Updated tests to work with new example data and ebirdst 3.2022.0 (#145)

Update tests for BirdFlowModels v 0.0.2.9002 and package new ebirdst Updated tests to work with new amewoo model in BirdFlowModels Changes to pass tests with ebirdst 3.2022.0 * Added ebird/ebirdst to remotes (to install dev version) Revert this after changes in ebirdst 47bbdfc87 are on CRAN * Add skip_if_unsupported_ebirdst_version() to preprocess species tests * Add copy of ebirdst_weeks to BirdFlowR as internal data
birdflow-science · Dec 5, 2023 · 43beefa · 43beefa
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -14,3 +14,4 @@
 ^man/figures/BirdFlowR_transparent.png
 ^man/figures/BirdFlowR_logo.R
 ^\.lintr
+^data-raw$
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: BirdFlowR
 Title: Predict and Visualize Bird Movement
-Version: 0.1.0.9038
+Version: 0.1.0.9039
 Authors@R: 
     c(person("Ethan", "Plunkett",  email = "plunkett@umass.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-4405-2251")),
@@ -11,9 +11,8 @@ Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Suggests: 
-    auk,
-    BirdFlowModels (>= 0.0.2),
-    ebirdst (<= 2.2021.3),
+    BirdFlowModels (>= 0.0.2.9002),
+    ebirdst,
     knitr,
     ragg,
     rmarkdown,
@@ -47,7 +46,10 @@ Imports:
     viridisLite
 VignetteBuilder: knitr
 Remotes:
-  birdflow-science/BirdFlowModels
+  birdflow-science/BirdFlowModels,
+  ebird/ebirdst
 URL: https://birdflow-science.github.io/BirdFlowR/, https://github.com/birdflow-science/BirdFlowR
 BugReports: https://github.com/birdflow-science/BirdFlowR/issues
 Language: en-US
+Depends: 
+    R (>= 3.5)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# BirdFlowR 0.1.0.9039
+2023-11-21*
+
+* Updated tests for new `amewoo` model in **BirdFlowModels** (R package)* 0.0.2.9002
+* Now depends on 
+
 # BirdFlowR 0.1.0.9038
 2023-11-16
 

diff --git a/R/get_dates.R b/R/get_dates.R
@@ -1,11 +1,31 @@
 #' Retrieve dates component of a BirdFlow model
 #'
-#' `get_dates()` retrieves the dates component of a BirdFlow model.  Most of
-#' the resulting data is derived from [ebirdst::ebirdst_weeks] and added
-#' to the model object by   [preprocess_species()].  [truncate_birdflow()]
-#' creates models with a subset of the intervals and renames them
-#' `1:[n_timesteps()]` of the truncated model so if it has been used the
-#' data may differ from [ebirdst::ebirdst_weeks()].
+#' `get_dates()` retrieves the dates component of a BirdFlow model.
+#'
+#'  \pkg{BirdFlowR} uses the same conventions for assigning dates to
+#'  eBird "weeks" as \pkg{ebirdst}. This changed with the 2022 release.
+#'
+#' \pkg{ebirdst} version <= 2.2021.3
+#'
+#' * Date table is derived from `ebirdst::ebirdst_weeks` and added
+#' to the model object by [preprocess_species()].
+#' * Julian date is converted to a proportion with `(jd - 0.5)/366`.
+#' * 52 even ranges are assigned to 0 to 1 and the proportional date is then
+#'   compared to these thresholds.
+#' * In a non-leap year two weeks have 8 days and the last week has 6.
+#' * In a leap-year two weeks have 8 days.
+#' * All other weeks have 7 days.
+#'
+#' \pkg{ebirdst} version  >= 3.2022.0
+#' * \pkg{ebirdst} dropped `ebirdst_weeks` and  `ebirdst::date_to_st_week()`
+#' *  Dates are assigned to weeks by finding which evenly spaced Julian date of
+#' a week center Julian date of the input is closest to.
+#' * All weeks but the last have 7 days.
+#' * On non-leap-years the last week has 8 days, on leap years it has 9.
+#'
+#' [truncate_birdflow()] creates models with a subset of the intervals
+#' and renames them `1:[n_timesteps()]` of the truncated model so if it
+#' has been used the data may differ from `ebirdst::ebirdst_weeks`.
 #'
 #' @param bf A BirdFlow object to retrieve dates from.
 #'
@@ -16,7 +36,7 @@
 #' equivalent to the week of the year but with truncated models may
 #' not be.}
 #'  \item{date}{The date associated with the interval's midpoint.}
-#'  \item{midpoint, star, end}{The midpoint, start, and end of each interval
+#'  \item{midpoint, start, end}{The midpoint, start, and end of each interval
 #' as a proportion of the total year that has elapsed.}
 #' \item{doy}{The day of year associated with the midpoint of each interval.}
 #' @export

