fast_recovery: Fast recovery of record using argument file

In EmmaLiTsai/recoverKBTDR: Recovering Records From Kooyman-Billups Time Depth Recorders (KBTDRs)

Fast recovery of record using argument file

Description

Recover a single record fast by using an argument csv file that passes arguments to different functions for recovery.

Usage

fast_recovery(
  filepath_trace = "WS_25_1981_trace.csv",
  col_x_trace = 1,
  col_y_trace = 2,
  filepath_timedots = "WS_25_1981_time_dots.csv",
  col_x_timedots = 1,
  col_y_timedots = 2,
  filepath_args = "WS_25_1981_args.csv"
)

Arguments

filepath_trace	file path of raw trace csv file
col_x_trace	position of trace x values column
col_y_trace	posiiton of trace y values column
filepath_timedots	file path of raw time dots csv file
col_x_timedots	posiiton of timedots x values column
col_y_timedots	position of timedots y values column
filepath_args	file path of csv file containing: radius : the length of the radius arm in cm. This is constant across all records, but some of the earlier records that I have were magnified by a slightly larger amount, and therefore the scale is slightly different. center_y: height of the pivot point of the transducer arm from depth = 0 in cm. In other words, the y-value of the center of the circle that draws the dive record. This value may change across records, but helper functions are available to provide estimates (?find_center_y). center_along_y: distance in cm used for centering the record. All time dots will be centered along y = -center_along_y time_period_min: time elapsed between two time dots. spar_h : spar value used for high depths of the records to increase resolution for the smooth_trace_dive() function. depth_thresh: depth threshold to use for the rolling mean function to determine what depths should be considered diving behavior. date_start: start of the record in y:m:d h:m:s format. max_depth: maximum depth to use for depth transformation. Only for records without a psi calibration curve. k_h : larger window to use for zoc() function, if needed. depth_bounds_l, depth_bounds_h: low and high depth bounds that encapsulate where depth = 0 is likely to be. Used for zoc() function. on_seal : time the tdr was placed on seal. In y:m:d h:m:s format. off_seal: time the tdr was taken off seal. In y:m:d h:m:s format.

Value

trace data frame after full recovery

Examples

## Not run: 
filepath <- system.file("extdata", "WS_25_1981", package = "recoverKBTDR")
filepath_trace <- paste(filepath, "WS_25_1981_trace.csv", sep = "/")
filepath_timedots <- paste(filepath, "WS_25_1981_time_dots.csv", sep = "/")
filepath_args <- paste(filepath, "WS_25_1981_args.csv", sep = "/")

fast_recovery(filepath_trace, col_x_trace = 1, col_y_trace = 2,
# filepath_timedots, col_x_timedots = 1, col_y_timedots =2, filepath_args)

## End(Not run)

EmmaLiTsai/recoverKBTDR documentation built on Aug. 29, 2024, 10:38 a.m.