longitudinal studies error metric

[qiime_user_jack]

Hello Qiime2 team,

Here is a snippet of the code. There is cut off from putty.exe. The python program runs. Can you please clarify what they mean by “metric” – bold.

The code follows the code you posted on github, however, we must be missing something. Any insight or suggestions are welcome and appreciated.
longitudinal-notebooks/analysis.ipynb at master · caporaso-lab/longitudinal-notebooks · GitHub

Sincerely,
Sally

………..
Lachnospiraceae='d__Bacteria; p__Firmicutes; c__Clostridia; o__Lachnospirales; f__Lachnospiracea$
Catenisphaera='d__Bacteria; p__Firmicutes; c__Bacilli; o__Erysipelotrichales; f__Erysipelotricha$
NK4A136_group='d__Bacteria; p__Firmicutes; c__Clostridia; o__Lachnospirales; f__Lachnospiraceae; Prevotella='d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Prevotellaceae; g
RC9_gut_group='d__Bacteria; p__Bacteroidota; c__Bacteroidia; o__Bacteroidales; f__Rikenellaceae;$

“stuff_to_test = [(Lachnospiraceae, t304, '304'),
(Catenisphaera, t304, '304'),
(NK4A136_group, t04, '04'),
(Prevotella, t03, '03'),
(RC9_gut_group, t304, '304')]

print("t304=",t304)

for target, tab, time in stuff_to_test:
# extract the genus name for saving files
print("time=",time,target,"\n\n")
print ("tab=",tab)
target_name = target.split('__')[-1]
# run LME
viz, = longitudinal.actions.linear_mixed_effects(
metadata=sample_md,metric="target", state_column='time', individual_id_column='pig',
group_columns='treatment', table=tab)
# save qzv

viz.save(os.path.join(results_dir, 'feat-volatility-genus_may6_2022', 'lme-' + target_name $

viz, = longitudinal.actions.linear_mixed_effects(
File "", line 2, in linear_mixed_effects
File "/root/miniconda2/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 245, in bound_callable
outputs = self.callable_executor(scope, callable_args,
File "/root/miniconda2/envs/qiime2-2021.11/lib/python3.8/site-packages/qiime2/sdk/action.py", line 453, in callable_executor
ret_val = self._callable(output_dir=temp_dir, **view_args)
File "/root/miniconda2/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_longitudinal/_longitudinal.py", line 186, in linear_mixed_effects
metadata = _add_metric_to_metadata(table, metadata, metric)
File "/root/miniconda2/envs/qiime2-2021.11/lib/python3.8/site-packages/q2_longitudinal/_utilities.py", line 448, in _add_metric_to_metadata
raise ValueError(
ValueError: metric must be a valid metadata or feature table column.

[J_Sh (sally)]

Any updates to this post? Thanks

[lizgehret]

Hi @J_Sh,

Thanks for your patience, and welcome to the forum!

The answer to your post's title question 'longitudinal studies error metric' can be found in our documentation on linear mixed effects modeling - I'd highly recommend reading through that (linked below) before moving forward here!

https://docs.qiime2.org/2022.2/plugins/available/longitudinal/linear-mixed-effects/

With regards to what's going on with your code - it seems to be a bit jumbled, and looks as though some segments may have been copy/pasted together, which is most likely where this error is coming from. In your code, you've set metric to "target" (from longitudinal.actions.linear_mixed_effects) - and the error message indicates that your chosen metric must be a valid metadata or feature table column.

Without wading in too deep here, I'd recommend starting with a fresh Python notebook or equivalent method (however you have been running your code thus far), and making sure you understand how each segment of code works that you are adding/writing. Print statements will be very helpful when debugging.

Cheers