Merge pull request #150 from birdflow-science/147-additional-testing

147 spelling, additional testing, and drop ability to import pre-dynamic-mask models

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BirdFlowR
 Title: Predict and Visualize Bird Movement
-Version: 0.1.0.9040
+Version: 0.1.0.9041
 Authors@R: 
     c(person("Ethan", "Plunkett",  email = "plunkett@umass.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-4405-2251")),

NEWS.md

@@ -1,7 +1,36 @@
+
+# BirdFlowR 0.1.0.9041
+2023-12-12
+
+* Dropped the ability to import pre-dynamic-mask models. This was announced 
+  in 0.1.0.9040 but not done. 
+* Fix spelling and minor documentation edits
+* Fix bug in `n_parameters()` for fitted models.
+* `birdflow_options()` now accepts a list with option names and their 
+  new values, as well as all the previously accepted argument forms.
+* Improve `validate_BirdFlowR()` error reporting.  
+* Add tests for:
+   *  Date lookup on preprocessed but not fitted models. Closes #147.
+   * `n_paramaters()`
+   * `load_model()`
+   * `load_collection_index()`
+   * `route_migration()`
+   * `marginal_stats()`, `calc_pct_zero()`, and `sum_marginals()`
+   * `find_threshold()`
+   * `print()` for `BirdFlow` and `BirdFlowRoutes` objects.
+   * `cache_path()`
+   * `compare_geom()`
+   * `birdflow_options()`
+   * `build_transitions()`, `drop_transitions()`
+
+* Expand testing for:
+   * `preprocess_species()`
+   * `validate_BirdFlow()`
+
 # BirdFlowR 0.1.0.9040
-2023-12-05
+2023-12-11
 
-## Support for **ebirdst** 3.2002.0 added.
+## Support for **ebirdst** 3.2022.0 added.
 **BirdFlowR** can now fit models based on eBird 2022 data or 2021 data and
 will preprocess using whichever version of **ebirdst** is loaded.
 Both types of fitted models can be used with BirdFlowR.
@@ -12,14 +41,15 @@ don't exist in the old version.
 ## Breaking
 *  `get_dates()` 
     * Models fit using **ebirdst** 2.2021  have `$dates` columns:
-    "interval", "date", "midpoint", "start", "end", "doy", and "week".
+    `"interval"`, `"date"`, `"midpoint"`, `"start"`, `"end"`, `"doy"`, and 
+    `"week"`.
     * Models fit with **ebirdst** 3.2022 have `$dates` columns: 
-    "timestep", "date", "label", "julian", "week".
+    `"timestep"`, `"date"`, `"label"`, `"julian"`, and `"week"`.
     * Regardless of the `$dates` format in the model object `get_dates()` 
-    returns the newer columns: "timestep", "date", "label", "julian", "week".
-    Previously it returned the older columns.
-    * Replacing `bf$dates` with `get_dates()` and adapting to the new column
-    names is recommended.
+    returns the newer columns:  `"timestep"`, `"date"`, `"label"`, `"julian"`, 
+    and `"week"`. Previously it returned the older columns.
+    * Users should replace `bf$dates` with `get_dates()` and use new column
+    names.
 
 *  Inconsistent weeks. **eBird** changed the way dates are assigned to weeks
    in the 2022 version.  See notes in `get_dates()` for details. 
@@ -48,7 +78,7 @@ don't exist in the old version.
 
 ## Updates
 
-* A number of interal changes were made to "`preprocess_species()` 
+* A number of internal changes were made to `preprocess_species()` 
   to work with  **ebirdst** v. 3.2022
   * `species` can be set to either `"example_date"` or `"yeseb-example"` to
   triggering using  **ebirdst** example data. **BirdFlowR** will silently
@@ -63,15 +93,15 @@ don't exist in the old version.
   `species_info()` (and `$species`) is unchanged.
   * A new `dates` format is now used with 2022 models.
 
