Merge pull request #138 from weecology/juniper_active

v0.10.0

.Rbuildignore

@@ -10,3 +10,4 @@
 ^\.zenodo\.json$
 ^inst/WORDLIST$
 ^notes.R$
+^docs$

.travis.yml

@@ -6,6 +6,7 @@ warnings_are_errors: false
 before_install:
   - sudo apt-get update -qq
   - sudo apt-get install texlive-latex-base
+  - sudo apt-get install gsl-bin libgsl0-dev
 
 r_packages:
   - covr

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: portalcasting
 Title: Functions Used in Predicting Portal Rodent Dynamics
-Version: 0.9.0
+Version: 0.10.0
 Authors@R: c(
     person(c("Juniper", "L."), "Simonis",
       email = "[email protected]", role = c("aut", "cre"),

NAMESPACE

@@ -4,10 +4,14 @@ export(AutoArima)
 export(ESSS)
 export(NMME_urls)
 export(NaiveArima)
+export(add_covered_to_cast_tab)
 export(add_date_from_components)
+export(add_err_to_cast_tab)
 export(add_extra_future_moons)
 export(add_future_moons)
+export(add_lead_to_cast_tab)
 export(add_moons_from_date)
+export(add_obs_to_cast_tab)
 export(all_species)
 export(append_csv)
 export(base_species)
@@ -57,6 +61,7 @@ export(last_census)
 export(last_moon)
 export(list_depth)
 export(main_path)
+export(measure_cast_level_error)
 export(messageq)
 export(model_control)
 export(model_controls)
@@ -72,6 +77,8 @@ export(path_no_ext)
 export(pevGARCH)
 export(plot_cast_point)
 export(plot_cast_ts)
+export(plot_casts_cov_RMSE)
+export(plot_casts_err_lead)
 export(portalcast)
 export(portalcast_goodbye)
 export(portalcast_welcome)
@@ -87,7 +94,9 @@ export(prep_rodents_table)
 export(prep_weather_data)
 export(process_rodent_data)
 export(raw_path)
+export(read_cast_metadata)
 export(read_cast_tab)
+export(read_cast_tabs)
 export(read_casts_metadata)
 export(read_climate_casts)
 export(read_covariate_casts)
@@ -151,6 +160,7 @@ importFrom(forecast,auto.arima)
 importFrom(forecast,ets)
 importFrom(forecast,forecast)
 importFrom(forecast,na.interp)
+importFrom(grDevices,grey)
 importFrom(grDevices,rgb)
 importFrom(graphics,abline)
 importFrom(graphics,axis)

NEWS.md

@@ -2,6 +2,21 @@
 
 Version numbers follow [Semantic Versioning](https://semver.org/).
 
+# [portalcasting 0.10.0](https://github.com/weecology/portalcasting/releases/tag/v0.10.0)
+*2019-09-13*
+
+### Model evaluation and ensembling added back in
+* Were removed with the updated version from 0.8.1 to 0.9.0 to allow time to develop the code with the new infrastructure. 
+* Model evaluation happens within the cast tab output as before.
+
+### Temporarily removed figures returned
+* Associated with the evaluation.
+* Plotting of error as a function of lead time for multiple species and multiple models. Now has a fall-back arrangement that works for a single species-model combination.
+* Plotting RMSE and coverage within species-model combinations.
+
+### Flexing model controls to allow user-defined lists for prefab models
+* For sandboxing with existing models, it is useful to be able to change a parameter in the model's controls, such as the data sets. Previously, that would require a lot of hacking around. Now, it's as simple as inputting the desired controls and flipping `arg_checks = FALSE`. 
+
 # [portalcasting 0.9.0](https://github.com/weecology/portalcasting/releases/tag/v0.9.0)
 *2019-09-06*
 
@@ -13,7 +28,7 @@ Version numbers follow [Semantic Versioning](https://semver.org/).
 
 ###  Directory tree structure simplified
 * `dirtree` was removed
-* `base` (both as a function and a concept) was removed. To make that structure use main = "./name"
+* `base` (both as a function and a concept) was removed. To make that structure use `main = "./name"`.
 * "PortalData" has been removed as a sub and replaced with "raw", which includes all raw versions of files (post unzipping) downloaded: Portal Data and Portal Predictions and covariate forecasts (whose saving is also new here).
 
 ### Tightened messaging

R/data_input_output.R

@@ -318,7 +318,8 @@ read_rodents <- function(main = ".", data_sets = c("all", "controls"),
 read_covariates <- function(main = ".", control_files = files_control(),
                             arg_checks = TRUE){
   check_args(arg_checks)
-  fpath <- file_path(main = main, sub = "data", files = "covariates.csv", 
+  fpath <- file_path(main = main, sub = "data", 
+                     files = control_files$filename_cov, 
                      arg_checks = arg_checks)
   if(!file.exists(fpath)){
     return(prep_covariates(main = main, arg_checks = arg_checks))
@@ -374,7 +375,9 @@ read_covariate_casts <- function(main = ".", control_files = files_control(),
 read_moons <- function(main = ".", control_files = files_control(),
                        arg_checks = TRUE){
   check_args(arg_checks = arg_checks)
-  fpath <- file_path(main, "data", "moon_dates.csv")
+  fpath <- file_path(main = main, sub = "data", 
+                     files = control_files$filename_moons, 
+                     arg_checks = arg_checks)
   if(!file.exists(fpath)){
     return(prep_moons(main = main, arg_checks = arg_checks))
   }
@@ -388,7 +391,9 @@ read_moons <- function(main = ".", control_files = files_control(),
 read_metadata <- function(main = ".", control_files = files_control(),
                           arg_checks = TRUE){
   check_args(arg_checks)
-  fpath <- file_path(main, "data", "metadata.yaml")
+  fpath <- file_path(main = main, sub = "data", 
+                     files = control_files$filename_meta, 
+                     arg_checks = arg_checks)
   if(!file.exists(fpath)){
     md <- prep_metadata(main = main, arg_checks = arg_checks)
     return(md)