In Novartis/xgxr: Exploratory Graphics for Pharmacometrics

knitr::opts_chunk$set(echo = TRUE)
library(testthat)

Brief Package Description

Supports a structured approach for exploring PKPD data https://opensource.nibr.com/xgx/. It also contains helper functions for enabling the modeler to follow best R practices (by appending the program name, figure name location, and draft status to each plot). In addition, it enables the modeler to follow best graphical practices (by providing a theme that reduces chart ink, and by providing time-scale, log-scale, and reverse-log-transform-scale functions for more readable axes). Finally, it provides some data checking and summarizing functions for rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.

Datasets used for testing

This describes the datasets (if any) or functions (if any) that are used to test the package.

nlmixr2data::theo_sd

Functions that are exported

GGproto functions

These functions are exported but are not expected to be used directly by the user and are not tested:

• StatSmoothOrdinal
• StatSummaryBinQuant
• StatSummaryOrdinal

Interactive only functions

These functions are based on interactive user input and are not tested:

• edit_rmd_template_str

Exported from other packages

• gtable
• nlsLM
• predict.nls

Functions that are display only, and do no calculation

• theme_xgr -- changes the ggplot2 theme to black and white

• xgx_annotate_filenames -- adds footnotes to figuers

• xgx_annotate_status -- Adds "DRAFT" to figures

• xgx_annotate_status_png -- nadds status to the png files

• xgx_theme

• xgx_theme_set

Testible functions without graphics

• xgx_breaks_log10 display log-10 breaks on scale

test_that("log10 breaks make sense", {
  expect_equal(xgx_breaks_log10(c(0.001, 2000)), 
               c(0.001, 0.01, 0.1, 1, 10, 100, 1000))
})

• xgx_breaks_time displays breaks with time

test_that("xgx_breaks_time makes sense", {
  expect_equal(xgx_breaks_time(c(0, 24*10), "h"),
               c(0, 60, 120, 180, 240))

})

• xgx_check_data

test_that("xgx_check_data produces no errors", {
  expect_error(xgx_check_data(nlmixr2data::theo_sd), NA)
})

• xgx_conf_int

test_that("xgx_conf_int", {
  withr::with_seed(24,{
    expect_equal(xgx_conf_int(rnorm(1000)),
                 structure(list(y = -0.0469587129006418, ymin = -0.109521192672548, ymax = 0.0156037668712641), class = "data.frame", row.names = c(NA, -1L)))
  })
})

• xgx_dirs2char

test_that("xgx_dirs2char", {
  dirs <- list(parent_dir = "/your/parent/path/",
            rscript_dir = "./Rscripts/",
            rscript_name = "Example.R",
            results_dir = "./Results/",
            filename = "your_file_name.png")
caption <- xgx_dirs2char(dirs)
expect_equal("/your/parent/path/\n./Rscripts//Example.R\n./Results//your_file_name.png\nCreated: 2022-11-07 20:10:34",
             caption)
})

• xgx_labels_log10

test_that("xgx_breaks_time makes sense", {
  expect_equal(xgx_labels_log10(xgx_breaks_log10(c(0.001, 2000))),
               c("0.001", "0.01", "0.1", "1", "10", "100", "1000"))
})

• xgx_minor_breaks_log10

test_that("xgx_breaks_time makes sense", {
  expect_equal(xgx_minor_breaks_log10(c(0.001, 2000)),
               c(0.002, 0.003, 0.004, 0.005, 0.006, 0.007, 0.008, 0.009, 
                 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.09, 
                 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 
                 2, 3, 4, 5, 6, 7, 8, 9, 
                 20, 30, 40, 50, 60, 70, 80, 90, 
                 200, 300, 400, 500, 600, 700, 800, 900, 
                 2000))
})

Interfaces that allow creation of ggplots

• xgx_plot -- This simply is a wrapper around ggplot, not sure the rationale. This is a display-only style function

Save ggplot2 objects

• xgx_save -- Save ggplot

• xgx_save_table -- saves table as image

Scales/stats/geom

These produce graphical output and need to be tested further in the future, probably using vdiffr

• xgx_geom_ci
• xgx_geom_pi
• xgx_geom_smooth, use "polr", "nls", "nlsLM"
• xgx_geom_smooth uses minpack.lm::nlsLM
• xgx_scale_x_log10
• xgx_scale_x_percentchangelog10
• xgx_scale_x_reverselog10
• xgx_scale_x_time_units
• xgx_scale_y_log10
• xgx_scale_y_percentchangelog10
• xgx_scale_y_reverselog10
• xgx_scale_y_time_units
• xgx_stat_ci
• xgx_stat_pi
• xgx_stat_smooth
• xgx_summarize_covariates
• xgx_summarize_data

Novartis/xgxr documentation built on Oct. 20, 2023, 4:35 a.m.