-* Date lookup code was overhauled througout the package. 
+* Date lookup code was overhauled throughout the package. 
   * Most use of `$dates`  was dropped in favor of `get_dates()` to handle the 
   two date formats in use.
 
 * `preprocess_species()` snapshot tests were updated to use eBird 2022 derived
-  snapshots and are skipped if older versions of **eBirdst** are loaded, but
+  snapshots and are skipped if older versions of **ebirdst** are loaded, but
   most `preprocess_species()` tests are still run.
 
-* Several internal functions documented in `ebirdst-compatability` help
+* Several internal functions documented in `ebirdst-compatibility` help
   insulate **BirdFlowR** from the changes in the **ebirdst** API and facilitate
   working with both versions.
 
@@ -83,11 +113,12 @@ Updated tests to work with new example data and ebirdst 3.2022.0
 * Updated tests for new `amewoo` model in **BirdFlowModels** 
   (R package) v. 0.0.2.9002
 * Added formal dependency on BirdFlowModels >= 0.0.2.9002.
-* Updates to pass CRAN checks but not preproces with ebirdst 3.2022.0 
-        * Added ebird/ebirdst to remotes (to force installing dev version)
-          Revert this after changes in ebirdst  47bbdfc87 are on CRAN
+* Updates to pass CRAN checks but not preprocess with **ebirdst** 3.2022.0 
+        * Added `ebird/ebirdst` to remotes (to force installing development 
+          version). Revert this after changes in **ebirdst**  
+          47bbdfc87 are on CRAN
         * Add skip_if_unsupported_ebirdst_version() to preprocess species tests
-          as it currently does for ebirdst 3.2022.0. 
+          as it currently does for **ebirdst** 3.2022.0. 
         * Add copy of `ebirdst_weeks` to BirdFlowR as internal data.
 
 # BirdFlowR 0.1.0.9038
@@ -109,7 +140,7 @@ Trying to pass all CI checks while still using ebirdst 2.2021
 
 * Spelling
   * Checked spelling on package documentation and vignettes. 
-  * Added wordlist (extending dictionary of valid words). 
+  * Added `inst\WORDLIST` (extending dictionary of valid words). 
   * To check package spelling use `devtools::spell_check()`
   * Added section on spelling to  `./.github/CONTRIBUTING.html` 
 

R/birdflow_options.R

@@ -60,11 +60,14 @@
 #'}
 #'
 #'
-#' @param ... One of: (1) one or more named arguments where the name is a
-#'   an option and the value its new setting e.g. `verbose = FALSE` ; (2) a
-#'   single unnamed argument stating an option to retrieve e.g. `"verbose"`
-#'   with an option to retrieve; or (3) No arguments, indicating that all
-#'   options and their current settings should be returned in a list.
+#' @param ... One of:
+#'   (1) one or more named arguments where the name is a
+#'   an option and the value its new setting e.g. `verbose = FALSE` ;
+#'   (2) a single unnamed argument stating an option to retrieve e.g.
+#'   `"verbose"` with an option to retrieve.
+#'   (3) No arguments, indicating that all options and their current settings
+#'   should be returned in a list; or
+#'   (4) a single list argument with named items and their new values.
 #'
 #' @return If no arguments are used than all options will be returned as a list.
 #'   If there is a single, unnamed argument with a character value indicating an
@@ -89,7 +92,7 @@ birdflow_options <- function(...) {
   }
 
   # Process single unnamed arguments by returning the relevant option(s)
-  if (length(args) == 1 && is.null(names(args))) {
+  if (length(args) == 1 && is.null(names(args)) && !is.list(args[[1]])) {
     if (length(args[[1]]) > 1) {
       stop("You can only retrieve one option by name. Use birdflow_options() ",
            "(no arguments) to retrieve all options.")
@@ -103,10 +106,14 @@ birdflow_options <- function(...) {
     }
   }
 
