remove defunct functions

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 5.8.0.0
-Date: 2024-05-01
+Version: 5.8.1.0
+Date: 2024-05-02
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="kingaa@umich.edu",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Edward","L."),family="Ionides",role="aut",comment=c(ORCID="0000-0002-4190-0174"))	,
 	  person(given="Carles",family="Bretó",role="aut",comment=c(ORCID="0000-0003-4695-4902")),
@@ -86,7 +86,6 @@ Collate:
     'cond_logLik.R'
     'covmat.R'
     'dacca.R'
-    'defunct.R'
     'design.R'
     'ebola.R'
     'eff_sample_size.R'

NAMESPACE

@@ -14,22 +14,18 @@ S3method(as.data.frame,probed_pomp)
 S3method(as.data.frame,wpfilterd_pomp)
 S3method(c,Pomp)
 export(Csnippet)
-export(as.pomp)
 export(as_pomp)
 export(bake)
 export(blowflies1)
 export(blowflies2)
-export(bspline.basis)
 export(bspline_basis)
 export(concat)
-export(cond.logLik)
 export(continue)
 export(dacca)
 export(dbetabinom)
 export(deulermultinom)
 export(discrete_time)
 export(ebolaModel)
-export(eff.sample.size)
 export(euler)
 export(expit)
 export(freeze)
@@ -46,30 +42,14 @@ export(logmeanexp)
 export(lookup)
 export(map)
 export(mcap)
-export(mvn.diag.rw)
-export(mvn.rw)
-export(mvn.rw.adaptive)
 export(mvn_diag_rw)
 export(mvn_rw)
 export(mvn_rw_adaptive)
 export(onestep)
 export(ou2)
 export(parameter_trans)
-export(periodic.bspline.basis)
 export(periodic_bspline_basis)
 export(pomp)
-export(pred.mean)
-export(pred.var)
-export(probe.acf)
-export(probe.ccf)
-export(probe.marginal)
-export(probe.mean)
-export(probe.median)
-export(probe.nlar)
-export(probe.period)
-export(probe.quantile)
-export(probe.sd)
-export(probe.var)
 export(probe_acf)
 export(probe_ccf)
 export(probe_marginal)
@@ -86,11 +66,9 @@ export(reulermultinom)
 export(rgammawn)
 export(ricker)
 export(runif_design)
-export(rw.sd)
 export(rw2)
 export(rw_sd)
 export(sannbox)
-export(saved.states)
 export(sir)
 export(sir2)
 export(slice_design)

R/mif2.R

@@ -22,7 +22,7 @@
 ##' @param Nmif The number of filtering iterations to perform.
 ##' @param rw.sd specification of the magnitude of the random-walk perturbations that will be applied to some or all model parameters.
 ##' Parameters that are to be estimated should have positive perturbations specified here.
-##' The specification is given using the \code{\link{rw.sd}} function, which creates a list of unevaluated expressions.
+##' The specification is given using the \code{\link{rw_sd}} function, which creates a list of unevaluated expressions.
 ##' The latter are evaluated in a context where the model time variable is defined (as \code{time}).
 ##' The expression \code{ivp(s)} can be used in this context as shorthand for \preformatted{ifelse(time==time[1],s,0).}
 ##' Likewise, \code{ivp(s,lag)} is equivalent to \preformatted{ifelse(time==time[lag],s,0).}
@@ -50,12 +50,12 @@
 ##' \item{\code{\link{logLik}}}{ returns the so-called \dfn{mif log likelihood} which is the log likelihood of the perturbed model, not of the focal model itself.
 ##' To obtain the latter, it is advisable to run several \code{\link{pfilter}} operations on the result of a \code{mif2} computatation.}
 ##' \item{\code{\link{coef}}}{ extracts the point estimate }
-##' \item{\code{\link{eff.sample.size}}}{ extracts the effective sample size of the final filtering iteration}
+##' \item{\code{\link{eff_sample_size}}}{ extracts the effective sample size of the final filtering iteration}
 ##' }
 ##' Various other methods can be applied, including all the methods applicable to a \code{\link[=pfilter]{pfilterd_pomp}} object and all other \pkg{pomp} estimation algorithms and diagnostic methods.
 ##'
 ##' @section Specifying the perturbations:
-##' The \code{rw.sd} function simply returns a list containing its arguments as unevaluated expressions.
+##' The \code{rw_sd} function simply returns a list containing its arguments as unevaluated expressions.
 ##' These are then evaluated in a context containing the model \code{time} variable.
 ##' This allows for easy specification of the structure of the perturbations that are to be applied.
 ##' For example,

R/pfilter.R

@@ -37,7 +37,7 @@
 ##' If \code{save.states="weighted"}, the state-vector for each weighted particle at each time is saved, along with the corresponding weight.
 ##' If \code{save.states="no"}, information on the latent states is not saved.
 ##' \code{"FALSE"} is a synonym for \code{"no"} and \code{"TRUE"} is a synonym for \code{"unweighted"}.
-##' To retrieve the saved states, applying \code{\link{saved.states}} to the result of the \code{pfilter} computation.
+##' To retrieve the saved states, applying \code{\link{saved_states}} to the result of the \code{pfilter} computation.
 ##'
 ##' @return
 ##' An object of class \sQuote{pfilterd_pomp}, which extends class \sQuote{pomp}.

inst/NEWS

@@ -1,5 +1,10 @@
 _N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_o_m_p'
 
+_C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _5._8._1:
+
+        • Functions with names that include dots (‘.’), which have been
+          defunct since version 4.7, have been expunged.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _5._7._1:
 
         • The ‘err()’ and ‘warn()’ C-level macros have been redefined

inst/NEWS.Rd

@@ -1,5 +1,10 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 5.8.1}{
+  \itemize{
+    \item Functions with names that include dots (\code{.}), which have been defunct since version 4.7, have been expunged.
+  }
+}
 \section{Changes in \pkg{pomp} version 5.7.1}{
   \itemize{
     \item The \code{err()} and \code{warn()} C-level macros have been redefined to forestall problems that would arise when these macros are included in C++ code under forthcoming versions of \R.