In metrumresearchgroup/pmplots: Plots for Pharmacometrics

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library(dplyr)
library(pmplots)
data <- pmplots_data_obs()

data <- filter(data, ID <= 9*2)
data <- mutate(data, OCC = as.integer(TIME > 12))

head(data)

count(data, ID, OCC)

data1 <- filter(data, ID <= 9)

Chunk

• 2 chunks

pmplots:::chunk_by_cols(
  data, 
  cols = "ID", 
  id_per_chunk = 9
)

• 6 chunks

pmplots:::chunk_by_cols(
  data, 
  cols = "ID", 
  id_per_chunk = 3) %>% length()

• 12 chunks

pmplots:::chunk_by_cols(
  data, 
  cols = c("ID", "OCC"), 
  id_per_chunk = 3) %>% length()

Basic plot

Faceted by ID

• including x and y labels

ans <- dv_pred_ipred(
  data, 
  facets = "ID", 
  id_per_plot = 4, ncol = 2, 
  xlab  = "Time (hr)", 
  ylab = "Concentration (ng/ml)"
)

length(ans)

ans[1:2]

Faceted by ID and OCC

This has twice as many plots because every

ans <- dv_pred_ipred(
  data, 
  facets = c("ID", "OCC"),
  id_per_plot = 4, ncol = 2
)
length(ans)

ans[1:2]

Glue in better strip labels

• If we ask for OCC and that takes values of 0 and 1, the strip labels will show 0 and 1
• With the glue syntax, rather than specifying OCC we pass OCC//Occasion: {OCC} so that the strip will say Occasion: 1 and Occasion: 2

ans <- dv_pred_ipred(
  data, 
  facets = c("ID//ID: {ID}", "OCC//Occasion: {OCC}"),
  id_per_plot = 4, ncol = 2
)

ans[1]

Lines

• ipred_lty: linetype for ipred; use 0 to suppress the line
• pred_lty: linetype for pred; use 0 to suppress the line

The plot will drop lines for PRED and IPRED in the plot and legend

dv_pred_ipred(data1, ipred_lty = 0, pred_lty = 0)[[1]]

Points

• ipred_point: logical indicating if points should be plotted; shape is same as dv
• pred_point: logical indicating if points should be plotted; shape is same as dv

The plot will drop points for PRED and IPRED in the plot and legend

dv_pred_ipred(data1, ipred_point = FALSE, pred_point = FALSE)[[1]]

Colors

• ipred_color: color for ipred data
• pred_color: color for pred data

The plot will drop points for PRED and IPRED in the plot and legend

dv_pred_ipred(data1, ipred_color = "green4", pred_color = "orange3")[[1]]

Margin

• We want to put in extra margin if needed
• margin is deprecated; use plot.margin instead

dv_pred_ipred(
  data1, 
  plot.margin = margin(0, 2, 0, 0, unit = "in")
)[[1]]

Format the strip

• This was manipulated by default before
• Now, you need to pass strip.text

dv_pred_ipred(
  data1, 
  strip.text = element_text(size = 5, margin = margin(3,0,3,0))
)[[1]]

Log y

dv_pred_ipred(data1, log_y = TRUE)[[1]]

metrumresearchgroup/pmplots documentation built on Oct. 15, 2024, noon