Athemis/pyKinetics
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calculate adjusted r-squared

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This commit is contained in:
Alexander Minges 2016-04-14 14:04:18 +02:00
parent b8a950fbc8
commit 65ce7e7e72
2 changed files with 22 additions and 11 deletions
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7
analyze-cli.py
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@ -267,6 +267,7 @@ def main():
# grab fitting window from provided arguments
fitting_window = (args.start, args.end)
# scaling of axes in kinetics plot
if args.log_x:
logx = args.log_x
else:
@ -276,17 +277,21 @@ def main():
logy = args.log_y
else:
logy = False
# suppress calculation of Michaelis-Menten kinetics
if args.no_michaelis:
no_mm = args.no_michaelis
else:
no_mm = False
# do Hill kinetics
if args.hill:
do_hill = args.hill
else:
do_hill = False
# perform global fit of kinetic function(s) to all replicates
# instead of their means
if args.replicates:
fit_to_replicates = args.replicates
else:

26
libkinetics/__init__.py
View file

@ -82,22 +82,28 @@ class Replicate():
) = stats.linregress(x_for_fit, y_for_fit)
r_squared = r_value ** 2
n = len(x_for_fit[0]) # number of observations
k = 2 # independent variables: slope and intercept
# calculcate adjusted R²
adj_r_squared = r_squared - (1 - r_squared) * k/(n - k - 1)
conc = '{} {}'.format(self.owner.concentration,
self.owner.concentration_unit)
self.logger.info('Linear fit for {} #{}:'.format(conc, self.num))
if r_squared < 0.9 and r_squared > 0.7:
msg = ' r-squared: {} < 0.9; Check fit manually!'
self.logger.warning(msg.format(round(r_squared, 4)))
elif r_squared < 0.7:
msg = ' r-squared: {} < 0.7; Linear fit probably failed!'
self.logger.warning(msg.format(round(r_squared, 4)))
else:
msg = ' r-squared: {}'
self.logger.info(msg.format(round(r_squared, 4)))
if adj_r_squared < 0.9 and adj_r_squared > 0.7:
msg = ' adjusted R² < 0.9; Check fit manually!'
self.logger.warning(msg.format(round(adj_r_squared, 4)))
elif adj_r_squared < 0.7:
msg = ' adjusted R² < 0.7; Linear fit probably failed!'
self.logger.warning(msg.format(round(adj_r_squared, 4)))
self.logger.info(' R²/adjusted R²: {}/{}'.format(round(r_squared, 4), round(adj_r_squared, 4)))
self.logger.info(' slope: {}'.format(slope))
if slope < 0:
self.logger.info(' Slope is negative. Will use absolute '
self.logger.info(' → Slope is negative. Will use absolute '
'value for further calculations!')
self.logger.info(' intercept: {}'.format(slope))