version 1.19

cran · Dec 13, 2018 · 0aec292 · 0aec292
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical Inference for Partially Observed Markov Processes
-Version: 1.18
-Date: 2018-07-09
+Version: 1.19
+Date: 2018-12-13
 Authors@R: c(person(given=c("Aaron","A."),family="King",
 		role=c("aut","cre"),email="kingaa@umich.edu"),
 	  person(given=c("Edward","L."),family="Ionides",role=c("aut")),
@@ -21,7 +21,7 @@ Authors@R: c(person(given=c("Aaron","A."),family="King",
 	  )
 URL: https://kingaa.github.io/pomp/
 Description: Tools for working with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models).  The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods.  It is also a versatile platform for implementation of inference methods for general POMP models.
-Depends: R(>= 3.1.2), methods
+Depends: R(>= 3.4.0), methods
 Imports: stats, graphics, digest, mvtnorm, deSolve, coda, subplex,
         nloptr
 Suggests: magrittr, plyr, reshape2, ggplot2, knitr
@@ -32,19 +32,21 @@ LazyData: true
 Contact: kingaa at umich dot edu
 BugReports: https://github.com/kingaa/pomp/issues/
 Collate: aaa.R authors.R bake.R generics.R eulermultinom.R csnippet.R
-        safecall.R pomp_fun.R plugins.R builder.R parmat.R logmeanexp.R
-        slice_design.R profile_design.R sobol.R bsplines.R sannbox.R
-        pomp_class.R load.R pomp.R pomp_methods.R rmeasure_pomp.R
-        rprocess_pomp.R initstate_pomp.R dmeasure_pomp.R
-        dprocess_pomp.R skeleton_pomp.R dprior_pomp.R rprior_pomp.R
-        simulate_pomp.R trajectory_pomp.R plot_pomp.R pfilter.R
-        pfilter_methods.R minim.R traj_match.R bsmc.R bsmc2.R kalman.R
-        kalman_methods.R mif.R mif_methods.R mif2.R mif2_methods.R
-        proposals.R pmcmc.R pmcmc_methods.R nlf_funcs.R nlf_guts.R
-        nlf_objfun.R nlf.R probe.R probe_match.R basic_probes.R spect.R
-        spect_match.R abc.R abc_methods.R covmat.R example.R
+        safecall.R pomp_fun.R plugins.R templates.R builder.R parmat.R
+        logmeanexp.R slice_design.R profile_design.R sobol.R bsplines.R
+        sannbox.R pomp_class.R load.R pomp.R pomp_methods.R
+        rmeasure_pomp.R rprocess_pomp.R initstate_pomp.R
+        dmeasure_pomp.R dprocess_pomp.R skeleton_pomp.R dprior_pomp.R
+        rprior_pomp.R simulate_pomp.R trajectory_pomp.R plot_pomp.R
+        pfilter.R pfilter_methods.R minim.R traj_match.R bsmc.R bsmc2.R
+        kalman.R kalman_methods.R mif.R mif_methods.R mif2.R
+        mif2_methods.R proposals.R pmcmc.R pmcmc_methods.R nlf_funcs.R
+        nlf_guts.R nlf_objfun.R nlf.R probe.R probe_match.R
