("inside", "outside"),
  strip_outline = TRUE,
  facet_spacing = 5.5,
  major_x_ticks = NULL,
  major_x_labels = NULL,
  minor_x_ticks = NULL,
  x_range = NULL,
  logxscale = FALSE,
  show_yaxis_gridlines = TRUE,
  show_xaxis_gridlines = TRUE,
  show_table_facet_strip = "none",
  table_facet_switch = c("both", "y", "x", "none"),
  show_table_yaxis_tick_label = FALSE,
  reserve_table_xaxis_label_space = TRUE,
  table_panel_border = TRUE,
  table_position = c("right", "below", "none"),
  plot_table_ratio = 4,
  vertical_dodge_height = 0.8,
  legend_space_x_mult = 1,
  legend_ncol_interval = 1,
  legend_ncol_shape = 1,
  plot_margin = c(5.5, 5.5, 5.5, 5.5),
  table_margin = c(5.5, 5.5, 5.5, 5.5),
  legend_margin = c(0, 0.1, -0.1, 0),
  parse_xlabel = FALSE,
  parse_ylabel = FALSE,
  plot_title = "\n",
  return_list = FALSE
)

Arguments

data	Data to use.
facet_formula	Facet formula.
xlabel	X axis title.
ylabel	Y axis title.
x_facet_text_size	Facet text size X.
y_facet_text_size	Facet text size Y.
x_facet_text_angle	Facet text angle X.
y_facet_text_angle	Facet text angle Y.
x_facet_text_vjust	Facet text vertical justification.
y_facet_text_vjust	Facet text vertical justification.
x_facet_text_hjust	Facet text horizontal justification.
y_facet_text_hjust	Facet text horizontal justification.
x_facet_text_col	Facet text color default to black.
y_facet_text_col	Facet text color default to black.
xy_facet_text_bold	Bold Facet text. Logical TRUE FALSE.
x_label_text_size	X axis labels size.
y_label_text_size	Y axis labels size.
legend_title_size	Legend title size if present.
break_ylabel	Split Y axis labels into multiple lines. Logical FALSE TRUE.
y_label_text_width	Number of characters to break Y axis labels.
table_text_size	Table text size.
table_text_colour_overwrite	Logical TRUE FALSE.
table_text_colour	Table text color to be used and overwrites mapped color
base_size	theme_bw base_size for the plot and table.
theme_benrich	apply Benjamin Rich's theming.
table_title	What text to use for table title (theme_benrich has a default).
table_title_size	table title size.
ref_legend_text	Reference legend text.
area_legend_text	Area legend text.
interval_legend_text	Pointinterval legend text.
interval_legend_title	Pointinterval legend title defaults to empty.
shape_legend_title	Shape legend title defaults to empty.
legend_order	Legend order. A four-element vector with the following items ordered in your desired order: "pointinterval", "ref", "area", "shape". if an item is absent the legend will be omitted.
combine_area_ref_legend	Combine reference and area legends if they share the same text?
combine_interval_shape_legend	Combine interval and shape legends?
legend_position	where to put the legend: "top", "bottom","right","none"
show_ref_area	Show reference window?
ref_area	Reference area. Two-element numeric vector multiplying the ref_value.
ref_area_col	Reference area background color.
show_ref_value	Show reference line?
ref_value	X intercept of reference line.
ref_value_col	Reference line color.
ref_value_size	Reference line size.
ref_value_linetype	Reference line linetype.
ref_value_by_panel	The ref_value vary by panel TRUE or FALSE.
ref_value_by_panel_data	if ref_value_by_panel is TRUE, data.frame to use for Reference (lines).
interval_col	Point range color. One or Multiple values.
interval_size	Point range size. Default to 1
interval_fatten	Point range fatten. Default to 4
interval_linewidth	Point range line width. Default to 1
interval_shape	Shape used for the Point Range. Default to "circle small".
bsv_col	BSV pointinterval color. One value.
bsv_shape	Shape used for the BSV Point Range. Default to "circle small".
bsv_text_id	Text string(s) to identify BSV. Default to c("BSV","bsv","IIV","Bsv")
interval_bsv_text	BSV legend text.
strip_col	Strip background color.
paramname_shape	Map symbol to parameter(s) name? TRUE or FALSE.
paramname_color	Map color to parameter(s) name? TRUE or FALSE.
legend_shape_reverse	TRUE or FALSE.
legend_color_reverse	TRUE or FALSE.
facet_switch	Facet switch to near axis. Possible values: "both", "y", "x", "none".
facet_scales	Facet scales. Possible values: "free_y", "fixed", "free_x", "free".
facet_space	Facet spaces. Possible values: "fixed", "free_x", "free_y", "free".
facet_labeller	Facet Labeller. Default "label_value" any other valid 'facet_grid' labeller can be specified.
label_wrap_width	How many characters before breaking the line. Numeric value. any other valid 'facet_grid' labeller can be specified.
facet_labeller_multiline	break facet strips into multiple lines. Logical TRUE FALSE.
strip_placement	Strip placement. Possible values: "inside", "outside".
strip_outline	Draw rectangle around the Strip. Logical TRUE FALSE.
facet_spacing	Control the space between facets in points.
major_x_ticks	X axis major ticks. Numeric vector.
major_x_labels	X axis labels. Character vector should be same length as major_x_ticks.
minor_x_ticks	X axis minor ticks. Numeric vector.
x_range	Range of X values. Two-element numeric vector.
logxscale	X axis log scale. Logical TRUE FALSE.
show_yaxis_gridlines	Draw the y axis gridlines. Logical TRUE FALSE.
show_xaxis_gridlines	Draw the x axis gridlines. Logical TRUE FALSE.
show_table_facet_strip	Possible values: "none", "both", "y", "x".
table_facet_switch	Table facet switch to near axis. Possible values: "both", "y", "x", "none".
show_table_yaxis_tick_label	Show table y axis ticks and labels?
reserve_table_xaxis_label_space	keep space for the x axis label to keep alignment.
table_panel_border	Draw the panel border for the table. Logical TRUE FALSE.
table_position	Table position. Possible values: "right", "below", "none".
plot_table_ratio	Plot-to-table ratio. Suggested value between 1-5.
vertical_dodge_height	Amount of vertical dodging to apply on segments and table text.
legend_space_x_mult	Multiplier to adjust the spacing between legend items.
legend_ncol_interval	Control the number of columns for the pointinterval legend.
legend_ncol_shape	Control the number of columns for the shape legend.
plot_margin	Control the white space around the main plot. Vector of four numeric values for the top, right, bottom and left sides.
table_margin	Control the white space around the table. Vector of four numeric values for the top, right, bottom and left sides.
legend_margin	Control the white space around the plot legend. Vector of four numeric values for the top, right, bottom and left sides.
parse_xlabel	treat xlabel as an expression. Logical FALSE TRUE.
parse_ylabel	treat ylabel as an expression. Logical FALSE TRUE.
plot_title	main plot title default to a line break.
return_list	What to return if True a list of the main and table plots is returned instead of the gtable/plot.

