## ----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()