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estimates regressions for SDA (digestion) measurements

SDA.Rd

Estimates metabolic performances associated with digestion (SDA refers to specific dynamic action, digestion costs). (updates in progress)

Usage

SDA(
  AnimalID,
  BW.animal,
  resp.V,
  r2_threshold_smr,
  sda_threshold_level,
  scaling_exponent_smr = 1,
  date_format = c("%Y-%m-%d %H:%M:%S", "GMT"),
  data.SDA = NULL,
  analyzed_MR = NULL,
  SMR_calc = TRUE,
  SMR_vals = c(NULL, NULL, NULL, NULL),
  drop_ch = NULL,
  N_Ch = 4,
  end_SDA_Ch = c(NA, NA, NA, NA),
  MLND = TRUE,
  verbose.MLND = FALSE,
  background_prior = NULL,
  background_post = NULL,
  background_slope = NULL,
  background.V = NULL,
  match_background_Ch = FALSE,
  background_gr = NULL,
  local_path = TRUE,
  handling_delay = c(0, 0, 0, 0),
  begin_smr_hr_zero = FALSE
)

Arguments

AnimalID

Indicates individual ID; must be a vector of 4 characters. When missing, enter "NA"

BW.animal

Indicates individual mass; must be a vector of 4 characters. When missing, enter "0"

resp.V

Indicated the volume (L) of respirometry chambers; must be a vector of 4 numbers (e.g., c(1, 1, 1, 1), for four 1-L respirometers)

r2_threshold_smr

R2 threshold for SMR, measurements below the threshold are excluded

sda_threshold_level

Indicates the threshold relevant to an individuals SMR to calculate the end time of recovery (the time at which metabolic rate has returned to sda_threshold). The default is the SMR level (1; At 100 percent SMR). To use 120 percent SMR as threshold for full digestion, enter sda_threshold = 1.2.

scaling_exponent_smr

Body mass scaling exponent to correct SMR values for body size. MR=aBM^b (MR = metabolic rate, BW = body mass, a = scaling coefficient [the intercept], and b = scaling exponent [the power term])

date_format

The date format used in the original data files. Argument is passed to strptime. default is c("%Y-%m-%d %H:%M:%S", "GMT").

data.SDA

The name of the SDA data file (“…analyzed.csv”; a character string); an output file from the SMR function.

analyzed_MR

The name of the data file with estimated SMR values

SMR_calc

Logical, indicates whether to calculate SMR from the present data trend

SMR_vals

allows a user to input their own SMR values

drop_ch

Indicates which channel is dropped or entirely excluded from the analysis. Must be a numerical vector, e.g., c(1,3)

N_Ch

The number of channels of the FireSting. It must be either 4 or 8.

end_SDA_Ch

Manually assigned end time (min) of digestion (SDA). The time can be assigned for each channel independently; use a numerical vector of 4 variables, one for each channel (e.g., c(120, 120, NA, 180), for 2 h, 2h, SMR level, and 3 h SDA end times, respectively)

MLND

Logical argument. If TRUE, SMR is estimated also using Mean Lowest Normal Distribution analysis. More details in Chabot et al 2016.

verbose.MLND

From MLND: A logical controlling if a text progress bar from MLND is displayed during the fitting procedure. (see 'verbose' in mclust package functions).

background_prior

The name of the analyzed background “…analyzed.csv” file, an output file from the SMR function (respiration in an empty respirometer measured before the respirometry trial).

background_post

The same as background_prior, only post respirometry trial

background_slope

Manually assigned background slope used to correct metabolic rate in all individuals. Provide numeric value in mgO2 L-1 h-1v

background.V

Manually assigned respirometry chamber volumes (L). A vector with 4 numeric variables, one for each channel.

match_background_Ch

Logical. If TRUE, the background respiration is estimated and applied channel-specific. The background_prior and background_post are used to estimate background respiration specific to each channel (or individual), which then is used to correct each individual’s MO2 independently. By default, the mean background respiration rate from all channels is calculated and applied to correct all individual’s MO2

background_gr

Specify whether to assume that bacterial growth (thus respiration rates) changed linearly or in exponentially across the duration of the respirometry trial. Must specify either "linear" or "exp": metabolic rate values across the given trial are corrected using the estimated background values from the indicated growth curve. Both background_prior and background_post must be provided to enable this.

local_path

Logical. If TRUE (default) all returned files will be saved in the local working directory.

handling_delay

a delay of SDA due to handling, anesthesia, or any other experimental factor. in hours

begin_smr_hr_zero

logical. Whether to force the integral SDA costs still be calculated from hour 0, that is assumed to be at SMR level (refer to sda_threshold_level)

Value

The output from print