CopulaDTA (version 1.0.1)

forestplot.cdtafit: Produce forest plots for categorical covariates.

Description

Produce forest plots for categorical covariates.

Usage

forestplot.cdtafit(
  x,
  title.1 = NULL,
  title.2 = NULL,
  title.3 = NULL,
  graph = NULL,
  width = 0.2,
  shape.1 = 19,
  size.1 = 2.5,
  shape.2 = 8,
  size.2 = 2.5,
  shape.O = 9,
  size.O = 3.5,
  cols.1 = NULL,
  cols.2 = NULL,
  digits = 3,
  ...
)

Value

forest plots by ggplot2.

Arguments

x

A cdtafit object from fit.

title.1

An optional string indicating the title of graph 1.

title.2

An optional string indicating the title of graph 2.

title.3

An optional string indicating the title of graph 3.

graph

An optional numeric value indicating which forest to plot(s) to graph. Valid values are:0 - for no graph, 1 - yielding a forest plot of the sensitivity and specificity with a 95 percent exact confidence intervals, 2 - yielding a forest plot of the posterior study-specific sensitivity and specificity and the marginal mean sensitivity and specificity and their corresponding 95 percent credible intervals, 3 - yielding a combination of 1 and 2 in one plot, and NULL(default) - yielding plots of 1, 2 and 3.

width

An optional numeric value to adjust the dogding position. The default is 0.2.

shape.1

An optional numeric value(0-255) indicating the symbol to plot in graph 1. The default is 19 which is a solid circle. See points for more details.

size.1

An optional positive numeric value indicating the size of symbols in graph 1. The default is 2.5.

shape.2

An optional numeric value(0-255) indicating the symbol to plot in graph 2. The default is 8 which is a star. See points for more details.

size.2

An optional positive numeric value indicating the size of symbols in graph 2. The default is 2.5.

shape.O

An optional numeric value(0-255) indicating the symbol representing the posterior marginal mean in graph 2. The default is 19 which is a solid circle. See points for more details.

size.O

An optional numeric value indicating the size of symbols representing the posterior marginal means in graph 2.

cols.1

An optional string vector specifying colours of shapes in graph 1.

cols.2

An optional string vector specifying colours of shapes in graph 2.

digits

An optional positive value to control the number of digits to print when printing numeric values. The default is 3.

...

other stan options.

Author

Victoria N Nyaga <[e-mail]>

References

Watanabe S (2010). Asymptotic Equivalence of Bayes Cross Validation and Widely Applicable Information Criterion in Singular Learning Theory. Journal of Machine Learning Research, 11, 3571-3594.

Vehtari A, Gelman A (2014). WAIC and Cross-validation in Stan. Unpublished, pp. 1-14.

Examples

data(telomerase)
model1 =  cdtamodel(copula = 'fgm')

model2 = cdtamodel(copula = 'fgm',
               modelargs=list(param=2,
                              prior.lse='normal',
                              par.lse1=0,
                              par.lse2=5,
                              prior.lsp='normal',
                              par.lsp1=0,
                              par.lsp2=5))

model3 =  cdtamodel(copula = 'fgm',
               modelargs = list(formula.se = StudyID ~ Test - 1))
if (FALSE) {
fit1 <- fit(model1,
                SID='ID',
                data=telomerase,
                iter=2000,
                warmup=1000,
                thin=1,
                seed=3)

plot(fit1)
}