+        basic_probes.R spect.R spect_match.R abc.R abc_methods.R
+        covmat.R example.R show.R
+RoxygenNote: 6.1.0
 NeedsCompilation: yes
-Packaged: 2018-07-09 14:56:52 UTC; kingaa
+Packaged: 2018-12-13 22:55:05 UTC; kingaa
 Author: Aaron A. King [aut, cre],
   Edward L. Ionides [aut],
   Carles Breto [aut],
@@ -61,4 +63,4 @@ Author: Aaron A. King [aut, cre],
   Eamon O'Dea [ctb]
 Maintainer: Aaron A. King <kingaa@umich.edu>
 Repository: CRAN
-Date/Publication: 2018-07-09 18:20:03 UTC
+Date/Publication: 2018-12-13 23:10:13 UTC
diff --git a/MD5 b/MD5
@@ -1,89 +1,93 @@
-ab6ace3a817dcafb4801db003b56b1ec *DESCRIPTION
-536699c34e2972a0d2b25ad3b90d7992 *NAMESPACE
-7d8ac54ea547777f454ffca21189460f *R/aaa.R
-6bfd68ee84374f95813e1d82960509cf *R/abc.R
+bf905d38891390a61517f599de7f074d *DESCRIPTION
+08aae488544578871bc16e3836fd428f *NAMESPACE
+3ba330bf77b6b2672c7255706e7e2665 *R/aaa.R
+e86f1da05a6b89ce91f34228774e3682 *R/abc.R
 12a580e0fa06f33454bc86179cfc35af *R/abc_methods.R
 84a26c9552920e388f398b2cb0e9e700 *R/authors.R
 a5113685b1309724923fdaa4395a62e2 *R/bake.R
 75f28997fddc110c5a92a84dbea23c69 *R/basic_probes.R
-13be453291e459ba97a6733bdf5c862f *R/bsmc.R
+331d1fdf61cdece9dac9cb8afa3415b0 *R/bsmc.R
 4aef35d79f42358d8bfa5536d9553ead *R/bsmc2.R
 ff92e2637405b8d01b919bb405c5c40d *R/bsplines.R
-009d15b9b86483987813eee4c5efb433 *R/builder.R
+bd334bc59a12a6fcd4990af00357e3af *R/builder.R
 4bc24391f645b1932d8b06db7699d7a5 *R/covmat.R
 5f66458a356676c2af6a2aa0ff1b8beb *R/csnippet.R
 da8b00318efabc8fe4ed6391dedcfcff *R/dmeasure_pomp.R
 e0eca97daed45a7027cb91e495af6312 *R/dprior_pomp.R
-89739ec4b6afd0385644dd6459ed459f *R/dprocess_pomp.R
+b66506b34ff8695ac9066f2e363f0640 *R/dprocess_pomp.R
 5df5e2921aefb89e06c32a201b70dddb *R/eulermultinom.R
 e557deae938c8447956eb53a4e23b332 *R/example.R
-e6e808e02df8ebc501ff047093871634 *R/generics.R
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 5f4b153993a048fe20345d499640ee5a *R/initstate_pomp.R
 5be6c22cc36d5eb112effb8858bfb53b *R/kalman.R
 b04512d656b21d8e5a39516ca974b2dd *R/kalman_methods.R
-9f0997ddf85ea2653a6fd2d6b93ff7cb *R/load.R
+f588b9074a27a1c252e4ea431a8db681 *R/load.R
 9d02dec82f3bb7ac32dfba0bd5643e0c *R/logmeanexp.R
-52fa81aca56347a7a989e3778f4ac1a6 *R/mif.R
-80a4bdae7a08ee84e979e8b68564e5e6 *R/mif2.R
+da05bf130f3e467a97e614b9a0ce4f80 *R/mif.R
+8631f7457d77817e5e4a9c63fd362077 *R/mif2.R
 a1e892ea8dafe64d087fab8df5a9d47f *R/mif2_methods.R
 c58a68e0707a575eda5687917bd501c0 *R/mif_methods.R
 0b95486f66e863471ce9a1dbea92c080 *R/minim.R
 6ef56f949fe6b701fc4b822aca84fe16 *R/nlf.R
 e04a51fbbe63656357a31f63615b9480 *R/nlf_funcs.R
