make additional arguments an error

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 5.11.1.0
-Date: 2024-12-07
+Version: 6.0.0.0
+Date: 2024-12-08
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]",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")),

R/pomp.R

@@ -477,16 +477,14 @@ pomp_internal <- function (
 
   added.userdata <- list(...)
   if (length(added.userdata)>0L) {
-    pWarn_("The provided ",
-      ngettext(length(added.userdata),"object","objects")," ",
+    pStop_("The ",
+      ngettext(length(added.userdata),"argument","arguments")," ",
       paste(sQuote(names(added.userdata)),collapse=","),
-      ngettext(length(added.userdata)," is"," are"),
-      " available for use by POMP basic components.\n",
-      "This option is deprecated: use ",sQuote("userdata"),
-      " to specify the list of such objects explicitly.\n",
-      "In a future release, this warning will become an error."
+      ngettext(length(added.userdata),"is","are"),
+      " not recognized.\nUse the ",sQuote("userdata"),
+      " argument to supply extra objects to basic model components.",
+      " See ",sQuote("?userdata"),"."
     )
-    .userdata[names(added.userdata)] <- added.userdata
   }
   .userdata[names(userdata)] <- userdata
 

inst/NEWS

@@ -1,5 +1,15 @@
 _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 _6._0._0:
+
+        • From version 5.8.4, the manner in which extra model elements
+          (‘userdata’) are supplied has changed.  As of that version,
+          use of the old method generated a warning.  As of this
+          version, an error will be generated.  To supply additional
+          elements (i.e., beyond parameters, latent-state variables,
+          observations, and covariates) to the basic model components,
+          provide them as a list via the ‘userdata’ argument.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _5._1_1._1:
 
         • A new addition to the C API allows one to easily compute the

inst/NEWS.Rd

@@ -1,5 +1,13 @@
 \name{NEWS}
 \title{News for package `pomp'}
+\section{Changes in \pkg{pomp} version 6.0.0}{
+  \itemize{
+    \item From version 5.8.4, the manner in which extra model elements (\code{userdata}) are supplied has changed.
+    As of that version, use of the old method generated a warning.
+    As of this version, an error will be generated.
+    To supply additional elements (i.e., beyond parameters, latent-state variables, observations, and covariates) to the basic model components, provide them as a list via the \code{userdata} argument.
+  }
+}
 \section{Changes in \pkg{pomp} version 5.11.1}{
   \itemize{
     \item A new addition to the C API allows one to easily compute the expectation of the Euler-multinomial.

tests/kalman.R

@@ -111,12 +111,12 @@ try(enkf(pf,Np=-10))
 try(enkf(pf,Np="10b"))
 try(enkf(pf,Np=100,emeasure=NULL))
 try(enkf(enkf,Np=100,vmeasure=NULL))
-try(enkf(enkf,C=matrix(1,2,4,dimnames=list(c("y2","y1"),NULL)),Np=100))
-try(enkf(enkf,C=matrix(1,3,4,dimnames=list(c("a","b","c"),NULL)),Np=100))
-try(enkf(enkf,R=matrix(1,1,1,dimnames=list(c("y1"),NULL)),Np=100))
-try(enkf(enkf,R=matrix(1,2,2,dimnames=list(c("y2","y1"),NULL)),Np=100))
-try(enkf(enkf,R=matrix(1,2,2,dimnames=list(c("a","b"),NULL)),Np=100))
-try(enkf(enkf,R=matrix(1,3,3,dimnames=list(c("a","b","c"),NULL)),Np=100))
+try(enkf(enkf,userdata=list(C=matrix(1,2,4,dimnames=list(c("y2","y1"),NULL))),Np=100))
+try(enkf(enkf,userdata=list(C=matrix(1,3,4,dimnames=list(c("a","b","c"),NULL))),Np=100))
+try(enkf(enkf,userdata=list(R=matrix(1,1,1,dimnames=list(c("y1"),NULL))),Np=100))
+try(enkf(enkf,userdata=list(R=matrix(1,2,2,dimnames=list(c("y2","y1"),NULL))),Np=100))
+try(enkf(enkf,userdata=list(R=matrix(1,2,2,dimnames=list(c("a","b"),NULL))),Np=100))
+try(enkf(enkf,userdata=list(R=matrix(1,3,3,dimnames=list(c("a","b","c"),NULL))),Np=100))
 enkf(enkf)
 enkf(enkf,Np=100)
 
