A set of “use” functions help you search, read, manipulate, plot, and save ecocomDP data.

Read

Read data from host APIs to get the newest authoritative version.

Read from the host API:

dataset_1 <- read_data("edi.193.5")
#> Reading edi.193.5
#>  [0%] Downloaded 0 bytes...
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#>
#> Validating edi.193.5:
#>   Required tables
#>   Column names
#>   Required columns
#>   Column classes
#>   Datetime formats
#>   Primary keys
#>   Composite keys
#>   Referential integrity
#>   Latitude and longitude format
#>   Latitude and longitude range
#>   Elevation
#>   variable_mapping

Read from the host API with filters when datasets are large (currently only for NEON datasets):

dataset_2 <- read_data(
  id = "neon.ecocomdp.20120.001.001", 
  site = c("COMO", "LECO", "SUGG"),
  startdate = "2017-06", 
  enddate = "2019-09",
  check.size = FALSE)
#> Finding available files
#>   |==================================================================| 100%
#> 
#> Downloading files totaling approximately 1.588594 MB
#> Downloading 20 files
#>   |====================================================================| 100%
#> 
#> Unpacking zip files using 1 cores.
#>   |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
#> Stacking operation across a single core.
#> Stacking table inv_fieldData
#>   |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
#> Stacking table inv_persample
#>   |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
#> Stacking table inv_pervial
#>   |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s  
#> Stacking table inv_taxonomyProcessed
#>   |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02s  
#> Stacking table inv_taxonomyRaw
#>   |++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=02s  
#> Copied the most recent publication of validation file to /stackedFiles
#> Copied the most recent publication of categoricalCodes file to /stackedFiles
#> Copied the most recent publication of variable definition file to /stackedFiles
#> Finished: Stacked 5 data tables and 3 metadata tables!
#> Stacking took 4.732454 secs
#> Joining, by = c("uid", "sampleID")
#> Joining, by = "sampleID"
#>
#> Validating neon.ecocomdp.20120.001.001:
#>   Required tables
#>   Column names
#>   Required columns
#>   Column classes
#>   Datetime formats
#>   Primary keys
#>   Composite keys
#>   Referential integrity
#>   Latitude and longitude format
#>   Latitude and longitude range
#>   Elevation
#>   variable_mapping

A data are returned as a list of metadata, tables, and validation issues (if there are any). The dataset identifier is at the top of this list.

