enforce named arguments

kingaa · Dec 9, 2024 · 2a13c1b · 2a13c1b
1 parent 9051136
commit 2a13c1b
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Showing 48 changed files with 713 additions and 351 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 6.0.0.0
+Version: 6.0.1.0
 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"))	,

diff --git a/R/abc.R b/R/abc.R
@@ -112,15 +112,19 @@ setMethod(
 setMethod(
   "abc",
   signature=signature(data="data.frame"),
-  definition=function (data,
+  definition=function (
+    data,
+    ...,
     Nabc = 1, proposal, scale, epsilon,
     probes,
     params, rinit, rprocess, rmeasure, dprior,
-    ..., verbose = getOption("verbose", FALSE)) {
+    verbose = getOption("verbose", FALSE)
+  ) {
 
     tryCatch(
       abc_internal(
         data,
+        ...,
         Nabc=Nabc,
         proposal=proposal,
         scale=scale,
@@ -131,7 +135,6 @@ setMethod(
         rprocess=rprocess,
         rmeasure=rmeasure,
         dprior=dprior,
-        ...,
         verbose=verbose
       ),
       error = function (e) pStop(who="abc",conditionMessage(e))
@@ -145,20 +148,23 @@ setMethod(
 setMethod(
   "abc",
   signature=signature(data="pomp"),
-  definition=function (data,
+  definition=function (
+    data,
+    ...,
     Nabc = 1, proposal, scale, epsilon,
     probes,
-    ..., verbose = getOption("verbose", FALSE)) {
+    verbose = getOption("verbose", FALSE)
+  ) {
 
     tryCatch(
       abc_internal(
         data,
+        ...,
         Nabc=Nabc,
         proposal=proposal,
         scale=scale,
         epsilon=epsilon,
         probes=probes,
-        ...,
         verbose=verbose
       ),
       error = function (e) pStop(who="abc",conditionMessage(e))
@@ -172,15 +178,19 @@ setMethod(
 setMethod(
   "abc",
   signature=signature(data="probed_pomp"),
-  definition=function (data, probes, ...,
-    verbose = getOption("verbose", FALSE)) {
+  definition=function (
+    data,
+    ...,
+    probes,
+    verbose = getOption("verbose", FALSE)
+  ) {
 
     if (missing(probes)) probes <- data@probes
 
     abc(
       as(data,"pomp"),
-      probes=probes,
       ...,
+      probes=probes,
       verbose=verbose
     )
 
@@ -192,10 +202,13 @@ setMethod(
 setMethod(
   "abc",
   signature=signature(data="abcd_pomp"),
-  definition=function (data,
+  definition=function (
+    data,
+    ...,
     Nabc, proposal, scale, epsilon,
     probes,
-    ..., verbose = getOption("verbose", FALSE)) {
+    verbose = getOption("verbose", FALSE)
+  ) {
 
     if (missing(Nabc)) Nabc <- data@Nabc
     if (missing(proposal)) proposal <- data@proposal
@@ -205,12 +218,12 @@ setMethod(
 
     abc(
       as(data,"pomp"),
+      ...,
       Nabc=Nabc,
       proposal=proposal,
       scale=scale,
       epsilon=epsilon,
       probes=probes,
-      ...,
       verbose=verbose
     )
 
@@ -223,12 +236,16 @@ setMethod(
 setMethod(
   "continue",
   signature=signature(object="abcd_pomp"),
-  definition=function (object, Nabc = 1, ...) {
+  definition=function (
+    object,
+    ...,
+    Nabc = 1
+  ) {
 
     ndone <- object@Nabc
     accepts <- object@accepts
 
-    obj <- abc(object,Nabc=Nabc,.ndone=ndone,.accepts=accepts,...)
+    obj <- abc(object,...,Nabc=Nabc,.ndone=ndone,.accepts=accepts)
 
     obj@traces <- rbind(
       object@traces[,colnames(obj@traces)],
@@ -242,11 +259,13 @@ setMethod(
   }
 )
 
-abc_internal <- function (object,
-  Nabc, proposal, scale, epsilon, probes,
+abc_internal <- function (
+  object,
   ...,
+  Nabc, proposal, scale, epsilon, probes,
   verbose,
-  .ndone = 0L, .accepts = 0L, .gnsi = TRUE) {
+  .ndone = 0L, .accepts = 0L, .gnsi = TRUE
+) {
 
   verbose <- as.logical(verbose)
 

diff --git a/R/bsmc2.R b/R/bsmc2.R
@@ -88,14 +88,18 @@ setMethod(
 setMethod(
   "bsmc2",
   signature=signature(data="data.frame"),
-  definition = function (data,
+  definition = function (
+    data,
+    ...,
     Np, smooth = 0.1,
     params, rprior, rinit, rprocess, dmeasure, partrans,
-    ..., verbose = getOption("verbose", FALSE)) {
+    verbose = getOption("verbose", FALSE)
+  ) {
 
     tryCatch(
       bsmc2_internal(
         data,
+        ...,
         Np=Np,
         smooth=smooth,
         params=params,
@@ -104,7 +108,6 @@ setMethod(
         rprocess=rprocess,
         dmeasure=dmeasure,
         partrans=partrans,
-        ...,
         verbose=verbose
       ),
       error = function (e) pStop(who="bsmc2",conditionMessage(e))
@@ -118,16 +121,19 @@ setMethod(
 setMethod(
   "bsmc2",
   signature=signature(data="pomp"),
-  definition = function (data,
+  definition = function (
+    data,
+    ...,
     Np, smooth = 0.1,
-    ..., verbose = getOption("verbose", FALSE)) {
+    verbose = getOption("verbose", FALSE)
+  ) {
 
     tryCatch(
       bsmc2_internal(
         data,
+        ...,
         Np=Np,
         smooth=smooth,
-        ...,
         verbose=verbose
       ),
       error = function (e) pStop(who="bsmc2",conditionMessage(e))
@@ -158,7 +164,12 @@ setMethod(
   }
 )
 
