download_w2_data: Download Turtle Tagging data from WAMTRAM2.

In dbca-wa/wastdr: WA Sea Turtle Database 'WAStD' API Wrapper

Download Turtle Tagging data from WAMTRAM2.

Description

This function requires an installed ODBC driver for MS SQL Server 2012. The database credentials are handled via environment variables.

Usage

download_w2_data(
  ord = c("YmdHMS", "Ymd"),
  tz = "Australia/Perth",
  db_drv = Sys.getenv("W2_DRV"),
  db_srv = Sys.getenv("W2_SRV"),
  db_name = Sys.getenv("W2_DB"),
  db_user = Sys.getenv("W2_UN"),
  db_pass = Sys.getenv("W2_PW"),
  db_port = Sys.getenv("W2_PT"),
  verbose = wastdr::get_wastdr_verbose(),
  dsn = Sys.getenv("W2_DSN"),
  use_rodbc = Sys.getenv("W2_RODBC", FALSE),
  save = NULL,
  compress = "xz"
)

Arguments

ord	Lubridate orders, default: c("YmdHMS", "Ymd").
tz	Timezone, default: "Australia/Perth".
db_drv	Database driver, default: Sys.getenv("W2_DRV") which should resolve to e.g. "/usr/lib/x86_64-linux-gnu/odbc/libtdsodbc.so".
db_srv	Database server, default: Sys.getenv("W2_SRV"), which should resolve to a valid server hostname, e.g. "myserver.corporateict.domain".
db_name	The database name, default: Sys.getenv("W2_DB"), which should resolve to a valid database name, e.g. turtle_tagging.
db_user	The read-permitted database user, default: Sys.getenv("W2_UN").
db_pass	The database user's password, default: Sys.getenv("W2_PW").
db_port	The database port, default: Sys.getenv("W2_PT"), which should resolve to a numeric port, e.g. 1234.
verbose	Whether to show debug messages. Default: wastdr::get_wastdr_verbose()
dsn	The DSN for Windows systems, default: Sys.getenv("W2_DSN").
use_rodbc	Whether to use the RODBC library (if TRUE, best for Windows systems), or the odbc/DBI library (if FALSE, default, best for GNU/Linux systems).
save	If supplied, the filepath to save the data object to.
compress	The saveRDS compression parameter, default: "xz". Set to FALSE for faster writes and reads but larger filesize.

Details

In Windows systems, create a user defined DSN with settings

• name WAMTRAMPROD

• server kens-mssql-001-prod.corporateict.domain

• SQL auth using login ID and password entered by user

• trust server certificate (this is where odbc falls over)

Add to .Renviron: W2_RODBC=TRUE W2_DSN="WAMTRAMPROD"

Value

A structure of class "wamtram_data" containing a named list of sanitised tables from the Turtle Tagging DB:

• Metadata:

  • downloaded_on

  • w2_tables

• Personnel:

  • persons

• Data entry:

  • data_entry_batches "TRT_ENTRY_BATCHES"

  • data_entry

  • data_entry_operators

• Lookups:

  • lookup_beach_positions

  • lookup_body_parts

  • lookup_conditions

  • lookup_damage_causes

  • lookup_damage_codes

  • lookup_datum_codes

  • lookup_egg_count_methods

  • lookup_id_types

  • lookup_measurement_types

  • lookup_pit_tag_states

  • lookup_sample_tissue_type

  • lookup_tag_states

• Places:

  • sites

• Encounters:

  • enc

    • location_code: the original rookery (where first encountered)

    • place_code: the place of the encounter (where currently found)

  • enc_qa

• Observations:

  • obs_flipper_tags

  • obs_pit_tags

  • obs_damages

  • obs_measurements

  • obs_samples

• Reconstructed:

  • reconstructed_pit_tags

  • reconstructed_tags

  • reconstructed_turtles

See Also

Other wamtram: map_wamtram(), w2_online()

Examples

## Not run: 
# Credentials are set in .Renviron

wamtram_data <- download_w2_data()


# develop:
ord <- c("YmdHMS", "Ymd")
tz <- "Australia/Perth"
verbose <- wastdr::get_wastdr_verbose()

con <- DBI::dbConnect(
  odbc::odbc(),
  Driver   = Sys.getenv("W2_DRV"),
  Server   = Sys.getenv("W2_SRV"),
  Database = Sys.getenv("W2_DB"),
  UID      = Sys.getenv("W2_UN"),
  PWD      = Sys.getenv("W2_PW"),
  Port     = Sys.getenv("W2_PT")
)

## End(Not run)

dbca-wa/wastdr documentation built on Nov. 20, 2022, 12:25 p.m.