str(dataset_1)
#> List of 4
#>  $ id               : chr "edi.193.5"
#>  $ metadata         :List of 1
#>   ..$ url: chr "https://portal.edirepository.org/nis/mapbrowse?packageid=edi.193.5"
#>  $ tables           :List of 8
#>   ..$ location             : tibble [10 x 6] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ location_id       : chr [1:10] "a1" "a2" "1" "2" ...
#>   .. ..$ location_name     : chr [1:10] "block__Ridge" "block__Valley" "plot__1" "plot__2" ...
#>   .. ..$ latitude          : num [1:10] NA NA 42.5 42.5 42.5 ...
#>   .. ..$ longitude         : num [1:10] NA NA -72.2 -72.2 -72.2 ...
#>   .. ..$ elevation         : num [1:10] NA NA 220 220 220 220 220 220 220 220
#>   .. ..$ parent_location_id: chr [1:10] NA NA "a2" "a2" ...
#>   ..$ taxon                : tibble [53 x 5] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ taxon_id          : chr [1:53] "1" "2" "3" "4" ...
#>   .. ..$ taxon_rank        : chr [1:53] "Species" "Species" "Species" "Species" ...
#>   .. ..$ taxon_name        : chr [1:53] "Aphaenogaster fulva" "Aphaenogaster picea" "Camponotus chromaiodes" "Camponotus herculeanus" ...
#>   .. ..$ authority_system  : chr [1:53] "ITIS" "ITIS" "ITIS" "ITIS" ...
#>   .. ..$ authority_taxon_id: chr [1:53] "578383" "578440" "575766" "575995" ...
#>   ..$ observation          : tibble [2,931 x 9] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ observation_id: chr [1:2931] "1" "2" "3" "4" ...
#>   .. ..$ event_id      : chr [1:2931] "1" "1" "1" "1" ...
#>   .. ..$ package_id    : chr [1:2931] "edi.193.5" "edi.193.5" "edi.193.5" "edi.193.5" ...
#>   .. ..$ location_id   : chr [1:2931] "4" "4" "4" "4" ...
#>   .. ..$ datetime      : Date[1:2931], format: "2003-06-01" "2003-06-01" ...
#>   .. ..$ taxon_id      : chr [1:2931] "1" "2" "53" "2" ...
#>   .. ..$ variable_name : chr [1:2931] "abundance" "abundance" "abundance" "abundance" ...
#>   .. ..$ value         : num [1:2931] 2 2 1 2 1 1 1 1 1 1 ...
#>   .. ..$ unit          : chr [1:2931] "number" "number" "number" "number" ...
#>   ..$ location_ancillary   : tibble [8 x 6] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ location_ancillary_id: chr [1:8] "1" "2" "3" "4" ...
#>   .. ..$ location_id          : chr [1:8] "1" "2" "3" "4" ...
#>   .. ..$ datetime             : Date[1:8], format: NA NA ...
#>   .. ..$ variable_name        : chr [1:8] "treatment" "treatment" "treatment" "treatment" ...
#>   .. ..$ value                : chr [1:8] "Girdled" "Logged" "HemlockControl" "Logged" ...
#>   .. ..$ unit                 : chr [1:8] NA NA NA NA ...
#>   ..$ taxon_ancillary      : tibble [742 x 7] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ taxon_ancillary_id: chr [1:742] "1" "2" "3" "4" ...
#>   .. ..$ taxon_id          : chr [1:742] "1" "1" "1" "1" ...
#>   .. ..$ datetime          : Date[1:742], format: NA NA ...
#>   .. ..$ variable_name     : chr [1:742] "subfamily" "hl" "rel" "rll" ...
#>   .. ..$ value             : chr [1:742] "Myrmicinae" "1.1582" "0.172681748" "1.323778277" ...
#>   .. ..$ unit              : chr [1:742] NA "millimeter" "millimeter" "millimeter" ...
#>   .. ..$ author            : chr [1:742] NA NA NA NA ...
#>   ..$ observation_ancillary: tibble [8,793 x 5] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ observation_ancillary_id: chr [1:8793] "1" "2" "3" "4" ...
#>   .. ..$ observation_id          : chr [1:8793] "1" "1" "1" "2" ...
#>   .. ..$ variable_name           : chr [1:8793] "trap.type" "trap.num" "moose.cage" "trap.type" ...
#>   .. ..$ value                   : chr [1:8793] "bait" "1 hour" NA "bait" ...
#>   .. ..$ unit                    : chr [1:8793] NA NA NA NA ...
#>   ..$ dataset_summary      : tibble [1 x 7] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ package_id                 : chr "edi.193.5"
#>   .. ..$ original_package_id        : chr "knb-lter-hfr.118.33"
#>   .. ..$ length_of_survey_years     : num 15
#>   .. ..$ number_of_years_sampled    : num 13
#>   .. ..$ std_dev_interval_betw_years: num 0.67
#>   .. ..$ max_num_taxa               : num 53
#>   .. ..$ geo_extent_bounding_box_m2 : num 913451
#>   ..$ variable_mapping     : tibble [19 x 6] (S3: tbl_df/tbl/data.frame)
#>   .. ..$ variable_mapping_id: chr [1:19] "1" "2" "3" "4" ...
#>   .. ..$ table_name         : chr [1:19] "observation" "observation_ancillary" "observation_ancillary" "observation_ancillary" ...
#>   .. ..$ variable_name      : chr [1:19] "abundance" "trap.type" "trap.num" "moose.cage" ...
#>   .. ..$ mapped_system      : chr [1:19] "Darwin Core" "The Ecosystem Ontology" NA NA ...
#>   .. ..$ mapped_id          : chr [1:19] "http://rs.tdwg.org/dwc/terms/individualCount" "http://purl.dataone.org/odo/ECSO_00001591" NA NA ...
#>   .. ..$ mapped_label       : chr [1:19] "individualCount" "type of trap" NA NA ...
#>  $ validation_issues: list()

