Merge pull request weecology#141 from weecology/juniper_active

[WIP] v0.12.0

.Rbuildignore

@@ -9,5 +9,6 @@
 ^LICENSE\.md$
 ^\.zenodo\.json$
 ^inst/WORDLIST$
+^codecov\.yml$
 ^notes.R$
 ^docs$

.travis.yml

@@ -8,6 +8,9 @@ before_install:
   - sudo apt-get install texlive-latex-base
   - sudo apt-get install gsl-bin libgsl0-dev
 
+r_binary_packages:
+  - runjags
+
 r_packages:
   - covr
 
@@ -23,7 +26,7 @@ matrix:
     after_success:
     - R CMD INSTALL .
     - Rscript -e 'pkgdown::build_site(examples = FALSE)'
-    - travis_wait 40 Rscript -e 'library(covr); codecov()'
+    - travis_wait 40 Rscript -e 'covr::codecov()'
     deploy:
       provider: pages
       skip-cleanup: true

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: portalcasting
 Title: Functions Used in Predicting Portal Rodent Dynamics
-Version: 0.11.0
+Version: 0.12.0
 Authors@R: c(
     person(c("Juniper", "L."), "Simonis",
       email = "[email protected]", role = c("aut", "cre"),
@@ -28,18 +28,21 @@ Depends: R (>= 3.2.3)
 License: MIT + file LICENSE
 LazyData: true
 Imports:
-  curl,
-  DesignLibrary,
-  dplyr,
-  forecast,
-  httr,
-  lubridate,
-  portalr,
-  readr,
-  rlang,
-  tscount,
-  viridis,
-  yaml
+    coda,
+    curl,
+    DesignLibrary,
+    dplyr,
+    forecast,
+    httr,
+    lubridate,
+    portalr,
+    readr,
+    rlang,
+    runjags,
+    tscount,
+    viridis,
+    yaml,
+    rEDM (>= 0.7.4)
 Suggests:
   knitr,
   pkgdown,
@@ -48,3 +51,5 @@ Suggests:
 RoxygenNote: 6.1.1
 VignetteBuilder: knitr
 Encoding: UTF-8
+Remotes:  
+    ha0ye/rEDM

NAMESPACE

@@ -32,7 +32,10 @@ export(create)
 export(create_dir)
 export(create_main)
 export(create_subs)
+export(creation_message)
 export(data_path)
+export(data_readying_message)
+export(data_resetting_message)
 export(download)
 export(download_climate_casts)
 export(download_destin)
@@ -57,17 +60,23 @@ export(foy)
 export(ifna)
 export(ifnull)
 export(is_sp_col)
+export(jags_RW)
+export(jags_ss)
 export(lag_covariates)
 export(last_census)
 export(last_moon)
 export(list_depth)
 export(main_path)
 export(measure_cast_level_error)
 export(messageq)
+export(messageq_break)
 export(model_control)
 export(model_controls)
+export(model_done_message)
+export(model_running_message)
 export(model_template)
 export(models_path)
+export(models_running_message)
 export(models_to_cast)
 export(most_abundant_species)
 export(na_conformer)
@@ -114,13 +123,16 @@ export(return_if_null)
 export(rodent_species)
 export(rodents_control)
 export(rodents_controls)
+export(runjags_control)
 export(sandbox_welcome)
 export(save_cast_cov_csv)
 export(save_cast_output)
 export(select_casts)
+export(setup_completion_message)
 export(setup_dir)
 export(setup_production)
 export(setup_sandbox)
+export(simplexEDM)
 export(species_from_table)
 export(sub_path)
 export(summarize_daily_weather_by_moon)
@@ -131,16 +143,20 @@ export(unzip_destins)
 export(unzip_download)
 export(update_directory_config)
 export(update_list)
+export(update_models)
 export(verify)
 export(verify_models)
 export(verify_raw_data)
+export(version_message)
 export(write_data)
 export(write_directory_config)
 export(write_model)
 export(zenodo_downloads)
 export(zenodo_url)
 export(zenodo_versions)
 importFrom(DesignLibrary,match.call.defaults)
+importFrom(coda,HPDinterval)
+importFrom(coda,as.mcmc)
 importFrom(curl,curl)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,arrange)
@@ -190,14 +206,18 @@ importFrom(rlang,"!!")
 importFrom(rlang,.data)
 importFrom(rlang,quo)
 importFrom(rlang,quos)
+importFrom(runjags,run.jags)
+importFrom(runjags,runjags.options)
 importFrom(stats,AIC)
 importFrom(stats,lm)
 importFrom(stats,na.omit)
 importFrom(stats,predict)
 importFrom(stats,qnorm)
 importFrom(stats,quantile)
+importFrom(stats,rgamma)
 importFrom(stats,rnorm)
 importFrom(stats,runif)
+importFrom(stats,sd)
 importFrom(tscount,tsglm)
 importFrom(utils,download.file)
 importFrom(utils,packageDescription)