Examples

library(dplyr)
library(ggplot2)

# Example 1

plotdata <- get_sample_data("forest-plot-table.csv")
plotdata <- plotdata %>%
  mutate(midlabel = format(round(mid,2), nsmall = 2),
         lowerlabel = format(round(lower,2), nsmall = 2),
         upperlabel = format(round(upper,2), nsmall = 2),
         LABEL = paste0(midlabel, " [", lowerlabel, "-", upperlabel, "]"))
param <- "BZD AUC"
plotdata <-  filter(plotdata,paramname==param)
plotdata$covname <- reorder(plotdata$covname,plotdata$upper,FUN =max)
plotdata$label <- reorder(plotdata$label,plotdata$scen)
covs <- c("WEIGHT","AGE")
plotdata <-  filter(plotdata,covname%in%covs)
forest_plot(plotdata,
            ref_legend_text = "Reference (vertical line)",
            area_legend_text = "Reference (vertical line)",
            xlabel = paste("Fold Change in", param, "Relative to Reference"),
            logxscale = TRUE, major_x_ticks =c(0.1,1,1.5),
            show_ref_area = FALSE,
            paramname_color =TRUE,
            interval_col =c("steelblue","red","steelblue","red"),
            facet_formula = "covname~.",
            facet_scales = "free_y",
            facet_space = "free_y",
            show_table_facet_strip = "none",
            table_position = "right",
            plot_title = "",
            plot_table_ratio = 4)

