fix errors in docs

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp2
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 2.0.9.2
-Date: 2019-01-22
+Version: 2.0.9.3
+Date: 2019-01-23
 Authors@R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="[email protected]"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),

R/parameter_trans.R

@@ -33,7 +33,8 @@
 ##'   Therefore, neither the time, nor any state variables, nor any of the covariates will be available in the context within which a parameter transformation snippet is executed.
 ##' }
 ##'
-##' These transformations can also be specified using \R functions with arguments \code{params} and \code{\dots}.
+##' These transformations can also be specified using \R functions with arguments chosen from among the parameters.
+##' Such an \R function must also have the argument \sQuote{\code{...}}.
 ##' In this case, \code{toEst} should transform parameters from the scale that the basic components use internally to the scale used in estimation.
 ##' \code{fromEst} should be the inverse of \code{toEst}.
 ##'

R/plot.R

@@ -7,7 +7,7 @@
 ##' @include pomp_class.R
 ##' @include abc.R mif2.R pmcmc.R pfilter.R spect.R
 ##' @include listie.R
-##' @aliases plot,missing-method plot,ANY-method
+##' @aliases plot,missing-method
 ##'
 ##' @importFrom graphics plot par abline pairs matplot box axis mtext points polygon lines plot.default legend hist rect text title
 ##' @importFrom grDevices rgb dev.interactive

R/rmeasure_spec.R

@@ -31,16 +31,10 @@
 ##' It is also possible, though far less efficient, to specify \code{rmeasure} using an \R function.
 ##' In this case, specify the measurement model simulator by furnishing \preformatted{
 ##'   rmeasure = f}
-##' to \code{pomp}, where \code{f} is an \R function with prototype \preformatted{
-##'   f(x, t, params, \dots)}
-##' It can also take any additional arguments if these are passed along with it in the call to \code{pomp}.
-##' When \code{f} is called,
-##' \itemize{
-##'   \item \code{x} will be a named numeric vector of length \code{nvar}, the number of state variables.
-##'   \item \code{t} will be a scalar quantity, the time at which the measurement is made.
-##'   \item \code{params} will be a named numeric vector of length \code{npar}, the number of parameters.
-##' }
-##' \code{f} must return a named numeric vector of length \code{nobs}, the number of observable variables.
+##' to \code{pomp}, where \code{f} is an \R function.
+##' The arguments of \code{f} should be chosen from among the state variables, parameters, covariates, and time.
+##' It must also have the argument \code{...}.
+##' \code{f} must return a named numeric vector of length equal to the number of observable variables.
 ##'
 ##' @section Default behavior:
 ##' The default \code{rmeasure} is undefined.

R/rprocess_spec.R

@@ -16,14 +16,11 @@
 ##' See \code{\link{Csnippet}} for general rules on writing C snippets.
 ##' Examples are to be found in the tutorials on the \href{https://kingaa.github.io/pomp/}{package website}.
 ##'
-##' If \code{f} is given as an \R function, it should have prototype
-##' \preformatted{
-##'     f(x, t, params, delta.t, ...)
-##' }
-##' When \code{f} is called, \code{x} will be a named numeric vector containing the value of the state process at time \code{t},
-##' \code{params} will be a named numeric vector containing parameters,
-##' and \code{delta.t} will be the time-step.
-##' It should return a named vector of the same length, and with the same set of names, as \code{x}, representing a draw from the distribution of the state process at time \code{t+delta.t}, conditional on its having value \code{x} at time \code{t}.
+##' If \code{f} is given as an \R function, its arguments should come from the state variables, parameters, covariates, and time.
+##' It may also take the argument \sQuote{\code{delta.t}};
+##' when called, the latter will be the time-step.
+##' It must also have the argument \sQuote{\code{...}}.
+##' It should return a named vector of length equal to the number of state variables, representing a draw from the distribution of the state process at time \code{t+delta.t} conditional on its value at time \code{t}.
 ##'
 ##' @section Continuous-time processes:
 ##' If the state process evolves in continuous time, but you can use an Euler approximation, implement \code{rprocess} using the \code{euler} plug-in.

R/skeleton_spec.R

@@ -34,16 +34,10 @@
 ##' }
 ##' The tutorials on the \href{https://kingaa.github.io/pomp/}{package website} give some examples.
 
-##' If \code{f} is an \R function, it must be of prototype \preformatted{
-##'   f(x, t, params, \dots)}
-##' where, as usual,
-##' \itemize{
-##'   \item \code{x} is a numeric vector (length \code{nvar}) containing the coordinates of a point in state space at which evaluation of the skeleton is desired.
-##'   \item \code{t} is a scalar value giving the time at which evaluation of the skeleton is desired.
-##'   \item \code{params} is a numeric vector (length \code{npar}) holding the parameters.
-##' }
+##' If \code{f} is an \R function, its arguments should be taken from among the state variables, parameters, covariates, and time.
+##' It must also take the argument \sQuote{\code{...}}.
 ##' As with the other basic components, \code{f} may take additional arguments, provided these are passed along with it in the call to \code{pomp}.
-##' The function \code{f} must return a numeric vector of the same length as \code{x}, which contains the value of the map or vectorfield at the required point and time.
+##' The function \code{f} must return a numeric vector of the same length as the number of state variables, which contains the value of the map or vectorfield at the required point and time.
 ##'
 ##' @section Default behavior:
 ##' The default \code{skeleton} is undefined.

R/time.R

@@ -4,7 +4,7 @@
 ##'
 ##' @name time
 ##' @rdname time
-##' @aliases time time<- time,ANY-method time,missing-method
+##' @aliases time time<- time,missing-method
 ##'
 ##' @importFrom stats time
 NULL

inst/NEWS

@@ -11,6 +11,8 @@ _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _2._0._9:
         • A bug, whereby the ‘coef’ method from other packages was
           masked, has been fixed.
 
+        • Errors in the documentation have been corrected.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _2._0._8:
 
         • There is a new ‘as.data.frame’ method for ‘listie’s.

inst/NEWS.Rd

@@ -5,6 +5,7 @@
     \item When \code{coef} is applied to a \sQuote{listie}, the result can be more usefully \code{melt}ed.
     \item The probe-names returned by \code{probe.acf} and \code{probe.ccf} have changed.
     \item A bug, whereby the \sQuote{coef} method from other packages was masked, has been fixed.
+    \item Errors in the documentation have been corrected.
   }
 }
 \section{Changes in \pkg{pomp} version 2.0.8}{