Add getters/counters for new API endpoints

[regetz]

What

This PR adds vb_get_*() and vb_count_*() wrapper functions for the following new endpoints:

• GET /taxon-importances
• GET /stem-counts
• GET /strata
• GET /named-places
• GET /roles
• GET /user-datasets

... and also enables the use of cross-resource queries for plot observations associated with a given named place or user dataset, e.g. vb_get_plot_observations("ds.199635") to get all plot observations associated with dataset ds.199635.

Why

So that package users can conveniently leverage these new API features.

How

For each of the 6 new resource types:

• Updated the table code lookup vector
• Added a new vb_get_*() wrapper
• Added a new vb_count_*() wrapper

Testing and documentation

• Included roxygen-based documentation for all new functions, and generated man files
• Added functional tests with JSON input fixtures as needed, for all new vb_get_*() and vb_count_*() functions
• Added new sets of API integration and e2e tests
• Updated these API tests with respect to the plot observation response schema
• Added integration tests for the new cross-resource queries for plot observations
• Verified that all tests pass, and test coverage is 100%
• Verified that R check passes: devtools::check(cran=TRUE, remote = TRUE, incoming = TRUE)

Demo

Taxon importances

> vb_count_taxon_importances()
[1] 3599923

> vb_get_taxon_importances(limit=5)
# A tibble: 5 × 12
  tm_code  to_code  ob_code sr_code  stratum_name  cover cover_code basal_area
  <chr>    <chr>    <chr>   <chr>    <chr>         <dbl> <chr>           <int>
1 tm.67083 to.64982 ob.2948 sr.17458 Nonvascular  63.3   05                 NA
2 tm.67084 to.64982 ob.2948 NA       <All>        63.3   05                 NA
3 tm.67085 to.64983 ob.2948 sr.17458 Nonvascular   0.562 01                 NA
4 tm.67086 to.64983 ob.2948 NA       <All>         0.562 01                 NA
5 tm.67087 to.64984 ob.2948 NA       <All>         0.188 01                 NA
# ℹ 4 more variables: biomass <int>, inference_area <int>, stratum_base <int>,
#   stratum_height <int>

Stem counts

> vb_count_stem_counts()
[1] 600241

> vb_get_stem_counts(limit=5)
# A tibble: 5 × 12
  ob_code to_code  tm_code  sr_code  stratum_name sc_code diameter
  <chr>   <chr>    <chr>    <chr>    <chr>        <chr>      <dbl>
1 ob.3062 to.68185 tm.74081 sr.22374 Canopy       sc.2056     22
2 ob.3062 to.68185 tm.74081 sr.22374 Canopy       sc.2057     17.2
3 ob.3062 to.68185 tm.74081 sr.22374 Canopy       sc.2058     12.4
4 ob.3062 to.68185 tm.74081 sr.22374 Canopy       sc.2059     14.3
5 ob.3062 to.68185 tm.74081 sr.22374 Canopy       sc.2060     13.4
# ℹ 5 more variables: diameter_accuracy <int>, height <int>,
#   height_accuracy <int>, count <dbl>, taxon_area <int>

Strata

> vb_count_strata()
[1] 347097

> vb_get_strata(limit=5)
# A tibble: 5 × 11
  ob_code sr_code  name        height  base cover description sm_code
  <chr>   <chr>    <chr>        <int> <int> <dbl>       <int> <chr>
1 ob.2948 sr.17456 Tall Shrub      NA    NA     0          NA sm.5
2 ob.2948 sr.17457 Short Shrub     NA    NA     0          NA sm.5
3 ob.2948 sr.17458 Nonvascular     NA    NA    90          NA sm.5
4 ob.2948 sr.17459 Herbaceous      NA    NA     7          NA sm.5
5 ob.2948 sr.17460 Epiphyte        NA    NA     0          NA sm.5
# ℹ 3 more variables: stratum_method_name <chr>, sy_code <chr>,
#   stratum_type_name <chr>

Named places

> vb_count_named_places()
[1] 64563

> vb_get_named_places(limit=5)
# A tibble: 5 × 8
  np_code system                name  description code  owner rf_label obs_count
  <chr>   <chr>                 <chr>       <int> <chr> <int> <chr>        <dbl>
1 np.1    continent             Afri…          NA f        NA USLC pl…         0
2 np.2    area|country|territo… Afri…          NA fc       NA USLC pl…         0
3 np.3    area|country|territo… Afri…          NA fe       NA USLC pl…         0
4 np.4    area|country|territo… Afri…          NA fq       NA USLC pl…         0
5 np.5    area|country|territo… Afri…          NA ff       NA USLC pl…         0

Plot observations for a given named place

> vb_get_plot_observations("np.1000", limit=5)
# A tibble: 5 × 11
  author_plot_code pl_code  latitude longitude  area elevation country
  <chr>            <chr>       <dbl>     <dbl> <dbl>     <dbl> <chr>
1 016-01-0047      pl.79523     32.0     -81.8  1000        42 United States
2 016-01-0048      pl.79524     32.0     -81.8  1000        43 United States
3 016-01-0062      pl.79538     31.9     -82.1  1000        27 United States
4 016-01-0063      pl.79539     31.9     -82.1  1000        26 United States
5 016-01-0064      pl.79540     31.9     -82.1  1000        30 United States
# ℹ 4 more variables: state_province <chr>, ob_code <chr>,
#   author_obs_code <chr>, year <dbl>

Roles

> vb_count_roles()
[1] 21

> vb_get_roles(limit=5)
# A tibble: 5 × 3
  ar_code name         description
  <chr>   <chr>        <chr>
1 ar.16   Author       NA
2 ar.17   Contact      VegBank Contact Party
3 ar.18   PI           Primary Investigator
4 ar.19   Data Manager NA
5 ar.34   Classifier   NA

User datasets

> vb_count_user_datasets()
[1] 57

> vb_get_user_datasets(limit=5)
# A tibble: 5 × 10
  ds_code   accession_code     start                stop name  description type
  <chr>     <chr>              <dttm>              <int> <chr> <chr>       <chr>
1 ds.196903 VB.ds.196903.6A18… 2005-08-13 23:49:13    NA exam… "some plot… norm…
2 ds.196904 VB.ds.196904.2707… 2005-08-13 23:51:54    NA exam… "some plot… norm…
3 ds.196917 VB.ds.196917.OBCC… 2005-08-24 13:00:38    NA test2 ""          norm…
4 ds.199634 VB.ds.199634.CEGL… 2013-06-10 07:00:00    NA CEGL…  NA         norm…
5 ds.199635 VB.ds.199635.CEGL… 2013-06-10 07:00:00    NA CEGL…  NA         norm…
# ℹ 3 more variables: owner_label <chr>, owner_email <chr>, obs_count <dbl>

Plot observations for a given user dataset

> vb_get_plot_observations("ds.199635", limit=5)
# A tibble: 5 × 11
  author_plot_code pl_code  latitude longitude  area elevation country
  <chr>            <chr>       <dbl>     <dbl> <dbl>     <dbl> <chr>
1 002-01-0042      pl.79110     34.7     -79.2   200        52 United States
2 003-02-0082      pl.79271     34.7     -78.6  1000        29 United States
3 003-03-0085      pl.79297     34.6     -78.4  1000        20 United States
4 003-06-0101      pl.79388     34.8     -79.6  1000        80 United States
5 044-07-0613      pl.80450     34.3     -79.3  1000        22 United States
# ℹ 4 more variables: state_province <chr>, ob_code <chr>,
#   author_obs_code <chr>, year <dbl>

[regetz]

Merging and moving forward :)