This package is use to read the data of LI-6800 photosynthesis system
from LICOR. Currently it only contains 2 functions, one is for read a
single excel file (read_li6800), and another (read_li6800_folder) is
read a folder contains data files from LI-6800 as a dataframe, with a
coloum of tags.
I use openxlsx to read the excel data, because it can deal with the
Formulas in LI-6800 excel data without any further pre-processing.
You can install the development version of ReadLICOR6800 from GitHub with:
# install.packages("devtools")
devtools::install_github("zhujiedong/ReadLICOR6800")This is a basic example which shows you how to solve a common problem:
library(ReadLICOR6800)
aci <- read_li6800('inst/extdata/racirtest1.xlsx', startRow = 15)
aci[1:3, 1:6]
#> obs time elapsed date hhmmss averaging
#> 2 1 1617082892.5 0 20210330 13:41:32 13:41:32 2
#> 3 2 1617082895 2.5 20210330 13:41:35 13:41:35 2
#> 4 3 1617082896.5 4 20210330 13:41:36 13:41:36 2
names(aci)
#> [1] "obs" "time" "elapsed" "date"
#> [5] "hhmmss" "averaging" "TIME" "E"
#> [9] "Emm" "A" "Ca" "Ci"
#> [13] "Pci" "Pca" "gsw" "gbw"
#> [17] "gtw" "gtc" "Rabs" "TleafEB"
#> [21] "TleafCnd" "SVPleaf" "RHcham" "VPcham"
#> [25] "SVPcham" "VPDleaf" "LatHFlux" "SenHFlux"
#> [29] "NetTherm" "EBSum" "Asty" "Esty"
#> [33] "Adyn" "Crd" "Csd" "dCsd/dt"
#> [37] "αVc" "Edyn" "Hr" "Hs"
#> [41] "dHs/dt" "αVh" "Leak" "LeakPct"
#> [45] "CorrFact" "CorrFactPct" "Fan" "DarkAdaptedID"
#> [49] "Qmax_d" "Fo" "Fm" "Fv/Fm"
#> [53] "A_dark" "LightAdaptedID" "Qmax" "Fs"
#> [57] "Fm'" "PhiPS2" "PS2/1" "Qabs_fs"
#> [61] "A_fs" "ETR" "PhiCO2" "NPQ"
#> [65] "alt..Fo'" "DarkPulseID" "Fmin" "Fo'"
#> [69] "Fv'/Fm'" "qP" "qN" "qP_Fo"
#> [73] "qN_Fo" "qL" "1-qL" "Qin"
#> [77] "Qabs" "alpha" "convert" "S"
#> [81] "K" "Geometry" "Custom" "UseDynamic"
#> [85] "TIME" "CO2_s" "CO2_r" "H2O_s"
#> [89] "H2O_r" "CO2_a" "H2O_a" "Flow"
#> [93] "Pa" "ΔPcham" "Tair" "Tleaf"
#> [97] "Tleaf2" "Offset" "Offset2" "Fan_speed"
#> [101] "Qamb_in" "Qamb_out" "Q" "f_red"
#> [105] "f_blue" "f_farred" "F" "Q_modavg"
#> [109] "F_dc" "Pc" "Tled" "TDigital"
#> [113] "TPreamp" "TPwrSpy" "TDrive" "Q_red"
#> [117] "Q_blue" "Q_farred" "TSPF" "state"
#> [121] "F_avg" "dF/dt" "dF_dc/dt" "F_dc_avg"
#> [125] "period" "time" "hhmmss" "co2_t"
#> [129] "h2o_t" "count" "co2_adj" "h2o_adj"
#> [133] "co2_match" "h2o_match" "co2_at" "h2o_at"
#> [137] "co2_cv" "h2o_cv" "MatchValveR" "MatchValveS"
#> [141] "MatchCO2" "MatchH2O" "cf_co2_a" "cf_co2_b"
#> [145] "cf_co2_c" "cf_co2_d" "cf_h2o_a" "cf_h2o_b"
#> [149] "cf_h2o_c" "cf_h2o_d" "co2_fit_low" "co2_fit_high"
#> [153] "h2o_fit_low" "h2o_fit_high" "co2_elapsed" "h2o_elapsed"
#> [157] "DIAG" "Flow_s" "Flow_r" "Txchg"
#> [161] "Tirga" "Tchopper" "Ts" "Tr"
#> [165] "CO2_%" "Desiccant_%" "Humidifier_%" "Txchg_sp"
#> [169] "CO2_r_sp" "H2O_r_sp" "SS_s" "SS_r"
#> [173] "data_tag"
aci$data_tag
#> [1] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [6] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [11] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [16] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [21] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [26] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [31] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [36] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [41] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [46] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [51] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [56] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [61] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [66] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [71] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [76] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [81] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [86] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [91] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [96] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [101] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [106] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [111] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [116] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [121] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [126] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [131] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [136] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [141] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [146] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [151] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [156] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [161] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [166] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [171] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [176] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [181] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [186] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [191] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [196] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [201] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [206] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [211] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [216] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [221] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [226] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [231] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [236] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [241] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [246] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [251] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [256] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [261] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [266] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [271] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [276] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [281] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [286] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [291] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [296] "racirtest1" "racirtest1" "racirtest1"by use the default arguments, the returned dataframe will contain a new
column contains the name of the file called data_tag, it is used to
distinguish files when reading all the files in a folder. the data_tag
can also be changed to a custom one, use the tags="custom tags", where
custom tags is what you need.
