The licorer package is designed to aid in the reading and processing of LI-6800 data files. It uses the R package units to ensure that values recorded with units have the correct scientific units.
from GitHub:
# install.packages("remotes")
remotes::install_github("muir-lab/licorer")
and load licorer
library("licorer")
The licorer package streamlines reading and validating data from raw
LI-6800 files in R. To read a raw LI-6800 data file, use the licor()
method. This will create a licor
object, which stores the data in a
tibble data object with header data stored in attributes.
library(licorer)
test_data <- read_li6800_raw(system.file("extdata", "2020-06-23_ECT_hib",
package = "licorer", mustWork = TRUE))
Example
obs |
time_Sys |
elapsed |
date |
hhmmss_Sys |
TIME_GasEx |
E |
A |
Ca |
Ci |
Pci |
Pca |
gsw |
gbw |
gtw |
gtc |
Rabs |
TleafEB |
TleafCnd |
SVPleaf |
RHcham |
VPcham |
SVPcham |
VPDleaf |
LatHFlux |
SenHFlux |
NetTherm |
EBSum |
blfa_1 |
blfa_2 |
blfa_3 |
Leak |
LeakPct |
CorrFact |
CorrFactPct |
Fan |
DarkAdaptedID |
Fo |
Fm |
Fv |
Fv/Fm |
Adark |
LightAdaptedID |
Fs |
Fm’ |
PhiPS2 |
PS2/1 |
Qabs_fs |
Afs |
ETR |
Fv’/Fm’ |
PhiCO2 |
NPQ |
DarkPulseID |
Fo’ |
Fv’ |
qP |
qN |
qP_Fo |
qN_Fo |
ID |
P1_dur |
P2_dur |
P3_dur |
P1_Qmax |
P1_Fmax |
P2_dQdt |
P3_(delta)F |
Qin |
Qabs |
alpha |
convert |
S |
K |
Geometry |
TIME_Meas |
CO2_s |
CO2_r |
H2O_s |
H2O_r |
Flow |
Pa |
(delta)Pcham |
Tair |
Tleaf |
Tleaf2 |
Offset |
Offset2 |
Fan_speed |
Qamb_in |
Qamb_out |
Q |
f_red |
f_blue |
f_farred |
F |
Q_modavg |
F_dc |
Pc |
Tled |
TDigital |
TPreamp |
TPwrSpy |
TDrive |
Q_red |
Q_blue |
Q_farred |
TSPF |
F_avg |
dF/dt |
dF_dc/dt |
F_dc_avg |
period |
time_Match |
hhmmss_Match |
count |
co2_adj |
h2o_adj |
co2_at |
h2o_at |
co2_cv |
h2o_cv |
(delta)CO2:MN |
(delta)CO2:SLP |
(delta)CO2:SD |
(delta)CO2:OK |
F:MN |
F:SLP |
F:SD |
F:OK |
(delta)H2O:MN |
(delta)H2O:SLP |
(delta)H2O:SD |
(delta)H2O:OK |
Stable |
Total |
State |
MatchValveR |
MatchValveS |
MatchCO2 |
MatchH2O |
DIAG |
Flow_s |
Flow_r |
Txchg |
Tirga |
Tchopper |
Ts |
Tr |
CO2_% |
Desiccant_% |
Humidifier_% |
Txchg_sp |
CO2_r_sp |
H2O_r_sp |
SS_s |
SS_r |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
1592958038 [s] |
0 |
2020-06-23 14:20:37 |
14:20:37 |
1592958012 [s] |
0.0018939311 [mol/m^2/s] |
7.3868079 [µmol/m^2/s] |
401.4031 [µmol/mol] |
262.9298 [µmol/mol] |
26.61081 [Pa] |
40.62553 [Pa] |
0.09444315 [mol/m^2/s] |
2.279358 [mol/m^2/s] |
0.09232184 [mol/m^2/s] |
0.057887775 [mol/m^2/s] |
161.8296 [W/m^2] |
33.76014 [°C] |
32.37763 [°C] |
4.878100 [kPa] |
56.45732 [%] |
2.881449 [kPa] |
5.103765 [kPa] |
1.996651 [kPa] |
-83.52236 [W/m^2] |
98.74384103 [W/m^2] |
9.899975210 [W/m^2] |