 e48c244d2bbd6ec5a4b9cc604f393d02 *R/nlf_guts.R
-722da4768979a0e7a7fe9c5864a94a5c *R/nlf_objfun.R
+25ac8e887baddf2d7c94bcba398c6378 *R/nlf_objfun.R
 f6a4731c9922c175f79d3302b6a47aaa *R/parmat.R
-f13ac4c0dd7e627cda86b0fcbc337a22 *R/pfilter.R
+9534473f5f19ec902d825d0b16c3c3e9 *R/pfilter.R
 2c425b2f48f1ada0c84b6a8e950486e2 *R/pfilter_methods.R
 7bd1c22460fa623c2779f47ca2d23714 *R/plot_pomp.R
-569b1586d88184de4d17fe0a67c8c052 *R/plugins.R
-7dd6cf7205a32c8dae9709a9d3b3a942 *R/pmcmc.R
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 388ec16e3ffc336aab6e23301e76ee17 *R/pmcmc_methods.R
-56c2c050dc2fa40e1c1fc99d2c6c2f2a *R/pomp.R
-fd9d3138864b848dc07ce0b4453f612c *R/pomp_class.R
-5643f6f8d7f43a36d8108e7af03bea0b *R/pomp_fun.R
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-b7ec130166b8bd9ed98efbe48265f71d *R/probe.R
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 473707deff50cf6ba948620dcfea628e *R/profile_design.R
 54ee5ac2ac3186ae4b504e72eacaec04 *R/proposals.R
 d6fc5ce9a73ca8b23f4e9b1d334a90a5 *R/rmeasure_pomp.R
 4422f25282c7d86931dd5192315eb196 *R/rprior_pomp.R
-de09d8d6782aaba95383c82ff3169ccb *R/rprocess_pomp.R
+4a2aaa99d2fa255c9c3d11039fc06827 *R/rprocess_pomp.R
 8adbdd40cd86249185e56fcb9eb8315e *R/safecall.R
-e10bd2e7489b4061809276ff5d62b6c9 *R/sannbox.R
-9dee8f52fe224b5558891a4b3dbf6242 *R/simulate_pomp.R
+a369cddbbd6f073961b710a214404c79 *R/sannbox.R
+266f3b1173e7ff242fc4e7d2adbb56bc *R/show.R
+41c987db3d0f04470b1b7ac96fad73b3 *R/simulate_pomp.R
 6705920fb9d53657ec787de781f6a831 *R/skeleton_pomp.R
 7fee39340bacf0e24bdd06708021c68b *R/slice_design.R
 08b59d1f948099d1f49408b978fd4ac4 *R/sobol.R
-3cab0c8be5b14ad16189892d1591a8a0 *R/spect.R
+0f3f20b931402cb14a6a4dea8d672194 *R/spect.R
 51c2f65ed8ae4da74574185adb21ee31 *R/spect_match.R
+2f37dd1477380c6494cc2b9aafea9e80 *R/templates.R
 5bc3bc0d76399d817ceddcc4b41c64cd *R/traj_match.R
-de9e04a0061311ef787f1d9bd5fe0e47 *R/trajectory_pomp.R
-3435872604613edc818ac6fd7ffba333 *build/partial.rdb
+a9e170b930acfc95f57b16fb4881e224 *R/trajectory_pomp.R
+28b9ca03de376997103817e44dde53d9 *build/partial.rdb
 9adea5ed10aa288f9728826f172ccf23 *data/LondonYorke.rda
 345f7c1351355deb8cf5665b841f61b2 *data/ewcitmeas.rda
 0f0baf1144f221a53bf591c354993b78 *data/ewmeas.rda
 21934c68ab97747102fe8c6c5c6d0644 *demo/00Index
 17a8e8d0c17c5b2404968b3e697b0378 *demo/gompertz.R
-c63ec645a0dc5f8712fbfe01084ad1cb *demo/logistic.R
-0ae5f93beee0f68eb2a3ccbea82649b7 *demo/rw2.R
+c6b490bc7211bdb8eb8e02356df23cb5 *demo/logistic.R
+49fd37d5cb6859a8d72d4ed5d2cb3fd5 *demo/rw2.R
 806e8c68983d666a2aa362a1fd7fcf14 *demo/sir.R