-bsmc2_internal <- function (object, Np, smooth, ..., verbose, .gnsi = TRUE) {
+bsmc2_internal <- function (
+  object,
+  ...,
+  Np, smooth,
+  verbose, .gnsi = TRUE
+) {
 
   verbose <- as.logical(verbose)
 

diff --git a/R/kalman.R b/R/kalman.R
@@ -89,20 +89,24 @@ setMethod(
 setMethod(
   "enkf",
   signature=signature(data="data.frame"),
-  function (data, Np,
+  function (
+    data,
+    ...,
+    Np,
     params, rinit, rprocess, emeasure, vmeasure,
-    ..., verbose = getOption("verbose", FALSE)) {
+    verbose = getOption("verbose", FALSE)
+  ) {
 
     tryCatch(
       enkf_internal(
         data,
+        ...,
         Np=Np,
         params=params,
         rinit=rinit,
         rprocess=rprocess,
         emeasure=emeasure,
         vmeasure=vmeasure,
-        ...,
         verbose=verbose
       ),
       error = function (e) pStop(who="enkf",conditionMessage(e))
@@ -116,14 +120,18 @@ setMethod(
 setMethod(
   "enkf",
   signature=signature(data="pomp"),
-  function (data, Np,
-    ..., verbose = getOption("verbose", FALSE)) {
+  function (
+    data,
+    ...,
+    Np,
+    verbose = getOption("verbose", FALSE)
+  ) {
 
     tryCatch(
       enkf_internal(
         data,
-        Np=Np,
         ...,
+        Np=Np,
         verbose=verbose
       ),
       error = function (e) pStop(who="enkf",conditionMessage(e))
@@ -137,14 +145,18 @@ setMethod(
 setMethod(
   "enkf",
   signature=signature(data="kalmand_pomp"),
-  function (data, Np,
-    ..., verbose = getOption("verbose", FALSE)) {
+  function (
+    data,
+    ...,
+    Np,
+    verbose = getOption("verbose", FALSE)
+  ) {
     if (missing(Np)) Np <- data@Np
     tryCatch(
       enkf_internal(
         as(data,"pomp"),
-        Np=Np,
         ...,
+        Np=Np,
         verbose=verbose
       ),
       error = function (e) pStop(who="enkf",conditionMessage(e))
@@ -167,7 +179,12 @@ setMethod(
 ## Updated ensemble: $X^u_{t}=X_t + K_t\,(O_t - Y_t)$
 ## Filter mean: $m_t=\langle X^u_t \rangle = \frac{1}{q} \sum\limits_{i=1}^q x^{u_i}_t$
 
-enkf_internal <- function (object, Np, ..., verbose) {
+enkf_internal <- function (
+  object,
+  ...,
+  Np,
+  verbose
+) {
 
   verbose <- as.logical(verbose)
 
@@ -306,20 +323,24 @@ setMethod(
 setMethod(
   "eakf",
   signature=signature(data="data.frame"),
-  function (data,
-    Np, params, rinit, rprocess, emeasure, vmeasure,
-    ...,verbose = getOption("verbose", FALSE)) {
+  function (
+    data,
+    ...,
+    Np,
+    params, rinit, rprocess, emeasure, vmeasure,
+    verbose = getOption("verbose", FALSE)
+  ) {
 
     tryCatch(
       eakf_internal(
         data,
+        ...,
         Np=Np,
         params=params,
         rinit=rinit,
         rprocess=rprocess,
         emeasure=emeasure,
         vmeasure=vmeasure,
-        ...,
         verbose=verbose
       ),
       error = function (e) pStop(who="eakf",conditionMessage(e))
@@ -333,14 +354,18 @@ setMethod(
 setMethod(
   "eakf",
   signature=signature(data="pomp"),
-  function (data,
-    Np, ..., verbose = getOption("verbose", FALSE)) {
+  function (
+    data,
+    ...,
+    Np,
+    verbose = getOption("verbose", FALSE)
+  ) {
 
     tryCatch(
       eakf_internal(
         data,
-        Np=Np,
         ...,
+        Np=Np,
         verbose=verbose
       ),
       error = function (e) pStop(who="eakf",conditionMessage(e))
@@ -361,7 +386,12 @@ setMethod(
 ## Filter mean: $m_t=M_t+K_t\,(y_t-C\,M_t)$
 ## Updated ensemble: $x_{t}=B\,(X_t-M_t\,\mathbb{1})+m_t\,\mathbb{1}$
 
-eakf_internal <- function (object, Np, ..., verbose) {
+eakf_internal <- function (
+  object,
+  ...,
+  Np,
+  verbose
+) {
 
   verbose <- as.logical(verbose)
 

diff --git a/R/kf.R b/R/kf.R
@@ -63,7 +63,8 @@
 ##
 ##' @export
 kalmanFilter <- function (
-  object, X0 = rinit(object),
+  object,
+  X0 = rinit(object),
   A, Q, C, R, tol = 1e-6
 ) {