186.951094 [W/m^2] |
-0.04197882 [1] |
0.04712491 [1] |
3.507846 [1] |
194 [µmol/s] |
39 [%] |
1 [1] |
0 [%] |
52311 [µmol/s] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [µmol/m^2/s] |
|
0 [1] |
0 [1] |
0 [1] |
0.5 [1] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [1] |
0.008781668 [µmol/µmol] |
0 [1] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [ms] |
0 [ms] |
0 [ms] |
0 [µmol/m^2/s] |
0 [1] |
0 [mol/m2/s2] |
0 [1] |
999.9622 [µmol/m^2/s] |
841.1623 [µmol/m^2/s] |
0.8411941 [1] |
0.1923881 [J/µmol] |
6 [cm^2] |
0.5 [1] |
0: Broadleaf |
1592958012 [s] |
401.4031 [µmol/mol] |
411.1766 [µmol/mol] |
28.47034 [mmol/mol] |
26.26298 [mmol/mol] |
500.1482 [µmol/s] |
101.1728 [kPa] |
0.03603505 [kPa] |
33.18117 [°C] |
32.37763 [°C] |
999.9 [°C] |
0 [°C] |
0 [°C] |
10006.049 [rpm] |
0 [µmol/m^2/s] |
2.905401 [µmol/m^2/s] |
999.9622 [µmol/m^2/s] |
0.9599963 [1] |
0.04000360 [1] |
0 [1] |
1100.612903 [1] |
5.00059 [µmol/m^2/s] |
11069.732 [1] |
9587.389 [1] |
42.80800 [°C] |
45.50000 [°C] |
44.30400 [°C] |
45.17500 [°C] |
45.12500 [°C] |
955.1610 [µmol/m^2/s] |
39.80065 [µmol/m^2/s] |
0 [µmol/m^2/s] |
1592958037 [s] |
1084.758846 [1] |
-43.6229060 [1/min] |
-442.92650 [1/min] |
10908.308 [1] |
15 [s] |
0 [s] |
NA |
0 [1] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
0 [µmol/mol] |
0 [mmol/mol] |
0 [%] |
0 [%] |
-1.6875699 [µmol/mol] |
15.34503554 [µmol/min/mol] |
2.44379221 [µmol/mol] |
0 [1] |
1086.678235 [1] |
-46.3353045 [1/min] |
4.5338709 [1] |
0 [1] |
0.2848114 [mmol/mol] |
-3.6686192 [mmol/min/mol] |
0.57995206 [mmol/mol] |
0 [1] |
0 [1] |
3 [1] |
0/3 |
100 [%] |
100 [%] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
2 [1] |
292.802 [µmol/s] |
269.236 [µmol/s] |
32.0927 [°C] |
30.9563 [°C] |
29.9984 [°C] |
31.0102 [°C] |
30.9831 [°C] |
19.7327 [%] |
26.5253 [%] |
0.00000 [%] |
32.0765 [°C] |
408.431 [µmol/mol] |
26.8672 [mmol/mol] |
98.6756 [%] |
100.223 [%] |
2 |
1592958098 [s] |
60 |
2020-06-23 14:21:37 |
14:21:37 |
1592958090 [s] |
0.0016173786 [mol/m^2/s] |
7.4274865 [µmol/m^2/s] |
400.2433 [µmol/mol] |
239.0048 [µmol/mol] |
24.18958 [Pa] |
40.50847 [Pa] |
0.08015180 [mol/m^2/s] |
2.278125 [mol/m^2/s] |
0.07861749 [mol/m^2/s] |
0.049271339 [mol/m^2/s] |
161.8387 [W/m^2] |
33.91098 [°C] |
32.49805 [°C] |
4.911354 [kPa] |
56.81719 [%] |
2.909643 [kPa] |
5.121062 [kPa] |
2.001711 [kPa] |
-71.32640 [W/m^2] |
91.30744429 [W/m^2] |
9.167485207 [W/m^2] |
190.987280 [W/m^2] |
-0.04194523 [1] |
0.04708719 [1] |
3.505630 [1] |
0 [µmol/s] |
0 [%] |
1 [1] |
0 [%] |
52489 [µmol/s] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [µmol/m^2/s] |
|
0 [1] |
0 [1] |
0 [1] |
0.5 [1] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [1] |