diff --git a/R/import_birdflow.R b/R/import_birdflow.R
@@ -39,13 +39,7 @@
 #'
 #' @param hdf5 Path to an HDF5 file containing a fitted BirdFlow model.
 #' @param ... Arguments to be passed to a version specific internal function.
-#'    Likely will only be used with
-#'    version 1 which takes two additional arguments: \describe{
-#'        \item{tiff}{Path to the model GeoTIFF.}
-#'        \item{species}{An eBird species code.  It should appear in the
-#'   `species_code` column of the data.frame returned by
-#'   [auk::get_ebird_taxonomy()]}
-#'    }
+#'  Currently deprecated was used in early BirdFlow models.
 #' @param version (optional) force reading of BirdFlow models as a particular
 #'   version. Normally, this will be determined from metadata in the HDF5
 #'   file.

diff --git a/R/preprocess_species.R b/R/preprocess_species.R
@@ -374,7 +374,9 @@ preprocess_species <- function(species = NULL,
 
   # Reformat and export dates
 
-  dates <- as.data.frame(ebirdst::ebirdst_weeks)
+  dates <- as.data.frame(ebirdst_weeks)
+    # Note ebirdst_weeks now stored in BirdFlowR is a copy of the ebirdst
+    # version that was dropped with the 2022 data release (nov 2023)
   names(dates)[names(dates) == "week_number"] <- "interval"
   dates$doy <- lubridate::yday(dates$date) + 0.5
   dates$date <- as.character(dates$date)

diff --git a/R/sysdata.rda b/R/sysdata.rda
diff --git a/data-raw/ebirdst_weeks.R b/data-raw/ebirdst_weeks.R
@@ -0,0 +1,42 @@
+#  This adds ebirdst_weeks as an internal dataset to the BirdFlowR package
+#  so that it no longer needs to pull it from ebirdst.
+#
+#  Note: Internal data is stored in R/sysdata.rda and must all be created in
+#  a single call.
+#
+#  ebirdst_weeks is from ebirdst version 2.2021.3.  It is added to BirdFlowR
+#  for use when preprocessing ebirdst 2021 data (with the old ebird package)
+#  without referencing the copy in that package as doing so - even conditioned
+#  on version - breaks CRAN checks when checking against newer ebirdst package
+#  versions that do not have it.
+
+#  ebirdst_weeks.rds added to data-raw with Using ebirdst v 2.2021.3
+#  with this: saveRDS(ebirdst::ebirdst_weeks, "data-raw/ebirdst_weeks.rds")
+#  which never need to run again.
+
+#  Add the data-raw/ebirdst_weeks.rds to R/sysdata.rda
+ebirdst_weeks <- readRDS("./data-raw/ebirdst_weeks.rds")
+usethis::use_data(ebirdst_weeks, internal = TRUE)
+
+### ROxygen Comments below copied from ebirdst/R/data.R  v 2.2021.3
+### They will not be rendered but kept here for reference.
+
+#' eBird Status and Trends weeks
+#'
+#' eBird Status and Trends predictions are made for each of 52 weeks of the
+#' year. This data frame provides the boundaries of the weeks.
+#'
+#' @format A data frame with 52 rows and 5 columns:
+#' \describe{
+#'   \item{week_number}{Integer week number from 1-52.}
+#'   \item{date}{Date of the midpoint of the week.}
+#'   \item{week_midpoint}{Date of the midpoint of the week expressed as a
+#'         fraction of the year, i.e. a number from 0-1.}
+#'   \item{week_start}{Date of the start of the week expressed as a fraction of
+#'         the year, i.e. a number from 0-1.}
+#'   \item{week_end}{Date of the end of the week expressed as a fraction of the
+#'         year, i.e. a number from 0-1.}
+#' }
+"ebirdst_weeks"
+
+
diff --git a/data-raw/ebirdst_weeks.rds b/data-raw/ebirdst_weeks.rds
diff --git a/man/get_dates.Rd b/man/get_dates.Rd
diff --git a/man/import_birdflow.Rd b/man/import_birdflow.Rd
diff --git a/tests/testthat/_snaps/calc_movement_vectors.md b/tests/testthat/_snaps/calc_movement_vectors.md
@@ -3,7 +3,7 @@
     Code
       mv
     Output
-          i start end start_x start_y   end_x   end_y       weight
-      1 797     5   6 1514879 5182031 1516433 5178565 6.633053e-08
-      2 798     5   6 1594875 5182031 1594266 5179248 8.513777e-08
+          i start end  start_x start_y     end_x    end_y       weight
+      1 154     5   6 -1725000  375000 -822249.8 60429.72 8.105351e-05
+      2 155     5   6 -1575000  375000 -820426.2 62271.54 4.196808e-06
 
