get_baseline_threshold: Get baseline noise threshold through activity data calculated...

Description Usage Arguments Value Examples

View source: R/BMR_calculations.R

Description

Given an activity dataset after 'run_curvep_batch()' and 'withdraw()', the function calculates the pooled variance of potency information (i.e., POD parameter) across chemicals derives the baseline noise threshold, which is the lowest threshold that variance of POD is sufficiently reduced and stabilized.

Usage

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get_baseline_threshold(df, endpoint = "endpoint", chemical = "chemical",
  threshold = "threshold", direction = "direction", potency = "POD",
  plot = TRUE, n_endpoint_page = 4)

Arguments

df

a tbl

endpoint

a chr that represents the column name of endpoint in 'df'

chemical

a chr that represents the column name of chemical in 'df'

threshold

a chr that represents the column name of threshold in 'df'

direction

a chr that represents the column name of direction in 'df'

potency

a chr that represents the column name of potency in 'df'

plot

default = TRUE, for diagnostic plots

n_endpoint_page

number of endpoints to be plotted per page

Value

an object of class 'rcurvep_thres_stats' with two named tbls:

stats
  • y_exp_fit, y_lm_fit: the y value from the fitting results (exponential or linear)

  • dist2l_exp, dist2l_raw: the calculated distance-to-line value based on the y from exponential fit or original y

  • curvature: the calculated curvature value using smooth.spline fit results

  • p1_raw, p2_raw: the index of points for the line using the original y values

outcome
  • thresDist_raw: the identified threshold based on distance approach using the original y values

  • thresDist_exp: the identified threshold based on distance approach using the y values from the exponential fitting results

  • thresComment: the flag to suggest whether to use the thresDist (OK, cautionary, check)

  • p1_raw, p2_raw: the index of points for the line using the original y values

  • cor_exp_fit, cor_lm_fit: the Pearson's correlation between the y values from fitting (exponential or linear) and the original y values

Examples

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data("zfishdev_act")
outthres <- get_baseline_threshold(zfishdev_act)

moggces/Rcurvep documentation built on May 28, 2019, 3:11 p.m.