 143111e3cd7a6bfc211dd50cb5cceec2 *inst/CITATION
 d32239bcb673463ab874e80d47fae504 *inst/GPL
-f82cc8b1f82883efe5767da7632f66d3 *inst/NEWS
-006c6e7d14677e0317c7428dbc1f20eb *inst/NEWS.Rd
-c87f669c0fac7551905fd03bc1c970ae *inst/doc/index.html
-59b1a54297507f9008263ae0cb418be3 *inst/examples/bbs.R
-255a7347df38adfcf9951a7f6cc8005f *inst/examples/blowflies.R
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+16a0870f1b19e625ea800f763106d4e1 *inst/doc/index.html
+a180be03351a98f9e22ef78088b902f0 *inst/doc/index.md
+ce390fb5e3a3f6fd8db7aeff7eccc1f8 *inst/examples/bbs.R
+e505649dcfe8d95a6aace8c63586a0fc *inst/examples/blowflies.R
 c9828f208fad49ab9acb9d462800adab *inst/examples/dacca.R
-6f7dfacc09bbbb74593afe389acd8295 *inst/examples/euler.sir.R
-fb926a0612d98d2d2bfb1111ae7f3e20 *inst/examples/gillespie.sir.R
+7ed5d4f14bd4cb822998041bc162886d *inst/examples/euler.sir.R
+0736982ca436e20319b78e5e73b9497c *inst/examples/gillespie.sir.R
 60ba9c1360df1a63eedb823a242444b1 *inst/examples/gompertz.R
-9d094cf0628e565ea9d058e66ad63063 *inst/examples/ou2.R
-c2acefabf9309393be2586608a04bae6 *inst/examples/ricker.R
-ca878dff891985f6ca8061bcf7fb3656 *inst/examples/rw2.R
-a558c185181b44b2ba42e956fe4466fd *inst/include/pomp.h
+875310229e5224d0b4b26b88e4fa6bf1 *inst/examples/ou2.R
+3e858538d3081c389837c3b67705bb50 *inst/examples/ricker.R
+76054473e577d0285fc4372c7d4dd73d *inst/examples/rw2.R
+cd9388f151042f25d64bcb33fda2f0c0 *inst/include/pomp.h
+1a7fe1842bbbd9bd4dbc5879475564f3 *inst/include/pomp_defines.h
 25cefbb8255be8592270fbcaa2565e61 *man/abc.Rd
 84eaf0e704b3cab46c72028306fd9716 *man/bake.Rd
 a7e63f3c3346745a298195e8490b31ba *man/basic_probes.Rd
@@ -95,9 +99,10 @@ a7e63f3c3346745a298195e8490b31ba *man/basic_probes.Rd
 32e288039126ca676a5d4b324d873e0d *man/eulermultinom.Rd
 e3516487ef181d65e676894929a9821f *man/example.Rd
 1298eb3b371d77d573dfd432bacb2594 *man/gompertz.Rd
+eadac5e4e542f3f8192e4777e7ef7e51 *man/hitch.Rd
 1556730d056ee7e8d6fee07599591622 *man/kalman.Rd
 7e38911fb09ebace7717655e249bce04 *man/logmeanexp.Rd
-152c4baacd1dd48c2357ca68412f3e79 *man/lowlevel.Rd
+d8e541726b21365120b94fbf4f2383a0 *man/lowlevel.Rd
 8ff8d2d3925b81703849382d24e5c07f *man/measles.Rd
 8f3fbfebb259b05202171223033a0e84 *man/mif.Rd
 91e51557f31c86a8f720f9bc0d9a1fda *man/mif2.Rd
@@ -107,54 +112,52 @@ e3516487ef181d65e676894929a9821f *man/example.Rd
 476478b241b178415a4d4a43a4f487e7 *man/parmat.Rd
 9cdb349c2303fc487562b3586aa07b2c *man/pfilter.Rd
 947b26e901b42ea4964a21b5a558ce86 *man/pmcmc.Rd
-c22f1aee123a372f756e84d41d632ae9 *man/pomp.Rd
+8a3534d78cec0d5324e1e5265e53cd66 *man/pomp.Rd