diff --git a/tests/testthat/_snaps/distribution_performance.md b/tests/testthat/_snaps/distribution_performance.md
@@ -4,10 +4,10 @@
       a
     Output
                         year spring-migration
-      min_step_cor    0.9726           0.9811
-      mean_step_cor   0.9918           0.9926
-      min_distr_cor   0.9479           0.9742
-      mean_distr_cor  0.9891           0.9906
-      st_traverse_cor 0.9863           0.9547
-      md_traverse_cor 0.9865           0.9554
+      min_step_cor    0.9645           0.9830
+      mean_step_cor   0.9881           0.9935
+      min_distr_cor   0.9615           0.9804
+      mean_distr_cor  0.9865           0.9920
+      st_traverse_cor 0.9863           0.9846
+      md_traverse_cor 0.9820           0.9907
 
diff --git a/tests/testthat/_snaps/evaluate_performance.md b/tests/testthat/_snaps/evaluate_performance.md
@@ -4,18 +4,18 @@
       stats
     Output
       $mean_step_cor
-      [1] 0.9918336
+      [1] 0.9881073
       
       $min_step_cor
-      [1] 0.9726291
+      [1] 0.9645225
       
       $traverse_cor
-      [1] 0.9863106
+      [1] 0.9863234
       
       $mean_distr_cor
-      [1] 0.9890949
+      [1] 0.9865373
       
       $min_distr_cor
-      [1] 0.9478764
+      [1] 0.9615346
       
 
diff --git a/tests/testthat/_snaps/get_transition.md b/tests/testthat/_snaps/get_transition.md
@@ -3,48 +3,48 @@
     Code
       histogram_counts
     Output
-         upper_bound   count
-      1        1e-04 2904514
-      2        2e-03    2678
-      3        3e-03     696
-      4        4e-03     425
-      5        5e-03     339
-      6        6e-03     252
-      7        7e-03     187
-      8        8e-03     146
-      9        9e-03     122
-      10       1e-02      79
-      11       2e-02     392
-      12       4e-02     165
-      13       6e-02      52
-      14       8e-02      18
-      15       1e-01      16
-      16       2e-01      22
-      17       6e-01      20
-      18       1e+00     313
+         upper_bound count
+      1        1e-04 10718
+      2        2e-03  1204
+      3        3e-03    65
+      4        4e-03    42
+      5        5e-03    22
+      6        6e-03    21
+      7        7e-03    13
+      8        8e-03    14
+      9        9e-03     7
+      10       1e-02     3
+      11       2e-02    45
+      12       4e-02    23
+      13       6e-02    13
+      14       8e-02     5
+      15       1e-01     2
+      16       2e-01     5
+      17       6e-01    11
+      18       1e+00   104
 
 # get_transition() is consistent for backwards transitions
 
     Code
       histogram_counts
     Output
-         upper_bound   count
-      1        1e-04 2904499
-      2        2e-03    2889
-      3        3e-03     673
-      4        4e-03     436
-      5        5e-03     339
-      6        6e-03     242
-      7        7e-03     196
-      8        8e-03     129
-      9        9e-03     123
-      10       1e-02      89
-      11       2e-02     280
-      12       4e-02      95
-      13       6e-02      20
-      14       8e-02      22
-      15       1e-01      15
-      16       2e-01      46
-      17       6e-01      25
-      18       1e+00     318
+         upper_bound count
+      1        1e-04  9307
+      2        2e-03  1874
+      3        3e-03   208
+      4        4e-03   124
+      5        5e-03    94
+      6        6e-03    72
+      7        7e-03    44
+      8        8e-03    49
+      9        9e-03    32
+      10       1e-02    34
+      11       2e-02   167
+      12       4e-02   103
+      13       6e-02    44
+      14       8e-02    19
+      15       1e-01    11
+      16       2e-01    26
+      17       6e-01    12
+      18       1e+00    97