Merge pull request #249 from aappling-usgs/develop

ODE refactor

.Rbuildignore

@@ -2,3 +2,5 @@
 ^\.Rproj\.user$
 ^\.travis\.yml$
 ^appveyor\.yml$
+man-roxygen
+temp

.travis.yml

@@ -4,33 +4,27 @@
 
 language: r
 sudo: required
-warnings_ar_errors: true
+warnings_are_errors: true
+
+r_build_args: --no-build-vignettes --no-manual --no-multiarch
+r_check_args: --no-build-vignettes --no-manual
 
 repos:
   CRAN: https://cloud.r-project.org
   GRAN: http://owi.usgs.gov/R
 
-before_install:
-  - wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.2.0.tar.gz
-  - tar xfvs JAGS-4.2.0.tar.gz
-  - cd JAGS-4.2.0
-  - sudo ./configure
-  - sudo make
-  - sudo make install
-  - cd ..
-  - sudo rm -f JAGS-4.2.0.tar.gz
-  - sudo rm -rf JAGS-4.2.0
-
 before_script:
   - Rscript -e "install.packages('knitr', repos='http://cran.cnr.Berkeley.edu/')"
   - Rscript -e "install.packages('rmarkdown', repos='http://cran.cnr.Berkeley.edu/')"
 
 r_packages:
  - modeest
+ - deSolve
 
 r_github_packages:
  - jimhester/covr
  - GLEON/LakeMetabolizer
+ - appling/unitted
 
 after_success:
   - Rscript -e 'covr::coveralls()'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: streamMetabolizer
 Type: Package
 Title: Estimate Stream Metabolism from Dissolved Oxygen Data
-Version: 0.9.8.3
-Date: 2016-08-11
+Version: 0.9.14
+Date: 2016-09-20
 Author: Alison Appling, Jordan Read, Luke Winslow, Bob Hall
 Maintainer: Alison Appling <aappling@usgs.gov>
 Description: Modeling package for stream metabolism.
@@ -35,7 +35,6 @@ Suggests:
     microbenchmark,
     plyr,
     RCurl,
-    runjags,
     rstan,
     testthat,
     XML,
@@ -44,10 +43,6 @@ Collate:
     '01-onLoad.R'
     'calc_DO_at_sat.R'
     'calc_DO_deficit.R'
-    'calc_DO_mod.R'
-    'calc_DO_mod_by_diff.R'
-    'calc_DO_mod_w_fixed_error.R'
-    'calc_DO_mod_w_sim_error.R'
     'calc_air_pressure.R'
     'calc_depth.R'
     'calc_is_daytime.R'
@@ -75,12 +70,17 @@ Collate:
     'metab_bayes.R'
     'metab_inputs.R'
     'metab_mle.R'
+    'metab_model.get_params.R'
+    'metab_model.predict_DO.R'
+    'metab_model.predict_metab.R'
+    'metab_model.show.R'
     'metab_model_interface.R'
     'metab_night.R'
     'metab_sim.R'
     'mm_check_mcmc_file.R'
     'mm_data.R'
     'mm_filter_dates.R'
+    'mm_filter_hours.R'
     'mm_filter_valid_days.R'
     'mm_validate_name.R'
     'mm_valid_names.R'
@@ -89,12 +89,16 @@ Collate:
     'mm_generate_mcmc_file.R'
     'mm_get_timestep.R'
     'mm_is_valid_day.R'
+    'mm_locate_filename.R'
     'mm_model_by_ply.R'
     'mm_model_by_ply_prototype.R'
-    'mm_predict_1ply.R'
+    'mm_predict_DO_1ply.R'
+    'mm_predict_metab_1ply.R'
+    'mm_sd_to_ci.R'
     'mm_validate_data.R'
     'plot_DO_preds.R'
     'plot_metab_preds.R'
+    'revise.R'
     'specs.R'
     'streamMetabolizer.R'
     'zz_build_docs.R'

NAMESPACE

@@ -8,6 +8,9 @@ S3method(get_info,metab_model)
 S3method(get_log,metab_bayes)
 S3method(get_mcmc,metab_bayes)
 S3method(get_mcmc_data,metab_bayes)
+S3method(get_params,metab_Kmodel)
+S3method(get_params,metab_bayes)
+S3method(get_params,metab_model)
 S3method(get_specs,metab_model)
 S3method(get_version,metab_model)
 S3method(predict_DO,metab_Kmodel)
@@ -17,16 +20,10 @@ S3method(predict_DO,metab_sim)
 S3method(predict_metab,metab_Kmodel)
 S3method(predict_metab,metab_bayes)
 S3method(predict_metab,metab_model)
-S3method(predict_metab,metab_sim)
 S3method(print,logs_metab)
-S3method(print,preds_metab)
 S3method(print,specs)
 export(calc_DO_at_sat)
 export(calc_DO_deficit)
-export(calc_DO_mod)
-export(calc_DO_mod_by_diff)
-export(calc_DO_mod_w_fixed_error)
-export(calc_DO_mod_w_sim_error)
 export(calc_air_pressure)
 export(calc_depth)
 export(calc_is_daytime)
@@ -55,6 +52,7 @@ export(get_info)
 export(get_log)
 export(get_mcmc)
 export(get_mcmc_data)
+export(get_params)
 export(get_specs)
 export(get_version)
 export(lookup_google_timezone)
@@ -82,6 +80,7 @@ export(plot_DO_preds)
 export(plot_metab_preds)
 export(predict_DO)
 export(predict_metab)
+export(revise)
 export(specs)
 exportClasses(metab_Kmodel)
 exportClasses(metab_bayes)
@@ -93,7 +92,6 @@ import(dplyr)
 import(methods)
 import(parallel)
 import(tibble)
-import(unitted)
 importFrom(LakeMetabolizer,is.day)
 importFrom(LakeMetabolizer,k600.2.kGAS.base)
 importFrom(LakeMetabolizer,o2.at.sat.base)

