include references with spect_match

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 5.6.1.0
-Date: 2024-03-27
+Version: 5.7.0.1
+Date: 2024-03-30
 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/spect_match.R

@@ -31,6 +31,11 @@
 ##' When called, it will return the (optionally weighted) \eqn{L^2}{L2} distance between the data spectrum and simulated spectra.
 ##' It is a stateful function:
 ##' Each time it is called, it will remember the values of the parameters and the discrepancy measure.
+##' @references
+##'
+##' \Reuman2006
+##'
+##' \Reuman2008
 ##' @inheritSection pomp Note for Windows users
 ##' @inheritSection objfun Important Note
 ##' @inheritSection objfun Warning! Objective functions based on C snippets

revdep/Outputs/check_CollocInfer_stdout.txt

@@ -1,10 +1,10 @@
 * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/CollocInfer.Rcheck'
-* using R version 4.3.2 (2023-10-31)
+* using R version 4.3.3 (2024-02-29)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
     gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
     GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
-* running under: Ubuntu 22.04.3 LTS
+* running under: Ubuntu 22.04.4 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'CollocInfer/DESCRIPTION' ... OK
@@ -18,7 +18,7 @@
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
 * checking serialization versions ... OK
-* checking whether package 'CollocInfer' can be installed ... [16s/17s] OK
+* checking whether package 'CollocInfer' can be installed ... [18s/19s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -83,9 +83,9 @@ Variables with usage in documentation object 'FhNest' but not in code:
 * checking examples ... OK
 Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
-Profile   2.867 10.974   1.401
-FitMatch  6.497  6.088   1.252
-ParsMatch 6.370  4.570   1.106
+Profile   4.790 20.101   2.358
+FitMatch  6.521  5.813   1.299
+ParsMatch 5.609  3.346   0.865
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK

revdep/Outputs/check_DTAT_stdout.txt

@@ -1,10 +1,10 @@
 * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/DTAT.Rcheck'
-* using R version 4.3.2 (2023-10-31)
+* using R version 4.3.3 (2024-02-29)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
     gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
     GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
-* running under: Ubuntu 22.04.3 LTS
+* running under: Ubuntu 22.04.4 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'DTAT/DESCRIPTION' ... OK
@@ -19,7 +19,7 @@
 * checking for hidden files and directories ... OK
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
-* checking whether package 'DTAT' can be installed ... [15s/15s] OK
+* checking whether package 'DTAT' can be installed ... [16s/16s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -42,7 +42,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [24s/18s] NOTE
+* checking R code for possible problems ... [25s/19s] NOTE
 dose.survfit: local variable ‘S’ assigned but may not be used
 as_d3_data,DE : rel_dose: local variable ‘where_na’ assigned but may
   not be used
@@ -66,7 +66,7 @@ initialize,DE: local variable ‘Q1’ assigned but may not be used
 ** found \donttest examples: check also with --run-donttest
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in 'inst/doc' ... OK
-* checking re-building of vignette outputs ... [29s/27s] OK
+* checking re-building of vignette outputs ... [28s/26s] OK
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK

revdep/Outputs/check_circumstance_stderr.txt

@@ -1,10 +1,6 @@
-  Running ‘mif2.R’ [11s/13s]
-  Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ... OK
-  Running ‘pfilter.R’
-  Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ... OK
-  Running ‘plot_matrix.R’
-  Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ... OK
-  Running ‘pmcmc.R’ [13s/15s]
-  Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ... OK
-
+  Running ‘mif2.R’ [11s/12s]
+  Comparing ‘mif2.Rout’ to ‘mif2.Rout.save’ ...  Running ‘pfilter.R’
+  Comparing ‘pfilter.Rout’ to ‘pfilter.Rout.save’ ...  Running ‘plot_matrix.R’
+  Comparing ‘plot_matrix.Rout’ to ‘plot_matrix.Rout.save’ ...  Running ‘pmcmc.R’ [14s/14s]
+  Comparing ‘pmcmc.Rout’ to ‘pmcmc.Rout.save’ ...
 

