fix bug in 'filter_traj' etc.

Author: kingaa

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 5.2.3.2
-Date: 2023-06-19
+Version: 5.2.3.3
+Date: 2023-06-21
 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")),

R/filter_mean.R

@@ -53,15 +53,17 @@ setMethod(
   signature=signature(object="kalmand_pomp"),
   definition=function (object, vars, ...,
     format = c("array", "data.frame")) {
-    if (missing(vars)) vars <- rownames(object@filter.mean)
-    format <- match.arg(format)
-    if (format == "array") {
-      object@filter.mean[vars,,drop=FALSE]
+    if (missing(vars)) {
+      x <- object@filter.mean
     } else {
+      x <- object@filter.mean[vars,,drop=FALSE]
+    }
+    format <- match.arg(format)
+    if (format == "data.frame") {
       x <- melt(object@filter.mean[vars,,drop=FALSE])
       x$time <- time(object)[as.integer(x$time)]
-      x
     }
+    x
   }
 )
 
@@ -72,14 +74,16 @@ setMethod(
   signature=signature(object="pfilterd_pomp"),
   definition=function (object, vars, ...,
     format = c("array", "data.frame")) {
-    if (missing(vars)) vars <- rownames(object@filter.mean)
-    format <- match.arg(format)
-    if (format == "array") {
-      object@filter.mean[vars,,drop=FALSE]
+    if (missing(vars)) {
+      x <- object@filter.mean
     } else {
+      x <- object@filter.mean[vars,,drop=FALSE]
+    }
+    format <- match.arg(format)
+    if (format == "data.frame") {
       x <- melt(object@filter.mean[vars,,drop=FALSE])
       x$time <- time(object)[as.integer(x$time)]
-      x
     }
+    x
   }
 )

R/filter_traj.R

@@ -50,15 +50,17 @@ setMethod(
   signature=signature(object="pfilterd_pomp"),
   definition=function (object, vars, ...,
     format = c("array", "data.frame")) {
-    if (missing(vars)) vars <- rownames(object@filter.traj)
-    format <- match.arg(format)
-    if (format == "array") {
-      object@filter.traj[vars,,,drop=FALSE]
+    if (missing(vars)) {
+      x <- object@filter.traj
     } else {
-      x <- melt(object@filter.traj[vars,,,drop=FALSE])
+      x <- object@filter.traj[vars,,drop=FALSE]
+    }
+    format <- match.arg(format)
+    if (format == "data.frame") {
+      x <- melt(x)
       x$time <- time(object,t0=TRUE)[as.integer(x$time)]
-      x
     }
+    x
   }
 )
 

R/forecast.R

@@ -39,15 +39,17 @@ setMethod(
   signature=signature(object="kalmand_pomp"),
   definition=function (object, vars, ...,
     format = c("array", "data.frame")) {
-    if (missing(vars)) vars <- rownames(object@forecast)
-    format <- match.arg(format)
-    if (format == "array") {
-      object@forecast[vars,,drop=FALSE]
+    if (missing(vars)) {
+      x <- object@forecast
     } else {
+      x <- object@forecast[vars,,drop=FALSE]
+    }
+    format <- match.arg(format)
+    if (format == "data.frame") {
       x <- melt(object@forecast[vars,,drop=FALSE])
       x$time <- time(object)[as.integer(x$time)]
-      x
     }
+    x
   }
 )
 

R/pred_mean.R

@@ -48,15 +48,17 @@ setMethod(
   signature=signature(object="kalmand_pomp"),
   definition=function (object, vars, ...,
     format = c("array", "data.frame")) {
-    if (missing(vars)) vars <- rownames(object@pred.mean)
-    format <- match.arg(format)
-    if (format == "array") {
-      object@pred.mean[vars,,drop=FALSE]
+    if (missing(vars)) {
+      x <- object@pred.mean
     } else {
+      x <- object@pred.mean[vars,,drop=FALSE]
+    }
+    format <- match.arg(format)
+    if (format == "data.frame") {
       x <- melt(object@pred.mean[vars,,drop=FALSE])
       x$time <- time(object)[as.integer(x$time)]
-      x
     }
+    x
   }
 )
 
@@ -67,14 +69,16 @@ setMethod(
   signature=signature(object="pfilterd_pomp"),
   definition=function (object, vars, ...,
     format = c("array", "data.frame")) {
-    if (missing(vars)) vars <- rownames(object@pred.mean)
-    format <- match.arg(format)
-    if (format == "array") {
-      object@pred.mean[vars,,drop=FALSE]
+    if (missing(vars)) {
+      x <- object@pred.mean
     } else {
+      x <- object@pred.mean[vars,,drop=FALSE]
+    }
+    format <- match.arg(format)
+    if (format == "data.frame") {
       x <- melt(object@pred.mean[vars,,drop=FALSE])
       x$time <- time(object)[as.integer(x$time)]
-      x
     }
+    x
   }
 )

R/pred_var.R

@@ -48,14 +48,16 @@ setMethod(
   signature=signature(object="pfilterd_pomp"),
   definition=function (object, vars, ...,
     format = c("array", "data.frame")) {
-    if (missing(vars)) vars <- rownames(object@pred.var)
-    format <- match.arg(format)
-    if (format == "array") {
-      object@pred.var[vars,,drop=FALSE]
+    if (missing(vars)) {
+      x <- object@pred.var
     } else {
+      x <- object@pred.var[vars,,drop=FALSE]
+    }
+    format <- match.arg(format)
+    if (format == "data.frame") {
       x <- melt(object@pred.var[vars,,drop=FALSE])
       x$time <- time(object)[as.integer(x$time)]
-      x
     }
+    x
   }
 )

inst/NEWS

@@ -5,6 +5,9 @@ _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _5._2._3:
         • The manual pages have been reorganized, with improved
           cross-linking.
 
+        • A bug in ‘filter_traj’ etc. arising when not all state
+          variables have names was fixed.
+
 _C_h_a_n_g_e_s _i_n '_p_o_m_p' _v_e_r_s_i_o_n _5._2._2:
 
         • This version adds the new basic component ‘dinit’ for

inst/NEWS.Rd

@@ -3,6 +3,7 @@
 \section{Changes in \pkg{pomp} version 5.2.3}{
   \itemize{
     \item The manual pages have been reorganized, with improved cross-linking.
+    \item A bug in \code{filter_traj} etc. arising when not all state variables have names was fixed.
   }
 }
 \section{Changes in \pkg{pomp} version 5.2.2}{