inst/doc/fqar.R

In fqar: Floristic Quality Assessment Tools for R

## ----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()