Merge pull request #52 from jeswheel/master

panelPomp V1.2.0

.Rbuildignore

@@ -8,7 +8,6 @@ man/roxygen
 LICENSE\.md$
 README\.md$
 CRAN\.md$
-TODO\.md$
 ^\.gitignore$
 \.github
 ^\.travis\.yml$

.github/workflows/r-cmd-check.yml

@@ -25,7 +25,6 @@ jobs:
           - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,  r: 'release'}
           - {os: ubuntu-20.04,   r: '4.1.0'}
-          - {os: macOS-11,       r: 'release'}
           - {os: macOS-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
 
@@ -56,7 +55,7 @@ jobs:
       _R_CHECK_CODETOOLS_PROFILE_: "suppressLocalUnused=FALSE,suppressPartialMatchArgs=FALSE,suppressParamUnused=TRUE,suppressUndefined=FALSE"
 
     steps:
-      - uses: actions/checkout@v3.1.0
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -75,10 +74,10 @@ jobs:
             any::subplex
             any::nloptr
             kingaa/pomp
-          
+
       - uses: r-lib/actions/check-r-package@v2
 
-      - uses: actions/upload-artifact@v3.1.1
+      - uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.config.os }}-${{ matrix.config.r }}-results
           path: check

.github/workflows/render-website.yml

@@ -68,6 +68,7 @@ jobs:
             any::devtools
             any::bib2df
             any::tidyverse
+            any::bookdown
 
       - name: Install package from source
         run: |
@@ -84,6 +85,13 @@ jobs:
           R CMD Rdconv -t html inst/NEWS.Rd -o website/NEWS.html
           ed -s website/html/00Index.html < website/changes.ed
 
+      - name: Copy Vignettes and Other Files
+        run: |
+          cp -r vignettes website/
+          Rscript --vanilla website/rmd2qmd.R website/vignettes/getting-started
+          rm website/vignettes/getting-started.Rmd
+          tree website
+
       - name: Render and Publish
         uses: quarto-dev/quarto-actions/publish@v2
         with:

.gitignore

@@ -33,3 +33,5 @@ covr.rds
 website/docs
 website/html
 website/help
+inst/doc
+website/vignettes/*

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: panelPomp
 Type: Package
 Title: Inference for Panel Partially Observed Markov Processes
-Version: 1.1.0.2
+Version: 1.2.0
 Date: 2023-05-22
 Authors@R: c(person(given="Carles",family="Breto",role=c("aut","cre"),email="carles.breto@uv.es",comment=c(ORCID="0000-0003-4695-4902")),
 	person(given=c("Edward","L."),family="Ionides",role="aut",comment=c(ORCID="0000-0002-4190-0174")),
@@ -13,11 +13,12 @@ Depends:
     R(>= 4.1.0),
     pomp(>= 4.5.2)
 Imports:
+    lifecycle,
     methods
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 Collate: 
-    'package.R'
+    'panelPomp-package.R'
     'aaa.R'
     'contacts.R'
     'generics.R'
@@ -34,5 +35,12 @@ Collate:
     'panelGompertz.R'
     'panelGompertzLikelihood.R'
     'panelRandomWalk.R'
+    'panel_designs.R'
     'plot.R'
     'simulate.R'
+Roxygen: list(markdown = TRUE)
+Suggests: 
+    knitr,
+    rmarkdown,
+    bookdown 
+VignetteBuilder: knitr

NAMESPACE

@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+export("shared<-")
+export("specific<-")
 export(contacts)
 export(fromVectorPparams)
 export(get_col)
@@ -11,17 +13,23 @@ export(panelPomp)
 export(panelRandomWalk)
 export(panel_logmeanexp)
 export(pparams)
+export(runif_panel_design)
+export(shared)
+export(specific)
 export(toMatrixPparams)
 export(toVectorPparams)
+export(unitLogLik)
+export(unit_objects)
 export(unitlogLik)
-export(unitobjects)
 export(wQuotes)
 exportClasses(mif2d.ppomp)
 exportClasses(panelPomp)
 exportClasses(pfilterd.ppomp)
 exportMethods("[")
 exportMethods("[[")
 exportMethods("coef<-")
+exportMethods("shared<-")
+exportMethods("specific<-")
 exportMethods(coef)
 exportMethods(length)
 exportMethods(logLik)
@@ -31,11 +39,14 @@ exportMethods(pfilter)
 exportMethods(plot)
 exportMethods(pparams)
 exportMethods(print)
+exportMethods(shared)
 exportMethods(show)
 exportMethods(simulate)
+exportMethods(specific)
 exportMethods(traces)
+exportMethods(unitLogLik)
+exportMethods(unit_objects)
 exportMethods(unitlogLik)
-exportMethods(unitobjects)
 exportMethods(window)
 import(methods)
 import(pomp)