0.008829534 [µmol/µmol] |
0 [1] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [ms] |
0 [ms] |
0 [ms] |
0 [µmol/m^2/s] |
0 [1] |
0 [mol/m2/s2] |
0 [1] |
1000.0181 [µmol/m^2/s] |
841.2093 [µmol/m^2/s] |
0.8411941 [1] |
0.1923882 [J/µmol] |
6 [cm^2] |
0.5 [1] |
0: Broadleaf |
1592958090 [s] |
400.2434 [µmol/mol] |
409.9327 [µmol/mol] |
28.74868 [mmol/mol] |
26.86371 [mmol/mol] |
500.0212 [µmol/s] |
101.1765 [kPa] |
0.03316085 [kPa] |
33.24148 [°C] |
32.49805 [°C] |
999.9 [°C] |
0 [°C] |
0 [°C] |
9997.678 [rpm] |
0 [µmol/m^2/s] |
2.903450 [µmol/m^2/s] |
1000.0181 [µmol/m^2/s] |
0.9599950 [1] |
0.04000482 [1] |
0 [1] |
1055.070000 [1] |
5.00059 [µmol/m^2/s] |
10606.690 [1] |
9587.918 [1] |
42.76200 [°C] |
45.48577 [°C] |
44.25000 [°C] |
45.12500 [°C] |
45.12500 [°C] |
955.2116 [µmol/m^2/s] |
39.80387 [µmol/m^2/s] |
0 [µmol/m^2/s] |
1592958097 [s] |
1055.026154 [1] |
-20.4061538 [1/min] |
-212.27009 [1/min] |
10605.688 [1] |
15 [s] |
0 [s] |
NA |
0 [1] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
0 [µmol/mol] |
0 [mmol/mol] |
0 [%] |
0 [%] |
-9.7459783 [µmol/mol] |
1.39610467 [µmol/min/mol] |
0.13998168 [µmol/mol] |
0 [1] |
1055.893235 [1] |
-21.1096632 [1/min] |
2.0798271 [1] |
0 [1] |
1.9123088 [mmol/mol] |
-0.5532088 [mmol/min/mol] |
0.05873102 [mmol/mol] |
0 [1] |
0 [1] |
3 [1] |
0/3 |
100 [%] |
100 [%] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
2 [1] |
516.716 [µmol/s] |
440.493 [µmol/s] |
32.2833 [°C] |
30.7026 [°C] |
29.9987 [°C] |
30.7458 [°C] |
30.7119 [°C] |
19.8223 [%] |
26.1552 [%] |
0.00000 [%] |
32.1519 [°C] |
409.582 [µmol/mol] |
27.0557 [mmol/mol] |
98.7211 [%] |
100.260 [%] |
3 |
1592958768 [s] |
730.400000095367 |
2020-06-23 14:32:48 |
14:32:48 |
1592958760 [s] |
0.0002354843 [mol/m^2/s] |
-0.4840734 [µmol/m^2/s] |
400.5528 [µmol/mol] |
455.5949 [µmol/mol] |
46.19508 [Pa] |
40.61408 [Pa] |
0.01116704 [mol/m^2/s] |
2.281568 [mol/m^2/s] |
0.01113676 [mol/m^2/s] |
0.006963189 [mol/m^2/s] |
161.8374 [W/m^2] |
33.33155 [°C] |
32.21135 [°C] |
4.832502 [kPa] |
57.29578 [%] |
2.768891 [kPa] |
4.832626 [kPa] |
2.063612 [kPa] |
-10.38486 [W/m^2] |
0.05555014 [W/m^2] |
0.005533068 [W/m^2] |
151.513658 [W/m^2] |
-0.04203905 [1] |
0.04719252 [1] |
3.511818 [1] |
0 [µmol/s] |
0 [%] |
1 [1] |
0 [%] |
52747 [µmol/s] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [µmol/m^2/s] |
|
0 [1] |
0 [1] |
0 [1] |
0.5 [1] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [1] |
-0.000575454 [µmol/µmol] |
0 [1] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [ms] |
0 [ms] |
0 [ms] |
0 [µmol/m^2/s] |
0 [1] |
0 [mol/m2/s2] |
0 [1] |
1000.0102 [µmol/m^2/s] |
841.2026 [µmol/m^2/s] |
0.8411941 [1] |
0.1923882 [J/µmol] |
