metaplot.data.frame: Create Metaplot for Data Frame.
In bergsmat/metaplot: Data-Driven Plot Design

metaplot.data.frame

R Documentation

Create Metaplot for Data Frame.

Description

Creates a metaplot for class 'data.frame'. Implements a rule to decided whether to make a density plot, a boxplot, a scatter plot, or a scatterplot matrix, given the supplied column names.

Usage

## S3 method for class 'data.frame'
metaplot(
  x,
  ...,
  univariate = metOption("univariate", "densplot"),
  mixedvariate = metOption("mixedvariate", "boxplot"),
  bivariate = metOption("bivariate", "scatter"),
  multivariate = metOption("multivariate", "corsplom"),
  categorical = metOption("categorical", "categorical"),
  verbose = metOption("verbose", FALSE)
)

Arguments

`x`	object
`...`	passed arguments
`univariate`	function for univariate arguments
`mixedvariate`	function for bivariate combinations of numeric and categoral arguments
`bivariate`	function for arguments that resolve to two numerics (see rules)
`multivariate`	function for more than two numeric arguments
`categorical`	function for categorical arguments
`verbose`	generate messages describing process; passed to called functions if explicitly supplied

Examples

## Not run: 
library(magrittr)
library(dplyr)
library(csv)
library(nlme)
x <- Theoph

# mixed effects model
m1 <- nlme(
  conc ~ SSfol(Dose, Time, lKe, lKa, lCl),
  data = x,
  fixed = lKe + lKa + lCl ~ 1,
  random = lKe + lKa + lCl ~ 1
)

# some numeric and categorical properties
names(x) <- tolower(names(x))
x %<>% mutate(arm = ifelse(as.numeric(as.character(subject)) %% 2 == 0, 1, 2))
x %<>% mutate(site = ifelse(as.numeric(as.character(subject)) < 6, 1, 2))
x %<>% mutate(cohort = ifelse(as.numeric(as.character(subject)) %in% c(1:2,6:8), 1,2))
x %<>% mutate(pred = predict(m1,level = 0) %>% signif(4))
x %<>% mutate(ipred = predict(m1) %>% signif(4))
x %<>% mutate(res = residuals(m1) %>% signif(4))
x %<>% mutate(sres = residuals(m1, type = 'pearson') %>% signif(4))
r <- ranef(m1) %>% signif(4)
r$subject <- rownames(r)
x %<>% left_join(r)
# metadata
attr(x$subject,'label') <- 'subject identifier'
attr(x$wt,'label') <- 'subject weight'
attr(x$dose,'label') <- 'theophylline dose'
attr(x$time,'label') <- 'time since dose administration'
attr(x$conc,'label') <- 'theophylline concentration'
attr(x$arm,'label') <- 'trial arm'
attr(x$site,'label') <- 'investigational site'
attr(x$cohort,'label') <- 'recruitment cohort'
attr(x$pred,'label') <- 'population-predicted concentration'
attr(x$ipred,'label') <- 'individual-predicted concentration'
attr(x$res,'label') <- 'residuals'
attr(x$sres,'label') <- 'standardized residuals'
attr(x$lKe,'label') <- 'natural log of elimination rate constant'
attr(x$lKa,'label') <- 'natural log of absorption rate constant'
attr(x$lCl,'label') <- 'natural log of clearance'
attr(x$subject,'guide') <- '....'
attr(x$wt,'guide') <- 'kg'
attr(x$dose,'guide') <- 'mg/kg'
attr(x$time,'guide') <- 'h'
attr(x$conc,'guide') <- 'mg/L'
attr(x$arm,'guide') <- '//1/Arm A//2/Arm B//'
attr(x$site,'guide') <- '//1/Site 1//2/Site 2//'
attr(x$cohort,'guide') <- '//1/Cohort 1//2/Cohort 2//'
attr(x$pred,'guide') <- 'mg/L'
attr(x$ipred,'guide') <- 'mg/L'

attr(x$lKe,'reference') <- 0
attr(x$lKa,'reference') <- 0
attr(x$lCl,'reference') <- 0
attr(x$res,'reference') <- 0
attr(x$sres,'reference') <- '//-1.96//1.96//'

attr(x$subject,'symbol') <- 'ID_i'
attr(x$wt,'symbol') <- 'W_i'
attr(x$dose,'symbol') <- 'A_i'
attr(x$time,'symbol') <- 't_i,j'
attr(x$conc,'symbol') <- 'C_i,j'
attr(x$arm,'symbol') <- 'Arm_i'
attr(x$site,'symbol') <- 'Site_i'
attr(x$cohort,'symbol') <- 'Cohort_i'
attr(x$pred,'symbol') <- 'C_pred_p'
attr(x$ipred,'symbol') <- 'C_pred_i'
attr(x$res,'symbol') <- '\\epsilon'
attr(x$sres,'symbol') <- '\\epsilon_st'
attr(x$lKe,'symbol') <- 'ln(K_e.)'
attr(x$lKa,'symbol') <- 'ln(K_a.)'
attr(x$lCl,'symbol') <- 'ln(Cl_c./F)'


x %>% unpack %>% as.csv('theoph.csv')

## End(Not run)

bergsmat/metaplot documentation built on Feb. 21, 2024, 1:18 p.m.