R/aaa.R

@@ -1,4 +1,4 @@
-#' @include package.R
+#' @include panelPomp-package.R
 NULL
 
 #' @title Interpret shortcuts for \code{sQuote()}s and \code{dQuote()}s in

R/generics.R

@@ -24,7 +24,7 @@ setGeneric(name = "pparams",
            def = function(object, ...) standardGeneric("pparams"))
 
 #' @title Extract units of a panel model
-#' @description \code{unitobjects()} is a generic function that extracts a list
+#' @description \code{unit_objects()} is a generic function that extracts a list
 #' of objects corresponding to units of panel objects returned by panel modeling
 #' functions.
 #' @param object an object for which extraction of panel units is meaningful.
@@ -39,26 +39,142 @@ setGeneric(name = "pparams",
 #' @seealso \link{panelPomp_methods}
 #' @author Carles \Breto
 #' @export
-setGeneric(name = "unitobjects",
-           def = function(object, ...) standardGeneric("unitobjects"))
+setGeneric(name = "unit_objects",
+           def = function(object, ...) standardGeneric("unit_objects"))
 
+#' @name unitLogLik
 #' @title Extract log likelihood of units of panel models
-#' @description \code{unitlogLik()} is a generic function that extracts the log
+#' @description \code{unitLogLik()} is a generic function that extracts the log
 #' likelihood for each unit of panel objects returned by panel modeling functions.
 #' While the \code{numeric} value with the log likelihood for the entire panel
 #' is useful and possible via S4 methods \code{logLik()}, the contributions to it
-#' by panel units can be implemented via \code{unitlogLik()}.
+#' by panel units can be implemented via \code{unitLogLik()}.
 #' @param object an object for which log likelihood values for units can be extracted.
 #' @param ... additional arguments.
 #' @details This is a generic function: methods can be defined for it.
 #' @return Log likelihood extracted for each unit of the panel model \code{object}.
 #'
-#' \unitlogLikReturn
+#' \unitLogLikReturn
 #' @example examples/pfrw.R
-#' @example examples/unitlogLik.R
+#' @example examples/unitLogLik.R
+#' @keywords internal
+#' @seealso \link{pfilter}
+#' @author Carles \Breto
+#' @export
+setGeneric(name = "unitLogLik",
+           def = function(object, ...) standardGeneric("unitLogLik"))
+
+
+#' @rdname unitlogLik-deprecated
+#' @name unitlogLik-deprecated
+#' @title (Deprecated) Extract log likelihood of units of panel models
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' In future versions, this generic is being replaced with [unitLogLik()].
+#'
+#' \code{unitlogLik()} is a generic function that extracts the log
+#' likelihood for each unit of panel objects returned by panel modeling functions.
+#' While the \code{numeric} value with the log likelihood for the entire panel
+#' is useful and possible via S4 methods \code{logLik()}, the contributions to it
+#' by panel units can be implemented via \code{unitlogLik()}.
+#' @param object an object for which log likelihood values for units can be extracted.
+#' @param ... additional arguments.
+#' @details This is a generic function: methods can be defined for it.
+#' @return Log likelihood extracted for each unit of the panel model \code{object}.
+#'
+#' When given objects of class \code{pfilterd.ppomp}, \code{unitloglik()} returns a \code{numeric} vector.
+#' @examples
+#' # filter, which generates log likelihoods
+#' pfrw <- pfilter(panelRandomWalk(),Np=10)
+#'
+#' # extract log likelihood for each panel unit
+#' unitlogLik(pfrw)
+#'
 #' @keywords internal
 #' @seealso \link{pfilter}
 #' @author Carles \Breto
+#' @aliases unitlogLik
 #' @export
 setGeneric(name = "unitlogLik",
            def = function(object, ...) standardGeneric("unitlogLik"))
+
+#' Extract unit-specific parameters from a panelPomp object
+#'
+#' This function is used to extract the unit-specific parameters from a
+#' panel pomp object.
+#'
+#' @param object an object that contains unit-specific parameters
+#' @param format character representing how the parameters should be returned
+#' @param ... additional arguments.
+#'
+#' @return a matrix or vector containing the unit-specific parameters
+#'
+#' @example examples/prw.R
+#' @example examples/get_specific.R
+#' @keywords internal
+#' @seealso \link{panelPomp_methods}
+#' @author Jesse Wheeler
+#' @export
+setGeneric(name = "specific",
+           def = function(object, ..., format = c('matrix', 'vector')) standardGeneric('specific')
+)
+
+#' Set unit-specific parameters of a panelPomp object
+#'
+#' This function is used to set the unit-specific parameters of a
+#' panel pomp object.
+#'
+#' @param object an object that contains unit-specific parameters.
+#' @param value a numeric matrix with column names matching the names of the
+#'    `unit_objects` slot, and row names matching the names of the unit-specific
+#'    parameters. Alternatively, this can be a named vector following the naming
+#'    convention `<parameter>[<unit_name>]`.
+#'
+#' @example examples/set_specific.R
+#' @keywords internal
+#' @seealso \link{panelPomp_methods}
+#' @author Jesse Wheeler
+#' @export
+setGeneric(name = "specific<-",
+           def = function(object, value) standardGeneric('specific<-')
+)
+
+#' Extract shared parameters from a panelPomp object
+#'
+#' This function is used to extract the shared parameters from a panelPomp
+#' object.
+#'
+#' @param object an object that contains shared parameters.
+#' @param ... additional arguments.
+#'
+#' @return vector containing the shared parameters
+#'
+#' @example examples/prw.R
+#' @example examples/get_shared.R
+#' @keywords internal
+#' @seealso \link{panelPomp_methods}
+#' @author Jesse Wheeler
+#' @export
+setGeneric(name = "shared",
+           def = function(object, ...) standardGeneric('shared')
+)
+
+#' Set shared parameters of a panelPomp object
+#'
+#' This function is used to set the shared parameters of a panel pomp object.
+#'
+#' @param object an object that contains shared parameters.
+#' @param value a named numeric vector containing the desired values of the
+#'    shared parameter vector.
+#'
+#' @example examples/prw.R
+#' @example examples/set_shared.R
+#' @keywords internal
+#' @seealso \link{panelPomp_methods}
+#' @author Jesse Wheeler
+#' @export
+setGeneric(name = "shared<-",
+           def = function(object, value) standardGeneric('shared<-')
+)
+

