seebirdr

IN DEVELOPMENT PHASE

To do:

• add license to DESCRIPTION
• improve documentation (e.g. examples)
• create hex sticker

Usage

Installation

remotes::install_github("jmhatch/seebirdr")

Database connectivity

Several of the functions require a connection to the internal NEFSC database following:

.channel <- DBI::dbConnect(odbc::odbc(), driver = [driver], DBQ = [dbq], UID = [uid], PWD = [pwd])

Or if you are already connected to the internal NEFSC network:

.channel <- DBI::dbConnect(odbc::odbc(), DSN = [dsn], UID = [uid], PWD = [pwd])

Example

An example workflow of how to use the functionality of seebirdr is provided below:

# load libraries
library(seebirdr)
library(dplyr)
library(magrittr)

# database connection
dbs_con <- .channel

# directory path to data
dir_path <- system.file("extdata", "GU1905_SeaScribe", package = "seebirdr")

# load data
gu1905 <- dir_path %>% upload_data_excel()

# format full dataset
gu1905 %<>% remove_apostrophe(observation_comment, species_common_name) %>%
  datetime_stampify(observation_timestamp) %>%
  observer_codify(dbs_con, observer)

# subset full dataset to get only sightings
sightings <- gu1905 %>% filter(!is.na(species_code) & species_code != "")

# format sightings data
sightings %<>% position_codify(dbs_con, position) %>%
  behavior_codify(dbs_con, behavior) %>%
  direction_codify(direction) %>%
  age_codify(dbs_con, age) %>%
  association_codify(dbs_con, association) %>%
  height_codify(dbs_con, flight_height) %>%
  plumage_codify(dbs_con, plumage) %>%
  sex_codify(sex)

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