 124903493d7846790adabba70e0548c3 *man/pomp_fun.Rd
-e240fd6534aada65a8e12c500cf0861f *man/pomp_methods.Rd
+2f242ef537de102a8f407039b7ae09f7 *man/pomp_methods.Rd
 1201060cf9d78104f454c9fbdb11f50d *man/probe.Rd
 beecb5088cafe2d4c318216830950aa2 *man/proposals.Rd
 3dd5f9036e036af5aaedfc98fc3b7da1 *man/ricker.Rd
 1539d1bc4226a799a83217aa581cb676 *man/rw2.Rd
 20d1d3d87216b1678a5ce9c034ad8fd9 *man/sannbox.Rd
-74abc53264d3b2154d1f3325ad354b1e *man/simulate_pomp.Rd
+541c7f5848bf052ded5bc3c58b486789 *man/simulate_pomp.Rd
 bf1ecc9573fa95278fc379824da0f7c4 *man/sir.Rd
 aacc12ccc8dcf3d911c94116b535edde *man/spect.Rd
-7976cebab487706b88b64d9382327d45 *man/traj_match.Rd
+bf583bd8b29edfe2bdf088e2a05c9beb *man/traj_match.Rd
 2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars
-149ecdbc6f53ec3071307b5c623c1b1d *src/blowfly.c
 5df2e1d1778196ee505d12ce6d18cd99 *src/bspline.c
 8bba7921d6a738384d9decb7af07647b *src/dmeasure.c
 1b22bbe5862d81d3d43bd3c373750a94 *src/dprior.c
-bf48499e2c4536c891c2c1109c4d404e *src/dprocess.c
-668ddb72697129486a14d0478ee34cfd *src/euler.c
+2c9023b2cc2a4937f8dc55ed186478e4 *src/dprocess.c
+9d3dea430cf13cf3e4a680008186a24a *src/euler.c
 42ca310dd0edfc736e8211117d36ab80 *src/eulermultinom.c
 75d4e5b83bc144f1709a207d12dac482 *src/gompertz.c
-7294241c95503c761156d52bb472121e *src/init.c
+c21a3ced562da2b9fc8026d521b1b83e *src/init.c
 79f883767e9907b014eb5785780ae639 *src/initstate.c
-2e097db81df8f613c7d620df58cfa401 *src/lookup_table.c
+39cd2a2f1a72488c875cfd0e6740f2a2 *src/lookup_table.c
 05c6ef9f5902ace7d6d2d33bef9b0572 *src/mif.c
 4a0696501ea8fa83fb8d576cc747ec41 *src/mif2.c
 5d2a6400971f0cdab2b239694e77eb26 *src/ou2.c
 2da42ff1762c58a00e1786b983741cd4 *src/partrans.c
-af05abc0b266185365dd1249ef34e50b *src/pfilter.c
-a558c185181b44b2ba42e956fe4466fd *src/pomp.h
-42f0ad985ebd89931c1939f318813f7b *src/pomp_fun.c
-00c8f3e565fa7c22340ea8ba5fa2db96 *src/pomp_internal.h
+3ee7f9a1a7e0113db40f5b24ec575458 *src/pfilter.c
+cd9388f151042f25d64bcb33fda2f0c0 *src/pomp.h
+1a7fe1842bbbd9bd4dbc5879475564f3 *src/pomp_defines.h
+39706ba56befd6c2fc05ab7d220aabc0 *src/pomp_fun.c
+eb687cc3c7ab8afce05127b2fc9a7a06 *src/pomp_internal.h
 5e2210aa36334af59cfa73662f0123cc *src/pomp_mat.h
-ab575d18ae6489128b685baadcda34bf *src/probe.c
+d4d37b1c03d0059dac42269c42614b5e *src/probe.c
 04c8ed0541ae01aa30333d65051c591f *src/probe_acf.c
 f3377bab720bc66992de0ff54a589ba9 *src/probe_marginal.c
 2f3fa99c841f11417e87dbf1e7ba223f *src/probe_nlar.c
 7c75ae3f991acaafc348573bcbf20db8 *src/resample.c
-7a1e6773f46a349186cfc7143e6d0642 *src/ricker.c
 e0d2f40cc346edc0acd7581f5f51c3b7 *src/rmeasure.c
