version 0.8-14

cran · Oct 7, 2021 · 27972f7 · 27972f7
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diff --git a/.Rinstignore b/.Rinstignore
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: simecol
-Version: 0.8-13
+Version: 0.8-14
 Title: Simulation of Ecological (and Other) Dynamic Systems
 Authors@R: c(person("Thomas","Petzoldt", role = c("aut", "cre"),
                      email = "thomas.petzoldt@tu-dresden.de",
@@ -18,6 +18,6 @@ Description: An object oriented framework to simulate
 License: GPL (>= 2)
 URL: http://www.simecol.de/
 NeedsCompilation: yes
-Packaged: 2019-07-15 20:53:54 UTC; thpe
+Packaged: 2021-10-06 21:47:19 UTC; thpe
 Repository: CRAN
-Date/Publication: 2019-07-15 21:20:05 UTC
+Date/Publication: 2021-10-07 06:40:02 UTC
diff --git a/MD5 b/MD5
@@ -1,4 +1,4 @@
-e2695431960016326b9b064099b96a9a *DESCRIPTION
+787684d3e5112c8373cf709aa29f4f5b *DESCRIPTION
 e7f1dabf77c24c20129c56fc5f8bf9f4 *NAMESPACE
 b8e065ecc0c11e42c920fd9faef1f5cc *R/aaa_classes.R
 dcdfcf37b1b245dd72d88302df9d0666 *R/accessors.R
@@ -23,8 +23,8 @@ ebdc21c2b9a30277a1505f80c50238c9 *R/sEdit.R
 e9ac2302312464bec9f29207e88e8645 *R/seedfill.R
 896d78634a193e0afdc17d6229355e01 *R/sim.R
 298cee7e5fb2ff9e8fd01613227eb124 *R/ssqOdeModel.R
-a822560da2f0f840979c57001f471a40 *build/partial.rdb
-9f5a75154f36837ff59ab33f03e34d0f *build/vignette.rds
+47c5e5f94271ce3afe89d70caf7fa3cc *build/partial.rdb
+97907ba2717880c1c268d97081e92bfc *build/vignette.rds
 29b6fb5733cd215588630781b1436c64 *data/CA.rda
 666abfe50ed7248313e334567511b13b *data/chemostat.rda
 8d093a41e7b4c8bba2e3b5103d87d471 *data/conway.rda
@@ -34,16 +34,16 @@ dde696004aa9bb419de2eade73b8e9e2 *data/lv.rda
 2e80d0874c93df7b90398c079c400cbe *data/upca.rda
 8609cb45cbc05486f13e258b1026ef2a *demo/00Index
 c5e1ac25087f98c1bc357fd5ad975561 *demo/jss.R
-9fba02e6e1f471777f3fcf7712dd4759 *inst/CITATION
+e4a851ac28f3c2b68cc087b235559772 *inst/CITATION
 a0e45d853a7be1b36de0087c212c667b *inst/FAQ.txt
-a532697b2ff58a84099c2726bd8d966f *inst/NEWS
+cea6c2407e0a9c6d2b3647ff029297d9 *inst/NEWS
 5ef8cae20fab098566d2c044345bb395 *inst/THANKS
-44be005510e552181c4884a60d501337 *inst/doc/a-simecol-introduction.R
-99fa2a58dc14263f0cbb271593f52a14 *inst/doc/a-simecol-introduction.Rnw
-dd8ad29503226655663ed3aaf655d879 *inst/doc/a-simecol-introduction.pdf
-4be63c999ed32450ba9986f87236e2c1 *inst/doc/b-simecol-howtos.R
-b101efdec89905934a25efc660be0098 *inst/doc/b-simecol-howtos.Rnw
-b4c80d57fa6d073dae1664acef7e2a3a *inst/doc/b-simecol-howtos.pdf
+4d340c5857e01fe5c5854fb74dadf4db *inst/doc/a-simecol-introduction.R
+14eb3b0cc9c380a0f6d3db40956c023c *inst/doc/a-simecol-introduction.Rnw
+85f33fbf08d4dd63be9d1764d17ae278 *inst/doc/a-simecol-introduction.pdf