# Example 2

plotdata <- get_sample_data("forest-plot-table.csv")
plotdata <- plotdata %>%
  mutate(midlabel = format(round(mid,2), nsmall = 2),
         lowerlabel = format(round(lower,2), nsmall = 2),
         upperlabel = format(round(upper,2), nsmall = 2),
         LABEL = paste0(midlabel, " [", lowerlabel, "-", upperlabel, "]"))
param <- c("BZD AUC","BZD Cmax")
plotdata <-  filter(plotdata,paramname%in%param)
plotdata <-  filter(plotdata,covname%in%"WEIGHT")
plotdata$covname <- reorder(plotdata$covname,plotdata$upper,FUN =max)
plotdata$label <- reorder(plotdata$label,plotdata$scen)
forest_plot(plotdata,
            ref_legend_text = "Reference (vertical line)",
            area_legend_text = "Reference (vertical line)",
            xlabel = paste("Fold Change of Parameter", "Relative to Reference"),
            show_ref_area = FALSE,
            facet_formula = "covname~paramname",
            facet_scales = "free_y",
            facet_space = "free_y",
            x_facet_text_size = 10,
            y_facet_text_size = 10,
            y_label_text_size = 10,
            y_label_text_width = 15,
            x_label_text_size = 10,
            facet_switch = "both",
            show_table_facet_strip = "both",
            show_table_yaxis_tick_label = TRUE,
            table_position = "below",
            plot_title = "",
            plot_table_ratio = 1)
## Not run: 

# Example 3a

plotdata <- get_sample_data("forest-plot-table.csv")
plotdata <- plotdata %>%
  mutate(midlabel = format(round(mid,2), nsmall = 2),
         lowerlabel = format(round(lower,2), nsmall = 2),
         upperlabel = format(round(upper,2), nsmall = 2),
         LABEL = paste0(midlabel, " [", lowerlabel, "-", upperlabel, "]"))
plotdata$covname <- reorder(plotdata$covname,plotdata$upper,FUN =max)
plotdata$label <- reorder(plotdata$label,plotdata$scen)

plotdata$compound <- c(rep("1-OH",30),rep("BZD",30))
plotdata$paramname <- c(rep("AUC",15),rep("CMAX",15),rep("AUC",15),rep("CMAX",15))

forest_plot(plotdata,
            ref_area = c(0.8, 1.2),
           x_facet_text_size = 13,
           y_facet_text_size = 13,
            ref_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
            area_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
            xlabel = "Fold Change Relative to Parameter",
            facet_formula = covname~compound,
            facet_switch = "both",
            facet_scales = "free",
            facet_space = "fixed",
            paramname_shape = TRUE,
            legend_shape_reverse = TRUE,
            interval_shape = c("square","triangle"),
            paramname_color =  FALSE,
            combine_interval_shape_legend = FALSE,
            table_position = "right", plot_title = "",
            ref_area_col = rgb( col2rgb("gray50")[1], col2rgb("gray50")[2],col2rgb("gray50")[3],
                                max = 255, alpha = 0.1*255 ) ,
            interval_col = c("steelblue"),
            strip_col = "lightblue",
            plot_table_ratio = 1.5)
            
# Example 3b
        
plotdata$paramname <- c(rep("1-OH",30),rep("BZD",30))
plotdata$paramname2 <- c(rep("AUC",15),rep("CMAX",15),rep("AUC",15),rep("CMAX",15))
forest_plot(plotdata,
           show_ref_area = TRUE,
           x_facet_text_size = 13,
           y_facet_text_size = 13,
           ref_legend_text = "Reference (vertical line)",
           area_legend_text = "Reference (vertical line)",
           xlabel = "Fold Change Relative to Parameter",
           facet_formula = covname~paramname2,
           facet_switch = "both",
           facet_scales = "free",
           facet_space = "free",
           legend_order = c("shape","pointinterval","ref"),
           paramname_shape = TRUE,
           interval_shape = c("diamond","diamond filled",
                              "diamond","diamond filled"),
           paramname_color =  TRUE,
           combine_interval_shape_legend = TRUE,
           legend_shape_reverse = TRUE,
           legend_color_reverse = TRUE,
           interval_legend_title="Median (points)\n95% CI (horizontal lines)",
           table_position = "right", plot_title = "",
           ref_area_col = "gray85" ,
           interval_col = c("#ee3124", "#fdbb2f"),
           strip_col = "#475c6b",
           y_facet_text_col = "white",x_facet_text_col = "white",
           major_x_labels         = c("1/2", "0.8","1", "1.25", "2"),
           logxscale = TRUE, major_x_ticks =c(0.5,0.8,1,1.25,2),
           table_text_size = 5,
           plot_table_ratio = 1.5,
           ref_value_by_panel = TRUE,
           ref_value_by_panel_data = as.data.frame(
           plotdata %>% 
           distinct(paramname2,covname) %>% 
           dplyr::mutate(xintercept=ifelse(paramname2=="CMAX",1,1.2))))