R/mif2.R

@@ -23,7 +23,7 @@ NULL
 #' @param specific.start matrix with row parameter names and column unit names;
 #' the starting guess of the specific parameters.
 #' @param start A named numeric vector of parameters at which to start the IF2 procedure.
-#' @param block A logical variable determining whther to carry out block
+#' @param block A logical variable determining whether to carry out block
 #' resampling of unit-specific parameters.
 #' @param rw.sd An unevaluated expression of the form \code{quote(rw.sd())} to
 #' be used for all panel units. If a \code{list} of such expressions of the
@@ -85,10 +85,10 @@ mif2.internal <- function (object, Nmif, start, Np, rw.sd, cooling.type,
   shnames <- names(start$shared)
   spnames <- rownames(start$specific)
 
-  if (!setequal(names(object@unit.objects),colnames(start$specific)))
+  if (!setequal(names(object@unit_objects),colnames(start$specific)))
     stop(ep,wQuotes("specific parameter column-names must match the names of the units"),
          call.=FALSE)
-  start$specific <- start$specific[,names(object@unit.objects),drop=FALSE]
+  start$specific <- start$specific[,names(object@unit_objects),drop=FALSE]
 
   ########################################################
   # Initialize objects
@@ -110,7 +110,7 @@ mif2.internal <- function (object, Nmif, start, Np, rw.sd, cooling.type,
     dimnames = list(
       variable = spnames,
       rep = NULL,
-      unit = names(unitobjects(object))
+      unit = names(unit_objects(object))
     )
   )
   # Initialize pconv.rec and pconv.rec.array
@@ -131,14 +131,14 @@ mif2.internal <- function (object, Nmif, start, Np, rw.sd, cooling.type,
       iteration = seq.int(.ndone, .ndone + Nmif),
       variable = c('unitLoglik',
         dimnames(start$specific)[[1]]),
-      unit = names(unitobjects(object))
+      unit = names(unit_objects(object))
     )
   )
   pconv.rec.array[1L, -1L, ] <- pparamArray[, 1L,]
   # Initialize output
   output <- vector(mode="list",length=U)
   # nameoutput
-  names(output) <- names(unitobjects(object))
+  names(output) <- names(unit_objects(object))
 
   ###########################################################
   # LOOP OVER MIF ITERATIONS AND PANEL UNITS
@@ -227,7 +227,7 @@ mif2.internal <- function (object, Nmif, start, Np, rw.sd, cooling.type,
     new(
       Class = "mif2d.ppomp",
       # panelPomp
-      unit.objects = output,
+      unit_objects = output,
       shared = pParams$shared,
       specific = pParams$specific,
       # pfilterd.ppomp