+b502c90902f7b761b70773f1eb7243a6 *inst/doc/b-simecol-howtos.R
+c0161e67b87234eea4e0adbf5d19a0ff *inst/doc/b-simecol-howtos.Rnw
+d25e2868ecfe9ab5dd9b1b4e6e65fccf *inst/doc/b-simecol-howtos.pdf
 83486c3a764fd74472c7fd81b22c82c1 *inst/doc/examples/CA.R
 892fa7f751313ae0d3c6d35533fd145a *inst/doc/examples/chemostat.R
 751963265a6ee8128dd653cd3345c148 *inst/doc/examples/competition.R
@@ -52,8 +52,8 @@ c308ab7633abd778d3f8fbec0545fda8 *inst/doc/examples/diffusion_A.R
 00e89beee89f984cd93c9dd0820d114e *inst/doc/examples/diffusion_B.R
 7e1f3aea7a19111e28733560c91b6e6f *inst/doc/examples/diffusion_barrier.R
 7170e1941d7668184bd7317eded7f31f *inst/doc/examples/dynload/clotka.c
-aacf0a7e33966588ce15c7484fbd9ba8 *inst/doc/examples/dynload/simecol_clotka.R
-9872804a6b014f79f2a869144d45d287 *inst/doc/examples/dynload/test_clotka.R
+1e03731740abe072d1bcee1da67f9a09 *inst/doc/examples/dynload/simecol_clotka.R
+89c27fda03d7ab84f2617114d1f8b251 *inst/doc/examples/dynload/test_clotka.R
 2464ee8ced5914537a35d5e6230c21f5 *inst/doc/examples/fitOdeModel/initval.R
 76e225a0e1e5454df7d8de79876a9374 *inst/doc/examples/fitOdeModel/weighted.R
 05c2930049e39a787be6f9dee83355a7 *inst/doc/examples/ibm_daphnia.R
@@ -73,7 +73,7 @@ fcc8075b0a4d95c97bb84c027840c1d5 *man/as.simObj.Rd
 08c8bf095c6932874a918f99dacc38f2 *man/diffusion.Rd
 5457c685ad2f98285b5414b5b089515c *man/editParms.Rd
 9ef15ca58ef8acb35a877ea9932120d6 *man/eightneighbours.Rd
-d3fbb365a02bb9d7ca95a9fa6d425487 *man/fitOdeModel.Rd
+c209ff243256aae94516903a806f12b4 *man/fitOdeModel.Rd
 223fa3d2fd5e838851e5204462ada3c3 *man/fromtoby.Rd
 a0462917439624aa4dfd41b32857cd7f *man/initialize-methods.Rd
 6e8f6bba35fb27b84ae9d543e67ab5e3 *man/iteration.Rd
@@ -86,9 +86,9 @@ b72d5cea7b5d6487f911cd39dac9a68c *man/modelFit-methods.Rd
 274b80320c68d7743bd047006ffbad70 *man/neighbours.Rd
 952741e1cfbbccf82ed3233f015f92b1 *man/observer.Rd
 e2b3468baae30d7a2f9a82b081c1ac24 *man/odeModel.Rd
-238f9f4ad71b826577c0d5d2929ac6df *man/p.constrain.Rd
+e19adb2a5a40e75d43750482f6d7ffc1 *man/p.constrain.Rd
 3b35e45ad62491202ec02d47c3fe9c3a *man/parms.Rd
-8428e7ec41667b0dca1c19e9ecb0acc8 *man/pcuseries.Rd
+d554c4de78bb9f84c13e24d80da5f40b *man/pcuseries.Rd
 c701f7bdb286ad8bb9e9e32796864784 *man/peaks.Rd
 5969564daf4bf7e85b8ec3e031276b92 *man/plot-methods.Rd
 44f62c2ed97bfd153793001f710752a3 *man/print-methods.Rd
@@ -100,8 +100,8 @@ d1e89494dd9cad4bd452bfc32be855c7 *man/simecol-package.Rd
 03e25c81b8ebbdda2e06feaac20f8700 *man/upca.Rd
 2a02dac2941789a7184ffe7136f2fd1b *src/R_init_simecol.c
 00e4ba34ac563c275f4a1e94b5567100 *src/simecol.c
-99fa2a58dc14263f0cbb271593f52a14 *vignettes/a-simecol-introduction.Rnw
-b101efdec89905934a25efc660be0098 *vignettes/b-simecol-howtos.Rnw
+14eb3b0cc9c380a0f6d3db40956c023c *vignettes/a-simecol-introduction.Rnw