revdep/Outputs/check_circumstance_stdout.txt

@@ -1,10 +1,10 @@
 * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/circumstance.Rcheck'
-* using R version 4.3.2 (2023-10-31)
+* using R version 4.3.3 (2024-02-29)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
     gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
     GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
-* running under: Ubuntu 22.04.3 LTS
+* running under: Ubuntu 22.04.4 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'circumstance/DESCRIPTION' ... OK
@@ -41,7 +41,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... OK
+* checking R code for possible problems ... [14s/11s] OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -55,11 +55,67 @@
 * checking examples ... OK
 Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
-pfilter 7.026  0.158   6.821
+pfilter 6.485  0.197   6.454
 ** found \donttest examples: check also with --run-donttest
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
- [34s/36s] OK
+9a10,17
+> Welcome to pomp!
+> 
+> As of version 4.6, no user-visible pomp function has a name that
+> includes a dot ('.'). Function names have been changed to replace the
+> dot with an underscore ('_'). For more information, see the pomp blog:
+> https://kingaa.github.io/pomp/blog.html.
+> 
+> 
+57,58c65
+< Removed 3 rows containing missing values or values outside the scale range
+< (`geom_line()`). 
+---
+> Removed 3 rows containing missing values (`geom_line()`). 
+88,89c95
+< Removed 3 rows containing missing values or values outside the scale range
+< (`geom_line()`). 
+---
+> Removed 3 rows containing missing values (`geom_line()`). 
+119,120c125
+< Removed 3 rows containing missing values or values outside the scale range
+< (`geom_line()`). 
+---
+> Removed 3 rows containing missing values (`geom_line()`). 
+138,139c143
+< Removed 3 rows containing missing values or values outside the scale range
+< (`geom_line()`). 
+---
+> Removed 3 rows containing missing values (`geom_line()`). 
+9a10,17
+> Welcome to pomp!
+> 
+> As of version 4.6, no user-visible pomp function has a name that
+> includes a dot ('.'). Function names have been changed to replace the
+> dot with an underscore ('_'). For more information, see the pomp blog:
+> https://kingaa.github.io/pomp/blog.html.
+> 
+> 
+17a18,25
+> Welcome to pomp!
+> 
+> As of version 4.6, no user-visible pomp function has a name that
+> includes a dot ('.'). Function names have been changed to replace the
+> dot with an underscore ('_'). For more information, see the pomp blog:
+> https://kingaa.github.io/pomp/blog.html.
+> 
+> 
+9a10,17
+> Welcome to pomp!
+> 
+> As of version 4.6, no user-visible pomp function has a name that
+> includes a dot ('.'). Function names have been changed to replace the
+> dot with an underscore ('_'). For more information, see the pomp blog:
+> https://kingaa.github.io/pomp/blog.html.
+> 
+> 
+ [34s/34s] OK
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK

revdep/Outputs/check_epimdr2_stdout.txt

@@ -1,10 +1,10 @@
 * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr2.Rcheck'
-* using R version 4.3.2 (2023-10-31)
+* using R version 4.3.3 (2024-02-29)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
     gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
     GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
-* running under: Ubuntu 22.04.3 LTS
+* running under: Ubuntu 22.04.4 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'epimdr2/DESCRIPTION' ... OK
@@ -18,7 +18,7 @@
 * checking for hidden files and directories ... OK
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
-* checking whether package 'epimdr2' can be installed ... [15s/15s] OK
+* checking whether package 'epimdr2' can be installed ... [17s/17s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -40,7 +40,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [22s/17s] NOTE
+* checking R code for possible problems ... [22s/15s] NOTE
 coyne: local variable ‘H1’ assigned but may not be used
 coyne: local variable ‘H2’ assigned but may not be used
 coyne: local variable ‘I’ assigned but may not be used
@@ -152,7 +152,7 @@ twostrain: local variable ‘res’ assigned but may not be used
 * checking data for non-ASCII characters ... OK
 * checking LazyData ... OK
 * checking data for ASCII and uncompressed saves ... OK
-* checking examples ... [15s/13s] OK
+* checking examples ... [13s/12s] OK
 ** found \donttest examples: check also with --run-donttest
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK

