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licorer

Build Status Lifecycle: experimental

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.

Get licorer

from GitHub:

# install.packages("remotes")
remotes::install_github("muir-lab/licorer")

and load licorer

library("licorer")

Vignette

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 [%]

The Data

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).

The Header

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.

Contributors

Comments and contributions

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

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