+  # Special case where first argument is a list of arguments to set
+  if (length(args) == 1 && is.list(args[[1]])) {
+    args <- args[[1]]
+  }
 
   if (any(is.null(names(args))))
-    stop("You can not set and retrieve options in the same call;",
-         " an unamed argument must be the only argument.")
+    stop('Use "all" or a single argument name to retreive arguments.",
+         "If setting multiple arguments all arguments must be named.')
 
   if (!all(names(args) %in% names(.birdflow_config))) {
     missing <- setdiff(names(args), names(.birdflow_config))
@@ -159,8 +166,6 @@ birdflow_options <- function(...) {
          length(lc) == 1 && !is.na(lc))) {
       stop("Invalid cache")
     }
-    lc <- gsub("(/|\\\\)*$", base::.Platform$file.sep, lc) # force end slash
-
     .birdflow_config$cache <- lc
   }
 }

R/determine_resolution.R

@@ -1,4 +1,3 @@
-# nolint start: cyclocomp_linter.
 #' Determine BirdFlow model resolution                                     ####
 #'
 #'  Internal function to determine the resolution to use when creating a
@@ -40,7 +39,7 @@
 #' @param sp_path The species path used with \pkg{ebirdst} to download and load
 #' data
 #' @param download_species The species code used with \pkg{ebirdst} this might
-#' be "example_data" or "yebsap-example" but otherwise will be a real
+#' be `"example_data"` or `"yebsap-example"` but otherwise will be a real
 #' species code.
 #' @param project_method This is the method used to reproject it is a local
 #' variable set within `preprocess_species`.
@@ -216,4 +215,3 @@ determine_resolution <- function(sp_path,
   return(res)
 
 }
-# nolint end

R/ebirdst_compatibility.R

@@ -1,19 +1,19 @@
-#' @title ebirdst version compatability functions:
+#' @title ebirdst version compatibility functions:
 #'
 #' @description
 #' Internal functions to facilitate working with both the 2021 and 2022
 #' versions of pkg{ebirdst} despite the significant changes to the API.
 #'
-#' @name ebirdst-compatability
+#' @name ebirdst-compatibility
 NULL
 
-#' @section  ebirdst_pkg_ver:
+#' @section `ebirdst_pkg_ver()`:
 #' `ebirdst_pkg_ver()` Look up the version of the currently installed
 #' \pkg{ebirdst}.
 #' @return `ebirdst_pkg_ver()`: The installed \pkg{ebirdst} package version or
 #' `NA` if none.
 #' @keywords internal
-#' @rdname ebirdst-compatability
+#' @rdname ebirdst-compatibility
 ebirdst_pkg_ver <- function() {
   res <- tryCatch(utils::packageVersion("ebirdst"), error = identity)
   if (inherits(res, "error"))
@@ -22,7 +22,7 @@ ebirdst_pkg_ver <- function() {
 }
 
 
-#' @section res_label():
+#' @section `res_label()`:
 #' Convert resolution labels so they are appropriate for the
 #' installed \pkg{ebirdst}
 #'
@@ -38,7 +38,7 @@ ebirdst_pkg_ver <- function() {
 #'
 #' @return `res_label()`: resolution labels appropriate for installed version
 #' of \pkg{ebirdst}.
-#' @rdname ebirdst-compatability
+#' @rdname ebirdst-compatibility
 #' @keywords internal
 res_label <- function(res) {
   crosswalk <- data.frame("v2021" = c("lr", "mr", "hr"),
@@ -60,7 +60,7 @@ res_label <- function(res) {
   res
 }
 
