Read FORCIS data

These functions read one specific csv file of the FORCIS database (see below) stored in the folder path. The function download_forcis_db() must be used first to store locally the database.

Usage

read_cpr_north_data(
  path,
  version = options()$forcis_version,
  check_for_update = options()$forcis_check_for_update
)

read_cpr_south_data(
  path,
  version = options()$forcis_version,
  check_for_update = options()$forcis_check_for_update
)

read_plankton_nets_data(
  path,
  version = options()$forcis_version,
  check_for_update = options()$forcis_check_for_update
)

read_pump_data(
  path,
  version = options()$forcis_version,
  check_for_update = options()$forcis_check_for_update
)

read_sediment_trap_data(
  path,
  version = options()$forcis_version,
  check_for_update = options()$forcis_check_for_update
)

Arguments

path

a character of length 1. The folder in which the FORCIS database has been saved.

version

a character of length 1. The version number (with two numbers, e.g. 08 instead of 8) of the FORCIS database to use. Default is the latest version. Note that this argument can be handle with the global option forcis_version. For example, if user calls options(forcis_version = "07"), the version 07 will be used by default for the current R session. Note that it is recommended to use the latest version of the database.

check_for_update

a logical. If TRUE (default) the function will check if a newer version of the FORCIS database is available on Zenodo and will print an informative message. Note that this argument can be handle with the global option forcis_check_for_update. For example, if user calls options(forcis_check_for_update = FALSE), the message to download the latest version will be disabled for the current R session.

Value

A tibble. See https://zenodo.org/doi/10.5281/zenodo.7390791 for a preview of the datasets.

Details

• read_plankton_nets_data() reads the FORCIS plankton nets data

• read_pump_data() reads the FORCIS pump data

• read_cpr_north_data() reads the FORCIS CPR North data

• read_cpr_south_data() reads the FORCIS CPR South data

• read_sediment_trap_data() reads the FORCIS sediment traps data

See also

download_forcis_db() to download the complete FORCIS database.

Examples

# \donttest{
# Folder in which the database will be saved ----
# N.B. In this example we use a temporary folder but you should select an
# existing folder (for instance "data/").
path <- tempdir()

# Download the database ----
download_forcis_db(path, timeout = 300)
#> The file 'iho_oceans_boundaries.rds' already exists. If you want to download again this file please use the argument 'overwrite'.
#> The file 'FORCIS_cpr_north_11072024.csv' already exists. If you want to download again this file please use the argument 'overwrite'.
#> The file 'FORCIS_data_template.xlsx' already exists. If you want to download again this file please use the argument 'overwrite'.
#> The file 'FORCIS_taxonomy_levels.xlsx' already exists. If you want to download again this file please use the argument 'overwrite'.
#> The file 'FORCIS_net_11072024.csv' already exists. If you want to download again this file please use the argument 'overwrite'.
#> The file 'FORCIS_cpr_south_11072024.csv' already exists. If you want to download again this file please use the argument 'overwrite'.
#> The file 'FORCIS_pump_11072024.csv' already exists. If you want to download again this file please use the argument 'overwrite'.
#> The file 'FORCIS_trap_11072024.csv' already exists. If you want to download again this file please use the argument 'overwrite'.

# Import plankton nets data ----
plankton_nets_data <- read_plankton_nets_data(path)
# }