Description Usage Arguments Value Examples
View source: R/BMR_calculations.R
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.
1 2 3  get_baseline_threshold(df, endpoint = "endpoint", chemical = "chemical",
threshold = "threshold", direction = "direction", potency = "POD",
plot = TRUE, n_endpoint_page = 4)

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 
an object of class 'rcurvep_thres_stats' with two named tbls:
y_exp_fit, y_lm_fit: the y value from the fitting results (exponential or linear)
dist2l_exp, dist2l_raw: the calculated distancetoline 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
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
1 2  data("zfishdev_act")
outthres < get_baseline_threshold(zfishdev_act)

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