+c0161e67b87234eea4e0adbf5d19a0ff *vignettes/b-simecol-howtos.Rnw
 686accaa04554feffe53df74eb20b150 *vignettes/ca.pdf
 c6f3372e18710befc0fe7a9a52f634f2 *vignettes/classes.pdf
 8fc613c62b53d20fa57cbba19f571f69 *vignettes/ibm_daphnia.R

diff --git a/NAMESPACE b/NAMESPACE
diff --git a/R/aaa_classes.R b/R/aaa_classes.R
diff --git a/R/accessors.R b/R/accessors.R
diff --git a/R/addtoenv.R b/R/addtoenv.R
diff --git a/R/approxTime.R b/R/approxTime.R
diff --git a/R/approxTime1.R b/R/approxTime1.R
diff --git a/R/coerce.R b/R/coerce.R
diff --git a/R/constructors.R b/R/constructors.R
diff --git a/R/edit.R b/R/edit.R
diff --git a/R/fitOdeModel.R b/R/fitOdeModel.R
diff --git a/R/fromtoby.R b/R/fromtoby.R
diff --git a/R/iteration.R b/R/iteration.R
diff --git a/R/mixNamedVec.R b/R/mixNamedVec.R
diff --git a/R/modelFit.R b/R/modelFit.R
diff --git a/R/neighbours.R b/R/neighbours.R
diff --git a/R/p.constrain.R b/R/p.constrain.R
diff --git a/R/pcuseries.R b/R/pcuseries.R
diff --git a/R/peaks.R b/R/peaks.R
diff --git a/R/plot.R b/R/plot.R
diff --git a/R/print.R b/R/print.R
diff --git a/R/sEdit.R b/R/sEdit.R
diff --git a/R/seedfill.R b/R/seedfill.R
diff --git a/R/sim.R b/R/sim.R
diff --git a/R/ssqOdeModel.R b/R/ssqOdeModel.R
diff --git a/build/partial.rdb b/build/partial.rdb
diff --git a/build/vignette.rds b/build/vignette.rds
diff --git a/data/CA.rda b/data/CA.rda
diff --git a/data/chemostat.rda b/data/chemostat.rda
diff --git a/data/conway.rda b/data/conway.rda
diff --git a/data/diffusion.rda b/data/diffusion.rda
diff --git a/data/lv.rda b/data/lv.rda
diff --git a/data/lv3.rda b/data/lv3.rda
diff --git a/data/upca.rda b/data/upca.rda
diff --git a/demo/00Index b/demo/00Index
diff --git a/demo/jss.R b/demo/jss.R
diff --git a/inst/CITATION b/inst/CITATION
@@ -8,17 +8,13 @@ citEntry(entry="Article",
   number   = "9",
   pages    = "1--31",
   year     = "2007",
-  CODEN    = "JSSOBK",
-  ISSN     = "1548-7660",
-  URL      = "http://www.jstatsoft.org/v22/i09",
-  DOI      = "10.18637/jss.v022.i09",
+  doi      = "10.18637/jss.v022.i09",
   keywords =  "ecological modeling, individual-based model,
                object-oriented programming (OOP),
                code-sharing, R.",
   textVersion =  paste(
     "Petzoldt, T. and K. Rinke (2007).",
     "simecol: An Object-Oriented Framework for Ecological Modeling in R.",
     "Journal of Statistical Software, 22(9), 1--31.",
-    "URL http://www.jstatsoft.org/v22/i09/.",
-    "DOI 10.18637/jss.v022.i09")
+    "doi:10.18637/jss.v022.i09")
 )
diff --git a/inst/FAQ.txt b/inst/FAQ.txt
diff --git a/inst/NEWS b/inst/NEWS
@@ -1,3 +1,6 @@
+0.8-14
+o usage of doi in references
+
 0.8-13
 o minor changes
 

diff --git a/inst/THANKS b/inst/THANKS