Manipulate

Working with a “flattened” dataset simplifies common tasks (select, filter, arrange, group, summarize). A “flat” version is where all tables have been joined and spread wide except for the core observation variables, which remain in long form.

flat <- flatten_data(dataset_1)
flat
#> # A tibble: 2,931 x 46
#>   observation_id event_id datetime   variable_name value unit   trap.type
#>   <chr>          <chr>    <date>     <chr>         <dbl> <chr>  <chr>    
#> 1 1              1        2003-06-01 abundance         2 number bait     
#> 2 2              1        2003-06-01 abundance         2 number bait     
#> 3 3              1        2003-06-01 abundance         1 number bait     
#> 4 4              1        2003-06-01 abundance         2 number bait     
#> # ... with 2,927 more rows, and 39 more variables: trap.num <chr>,
#> #   moose.cage <chr>, location_id <chr>, location_name <chr>, block <chr>,
#> #   plot <chr>, latitude <dbl>, longitude <dbl>, elevation <dbl>,
#> #   treatment <chr>, taxon_id <chr>, taxon_rank <chr>, taxon_name <chr>,
#> #   authority_system <chr>, authority_taxon_id <chr>, behavior <chr>,
#> #   biogeographic.affinity <chr>, colony.size <chr>, feeding.preference <chr>,
#> #   hl <dbl>, unit_hl <chr>, nest.substrate <chr>, primary.habitat <chr>, ...

Plot

Visually explore data with the plotting functions:

plot_taxa_diversity(flat, time_window_size = "month")

plot_taxa_diversity(flat, time_window_size = "year")


plot_taxa_rank(flat, facet_var = "location_id")


plot_taxa_occur_freq(
  data = flat,
  facet_var = "location_id",
  color_var = "taxon_rank")


plot_taxa_abund(
  data = flat,
  facet_var = "location_id",
  color_var = "taxon_rank",
  trans = "log10")
#> Warning: Removed 78 rows containing non-finite values (stat_boxplot).


plot_sites(flat)
#> Warning in showSRID(uprojargs, format = "PROJ", multiline = "NO", prefer_proj =
#> prefer_proj): Discarded datum unknown in Proj4 definition

Save

Save local copies and read them back in later.

Save a local copy as .rds:

datasets <- list(dataset_1, dataset_2)
mypath <- paste0(tempdir(), "/data")
dir.create(mypath)

save_data(datasets, mypath)

Read a local copy from .rds

datasets <- read_data(from = paste0(mypath, "/datasets.rds"))
#> Validating edi.193.5:
#>   Required tables
#>   Column names
#>   Required columns
#>   Column classes
#>   Datetime formats
#>   Primary keys
#>   Composite keys
#>   Referential integrity
#>   Latitude and longitude format
#>   Latitude and longitude range
#>   Elevation
#>   variable_mapping
#> Validating neon.ecocomdp.20120.001.001:
#>   Required tables
#>   Column names
#>   Required columns
#>   Column classes
#>   Datetime formats
#>   Primary keys
#>   Composite keys
#>   Referential integrity
#>   Latitude and longitude format
#>   Latitude and longitude range
#>   Elevation
#>   variable_mapping

Save a local copy as .csv:

save_data(datasets, mypath, type = ".csv")

Read a local copy from .csv:

datasets <- read_data(from = mypath)
#> Validating edi.193.5:
#>   Required tables
#>   Column names
#>   Required columns
#>   Column classes
#>   Datetime formats
#>   Primary keys
#>   Composite keys
#>   Referential integrity
#>   Latitude and longitude format
#>   Latitude and longitude range
#>   Elevation
#>   variable_mapping
#> Validating neon.ecocomdp.20120.001.001:
#>   Required tables
#>   Column names
#>   Required columns
#>   Column classes
#>   Datetime formats
#>   Primary keys
#>   Composite keys
#>   Referential integrity
#>   Latitude and longitude format
#>   Latitude and longitude range
#>   Elevation
#>   variable_mapping