# Example 3

plotdata <- get_sample_data("forestplotdatacpidata.csv")
forest_plot(plotdata,
            ref_area = c(0.8, 1.2),
            x_facet_text_size = 12,
            y_facet_text_size = 12,
            y_label_text_size = 10,
            x_label_text_size = 10,
            table_text_size = 6,
            plot_table_ratio = 1.5,
            ref_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
            area_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
            xlabel = "Fold Change Relative to RHZE",
            facet_formula = "covname~paramname",
            table_position = "below",
            show_table_facet_strip = "both",
            show_table_yaxis_tick_label = TRUE)

# Example 4
plotdata <- get_sample_data("dataforest.csv")
plotdata <- plotdata %>%
  dplyr::mutate(midlabel = format(round(mid,2), nsmall = 2),
         lowerlabel = format(round(lower,2), nsmall = 2),
         upperlabel = format(round(upper,2), nsmall = 2),
         LABEL = paste0(midlabel, " [", lowerlabel, "-", upperlabel, "]"))
plotdata <- plotdata %>%
  filter(covname%in%c("Weight"))
plotdata$label <- as.factor(as.character(plotdata$label))
plotdata$label <- factor(plotdata$label, c("36.2 kg","66 kg","110 kg"))
forest_plot(plotdata,
            ref_area = c(0.8, 1.2),
            x_facet_text_size = 13,
            y_facet_text_size = 13,
            ref_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
            area_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
            xlabel = "Fold Change Relative to Parameter",
            facet_formula = "covname~paramname",
            facet_switch = "both",
            facet_scales = "free",
            facet_space = "fixed",
            table_position = "below",
            plot_table_ratio = 1,
            show_table_facet_strip = "both",
            show_table_yaxis_tick_label = TRUE)

# Example 5

forest_plot(plotdata,
            ref_area = c(0.8, 1.2),
            x_facet_text_size = 13,
            y_facet_text_size = 13,
            ref_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
            area_legend_text = "Reference (vertical line)\n+/- 20% limits (colored area)",
            xlabel = "Fold Change Relative to Parameter",
            facet_formula = "covname~.",
            facet_switch = "both",
            facet_scales = "free",
            facet_space = "fixed",
            paramname_shape = TRUE,
            table_position = "none",
            ref_area_col = rgb( col2rgb("gray50")[1], col2rgb("gray50")[2],col2rgb("gray50")[3],
            max = 255, alpha = 0.1*255 ) ,
            interval_col = "steelblue",
            strip_col = "lightblue",
            plot_table_ratio = 1)

## End(Not run)

---

Get sample dataset

Description

Get a sample dataset that is included with the package to plot a forest plot.

Usage

get_sample_data(dataset = "dfall.csv")

Arguments

dataset

A sample dataset file.

---

Prezista Drug Label Data

Description

A dataset containing an excerpt from the official Prezista FDA Drug Label to help in the app exploration.

Usage

prezista

Format

A dataset with 33 rows and 6 variables

covname

Covariate Name, a character variable with two values Protease Inihibitors and Other Antiretrovirals

label

Covariate value label, a character variable with several possible values

paramname

Parameter on which the effects are shown, a character variable with three possible values Cmax, AUC and Cmin

mid

Middle value for the effects, the median from the uncertainty distribution

lower

Lower value for the effects usually the 5% from the uncertainty distribution

upper

Upper value for the effects usually the 95% from the uncertainty distribution

Source

Table 16 from https://www.accessdata.fda.gov/drugsatfda_docs/label/2017/021976s045_202895s020lbl.pdf

---

Run the interactiveforestplot application

Description

Run the interactiveforestplot application.

Usage

run_interactiveforestplot(data = NULL)

Arguments

data	optional data to load when the app is launched

Examples

if (interactive()) {
  run_interactiveforestplot()
}

---

Weight Age CDC growth charts data

Description

Weight-for-age, 2 to 20 years, LMS parameters and selected smoothed weight percentiles in kilograms, by sex and age.

Usage

wtage

Format

A dataset with 436 rows and 14 variables

Sex

1=male; 2=female

Agemos

Age in months

L

skewness distribution parameter

M

location distribution parameter

S

scale distribution parameter

P3

Smoothed third percentile

P5

Smoothed fifth percentile

P10

Smoothed tenth percentile

P25

Smoothed twenty fifth percentile

P50

Smoothed fiftieth percentile

P75

Smoothed seventy fifth percentile

P90

Smoothed ninetieth percentile

P95

Smoothed ninety fifth percentile

P97

Smoothed ninety seventh percentile

Source

CDC website https://www.cdc.gov/growthcharts/data/zscore/wtage.csv

---