6 [cm^2] |
0.5 [1] |
0: Broadleaf |
1592958760 [s] |
400.5528 [µmol/mol] |
400.0851 [µmol/mol] |
27.30794 [mmol/mol] |
27.03309 [mmol/mol] |
500.0235 [µmol/s] |
101.3627 [kPa] |
0.03240343 [kPa] |
32.21180 [°C] |
32.21135 [°C] |
999.9 [°C] |
0 [°C] |
0 [°C] |
10001.632 [rpm] |
0 [µmol/m^2/s] |
28.256684 [µmol/m^2/s] |
1000.0102 [µmol/m^2/s] |
0.9599955 [1] |
0.04000417 [1] |
0 [1] |
2.538268 [1] |
5.00059 [µmol/m^2/s] |
1412.695 [1] |
9587.846 [1] |
41.50997 [°C] |
45.06200 [°C] |
43.32826 [°C] |
44.52197 [°C] |
43.76384 [°C] |
955.2061 [µmol/m^2/s] |
39.80323 [µmol/m^2/s] |
0 [µmol/m^2/s] |
1592958768 [s] |
2.560638 [1] |
0.6414290 [1/min] |
25.39179 [1/min] |
1413.617 [1] |
15 [s] |
0 [s] |
NA |
0 [1] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
0 [µmol/mol] |
0 [mmol/mol] |
0 [%] |
0 [%] |
0.4673976 [µmol/mol] |
0.89352538 [µmol/min/mol] |
0.27749047 [µmol/mol] |
0 [1] |
2.530365 [1] |
0.3814049 [1/min] |
0.1936925 [1] |
1 [1] |
0.2785463 [mmol/mol] |
-0.1942422 [mmol/min/mol] |
0.03476224 [mmol/mol] |
0 [1] |
1 [1] |
3 [1] |
1/3 |
100 [%] |
100 [%] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
2 [1] |
514.985 [µmol/s] |
437.963 [µmol/s] |
33.8653 [°C] |
29.3023 [°C] |
30.0072 [°C] |
29.2929 [°C] |
29.2987 [°C] |
19.4896 [%] |
21.7097 [%] |
9.58107 [%] |
33.8550 [°C] |
399.469 [µmol/mol] |
27.2361 [mmol/mol] |
99.2096 [%] |
100.645 [%] |
4 |
1592958901 [s] |
863.400000095367 |
2020-06-23 14:35:01 |
14:35:01 |
1592958893 [s] |
0.0073598465 [mol/m^2/s] |
11.8661266 [µmol/m^2/s] |
399.3959 [µmol/mol] |
338.4365 [µmol/mol] |
34.31522 [Pa] |
40.49610 [Pa] |
0.41562142 [mol/m^2/s] |
2.284571 [mol/m^2/s] |
0.37772997 [mol/m^2/s] |
0.239197088 [mol/m^2/s] |
161.8387 [W/m^2] |
32.23319 [°C] |
32.40704 [°C] |
4.886205 [kPa] |
57.70930 [%] |
2.987320 [kPa] |
5.176496 [kPa] |
1.898885 [kPa] |
-324.56923 [W/m^2] |
126.43323574 [W/m^2] |
12.664674351 [W/m^2] |
-23.632629 [W/m^2] |
-0.04212099 [1] |
0.04728450 [1] |
3.517219 [1] |
0 [µmol/s] |
0 [%] |
1 [1] |
0 [%] |
52416 [µmol/s] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [µmol/m^2/s] |
|
0 [1] |
0 [1] |
0 [1] |
0.5 [1] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [1] |
0.014106024 [µmol/µmol] |
0 [1] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [ms] |
0 [ms] |
0 [ms] |
0 [µmol/m^2/s] |
0 [1] |
0 [mol/m2/s2] |
0 [1] |
1000.0188 [µmol/m^2/s] |
841.2099 [µmol/m^2/s] |
0.8411940 [1] |
0.1923880 [J/µmol] |
6 [cm^2] |
0.5 [1] |
0: Broadleaf |
1592958893 [s] |
399.3959 [µmol/mol] |
417.1597 [µmol/mol] |
29.46267 [mmol/mol] |
20.89248 [mmol/mol] |
500.0826 [µmol/s] |
101.3586 [kPa] |
0.03473805 [kPa] |
33.43357 [°C] |
32.40704 [°C] |
999.9 [°C] |
0 [°C] |
0 [°C] |