NEWS.md

@@ -3,6 +3,53 @@
 Version numbers follow [Semantic Versioning](https://semver.org/).
 
 
+# [portalcasting 0.12.0](https://github.com/weecology/portalcasting/releases/tag/v0.12.0)
+*2019-10-11*
+
+### `portalcast` updates model scripts according to `controls_model`
+* Previously, if you changed any controls of a prefab model, you had to manually re-write the models using `fill_models` before running `portalcast`.
+* Using `fill_models` would result in hand-made scripts being overwritten, so a specific function (`update_models`) for updating the models was created. 
+* `update_models` by default only updates the models listed in the `controls_model` input, to avoid overwriting model scripts. To change this behavior and also update all of the prefab models' scripts, set `update_prefab_models = TRUE`. This is particularly handy when changing a global (with respect to model scripts) argument: `main`, `quiet`, `verbose`, or `arg_checks`.
+* [addresses](https://github.com/weecology/portalcasting/issues/147)
+
+### Messaging around trying to use not-complete directory improved
+* Indication now made that a component of the directory is missing and suggestion is made to run `create_dir`.
+* [addresses](https://github.com/weecology/portalcasting/issues/137)
+
+### Patching data set bug in plotting
+* There was a bug with matching the interpolated to the non interpolated data sets within the ensembling, which has been fixed. 
+* [addresses](https://github.com/weecology/portalcasting/issues/140)
+
+### Updated messaging 
+* Moved most of the messaging into tidied functions.
+
+### Changed behavior of `prep_rodents_table` and `prep_rodents` 
+* Now there is no `start_moon` argument, and all of the data prior to `end_moon` are returned.
+* This aligns the rodents prep functions with the other (moons, covariates) prep functions.
+* Facilitates use of data prior to `start_moon` in forecasting models (e.g., for distributions of starting state variables).
+* Requires that model functions now explicitly trim the rodents table being used. This has been added to all prefab models. 
+
+### Fixed codecov targets
+* Previous targets were restrictively high due to earlier near-perfect coverage.
+* A codecov.yml file is now included in the repo (and ignored for the R build) which sets the target arbitrarily at the still-quite-high-but-not-restrictively-so 95%. 
+* It can be changed if needed in the future.
+
+### Simple EDM model added
+* [addresses](https://github.com/weecology/portalcasting/issues/115)
+
+### JAGS infrastructure added
+* Using the runjags package, with extensive access to the API of `run.jags` via a `control_runjags` `list` (see `runjags_control`).
+* Currently in place with a very simple random walk model. 
+* [addresses](https://github.com/weecology/portalcasting/issues/142)
+
+### Prepared rodents table includes more content
+* Expanded back in time to the start.
+* Added effort columns (all default options in `prefab_rodents_controls` have `effort = TRUE`).
+
+### Updated adding a model and data vignette
+* Added section at the end about just extending existing models to new data sets.
+* [addresses](https://github.com/weecology/portalcasting/issues/145)
+
 # [portalcasting 0.11.0](https://github.com/weecology/portalcasting/releases/tag/v0.11.0)
 *2019-09-14*