alternative filter scheme for SEIRS

Author: kingaa

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.17.2.0
-Date: 2026-04-10
+Version: 0.18.0.0
+Date: 2026-05-10
 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("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))
 	  )
@@ -17,7 +17,6 @@ LazyData: true
 Contact: kingaa at umich dot edu
 Encoding: UTF-8
 Roxygen: list(roclets = c("collate", "namespace", "rd"))
-RoxygenNote: 7.3.3
 Collate: 
     'package.R'
     'geneal.R'
@@ -52,3 +51,4 @@ Collate:
     'twospecies_pomp.R'
     'twoundead.R'
     'yaml.R'
+Config/roxygen2/version: 8.0.0

inst/NEWS

@@ -1,5 +1,21 @@
 _N_e_w_s _f_o_r _p_a_c_k_a_g_e '_p_h_y_l_o_p_o_m_p'
 
+_C_h_a_n_g_e_s _i_n '_p_h_y_l_o_p_o_m_p' _v_e_r_s_i_o_n _0._1_8:
+
+        • The integration of the filter for the SEIRS model has
+          changed.
+
+        • ‘sir_pomp’, ‘seirs_pomp’, and ‘strains_pomp’ now expect
+          initial conditions expressed as fractions of a specified host
+          population size (‘pop’).
+
+        • When times or branch-lengths are converted to decimal
+          representation (e.g., by ‘newick()’ or ‘yaml()’), more care
+          is taken to preserve precision.
+
+        • The ‘curtail’ function now takes arguments ‘t0’ and ‘time’,
+          consistent with the usage in the rest of the package.
+
 _C_h_a_n_g_e_s _i_n '_p_h_y_l_o_p_o_m_p' _v_e_r_s_i_o_n _0._1_7:
 
      This release contains a relatively large refactorization of the
@@ -34,17 +50,6 @@ _C_h_a_n_g_e_s _i_n '_p_h_y_l_o_p_o_m_p' _v_e_r_s_i_o_n
         • The use of palettes in the plotting routines is now more
           consistent.
 
-        • The ‘curtail’ now takes arguments ‘t0’ and ‘time’, consistent
-          with the usage in the rest of the package.
-
-        • ‘sir_pomp’, ‘seirs_pomp’, and ‘strains_pomp’ now expect
-          initial conditions expressed as fractions of a specified host
-          population size (‘pop’).
-
-        • When times or branch-lengths are converted to decimal
-          representation (e.g., by ‘newick()’ or ‘yaml()’), more care
-          is taken to preserve precision.
-
 _C_h_a_n_g_e_s _i_n '_p_h_y_l_o_p_o_m_p' _v_e_r_s_i_o_n _0._1_6:
 
         • ‘gendat()’ now returns the deme for samples.

inst/NEWS.Rd

@@ -1,5 +1,13 @@
 \name{NEWS}
 \title{News for package `phylopomp'}
+\section{Changes in \pkg{phylopomp} version 0.18}{
+  \itemize{
+    \item The integration of the filter for the SEIRS model has changed.
+    \item \code{sir_pomp}, \code{seirs_pomp}, and \code{strains_pomp} now expect initial conditions expressed as fractions of a specified host population size (\code{pop}).
+    \item When times or branch-lengths are converted to decimal representation (e.g., by \code{newick()} or \code{yaml()}), more care is taken to preserve precision.
+    \item The \code{curtail} function now takes arguments \code{t0} and \code{time}, consistent with the usage in the rest of the package.
+  }
+}
 \section{Changes in \pkg{phylopomp} version 0.17}{
   This release contains a relatively large refactorization of the C++ library.
   \itemize{
@@ -16,9 +24,6 @@
     \item Internally, \code{phylopomp} now represents the demes more carefully.
     The deme-number 0 is reserved for the \sQuote{undeme}, i.e., nodes or branches with unspecified deme.
     \item The use of palettes in the plotting routines is now more consistent.
-    \item The \code{curtail} now takes arguments \code{t0} and \code{time}, consistent with the usage in the rest of the package.
-    \item \code{sir_pomp}, \code{seirs_pomp}, and \code{strains_pomp} now expect initial conditions expressed as fractions of a specified host population size (\code{pop}).
-    \item When times or branch-lengths are converted to decimal representation (e.g., by \code{newick()} or \code{yaml()}), more care is taken to preserve precision.
   }
 }
 \section{Changes in \pkg{phylopomp} version 0.16}{