-#' @section date_to_week():
+#' @section `date_to_week()`:
 #'
 #' This is a slightly modified copy of `ebirdst::date_to_st_week()` that
 #' allows calculating weeks from dates without depending on \pkg{ebirdst}.
@@ -71,7 +71,7 @@ res_label <- function(res) {
 #' the closest of those two. The output of
 #' `ebirdst::ebirdst_version()$version_year` or
 #' `get_metadata(bf, "ebird_version_year")` is appropriate.
-#' @rdname ebirdst-compatability
+#' @rdname ebirdst-compatibility
 #' @return `date_to_week()`: A vector of week numbers associated with `dates`
 #' @keywords internal
 date_to_week <- function(dates, version = 2022) {
@@ -92,17 +92,16 @@ date_to_week <- function(dates, version = 2022) {
   return(findInterval(jd, breaks))
 }
 
-#' @section  ebirdst_example_species():
+#' @section `ebirdst_example_species()`:
 #' Lookup the example species name that is appropriate for the
 #' installed \pkg{ebirdst}.  The example species changed
-#' from "example_data" to "yebsap-example" in version 3.2022.0.
+#' from `"example_data"` to `"yebsap-example"` in version 3.2022.0.
 #' @return `ebirdst_example_species()`: The example species name for
 #'  \pkg{ebirdst}
 #' @keywords internal
-#' @rdname ebirdst-compatability
-ebirdst_example_species <- function(){
+#' @rdname ebirdst-compatibility
+ebirdst_example_species <- function() {
    ifelse(ebirdst_pkg_ver() < "3.2022.0",
                           "example_data",
                           "yebsap-example")
 }
-

R/get_dates.R

@@ -35,10 +35,10 @@
 #'   of whether it is a leap year. The label on leap years will thus be one
 #'   day off the date of the week center for most of the year.
 #'
-#' ### Retreiving dates
+#' ### Retrieving dates
 #'  The date columns stored within a birdflow model changes depending on the
-#'  ebirdst version year, so do NOT use `bf$dates` in your code. Instead use
-#'  `get_dates()` which will always return the same (newer) column names.
+#'  \pkg{ebirdst} version year, so do NOT use `bf$dates` in your code. Instead
+#'  use`get_dates()` which will always return the same (newer) column names.
 #'
 #' @note
 #' * [truncate_birdflow()] creates models with a subset of the intervals
@@ -59,8 +59,8 @@
 #' offset}
 #' \item{julian}{The Julian date (day of year) associated with the timestep
 #' center}
-#' \item{week}{The eBirdst week number associated with the date. For full year
-#' models this is identical to `timestep` but after
+#' \item{week}{The \pkg{ebirdst} week number associated with the date. For full
+#' year models this is identical to `timestep` but after
 #' [truncation](truncate_birdflow) they will differ.}
 #'
 #' Prior to \pkg{BirdFlowR} v. 0.1.0.9040 it returned columns:

R/ignore_unused_imports.R

@@ -26,4 +26,6 @@ ignore_unused_imports <- function() {
   # TLDS Although in theory BirdFlowR only directly depends on
   # rnaturalearth it imports rnaturalearthdata to streamline
   # installation and avoid relying on rnaturalearth::install_rnaturalearthdata.
+
+  NULL
 }

R/import_birdflow.R

@@ -70,11 +70,17 @@ import_birdflow <- function(hdf5, ..., version) {
   }
 
   version <- as.character(version)
-  return(switch(as.character(version),
-                "1" = stop("Importing Version 1  BirdFlow models is no longer",
-                "supported."),
-                "2" = import_birdflow_v2(hdf5 = hdf5, ...),
-                "3" = import_birdflow_v3(hdf5 = hdf5, ...),
-                stop("Unrecognized version. ",
-                     "Was this model fit with a newer version of BirdFlowR?")))
+
+
+
+  if (version == 1)
+    stop("Importing this version ", version,
+         " BirdFlow model is no longer supported")
+
+  if (version == 2)
+    stop("Importing this version ", version,
+         " BirdFlow model is no longer supported. ",
+         "Use BirdFlowR version 0.1.0.9039 to import it.")
+
+  return(import_birdflow_v3(hdf5 = hdf5, ...))
 }