@@ -125,12 +125,12 @@ try(eakf(enkf,Np=-10))
 try(eakf(enkf,Np="10b"))
 try(eakf(enkf,Np=100,emeasure=NULL))
 try(eakf(enkf,Np=100,vmeasure=NULL))
-try(eakf(enkf,C=matrix(1,2,4,dimnames=list(c("y2","y1"),NULL)),Np=100))
-try(eakf(enkf,C=matrix(1,3,4,dimnames=list(c("a","b","c"),NULL)),Np=100))
-try(eakf(enkf,R=matrix(1,1,1,dimnames=list(c("y1"),NULL)),Np=100))
-try(eakf(enkf,R=matrix(1,2,2,dimnames=list(c("y2","y1"),NULL)),Np=100))
-try(eakf(enkf,R=matrix(1,2,2,dimnames=list(c("a","b"),NULL)),Np=100))
-try(eakf(enkf,R=matrix(1,3,3,dimnames=list(c("a","b","c"),NULL)),Np=100))
+try(eakf(enkf,userdata=list(C=matrix(1,2,4,dimnames=list(c("y2","y1"),NULL))),Np=100))
+try(eakf(enkf,userdata=list(C=matrix(1,3,4,dimnames=list(c("a","b","c"),NULL))),Np=100))
+try(eakf(enkf,userdata=list(R=matrix(1,1,1,dimnames=list(c("y1"),NULL))),Np=100))
+try(eakf(enkf,userdata=list(R=matrix(1,2,2,dimnames=list(c("y2","y1"),NULL))),Np=100))
+try(eakf(enkf,userdata=list(R=matrix(1,2,2,dimnames=list(c("a","b"),NULL)),Np=100)))
+try(eakf(enkf,userdata=list(R=matrix(1,3,3,dimnames=list(c("a","b","c"),NULL))),Np=100))
 
 invisible(enkf(pf,Np=1000,params=as.list(coef(pf))))
 invisible(eakf(pf,Np=1000,params=as.list(coef(pf))))
@@ -161,11 +161,11 @@ eakf |>
 try({
   R <- matrix(c(1,0,1,0),2,2)
   rownames(R) <- rownames(C)
-  enkf(pf,Np=1000,R=R)
+  enkf(pf,Np=1000,userdata=list(R=R))
 })
 
 try({
-  eakf(pf,Np=1000,R=R)
+  eakf(pf,Np=1000,userdata=list(R=R))
 })
 
 try(enkf())

