## ----eval = FALSE-------------------------------------------------------------
#  databases <- index_fqa_databases()
#  head(databases)
#  #> # A tibble: 6 × 4
#  #>   database_id region                                year description
#  #>         <dbl> <chr>                                <dbl> <chr>
#  #> 1         206 "Allegheny Plateau, Glaciated"        2021 Faber-Lang…
#  #> 2          70 "Appalachian Mtn (EPA Ecoregions 66…  2013 Gianopulos…
#  #> 3         108 "Atlantic Coastal Pine Barrens (8.5…  2017 NEIWPCC FQ…
#  #> 4         136 "Atlantic Coastal Pine Barrens (8.5…  2018 NatureServ…
#  #> 5         204 "Atlantic Coastal Pine Barrens (8.5…  2021 Faber-Lang…
#  #> 6           1 "Chicago Region"                      1994 Swink, F. …

## ----eval = FALSE-------------------------------------------------------------
#  missouri_fqas <- index_fqa_assessments(database_id = 63)
#  head(missouri_fqas)
#  #> # A tibble: 6 × 5
#  #>      id assessment                     date       site  practitioner
#  #>   <dbl> <chr>                          <date>     <chr> <chr>
#  #> 1 30687 Bridge School Prairie Survey   2023-09-02 Vari… Nathan Aaron
#  #> 2 30115 Leatherwood Hollow Survey (Up… 2023-07-13 Pion… Nathan Aaro…
#  #> 3 29965 chi                            2023-06-28 CHI … chi
#  #> 4 29949 CHI List                       2023-06-27 CHI … ns
#  #> 5 29622 Interior Woodlands Survey      2023-05-26 WS I… Nathan Aaron
#  #> 6 29750 Wetland B                      2023-05-24 STL … Marion Well…

## ----eval = FALSE-------------------------------------------------------------
#  missouri_transects <- index_fqa_transects(database_id = 63)
#  head(missouri_transects)
#  #> # A tibble: 6 × 5
#  #>      id assessment        date       site               practitioner
#  #>   <dbl> <chr>             <date>     <chr>              <chr>
#  #> 1  8434 Hawn-Array-2-2023 2023-09-04 Hawn State Park    Parks
#  #> 2  8415 STJ-Array2-2023   2023-08-29 St. Joe State Park Parks
#  #> 3  8414 STJ-3-23          2023-07-20 St. Joe State Park Parks
#  #> 4  8347 TUCKER DNA        2023-07-06 DNA Floristic Sam… Lord/ Sutton
#  #> 5  8052 Golden DNA23      2023-06-28 DNA Floristic Sam… Lord/Sutton
#  #> 6  8053 Lindens DNA23     2023-06-28 DNA Floristic Sam… Lord/Sutton

## ----eval = FALSE-------------------------------------------------------------
#  grasshopper <- download_assessment(assessment_id = 25961)

## ----eval = FALSE-------------------------------------------------------------
#  ambrose <- download_assessment_list(database_id = 63,
#                                      site == "Ambrose Farm")

## ----eval = FALSE-------------------------------------------------------------
#  class(ambrose)
#  #> [1] "list"
#  length(ambrose)
#  #> [1] 3

## ----eval = FALSE-------------------------------------------------------------
#  rock_garden <- download_transect(transect_id = 6875)
#  golden <- download_transect_list(database_id = 63,
#                                   site == "Golden Prairie")

## ----eval = FALSE-------------------------------------------------------------
#  grasshopper_species <- assessment_inventory(grasshopper)
#  glimpse(grasshopper_species)
#  #> Rows: 317
#  #> Columns: 9
#  #> $ scientific_name <chr> "Acer rubrum var. rubrum", "Acer saccharum…
#  #> $ family          <chr> "Sapindaceae", "Sapindaceae", "Asteraceae"…
#  #> $ acronym         <chr> "ACERUR", "ACESUG", "ACHMIL", "ACOCAL", "A…
#  #> $ nativity        <chr> "native", "native", "native", "non-native"…
#  #> $ c               <dbl> 5, 5, 1, 0, 8, 2, 5, 4, 4, 0, 2, 7, 6, 4, …
#  #> $ w               <dbl> 0, 3, 3, -5, 3, 3, -3, 5, 3, -3, 3, -5, 3,…
#  #> $ physiognomy     <chr> "tree", "tree", "forb", "forb", "forb", "f…
#  #> $ duration        <chr> "perennial", "perennial", "perennial", "pe…
#  #> $ common_name     <chr> "red maple", "sugar maple", "yarrow", "swe…

