Commit 97e4841d authored by Chris Jewell's avatar Chris Jewell
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Added HaldDP.Rd autogenerated with roxygen2.

parent 1b78bec2
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/interface.R
\title{Runs the HaldDP source attribution model}
\format{Object of \code{\link{R6Class}} with methods for creating a HaldDP model, running the model, and accessing and plotting the results.}
Object of \code{\link{HaldDP}} with methods for creating a HaldDP model, running the model, and accessing and plotting the results.
Runs the HaldDP source attribution model
\item{\code{new(data, k, priors, a_q, inits = NULL)}}{Constructor takes
\code{data} dataframe (with columns containing the number of human cases named
\code{Human}, columns containing the number of positive source samples
(one column per source), a column with the time id's named \code{Time},
a column with the type id's named \code{Type}, and a column with the source
location id's \code{Location})
\code{k} prevalence dataframe (with columns named \code{Value, Time,
Location and Source})
\code{a_q} the Dirichlet Process concentration parameter
\code{inits} (optional) initial values for the mcmc algorithm. This is a list
that may contain any of the following items:
\code{alpha} (a data frame with
columns named \code{Value} contining the initial values, \code{Time}, \code{Location}, \code{Source}),
\code{q} (a data frame with columns names \code{Value} contining the initial values and \code{Type}), and
\code{r} (a data frame with columns:
a column with the initial r values named \code{Value}
(note these must sum to 1 for each source-time combination),
a column with the source id's named \code{Source},
a column with the time id's named \code{Time},
a column with the type id's named \code{Type}.)}
\item{\code{fit_params(n_iter = 1000, burn_in = 0, thin = 1,
n_r = ceiling(private$nTypes * 0.2), params_fix = NULL)}}{when called, sets the mcmc
\code{n_iter} sets the number of iterations returned (after removing
\code{burn_in} and thinning results by \code{thin} i.e. a total of
(n_iter * thin) + burn_in iterations are run)
\code{n_r} is a positive
integer that sets the total number of \code{r_{ijtl}} parameters to be updated
at each time-location-source combination (the default is 20 percent updated
per iteration)
\code{params_fix} is a list with a logical value for any of the model parameters
(any of \code{"alpha", "r", or "q"}). For each parameter, if set to \code{TRUE},
the parameters will be fixed at their initial values and not updated.}
\item{\code{update(n_iter, append = TRUE)}}{when called, updates the \code{HaldDP}
model by running \code{n_iter} iterations.
If missing \code{n_iter}, the \code{n_iter} last set using \code{fit_params()}
or \code{update()} is used.
is a logical value which determines whether the next \code{n_iter} iterations
are appended to any previous iterations, or overwrites them. When
\code{append = TRUE}, the starting values are the last iteration and no
\code{burn_in} is removed. Running the model for the first time, or changing any
model or fitting parameters will set \code{append = FALSE}.
\item{\code{print_data}}{returns a list containing the human data \code{y}
(an array y[types, times, locations]), the source data \code{X} (an array X[types, sources, times]),
the prevalence data (an array k[sources, times]), the type names, source names,
time names, location names and number of different types, sources, times and locations.
\item{\code{print_priors}}{returns a list containing the DP concentration
parameter \code{a_q}, and the priors (R6 class with members named \code{a_alpha}
(members are array \code{a_alpha[sources, times, locations]}), \code{a_r} (an array \code{a_r[types, sources, times]}),
\code{a_theta} and \code{b_theta}).}
\item{\code{print_inits}}{returns an R6 class holding the initial values
(members are \code{alpha} (an array \code{alpha[sources, times, locations]}),
\code{theta} (an array \code{theta[types, iters]}), \code{s} (an array
\code{s[types, iters]}), and \code{r} (an array \code{r[types, sources, times]})).}
\item{\code{print_fit_params}}{returns a list of fitting parameters (\code{n_iter},
\code{append}, \code{burn_in}, \code{thin}, \code{params_fix} (R6 class with members
\code{alpha}, \code{q}, \code{r})).}
\item{\code{print_acceptance}}{returns an R6 class containing the acceptance
rates for each parameter (members are \code{alpha} (an array \code{alpha[sources, times, locations]}),
and \code{r} (an array \code{r[types, sources, times]})).}
\item{\code{extract(params = c("alpha", "q", "s", "r", "lambda_i", "lambda_j", "lambda_j_prop"),
times = NULL, locations = NULL, sources = NULL, types = NULL, iters = NULL,
flatten = FALSE, drop = TRUE)}}{returns a list contining a subset of the parameters
(determined by the \code{params} vector, \code{times}, \code{locations}, \code{sources}, \code{types} and \code{iters}).