tests/kalman.Rout.save

@@ -140,42 +140,18 @@ In enkf_internal(data, Np = Np, ..., verbose = verbose) :
 Error : in 'enkf': 'emeasure' is a needed basic component.
 > try(enkf(enkf,Np=100,vmeasure=NULL))
 Error : in 'enkf': 'vmeasure' is a needed basic component.
-> try(enkf(enkf,C=matrix(1,2,4,dimnames=list(c("y2","y1"),NULL)),Np=100))
+> try(enkf(enkf,userdata=list(C=matrix(1,2,4,dimnames=list(c("y2","y1"),NULL))),Np=100))
 Error : in 'enkf': rownames of matrix returned by 'vmeasure' do not match those returned by 'emeasure'.
-In addition: Warning message:
-The provided object 'C' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> try(enkf(enkf,C=matrix(1,3,4,dimnames=list(c("a","b","c"),NULL)),Np=100))
+> try(enkf(enkf,userdata=list(C=matrix(1,3,4,dimnames=list(c("a","b","c"),NULL))),Np=100))
 Error : in 'enkf': number of observables returned by 'emeasure' does not match data.
-In addition: Warning message:
-The provided object 'C' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> try(enkf(enkf,R=matrix(1,1,1,dimnames=list(c("y1"),NULL)),Np=100))
+> try(enkf(enkf,userdata=list(R=matrix(1,1,1,dimnames=list(c("y1"),NULL))),Np=100))
 Error : in 'enkf': rownames of matrix returned by 'vmeasure' do not match those returned by 'emeasure'.
-In addition: Warning message:
-The provided object 'R' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> try(enkf(enkf,R=matrix(1,2,2,dimnames=list(c("y2","y1"),NULL)),Np=100))
+> try(enkf(enkf,userdata=list(R=matrix(1,2,2,dimnames=list(c("y2","y1"),NULL))),Np=100))
 Error : in 'enkf': rownames of matrix returned by 'vmeasure' do not match those returned by 'emeasure'.
-In addition: Warning message:
-The provided object 'R' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> try(enkf(enkf,R=matrix(1,2,2,dimnames=list(c("a","b"),NULL)),Np=100))
+> try(enkf(enkf,userdata=list(R=matrix(1,2,2,dimnames=list(c("a","b"),NULL))),Np=100))
 Error : in 'enkf': rownames of matrix returned by 'vmeasure' do not match those returned by 'emeasure'.
-In addition: Warning message:
-The provided object 'R' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> try(enkf(enkf,R=matrix(1,3,3,dimnames=list(c("a","b","c"),NULL)),Np=100))
+> try(enkf(enkf,userdata=list(R=matrix(1,3,3,dimnames=list(c("a","b","c"),NULL))),Np=100))
 Error : in 'enkf': rownames of matrix returned by 'vmeasure' do not match those returned by 'emeasure'.
-In addition: Warning message:
-The provided object 'R' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
 > enkf(enkf)
 <object of class 'kalmand_pomp'>
 > enkf(enkf,Np=100)
@@ -194,42 +170,18 @@ In eakf_internal(data, Np = Np, ..., verbose = verbose) :
 Error : in 'eakf': 'emeasure' is a needed basic component.
 > try(eakf(enkf,Np=100,vmeasure=NULL))
 Error : in 'eakf': 'vmeasure' is a needed basic component.
-> try(eakf(enkf,C=matrix(1,2,4,dimnames=list(c("y2","y1"),NULL)),Np=100))
+> try(eakf(enkf,userdata=list(C=matrix(1,2,4,dimnames=list(c("y2","y1"),NULL))),Np=100))
 Error : in 'eakf': rownames of matrix returned by 'vmeasure' do not match those returned by 'emeasure'.
-In addition: Warning message:
-The provided object 'C' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> try(eakf(enkf,C=matrix(1,3,4,dimnames=list(c("a","b","c"),NULL)),Np=100))
+> try(eakf(enkf,userdata=list(C=matrix(1,3,4,dimnames=list(c("a","b","c"),NULL))),Np=100))
 Error : in 'eakf': number of observables returned by 'emeasure' does not match data.
-In addition: Warning message:
-The provided object 'C' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> try(eakf(enkf,R=matrix(1,1,1,dimnames=list(c("y1"),NULL)),Np=100))
+> try(eakf(enkf,userdata=list(R=matrix(1,1,1,dimnames=list(c("y1"),NULL))),Np=100))
 Error : in 'eakf': rownames of matrix returned by 'vmeasure' do not match those returned by 'emeasure'.
-In addition: Warning message:
-The provided object 'R' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> try(eakf(enkf,R=matrix(1,2,2,dimnames=list(c("y2","y1"),NULL)),Np=100))
-Error : in 'eakf': rownames of matrix returned by 'vmeasure' do not match those returned by 'emeasure'.
-In addition: Warning message:
-The provided object 'R' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> try(eakf(enkf,R=matrix(1,2,2,dimnames=list(c("a","b"),NULL)),Np=100))
+> try(eakf(enkf,userdata=list(R=matrix(1,2,2,dimnames=list(c("y2","y1"),NULL))),Np=100))
 Error : in 'eakf': rownames of matrix returned by 'vmeasure' do not match those returned by 'emeasure'.
-In addition: Warning message:
-The provided object 'R' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> try(eakf(enkf,R=matrix(1,3,3,dimnames=list(c("a","b","c"),NULL)),Np=100))
+> try(eakf(enkf,userdata=list(R=matrix(1,2,2,dimnames=list(c("a","b"),NULL)),Np=100)))
+Error : in 'eakf': argument "Np" is missing, with no default
+> try(eakf(enkf,userdata=list(R=matrix(1,3,3,dimnames=list(c("a","b","c"),NULL))),Np=100))
 Error : in 'eakf': rownames of matrix returned by 'vmeasure' do not match those returned by 'emeasure'.
-In addition: Warning message:
-The provided object 'R' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
 > 
 > invisible(enkf(pf,Np=1000,params=as.list(coef(pf))))
 > invisible(eakf(pf,Np=1000,params=as.list(coef(pf))))
@@ -292,22 +244,14 @@ In a future release, this warning will become an error.
 > try({
 +   R <- matrix(c(1,0,1,0),2,2)
 +   rownames(R) <- rownames(C)
-+   enkf(pf,Np=1000,R=R)
++   enkf(pf,Np=1000,userdata=list(R=R))
 + })
 Error : in 'enkf': degenerate 'vmeasure': the leading minor of order 2 is not positive
-In addition: Warning message:
-The provided object 'R' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
 > 
 > try({
-+   eakf(pf,Np=1000,R=R)
++   eakf(pf,Np=1000,userdata=list(R=R))
 + })
 Error : in 'eakf': degenerate 'vmeasure': Lapack routine dgesv: system is exactly singular: U[2,2] = 0
-In addition: Warning message:
-The provided object 'R' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
 > 
 > try(enkf())
 Error : in 'enkf': 'data' is a required argument.