## ----eval = FALSE-------------------------------------------------------------
#  grasshopper_summary <- assessment_glance(grasshopper)
#  names(grasshopper_summary)
#  #>  [1] "title"                     "date"
#  #>  [3] "site_name"                 "city"
#  #>  [5] "county"                    "state"
#  #>  [7] "country"                   "fqa_db_region"
#  #>  [9] "fqa_db_publication_year"   "fqa_db_description"
#  #> [11] "custom_fqa_db_name"        "custom_fqa_db_description"
#  #> [13] "practitioner"              "latitude"
#  #> [15] "longitude"                 "weather_notes"
#  #> [17] "duration_notes"            "community_type_notes"
#  #> [19] "other_notes"               "private_public"
#  #> [21] "total_mean_c"              "native_mean_c"
#  #> [23] "total_fqi"                 "native_fqi"
#  #> [25] "adjusted_fqi"              "c_value_zero"
#  #> [27] "c_value_low"               "c_value_mid"
#  #> [29] "c_value_high"              "native_tree_mean_c"
#  #> [31] "native_shrub_mean_c"       "native_herbaceous_mean_c"
#  #> [33] "total_species"             "native_species"
#  #> [35] "non_native_species"        "mean_wetness"
#  #> [37] "native_mean_wetness"       "tree"
#  #> [39] "shrub"                     "vine"
#  #> [41] "forb"                      "grass"
#  #> [43] "sedge"                     "rush"
#  #> [45] "fern"                      "bryophyte"
#  #> [47] "annual"                    "perennial"
#  #> [49] "biennial"                  "native_annual"
#  #> [51] "native_perennial"          "native_biennial"

## ----eval = FALSE-------------------------------------------------------------
#  ambrose_summary <- assessment_list_glance(ambrose)

## ----eval = FALSE-------------------------------------------------------------
#  rock_garden_species <- transect_inventory(rock_garden)
#  rock_garden_summary <- transect_glance(rock_garden)
#  golden_summary <- transect_list_glance(golden)

## ----eval = FALSE-------------------------------------------------------------
#  rock_garden_phys <- transect_phys(rock_garden)
#  glimpse(rock_garden_phys)
#  #> Rows: 6
#  #> Columns: 6
#  #> $ physiognomy                       <chr> "Native forb", "Native g…
#  #> $ frequency                         <dbl> 115, 53, 20, 6, 4, 1
#  #> $ coverage                          <dbl> 628, 413, 180, 125, 78, 1
#  #> $ relative_frequency_percent        <dbl> 51.6, 23.8, 9.0, 2.7, 1.…
#  #> $ relative_coverage_percent         <dbl> 26.1, 17.2, 7.5, 5.2, 3.…
#  #> $ relative_importance_value_percent <dbl> 38.9, 20.5, 8.3, 4.0, 2.…

## ----eval = FALSE-------------------------------------------------------------
#  # Obtain a tidy data frame of all co-occurrences in the 1995 Southern Ontario database:
#  ontario <- download_assessment_list(database = 2)
#  
#  # Extract inventories as a list:
#  ontario_invs <- assessment_list_inventory(ontario)
#  
#  # Enumerate all co-occurrences in this database:
#  ontario_cooccurrences <- assessment_cooccurrences(ontario_invs)
#  
#  # Summarize co-occurrences in this database, one row per target species:
#  ontario_cooccurrences <- assessment_cooccurrences_summary(ontario_invs)

## ----eval = FALSE-------------------------------------------------------------
#  aster_profile <- species_profile("Aster lateriflorus",
#                                   ontario_invs,
#                                   native = TRUE)
#  aster_profile
#  #> # A tibble: 11 × 4
#  #>    species            target_c cospecies_c cospecies_n
#  #>    <chr>                 <dbl>       <dbl>       <dbl>
#  #>  1 Aster lateriflorus        3           0         176
#  #>  2 Aster lateriflorus        3           1          58
#  #>  3 Aster lateriflorus        3           2         139
#  #>  4 Aster lateriflorus        3           3         209
#  #>  5 Aster lateriflorus        3           4         212
#  #>  6 Aster lateriflorus        3           5         186
#  #>  7 Aster lateriflorus        3           6         127
#  #>  8 Aster lateriflorus        3           7          83
#  #>  9 Aster lateriflorus        3           8          26
#  #> 10 Aster lateriflorus        3           9           9
#  #> 11 Aster lateriflorus        3          10          15
#  
#  species_profile_plot("Aster lateriflorus",
#                       ontario_invs,
#                       native = TRUE)

## ----eval = FALSE-------------------------------------------------------------
#  ggplot(missouri, aes(x = native_species,
#                       y = native_mean_c)) +
#    geom_point() +
#    geom_smooth() +
#    scale_x_continuous(trans = "log10") +
#    labs(x = "Native Species (logarithmic scale)",
#         y = "Native Mean C") +
#    theme_minimal()