10021.525 [rpm] |
0 [µmol/m^2/s] |
16.781681 [µmol/m^2/s] |
1000.0188 [µmol/m^2/s] |
0.9600009 [1] |
0.03999945 [1] |
0 [1] |
1156.980968 [1] |
5.00059 [µmol/m^2/s] |
14070.177 [1] |
9587.940 [1] |
42.20939 [°C] |
44.96139 [°C] |
43.58232 [°C] |
44.89900 [°C] |
44.48171 [°C] |
955.2181 [µmol/m^2/s] |
39.80097 [µmol/m^2/s] |
0 [µmol/m^2/s] |
1592958901 [s] |
1154.790769 [1] |
-173.6519656 [1/min] |
-1697.15555 [1/min] |
14048.285 [1] |
15 [s] |
0 [s] |
NA |
0 [1] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
0 [µmol/mol] |
0 [mmol/mol] |
0 [%] |
0 [%] |
-17.7978415 [µmol/mol] |
0.96625505 [µmol/min/mol] |
0.11026062 [µmol/mol] |
0 [1] |
1166.682647 [1] |
-196.1255609 [1/min] |
19.3439275 [1] |
0 [1] |
8.5737571 [mmol/mol] |
-0.2241640 [mmol/min/mol] |
0.03991588 [mmol/mol] |
0 [1] |
0 [1] |
3 [1] |
0/3 |
100 [%] |
100 [%] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
2 [1] |
519.325 [µmol/s] |
431.134 [µmol/s] |
34.2703 [°C] |
29.8063 [°C] |
29.9953 [°C] |
29.6528 [°C] |
29.6364 [°C] |
20.0495 [%] |
39.5906 [%] |
6.78577 [%] |
34.7286 [°C] |
417.613 [µmol/mol] |
20.7953 [mmol/mol] |
98.7407 [%] |
100.215 [%] |
5 |
1592958999 [s] |
961 |
2020-06-23 14:36:38 |
14:36:38 |
1592958991 [s] |
0.0068614392 [mol/m^2/s] |
12.0639704 [µmol/m^2/s] |
399.9004 [µmol/mol] |
332.9966 [µmol/mol] |
33.76210 [Pa] |
40.54539 [Pa] |
0.37579717 [mol/m^2/s] |
2.281431 [mol/m^2/s] |
0.34448777 [mol/m^2/s] |
0.217900092 [mol/m^2/s] |
161.8337 [W/m^2] |
32.49134 [°C] |
32.50147 [°C] |
4.912303 [kPa] |
57.08953 [%] |
2.971376 [kPa] |
5.204764 [kPa] |
1.940928 [kPa] |
-302.58947 [W/m^2] |
126.60824981 [W/m^2] |
12.711597346 [W/m^2] |
-1.435918 [W/m^2] |
-0.04203533 [1] |
0.04718834 [1] |
3.511573 [1] |
0 [µmol/s] |
0 [%] |
1 [1] |
0 [%] |
52337 [µmol/s] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [µmol/m^2/s] |
|
0 [1] |
0 [1] |
0 [1] |
0.5 [1] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [1] |
0.014341684 [µmol/µmol] |
0 [1] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [ms] |
0 [ms] |
0 [ms] |
0 [µmol/m^2/s] |
0 [1] |
0 [mol/m2/s2] |
0 [1] |
999.9859 [µmol/m^2/s] |
841.1823 [µmol/m^2/s] |
0.8411942 [1] |
0.1923884 [J/µmol] |
6 [cm^2] |
0.5 [1] |
0: Broadleaf |
1592958991 [s] |
399.9004 [µmol/mol] |
417.6687 [µmol/mol] |
29.30677 [mmol/mol] |
21.31487 [mmol/mol] |
500.0331 [µmol/s] |
101.3527 [kPa] |
0.03600639 [kPa] |
33.53084 [°C] |
32.50147 [°C] |
999.9 [°C] |
0 [°C] |
0 [°C] |
10001.730 [rpm] |
0 [µmol/m^2/s] |
15.863703 [µmol/m^2/s] |
999.9859 [µmol/m^2/s] |
0.9599949 [1] |
0.04000518 [1] |
0 [1] |
1075.012581 [1] |
5.00059 [µmol/m^2/s] |
13185.452 [1] |
9587.616 [1] |
42.69729 [°C] |
45.17900 [°C] |
43.93700 [°C] |
45.16903 [°C] |
