minor documentation changes and adding xlim specification to plot met…

…hod for cd.fit objects
nickreich · Jul 17, 2013 · ebb10ce · ebb10ce
1 parent f46b26d
commit ebb10ce
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Showing 4 changed files with 19 additions and 13 deletions.
diff --git a/R/S4stuff.R b/R/S4stuff.R
@@ -113,6 +113,8 @@ setMethod("logLik",
 ##' 
 ##' @param add add to exisiting plot?
 ##' 
+##' @param xlim xlim for plot, defaults to the range of the data slot in x
+##' 
 ##' @param ... other options to pass to plot
 ##' @rdname plot-methods
 ##' @aliases plot plot,cd.fit-method
@@ -123,7 +125,7 @@ setMethod("plot",
  col.main=rgb(230, 85, 13,maxColorValue=255),
  col.samps=rgb(99,99,99,10,maxColorValue=255),
  plot.n.samps=200,
- add=F,
+ add=F, xlim=range(x@data),
  ...) {
 
  par1 <- x@ests[1,1]
@@ -134,9 +136,8 @@ setMethod("plot",
  plot.samples <- x@samples[sample(nrow(x@samples),min(plot.n.samps,nrow(x@samples))),]
  }
 
- xlims <- range(x@data)
- xs <-seq(xlims[1],xlims[2],length=100)
- if (!add) plot(-100,-100,xlim=xlims,ylim=c(0,1),...)
+ xs <-seq(xlim[1],xlim[2],length=100)
+ if (!add) plot(-100,-100,xlim=xlim,ylim=c(0,1),...)
  if (x@dist == "L"){
  if (plot.n.samps> 0 & nrow(x@samples) > 0){
  apply(plot.samples,1,function(y) lines(xs,plnorm(xs,meanlog=y[1],sdlog=y[2]),col=col.samps))

diff --git a/R/dic.fit.mcmc.R b/R/dic.fit.mcmc.R
@@ -11,7 +11,8 @@
 ##' \deqn{Gamma model: f(x) = \frac{1}{\theta^k \Gamma(k)} x^{k-1} exp\{-\frac{x}{\theta}\}}
 ##' 
 ##' \deqn{Gamma Default Prior Specification: p(k,\theta) \propto \frac{1}{\theta} * \sqrt{k*TriGamma(k)-1}}
-##' (Note: this is Jeffery's Prior when both parameters are unknown, and \eqn{Trigamma(x) = \frac{\partial}{\partial x^2} ln(\Gamma(x))}.)
+##' (Note: this is Jeffery's Prior when both parameters are unknown), and 
+##' \deqn{Trigamma(x) = \frac{\partial}{\partial x^2} ln(\Gamma(x))}.)
 ##' \deqn{Erlang model: f(x) = \frac{1}{\theta^k (k-1)!} x^{k-1} exp\{-\frac{x}{\theta}\}}
 ##' \deqn{Erlang Default Prior Specification: k \sim NBinom(100,1), log(\theta) \sim N(0,1000)}
 ##' (Note: parameters in the negative binomial distribution above represent mean and size, respectivley)

diff --git a/man/dic.fit.mcmc.Rd b/man/dic.fit.mcmc.Rd
@@ -63,13 +63,14 @@ as implemented in MCMCpack.}
 
  \deqn{Gamma Default Prior Specification: p(k,\theta)
  \propto \frac{1}{\theta} * \sqrt{k*TriGamma(k)-1}} (Note:
- this is Jeffery's Prior when both parameters are unknown,
- and \eqn{Trigamma(x) = \frac{\partial}{\partial x^2}
- ln(\Gamma(x))}.) \deqn{Erlang model: f(x) =
- \frac{1}{\theta^k (k-1)!} x^{k-1}
- exp\{-\frac{x}{\theta}\}} \deqn{Erlang Default Prior
- Specification: k \sim NBinom(100,1), log(\theta) \sim
- N(0,1000)} (Note: parameters in the negative binomial
- distribution above represent mean and size, respectivley)
+ this is Jeffery's Prior when both parameters are
+ unknown), and \deqn{Trigamma(x) =
+ \frac{\partial}{\partial x^2} ln(\Gamma(x))}.)
+ \deqn{Erlang model: f(x) = \frac{1}{\theta^k (k-1)!}
+ x^{k-1} exp\{-\frac{x}{\theta}\}} \deqn{Erlang Default
+ Prior Specification: k \sim NBinom(100,1), log(\theta)
+ \sim N(0,1000)} (Note: parameters in the negative
+ binomial distribution above represent mean and size,
+ respectivley)
 }
 
diff --git a/man/plot-methods.Rd b/man/plot-methods.Rd
@@ -15,6 +15,9 @@
 
  \item{add}{add to exisiting plot?}
 
+ \item{xlim}{xlim for plot, defaults to the range of the
+ data slot in x}
+
  \item{...}{other options to pass to plot}
 }
 \description{