revdep/Outputs/check_epimdr_stdout.txt

@@ -1,10 +1,10 @@
 * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/epimdr.Rcheck'
-* using R version 4.3.2 (2023-10-31)
+* using R version 4.3.3 (2024-02-29)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
     gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
     GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
-* running under: Ubuntu 22.04.3 LTS
+* running under: Ubuntu 22.04.4 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'epimdr/DESCRIPTION' ... OK
@@ -19,7 +19,7 @@
 * checking for portable file names ... OK
 * checking for sufficient/correct file permissions ... OK
 * checking serialization versions ... OK
-* checking whether package 'epimdr' can be installed ... OK
+* checking whether package 'epimdr' can be installed ... [12s/10s] OK
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
@@ -41,7 +41,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [19s/13s] NOTE
+* checking R code for possible problems ... [18s/14s] NOTE
 chainSIR: local variable ‘I’ assigned but may not be used
 chainSIR: local variable ‘R’ assigned but may not be used
 chainSIR: local variable ‘S’ assigned but may not be used

revdep/Outputs/check_hte_stderr.txt

@@ -1,12 +1,12 @@
-  Running ‘fakery.R’ [17s/19s]
+  Running ‘fakery.R’ [14s/15s]
   Comparing ‘fakery.Rout’ to ‘fakery.Rout.save’ ... OK
   Running ‘filter.R’
   Comparing ‘filter.Rout’ to ‘filter.Rout.save’ ... OK
   Running ‘indep.R’
   Comparing ‘indep.Rout’ to ‘indep.Rout.save’ ... OK
   Running ‘stobfun.R’
   Comparing ‘stobfun.Rout’ to ‘stobfun.Rout.save’ ... OK
-  Running ‘transmiss.R’ [25s/24s]
+  Running ‘transmiss.R’ [21s/21s]
   Comparing ‘transmiss.Rout’ to ‘transmiss.Rout.save’ ... OK
 
 See

revdep/Outputs/check_hte_stdout.txt

@@ -1,15 +1,15 @@
 * using log directory '/home/kingaa/projects/Rpkg/pomp/revdep/hte.Rcheck'
-* using R version 4.3.2 (2023-10-31)
+* using R version 4.3.3 (2024-02-29)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * R was compiled by
     gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
     GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
-* running under: Ubuntu 22.04.3 LTS
+* running under: Ubuntu 22.04.4 LTS
 * using session charset: UTF-8
 * using option '--as-cran'
 * checking for file 'hte/DESCRIPTION' ... OK
 * checking extension type ... Package
-* this is package 'hte' version '0.0.15.0'
+* this is package 'hte' version '0.0.16.0'
 * package encoding: UTF-8
 * checking package namespace information ... OK
 * checking package dependencies ... OK
@@ -43,7 +43,7 @@
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... [18s/11s] NOTE
+* checking R code for possible problems ... [18s/12s] NOTE
 filterfun : fun: local variable ‘theta’ assigned but may not be used
 stobfun : ofun: local variable ‘theta’ assigned but may not be used
 * checking Rd files ... OK
@@ -64,15 +64,15 @@ stobfun : ofun: local variable ‘theta’ assigned but may not be used
 * checking compilation flags used ... OK
 * checking compiled code ... OK
 * checking installed files from 'inst/doc' ... OK
-* checking examples ... [94s/49s] OK
+* checking examples ... [96s/49s] OK
 Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
-fake_data        20.187 23.818  17.923
-simuldat         16.936 18.546  15.764
-bernoulli_filter  4.686  0.117   5.816
+fake_data        18.967 24.513  17.851
+simuldat         16.912 21.792  15.537
+bernoulli_filter  4.716  0.104   5.665
 * checking for unstated dependencies in 'tests' ... OK
 * checking tests ...
- [57s/53s] OK
+ [50s/48s] OK
 * checking PDF version of manual ... OK
 * checking HTML version of manual ... OK
 * checking for non-standard things in the check directory ... OK

revdep/Outputs/check_panelPomp_stderr.txt

@@ -2,7 +2,7 @@
   Comparing ‘_options.Rout’ to ‘_options.Rout.save’ ... OK
   Running ‘aaa.R’
   Comparing ‘aaa.Rout’ to ‘aaa.Rout.save’ ... OK
-  Running ‘contacts.R’ [14s/13s]
+  Running ‘contacts.R’ [12s/13s]
   Comparing ‘contacts.Rout’ to ‘contacts.Rout.save’ ...  Running ‘get_col_row.R’
   Comparing ‘get_col_row.Rout’ to ‘get_col_row.Rout.save’ ... OK
   Running ‘mif2.R’