If \code{flatten} is set to \code{TRUE}, it returns a dataframe with 1 column per
parameter, otherwise it returns a list containing \code{params} containing a
subset of the following arrays: \code{alpha[Sources, Times, Locations, iters]}, \code{q[Types, iters]},
\code{s[Types, iters]}, \code{r[Types, Sources, Times, iters]}, \code{lambda_i[Types, Times, Locations, iters]},
\code{lambda_j[Sources, Times, Locations, iters]}.
determines whether to delete the dimensions of an array which have only one
level when \code{flatten = FALSE}.}
\item{\code{summary(alpha = 0.05, params = c("alpha", "q", "s", "r", "lambda_i",
"lambda_j" ,"lambda_j_prop"), times = NULL, locations = NULL, sources = NULL,
types = NULL, iters = NULL, flatten = FALSE, drop = TRUE, CI_type = "c-s")}}{
returns a list contining the
median and credible intervals for a subset of the parameters. The default credible
interval type are Chen-Shao highest posterior density intervals (alternatives
are \code{"percentiles"} and \code{"spin"}).
See \code{extract} for details on the subsetting. \code{lambda_j_prop} returns the
proportion of cases attributed to each source \code{j} and is calculated by dividing
each iteration of \code{lambda_{jtl}} values by their sum within each time \code{t} and location \code{l}.}.}
\item{\code{plot_heatmap(iters, cols = c("blue","white"), hclust_method = "complete")}}{
Creates a dendrogram and heatmap for the type effect groupings (\code{s} parameter in the model).
This uses the heatmap.2 function from gplots.
\code{iters} is a vector containing the iterations to be used in constructing
the graph. Default is all iterations in posterior.
\code{hclust_method} allows the user to select the method used by \code{stats::hclust} to
cluster the type effect groupings \code{s}.
\code{cols} gives the colours for completely dissimilar (dissimilarity value
of 1), and identical (dissimilarity value of 0). All other values will be in
between the two chosen colours. See ?colorRampPalette for more details..}
zero_rows <- which(apply(campy[,c(2:7)], 1, sum) == 0)
campy <- campy[-zero_rows,]
prevs <- data.frame(Value = 1/c(181/ 239, 113/196, 109/127,
97/595, 165/552, 86/524),
Source = colnames(campy[, 2:7]),
Time = rep(1, 6),
Location = rep("A", 6))
priors <- list(a_alpha = 1, a_r = 1, a_theta = 0.01, b_theta = 0.00001)
res <- HaldDP$new(data = campy, k = prevs, priors = priors, a_q = 1)
res$fit_params(n_iter = 100, burn_in = 10, thin = 1)
res$plot_heatmap(iters = 10:100, hclust_method = "complete")
res$summary(params = c("alpha", "q", "lambda_i"),
times = "1", sources = c("ChickenA", "Bovine"),
iters = 10:100, flatten = TRUE, CI_type = "c-s")
res$extract(params = c("alpha", "r", "q", "lambda_j"),
sources = c("ChickenB", "Ovine"),
types = c("474", "52"),
iters = 50:100, drop = FALSE, flatten = FALSE)
Chris Jewell and Poppy Miller \email{}
Chen, M.-H. and Shao, Q.-M. (1998). Monte Carlo estimation of Bayesian credible and HPD intervals, \emph{Journal of Computational and Graphical Statistics}, 7.
Liu Y, Gelman A, Zheng T (2015). "Simulation-efficient shortest probability intervals." Statistics and Computing.
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