tests/mif2.R

@@ -85,9 +85,14 @@ try(mif2(po,Nmif=2,Np=100,rw.sd=rw_sd(sigma=0.01,X_0=ivp(0.01)),
   cooling.fraction.50=0.1,dmeasure=function(log,...)stop("blop")))
 try(mif2(po,Nmif=2,Np=100,rw.sd=rw_sd(sigma=0.01,X_0=ivp(0.01)),
   cooling.fraction.50=0.1,dmeasure=function(log,...)NA))
+try(
+  mif2(po,Nmif=2,Np=50,rw.sd=rw_sd(sigma=0.01),
+    cooling.type="hyper",cooling.fraction.50=0.1,
+    drpocess="oops",
+    dmeasure=function(log,...)0) -> mf3
+)
 mif2(po,Nmif=2,Np=50,rw.sd=rw_sd(sigma=0.01),
   cooling.type="hyper",cooling.fraction.50=0.1,
-  drpocess="oops",
   dmeasure=function(log,...)0) -> mf3
 try(mif2(po,Nmif=2,Np=50,rw.sd=rw_sd(sigma=0.01),cooling.fraction.50=0.1,dmeasure=NULL))
 try(mif2(po,Nmif=2,Np=50,rw.sd=rw_sd(sigma=0.01),cooling.fraction.50=0.1,rprocess=NULL))