44.96748 [°C] |
955.1797 [µmol/m^2/s] |
39.80581 [µmol/m^2/s] |
0 [µmol/m^2/s] |
1592958998 [s] |
1075.009615 [1] |
-4.9569231 [1/min] |
29.35043 [1/min] |
13185.519 [1] |
15 [s] |
0 [s] |
NA |
0 [1] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
0 [µmol/mol] |
0 [mmol/mol] |
0 [%] |
0 [%] |
-17.7702902 [µmol/mol] |
0.25286935 [µmol/min/mol] |
0.05753819 [µmol/mol] |
1 [1] |
1075.217647 [1] |
-4.7057052 [1/min] |
0.5085334 [1] |
0 [1] |
8.0152871 [mmol/mol] |
-0.6962752 [mmol/min/mol] |
0.07019443 [mmol/mol] |
0 [1] |
1 [1] |
3 [1] |
1/3 |
100 [%] |
100 [%] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
2 [1] |
518.827 [µmol/s] |
430.306 [µmol/s] |
32.7468 [°C] |
30.3814 [°C] |
30.0029 [°C] |
30.0849 [°C] |
30.0542 [°C] |
20.0667 [%] |
37.1472 [%] |
4.43732 [%] |
32.6668 [°C] |
417.623 [µmol/mol] |
21.5506 [mmol/mol] |
98.6002 [%] |
100.068 [%] |
6 |
1592959013 [s] |
975.5 |
2020-06-23 14:36:53 |
14:36:53 |
1592959005 [s] |
0.0066226329 [mol/m^2/s] |
12.1148589 [µmol/m^2/s] |
399.9555 [µmol/mol] |
331.6922 [µmol/mol] |
33.62895 [Pa] |
40.54989 [Pa] |
0.36665126 [mol/m^2/s] |
2.280490 [mol/m^2/s] |
0.33677120 [mol/m^2/s] |
0.212963314 [mol/m^2/s] |
161.8343 [W/m^2] |
32.45101 [°C] |
32.38387 [°C] |
4.879820 [kPa] |
57.30823 [%] |
2.963173 [kPa] |
5.170589 [kPa] |
1.916647 [kPa] |
-292.05811 [W/m^2] |
126.54966488 [W/m^2] |
12.696308607 [W/m^2] |
9.022135 [W/m^2] |
-0.04200967 [1] |
0.04715953 [1] |
3.509881 [1] |
0 [µmol/s] |
0 [%] |
1 [1] |
0 [%] |
52311 [µmol/s] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [µmol/m^2/s] |
|
0 [1] |
0 [1] |
0 [1] |
0.5 [1] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [µmol/m^2/s] |
0 [1] |
0.014402169 [µmol/µmol] |
0 [1] |
|
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [1] |
0 [ms] |
0 [ms] |
0 [ms] |
0 [µmol/m^2/s] |
0 [1] |
0 [mol/m2/s2] |
0 [1] |
999.9863 [µmol/m^2/s] |
841.1829 [µmol/m^2/s] |
0.8411945 [1] |
0.1923889 [J/µmol] |
6 [cm^2] |
0.5 [1] |
0: Broadleaf |
1592959005 [s] |
399.9555 [µmol/mol] |
417.6704 [µmol/mol] |
29.22665 [mmol/mol] |
21.51238 [mmol/mol] |
500.0406 [µmol/s] |
101.3523 [kPa] |
0.03367666 [kPa] |
33.41319 [°C] |
32.38387 [°C] |
999.9 [°C] |
0 [°C] |
0 [°C] |
9995.662 [rpm] |
0 [µmol/m^2/s] |
15.808339 [µmol/m^2/s] |
999.9863 [µmol/m^2/s] |
0.9599871 [1] |
0.04001312 [1] |
0 [1] |
1074.494194 [1] |
5.00059 [µmol/m^2/s] |
13212.958 [1] |
9587.608 [1] |
42.75000 [°C] |
45.19106 [°C] |
43.97765 [°C] |
45.24187 [°C] |
45.04000 [°C] |
955.1739 [µmol/m^2/s] |
39.81484 [µmol/m^2/s] |
0 [µmol/m^2/s] |
1592959013 [s] |
1074.492692 [1] |
-0.5425641 [1/min] |
109.04957 [1/min] |
13213.781 [1] |
15 [s] |
0 [s] |
NA |
0 [1] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
