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COMPASS-DOE / grossMethane

analysis code for paired data sets of laboratory-incubations of gross methane flux and associated field net methane and CO2 flux rates
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trial 2 data for AGU abstract #7

Closed kendalynnm closed 2 years ago

kendalynnm commented 2 years ago

Hi @bpbond, The branch "semi-automated processing" has all three Picarro csv files with the necessary meta-data for processing in the 'toy' model. Let me know if you have any questions about column ids - and warning that the default output column names are not very R friendly. Thank you! Kendal

bpbond commented 2 years ago

Hi @kendalynnm -

What do "HP" and "HR" stand for in the column names?

Ignoring units for the moment, does this look right?

This field in toy code... ...corresponds to this column in Picarro data
cal12CH4ml 12CO2 Mean
cal13CH4ml 13CO2 Mean
bpbond commented 2 years ago

Next question. All samples have a second T4 observation that's, well, weird; and sample 10 has a wacky T5 13C number:

> filter(incdat, id==10)
# A tibble: 7 × 8
# Groups:   id [1]
  Timestamp           id    round   vol mean12CO2 mean13CO2 notes                                        Elapsed        
  <dttm>              <fct> <chr> <dbl>     <dbl>     <dbl> <chr>                                        <drtn>         
1 2022-07-21 16:09:00 10    T0       10      378.      4.32 NA                                           0.00000000 days
2 2022-07-21 17:50:00 10    T1       10     1328.     15.1  NA                                           0.07013889 days
3 2022-07-21 20:39:00 10    T2       10     2290.     25.8  NA                                           0.18750000 days
4 2022-07-21 22:33:00 10    T3       10     3425.     38.7  something went deeply wrong with this sample 0.26666667 days
5 2022-07-22 20:13:00 10    T4       10     4141.     46.8  zero air added                               1.16944444 days
6 2022-07-22 20:23:00 10    T4        2      885.      9.76 zero air added                               1.17638889 days
7 2022-07-22 22:04:00 10    T5       10     4108.    767.   no zero air added                            1.24652778 days

t4

Drop these data? Or something else?

bpbond commented 2 years ago

samples were in the fridge overnight between T3 and T4

Hmmm.

bpbond commented 2 years ago

Dropping T4 vol=2 data and removing that one very high T5 13CO2:

over_time

Uh oh...that can't be right.

bpbond commented 2 years ago

Opening a PR for you to play with. Initial results:

ap_pred

   id        P       k
   <chr> <dbl>   <dbl>
 1 1     0.433 -0.0262
 2 2     6.80  -0.378 
 3 3     2.66  -0.187 
 4 4     3.91  -0.254 
 5 5     5.22  -0.304 
 6 6     4.48  -0.250 
 7 7     2.09  -0.159 
 8 8     4.89  -0.324 
 9 9     5.35  -0.408 
10 10    6.27  -0.337