indivplot: plot aggregated COD distribution

In InSilicoVA: Probabilistic Verbal Autopsy Coding with 'InSilicoVA' Algorithm

plot aggregated COD distribution

Description

Produce a bar plot of the aggregated COD distribution as approximate CSMFs for a fitted "insilico" object.

Usage

indivplot(
  x,
  type = c("errorbar", "bar")[1],
  top = 10,
  causelist = NULL,
  which.plot = NULL,
  xlab = "Causes",
  ylab = "COD distribution",
  title = "COD distributions for the top causes",
  horiz = TRUE,
  angle = 60,
  fill = "lightblue",
  err_width = 0.4,
  err_size = 0.6,
  point_size = 2,
  border = "black",
  bw = FALSE,
  ...
)

Arguments

x	object from get.indiv function.
type	An indicator of the type of chart to plot. "errorbar" for line plots of only the error bars on single population; "bar" for bar chart with error bars on single population.
top	The number of top causes to plot. If multiple sub-populations are to be plotted, it will plot the union of the top causes in all sub-populations.
causelist	The list of causes to plot. It could be a numeric vector indicating the position of the causes in the InterVA cause list (see causetext), or a vector of character string of the cause names. The argument supports partial matching of the cause names. e.g., "HIV/AIDS related death" could be abbreviated into "HIV"; "Other and unspecified infect dis" could be abbreviated into "Other and unspecified infect".
which.plot	Specification of which group to plot if there are multiple.
xlab	Labels for the causes.
ylab	Labels for the CSMF values.
title	Title of the plot.
horiz	Logical indicator indicating if the bars are plotted horizontally.
angle	Angle of rotation for the texts on x axis when horiz is set to FALSE
fill	The color to fill the bars when type is set to "bar".
err_width	Size of the error bars.
err_size	Thickness of the error bar lines.
point_size	Size of the points.
border	The color to color the borders of bars when type is set to "bar".
bw	Logical indicator for setting the theme of the plots to be black and white.
...	Not used.

Author(s)

Zehang Li, Tyler McCormick, Sam Clark

Maintainer: Zehang Li <[e-mail]>

References

Tyler H. McCormick, Zehang R. Li, Clara Calvert, Amelia C. Crampin, Kathleen Kahn and Samuel J. Clark Probabilistic cause-of-death assignment using verbal autopsies, Journal of the American Statistical Association (2016), 111(515):1036-1049.

See Also

insilico, summary.insilico

Examples

## Not run: 
# Toy example with 1000 VA deaths
data(RandomVA1)
fit1<- insilico(RandomVA1, subpop = NULL,  
              Nsim = 1000, burnin = 500, thin = 10 , seed = 1,
              auto.length = FALSE)
summary(fit1, id = "d199")

# update credible interval for individual probabilities to 90%
indiv.new <- get.indiv(fit1, CI = 0.9)
fit1$indiv.prob.lower <- indiv.new$lower
fit1$indiv.prob.upper <- indiv.new$upper
fit1$indiv.CI <- 0.9
summary(fit1, id = "d199")


# get empirical aggregated COD distribution 
agg.csmf <- get.indiv(data = RandomVA2, fit1, CI = 0.95, 
                      is.aggregate = TRUE, by = NULL)
head(agg.csmf)

# aggregate individual COD distribution by sex and age
# note the model was fitted assuming the same CSMF for all deaths
# this aggregation provides an approximate CSMF for each sub-groups
agg.by.sex.age <- get.indiv(data = RandomVA2, fit1, CI = 0.95, 
                        is.aggregate = TRUE, by = list("sex", "age"))
head(agg.by.sex.age$mean)

# plot of aggregated individual COD distribution
# 0. plot for all data
indivplot(agg.csmf, top = 10)
# 1. plot for specific one group
indivplot(agg.by.sex.age, which.plot = "Men 60-", top = 10)
# 2. comparing multiple groups
indivplot(agg.by.sex.age, which.plot = list("Men 60+", "Men 60-"), 
                          top = 5)
# 3. comparing multiple groups on selected causes
indivplot(agg.by.sex.age, which.plot = list("Men 60-", "Women 60-"), 
                          top = 0, causelist = c(
                            "HIV/AIDS related death", 
                            "Pulmonary tuberculosis", 
                            "Other and unspecified infect dis", 
                            "Other and unspecified NCD"))

## End(Not run) 

InSilicoVA documentation built on Sept. 29, 2022, 9:06 a.m.