R: Methods for fitted 'surveil' models

plot.surveil {surveil}

R Documentation

Methods for fitted `surveil` models

Description

Print and plot methods for surveil model results

Usage

## S3 method for class 'surveil'
print(x, scale = 1, ...)

## S3 method for class 'surveil'
plot(
  x,
  scale = 1,
  style = c("mean_qi", "lines"),
  facet = FALSE,
  facet_scales = c("fixed", "free"),
  ncol = NULL,
  base_size = 14,
  palette = "Dark2",
  M = 250,
  alpha,
  lwd,
  fill = "gray80",
  size = 1.5,
  ...
)

## S3 method for class 'list'
plot(
  x,
  scale = 1,
  style = c("mean_qi", "lines"),
  facet = FALSE,
  ncol,
  facet_scales = c("fixed", "free"),
  M = 250,
  base_size = 14,
  palette = "Dark2",
  fill = "gray80",
  size = 1.5,
  alpha,
  lwd,
  ...
)

Arguments

`x`	A fitted `surveil` model, or a list of `stand_surveil` objects (as produced by `standardize`).
`scale`	Scale the rates by this amount; e.g., `scale = 100e3` will print rates per 100,000 at risk.
`...`	For the plot method, additional arguments will be passed to '`theme`; for the print method, additional arguments will be passed to `print.data.frame`.
`style`	If `style = "mean_qi"`, then the posterior mean and 95 percent credible interval will be plotted; if `style = "lines"`, then `M` samples from the joint probability distribution of the annual rates will be plotted.
`facet`	If `facet = TRUE`, `facet_wrap` will be used instead of differentiating by line color.
`facet_scales`	When `facet = TRUE`, this argument controls behavior of the scales for each sub-plot. See the `scales` argument to `facet_wrap`.
`ncol`	Number of columns for the plotting device; optional and only used if `facet = TRUE`. If `ncol = 1`, the three plots will be aligned vertically in one column; if `ncol = 3` they will b aligned horizontally in one row. Defaults to `ncol = NULL` to allow `facet_wrap` to automatically determine the number of columns.
`base_size`	Passed to `theme_classic()` to control size of plot components (text).
`palette`	For multiple groups, choose the color palette. For a list of options, see `scale_color_brewer`. The default is `palette = "Dark2"`. Not used if `facet = TRUE`.
`M`	If `style = "lines"`, then `M` is the number of samples from the posterior distribution that will be plotted; the default is `M = 250`.
`alpha`	Numeric value from zero to one. When `style = "lines"`, this controls transparency of lines; passed to `geom_line`. For 'style = "mean_qi", this controls the transparency of the shaded credible interval; passed to `geom_ribbon`.
`lwd`	Numeric value indicating linewidth. Passed to `geom_line`
`fill`	Color for the shaded credible intervals; only used when `style = "mean_qi"`.
`size`	Positive numeric value. For `style = "mean_qi"`, this controls the size of the points representing crude rates. To exclude these points from the plot altogether, use `size = 0`.

Value

The plot method returns a ggplot object; the print method returns nothing but prints a summary of results to the R console. If x is a list of stand_surveil objects, the plotted lines will be labeled using the names returned by names(x); if elements of the list are not named, plotted lines will simply be numbered.

Author(s)

Connor Donegan (Connor.Donegan@UTSouthwestern.edu)

Examples

data(msa)
dat <- aggregate(cbind(Count, Population) ~ Year + Race, data = msa, FUN = sum)
fit <- stan_rw(dat, time = Year, group = Race,
               iter = 1e3, chains = 2) # for speed only, use 4 chains

print(fit)
plot(fit, facet = TRUE, scale = 100e3)

 ## as a ggplot, you can customize the output
library(ggplot2)
plot(fit) + theme_bw()

[Package surveil version 0.3.0 Index]

Methods for fitted surveil models