NEWS.md

@@ -1,3 +1,43 @@
+# streamMetabolizer 0.9.14
+
+* all tests are passing and all examples are running [again]. tests are 
+acceptably comprehensive [for now].
+
+* known issue: K binning in bayesian models is producing unlikely estimates. all
+bayesian models need further testing.
+
+# streamMetabolizer 0.9.14
+
+* ongoing bug fixes and re-integration of all model types into new ODE
+production/integration scheme
+
+# streamMetabolizer 0.9.12
+
+* removed JAGS from the package. Stan is better for us.
+
+# streamMetabolizer 0.9.11
+
+* this is the last version with JAGS in it.
+
+# streamMetabolizer 0.9.10
+
+* myriad bug fixes to accommodate changes from version 0.9.9.
+
+# streamMetabolizer 0.9.9
+
+* `metab_mle` and `metab_sim` now have several options for relationships among 
+GPP, light, ER, and temperature.
+
+* `metab_mle` and `metab_sim` now have several options for the method by which 
+the differential equation for dDO/dt is numerically integrated to produce a time
+series of DO predictions.
+
+* `metab_mle` has taken a performance hit to become more flexible in the 
+GPP-light relationship, the ODE method, and so on. Optimization is likely in the
+future.
+
+* `predict_metab` and `predict_DO` optionally attach units to their output.
+
 # streamMetabolizer 0.9.8
 
 * better error and warning handling in metab_bayes, including a new function 
@@ -8,9 +48,6 @@ files are now retrieved for both JAGS and Stan models.
 
 * more efficient specifications of JAGS and Stan models
 
-* more options, more maintainably coded, slightly slower, for ODE solutions in 
-metab_mle
-
 * incorporated feedback on vignette
 
 # streamMetabolizer 0.9.6

R/01-onLoad.R

@@ -2,22 +2,23 @@
 #' @importFrom utils available.packages contrib.url
 #' @keywords internal
 .onAttach <- function(libname, pkgname) {
-  packageStartupMessage("This package is in development. We are using it for our own early applications and welcome bold, flexible, resilient new users who can help us make the package better. Details of the user interface and model implementations will change. Please give us feedback at https://github.com/USGS-R/streamMetabolizer/issues/new.\n")
+  packageStartupMessage("This package is in development. We are using it for our own early applications and welcome flexible, resilient new users who can help us make the package better. Details of the user interface and model implementations will change. Please give us feedback at https://github.com/USGS-R/streamMetabolizer/issues/new.\n")
   packageStartupMessage("This information is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The information has not received final approval by the U.S. Geological Survey (USGS) and is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the information. Although this software program has been used by the USGS, no warranty, expressed or implied, is made by the USGS or the U.S. Government as to the accuracy and functioning of the program and related program material nor shall the fact of distribution constitute any such warranty, and no responsibility is assumed by the USGS in connection therewith.")
 
-  # Check whether this package is up to date
+  # Load deSolve because otherwise after a few model runs we're likely to get
+  # the following error
+  requireNamespace('deSolve', quietly=TRUE)
+  ## Error in .Call("call_rkFixed", as.double(y), as.double(times), Func, Initfunc,  :
+  ##   "call_rkFixed" not resolved from current namespace (deSolve)
+  ## Error in .C("unlock_solver") :
+  ##   "unlock_solver" not resolved from current namespace (deSolve)
 
+  # Check whether this package is up to date on GRAN
   GRAN_update_code <- paste0(
     '  update.packages(oldPkgs=c("streamMetabolizer","unitted"),\n',
-    '    dependencies=TRUE, repos=c("http://owi.usgs.gov/R", "https://cran.rstudio.com"))')
-  github_owner <- 'USGS-R'
-  github_branch <- 'develop'
-  github_pkg_ref <- paste0(github_owner,'/',pkgname,'@',github_branch)
-  github_update_code <- paste0(
-    '  devtools::install_github("',github_pkg_ref,'")')
-
+    '    dependencies=TRUE, repos=c("https://owi.usgs.gov/R", "https://cran.rstudio.com"))')
   tryCatch({
-    GRAN_pkg <- available.packages(contrib.url("http://owi.usgs.gov/R"))
+    GRAN_pkg <- available.packages(contrib.url("https://owi.usgs.gov/R"))
     GRAN_version <- package_version(GRAN_pkg[[pkgname, 'Version']])
     local_version <- packageVersion(pkgname)
     if(local_version < GRAN_version) {
@@ -29,6 +30,12 @@
     packageStartupMessage("Can't check GRAN for new package versions just now. We'll try again next time.")
   })
 
+  # Check whether this package is up to date on GitHub
+  github_owner <- 'USGS-R'
+  github_branch <- 'develop'
+  github_pkg_ref <- paste0(github_owner,'/',pkgname,'@',github_branch)
+  github_update_code <- paste0(
+    '  devtools::install_github("',github_pkg_ref,'")')
   if(requireNamespace('devtools', quietly=TRUE)) {
     tryCatch({
       github_ref <- devtools:::github_resolve_ref(