0 [µmol/mol] |
0 [mmol/mol] |
0 [%] |
0 [%] |
-17.7221146 [µmol/mol] |
-0.03887247 [µmol/min/mol] |
0.04125643 [µmol/mol] |
1 [1] |
1074.529412 [1] |
-0.7325754 [1/min] |
0.2037146 [1] |
1 [1] |
7.7737339 [mmol/mol] |
-1.1375774 [mmol/min/mol] |
0.11741928 [mmol/mol] |
0 [1] |
2 [1] |
3 [1] |
2/3 |
100 [%] |
100 [%] |
1.64 [µmol/mol] |
0.445 [mmol/mol] |
2 [1] |
518.649 [µmol/s] |
430.311 [µmol/s] |
32.4813 [°C] |
30.4664 [°C] |
30.0023 [°C] |
30.1542 [°C] |
30.1213 [°C] |
20.0702 [%] |
37.4194 [%] |
3.66987 [%] |
32.5041 [°C] |
417.470 [µmol/mol] |
21.4695 [mmol/mol] |
98.5810 [%] |
100.047 [%] |
As you can see, there is a lot of data. There are 20 rows and 157 columns.
All of the data is stored either as a unit (some have the “unitless” unit) or as an approprate class (character, hms, or date/time), which are automatically assigned and validated when the file is loaded, as they are read in from the file. We’ll discuss user-defined variables below.
LI-COR groups variables into a few different categories which are stored
as attributes of the data. This topic is covered in greater detail in
the vignette on data manipulation and by the
subset_options()
function described below.
subset_options(test_data)
#> [1] "Sys" "GasEx" "Leak" "FLR" "MPF" "LeafQ"
#> [7] "Const" "Meas" "FlrLS" "FlrStats" "Match" "Stability"
#> [13] "Status"
The data columns covered by each of these values are expressly stated in the LI-6800 manual “Summary of symbols” section (CDM: provide page # and edition, v1.4 in this case).
In addition to data, the licor
class stores meta-data from the header
of the LI-6800 data file. This information is accessible with the
header
attribute.
attributes(test_data)$header[1:5]
#> $`File opened`
#> [1] "2020-06-23 14:17:33"
#>
#> $`Console s/n`
#> [1] "68C-811937"
#>
#> $`Console ver`
#> [1] "Bluestem v.1.3.17"
#>
#> $`Scripts ver`
#> [1] "2018.12 1.3.16, Nov 2018"
#>
#> $`Head s/n`
#> [1] "68H-711927"
Once again we are showing a subset of the list, as the actual list of meta-data contains around 50 elements.
The licor_validator()
that ensures that the licor
class was created
correctly and that all variables have valid scientific units. It is
automatically called during the licor
method call, but not during the
read_li6800_raw()
method.
Currently, the data reader only supports reading from LI-6800 files, but we plan to add support for the LI-6400 as well.
Comments, criticisms, and contributions are welcomed! GitHub issues are the preferred way to report bugs, ask questions, or request new features. You can submit issues here: https://github.com/muir-lab/licorer/issues
- Please report any issues or bugs
- License: MIT + file LICENSE