FathomR is an R package designed to interface with the Fathom API. It allows users to authenticate, retrieve, and filter telemetry and deployment data from acoustic telemetry studies with ease. The resulting dataframes are in a format compatable with the actel package.
To install the package directly from GitHub, use the following commands in R:
# Install devtools if not already installed
install.packages("devtools")
# Install the package from GitHub
devtools::install_github("Eugies/FathomR")
# Load the package
library(FathomR)To authenticate user login details and select workspace, use the following commands in R:
# Authenticate using Fathom username and password
auth <- authenticate_wrapper()
# This will launch a browser window to log in and return a token and workspace ID
# Use default client ID if askedTo fetch all receiver deployment data, use the following commands in R:
# deployments
deployments<-get_deployments(token = auth$token, # if not specified then authentication will prompt a new login
ws_id = auth$ws_id) # if not specified then authentication will prompt a new loginTo fetch Spatial data of receivers, use the following commands in R:
# spatial
spatial <- get_spatial(
StationName = "all",
#StationName = c("BB", "Creole"), # For example: all stations containing BB or Creole (case sensative)
#Receivers = c("1361", "800"), # For example: all receivers containing these substrings
Receivers = "all",
#Area = list(lon = c(30.2, 30.6), lat = c(-89, -88)), #For example: all receivers inside the specified longitude and latitude
token = auth$token, # if not specified then authentication will prompt a new login
ws_id = auth$ws_id # if not specified then authentication will prompt a new login
)To fetch biometrics data of tagged individuals, use the following commands in R:
# biometrics
biometrics <- get_biometrics(token = auth$token, # if not specified then authentication will prompt a new login
ws_id = auth$ws_id) # if not specified then authentication will prompt a new loginTo fetch biometrics data of tagged individuals, use the following commands in R:
# detections
detections <- get_detections(
common_names = "all", # all common names
#common_names = c("Cownose',"Gulf Sturgeon), # specify common name
transmitters = "all",
#transmitters = c("A69-1604-60495","A69-1303-46570","A69-9001-16605"), # For example: To Specify specific Transmitters
transmitterTypes = "all", # for all transmitter types
#transmitterTypes = c("V13","V16"), # For example: to only get V13 and V16 transmitter types
start_date = "all", # use "all" or leave unspecified for all dates, or specify a start date in yyyy-mm-dd
end_date = "all", # use "all" or leave unspecified for all dates, or specify an end date in yyyy-mm-dd
token = auth$token, # if not specified then authentication will prompt a new login
ws_id = auth$ws_id # if not specified then authentication will prompt a new login
)