PlotLong: Wrapper for fitting model and adjusting to predicted values...

In lengning/gClinBiomarker: gClinBiomarker: an R package for clinical biomarker analyses

Description

Wrapper for fitting model and adjusting to predicted values and passing newly fitted model to ggplot geom_stat_ribbon

Usage

PlotLong(data, mapping = NULL, model = lm, model.per = NULL,
  model.formula = NULL, facet.fun = NULL, plot.style = "ribbons", ...)

Arguments

data	data to use for model fitting and plotting
mapping	ggplot aesthetic mapping to use for plotting
model	model function to use for fitting; defaults to lm
model.per	grouping variables by which to isolate individual models
model.formula	model formula to use for model fitting
facet.fun	function to use for ggplot faceting in ggplot2::facet_grid
plot.style	one of 'errorbars' or 'ribbons'
...	Additional arguments allow for an assortion of additional functionality. "Aesthetics" First, arguments which can be used as any of ggplot's default aesthetics will be pulled from ... args. . "ggplot layers" Arguments are passed to underlying ggplot components by prefixing value with ggplot call name. ("ribbons", "line", "text", "facet", "xlab", "ylab", "labs" or "theme" - e.g. ribbons.color = 'red')). "Model fitting" Arguments with prefixes of "model" will be passed to the model function if one is provided. "ggpackets" Additional arguments passed to ggpk_ribbons or ggpk_line_errorbar.

Value

a ggplot object

Author(s)

Doug Kelkhoff [e-mail]

Examples

# load data
nasa.data <- as.data.frame(dplyr::nasa)

# default representation
PlotLong(nasa.data, x = month, y = temperature)

# a more appropriate representation for large n
PlotLong(nasa.data, x = month, y = temperature, fun.data = 'quartiles')

# include linear adjustment accounting for amount of ozone
PlotLong(nasa.data, x = month, y = temperature,
         formula = temperature ~ ozone, fun.data = 'deciles',
         show.counts = T)

# adjusting by independent models for the northern and southern hemispheres
library(dplyr) # needed for %>%
PlotLong(nasa.data %>% mutate(hemi=ifelse(lat>0, "North", "South")),
         x = month, y = temperature, formula = temperature ~ ozone,
         model.per = ~ hemi, facet.fun = ~ hemi, fun.data = 'deciles',
         xlab = "Month", ylab = "Temperature Adjusted for Ozone",
         labs.title = "Temperature by Hemisphere",
         labs.caption = "*idependent models fit per hemisphere")

# including a table of value counts and subsetting value data to specific
# months
library(dplyr) # needed for %>%
PlotLong(nasa.data %>% mutate(hemisphere=ifelse(lat > 0, "North", "South")),
         x = month, y = temperature, group = hemisphere,
         color = hemisphere, fill = hemisphere,
         formula = temperature ~ ozone,
         model.per = ~ hemisphere, fun.data = 'deciles',
         plot.style = 'errorbars',
         show.counts = 'table',
         label.data = . %>% filter(month %in% c(1, 6, 12)),
         label.hjust = 'inward',
         xlab = "Month", ylab = "Temperature Adjusted for Ozone",
         labs.title = "Temperature by Hemisphere",
         labs.caption = "*idependent models fit per hemisphere")

lengning/gClinBiomarker documentation built on May 9, 2019, 2:55 p.m.