tests/mif2.Rout.save

@@ -179,14 +179,17 @@ loglik:           NA
  sigma:    0.0996772
    tau:          0.1
    X_0:     0.990808
+> try(
++   mif2(po,Nmif=2,Np=50,rw.sd=rw_sd(sigma=0.01),
++     cooling.type="hyper",cooling.fraction.50=0.1,
++     drpocess="oops",
++     dmeasure=function(log,...)0) -> mf3
++ )
+Error : in 'mif2': The argument 'drpocess'is not recognized.
+Use the 'userdata' argument to supply extra objects to basic model components. See '?userdata'.
 > mif2(po,Nmif=2,Np=50,rw.sd=rw_sd(sigma=0.01),
 +   cooling.type="hyper",cooling.fraction.50=0.1,
-+   drpocess="oops",
 +   dmeasure=function(log,...)0) -> mf3
-Warning message:
-The provided object 'drpocess' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
 > try(mif2(po,Nmif=2,Np=50,rw.sd=rw_sd(sigma=0.01),cooling.fraction.50=0.1,dmeasure=NULL))
 Error : in 'mif2': 'rprocess', 'dmeasure' are needed basic components.
 > try(mif2(po,Nmif=2,Np=50,rw.sd=rw_sd(sigma=0.01),cooling.fraction.50=0.1,rprocess=NULL))

tests/pomp.R

@@ -24,9 +24,6 @@ try(data.frame(a=1:10,b=1:10) |> pomp(times=1,t0=11))
 try(data.frame(a=1:10,b=1:10) |> pomp(times="a",t0=11))
 try(data.frame(a=1:10,b=1:10) |> pomp(times="b",t0=NULL))
 try(data.frame(a=1:10,b=1:10) |> pomp(times="a",t0=NA))
-stopifnot(data.frame(a=1:10,b=1:10) |>
-    pomp(covar=covariate_table(c=0:10,d=0:10,times="c"),
-      covarnames="d",times="a",t0=0,bob=3) |> class() == "pomp")
 stopifnot(data.frame(a=1:10,b=1:10) |>
     pomp(covar=covariate_table(c=0:10,d=0:10,times="c"),
       covarnames="d",times="a",t0=0,userdata=list(bob=3)) |> class() == "pomp")

tests/pomp.Rout.save

@@ -65,13 +65,6 @@ Error : 't0' must be a single number not greater than 'times[1]'.
 Error : 't0' must be a single number not greater than 'times[1]'.
 > stopifnot(data.frame(a=1:10,b=1:10) |>
 +     pomp(covar=covariate_table(c=0:10,d=0:10,times="c"),
-+       covarnames="d",times="a",t0=0,bob=3) |> class() == "pomp")
-Warning message:
-The provided object 'bob' is available for use by POMP basic components.
-This option is deprecated: use 'userdata' to specify the list of such objects explicitly.
-In a future release, this warning will become an error. 
-> stopifnot(data.frame(a=1:10,b=1:10) |>
-+     pomp(covar=covariate_table(c=0:10,d=0:10,times="c"),
 +       covarnames="d",times="a",t0=0,userdata=list(bob=3)) |> class() == "pomp")
 > try(data.frame(a=1:10,b=1:10) |>
 +     pomp(covar=covariate_table(c=1:10,d=1:10,d=1:10,times="c"),

tests/spy.R

@@ -4,7 +4,7 @@ library(pomp)
 
 gompertz() -> po
 
-pomp(po,partrans=NULL,bob=3,
+pomp(po,partrans=NULL,userdata=list(bob=3),
   covar=covariate_table(a=0:20,b=0:20,times="a")) -> po1
 spy(po1)
 
@@ -29,7 +29,7 @@ try(spy(list()))
 pomp(
   data=NULL,
   t0=0,times=1:10,
-  x0=as.double(1),
+  userdata=list(x0=as.double(1)),
   params=c(x_0=1,a=22),
   rinit=Csnippet(r"{x = *get_userdata_double("x0");}"),
   statenames="x",
@@ -40,7 +40,7 @@ pomp(
 pomp(
   data=NULL,
   t0=0,times=1:10,
-  x0=as.double(1),
+  userdata=list(x0=as.double(1)),
   params=c(x_0=1,a=22),
   globals=Csnippet("static double X0;"),
   rinit=Csnippet(r"{x = X0;}"),