 15e0106052110261340228b297c54137 *src/rprior.c
-9e39e2fb17c49892d25acb64ff645c23 *src/rprocess.c
+9786cfc24f39821b1879317e38da81c6 *src/rprocess.c
 e7e9b13d7ae750f8f141b574ec42cfe4 *src/simulate.c
-52abacb92560fc4dbacc17fe670a2d02 *src/sir.c
-d945c5746afacd229cf5ed589906e43d *src/skeleton.c
+38315ba47e80fbc964d6e6bbb09c4231 *src/skeleton.c
 f59dd0059cdd443a58c43bf2755f66e5 *src/soboldata.h
 d2ed11484e058e34104d3214d0980c7e *src/sobolseq.c
 b8d4e5f51e12253529b1fc8e5267b0e2 *src/ssa.c
 065c243df9f01c531e39b18127b284d1 *src/synth_lik.c
-45f68c3bfffe01be47c8a40ebd9e7d6b *src/trajectory.c
-c94527b269480b16ecf1516c8b684839 *src/userdata.c
+57ec85592091902498abb259308196c7 *src/trajectory.c
+6686ff3fb3560f22684f4fa71d5920e1 *src/userdata.c
diff --git a/NAMESPACE b/NAMESPACE
@@ -12,7 +12,7 @@ importFrom(stats,simulate,time,coef,logLik,window,fitted,
 importFrom(digest,digest)
 importFrom(mvtnorm,dmvnorm,rmvnorm)
 importFrom(subplex,subplex)
-importFrom(deSolve,ode)
+importFrom(deSolve,ode,diagnostics)
 importFrom(nloptr,nloptr)
 importFrom(coda,mcmc,mcmc.list)
 
@@ -35,6 +35,7 @@ exportMethods(
     plot,show,print,spy,
     coerce,summary,logLik,window,"$",
     pompLoad,pompUnload,
+    "solibs<-",
     dprocess,rprocess,rmeasure,dmeasure,init.state,skeleton,
     dprior,rprior,
     obs,partrans,coef,"coef<-",
@@ -61,7 +62,7 @@ S3method(as.data.frame,kalmand.pomp)
 export(
     pomp,
     bake,stew,freeze,
-    Csnippet,
+    Csnippet, hitch,
     reulermultinom,
     deulermultinom,
     rgammawn,
@@ -73,7 +74,7 @@ export(
     gillespie.hl.sim,
     mvn.diag.rw,mvn.rw,
     mvn.rw.adaptive,
-    rw.sd,
+    rw.sd,vectorfield,map,
     sobolDesign,
     sliceDesign,
     profileDesign,

diff --git a/R/aaa.R b/R/aaa.R
@@ -2,6 +2,14 @@
   exampleDir <- getOption("pomp.examples")
   pompExampleDir <- system.file("examples",package="pomp")
   options(pomp.examples=c(exampleDir,pompExampleDir,recursive=TRUE))
+  packageStartupMessage("Welcome to pomp version 1.19!\n",
+    "pomp version 2 is now available on https://kingaa.github.io/pomp/.\n",
+    "This new version contains many improvements but is not backward compatible.\n",
+    "To allow users time to modify their codes, 'pomp' version 2 will be provided as package 'pomp2' for a short while.\n\n",
+    "Around the middle of 2019, 'pomp2' will be renamed 'pomp' version 2.1 and will be released to CRAN. ",
+    "Until then, 'pomp' versions < 2 will continue to be available.\n\n",
+    "See the ",sQuote("pomp version 2 upgrade guide")," at ",
+    "https://kingaa.github.io/pomp/",".")
 }
 
 .onDetach <- function (...) {