if you need to read only one file, it is not needed:
aci <- read_li6800("inst/extdata/racirtest1.xlsx", add_tags = FALSE)
names(aci)
#> [1] "obs" "time" "elapsed" "date"
#> [5] "hhmmss" "averaging" "TIME" "E"
#> [9] "Emm" "A" "Ca" "Ci"
#> [13] "Pci" "Pca" "gsw" "gbw"
#> [17] "gtw" "gtc" "Rabs" "TleafEB"
#> [21] "TleafCnd" "SVPleaf" "RHcham" "VPcham"
#> [25] "SVPcham" "VPDleaf" "LatHFlux" "SenHFlux"
#> [29] "NetTherm" "EBSum" "Asty" "Esty"
#> [33] "Adyn" "Crd" "Csd" "dCsd/dt"
#> [37] "αVc" "Edyn" "Hr" "Hs"
#> [41] "dHs/dt" "αVh" "Leak" "LeakPct"
#> [45] "CorrFact" "CorrFactPct" "Fan" "DarkAdaptedID"
#> [49] "Qmax_d" "Fo" "Fm" "Fv/Fm"
#> [53] "A_dark" "LightAdaptedID" "Qmax" "Fs"
#> [57] "Fm'" "PhiPS2" "PS2/1" "Qabs_fs"
#> [61] "A_fs" "ETR" "PhiCO2" "NPQ"
#> [65] "alt..Fo'" "DarkPulseID" "Fmin" "Fo'"
#> [69] "Fv'/Fm'" "qP" "qN" "qP_Fo"
#> [73] "qN_Fo" "qL" "1-qL" "Qin"
#> [77] "Qabs" "alpha" "convert" "S"
#> [81] "K" "Geometry" "Custom" "UseDynamic"
#> [85] "TIME" "CO2_s" "CO2_r" "H2O_s"
#> [89] "H2O_r" "CO2_a" "H2O_a" "Flow"
#> [93] "Pa" "ΔPcham" "Tair" "Tleaf"
#> [97] "Tleaf2" "Offset" "Offset2" "Fan_speed"
#> [101] "Qamb_in" "Qamb_out" "Q" "f_red"
#> [105] "f_blue" "f_farred" "F" "Q_modavg"
#> [109] "F_dc" "Pc" "Tled" "TDigital"
#> [113] "TPreamp" "TPwrSpy" "TDrive" "Q_red"
#> [117] "Q_blue" "Q_farred" "TSPF" "state"
#> [121] "F_avg" "dF/dt" "dF_dc/dt" "F_dc_avg"
#> [125] "period" "time" "hhmmss" "co2_t"
#> [129] "h2o_t" "count" "co2_adj" "h2o_adj"
#> [133] "co2_match" "h2o_match" "co2_at" "h2o_at"
#> [137] "co2_cv" "h2o_cv" "MatchValveR" "MatchValveS"
#> [141] "MatchCO2" "MatchH2O" "cf_co2_a" "cf_co2_b"
#> [145] "cf_co2_c" "cf_co2_d" "cf_h2o_a" "cf_h2o_b"
#> [149] "cf_h2o_c" "cf_h2o_d" "co2_fit_low" "co2_fit_high"
#> [153] "h2o_fit_low" "h2o_fit_high" "co2_elapsed" "h2o_elapsed"
#> [157] "DIAG" "Flow_s" "Flow_r" "Txchg"
#> [161] "Tirga" "Tchopper" "Ts" "Tr"
#> [165] "CO2_%" "Desiccant_%" "Humidifier_%" "Txchg_sp"
#> [169] "CO2_r_sp" "H2O_r_sp" "SS_s" "SS_r"
head(aci$data_tags)
#> NULLBut be sure to supply the right startRow to read the data. It is the
header of the measuring data, start with ‘obs’(the first column)
It is similar with read_li6800, but usually we may need to specify the
tags to distinguish the combined dataframe that from lots of excel
files, if tags=NULL(default), data_tagcolumn will use the file name
as a tag:
list.files("inst/extdata/")
#> [1] "racirtest1.xlsx" "racirtest3.xlsx"
aci <- read_li6800_folder("inst/extdata/")
names(aci)
#> [1] "obs" "time" "elapsed" "date"
#> [5] "hhmmss" "averaging" "TIME" "E"
#> [9] "Emm" "A" "Ca" "Ci"
#> [13] "Pci" "Pca" "gsw" "gbw"
#> [17] "gtw" "gtc" "Rabs" "TleafEB"
#> [21] "TleafCnd" "SVPleaf" "RHcham" "VPcham"
#> [25] "SVPcham" "VPDleaf" "LatHFlux" "SenHFlux"
#> [29] "NetTherm" "EBSum" "Asty" "Esty"
#> [33] "Adyn" "Crd" "Csd" "dCsd/dt"
#> [37] "αVc" "Edyn" "Hr" "Hs"
#> [41] "dHs/dt" "αVh" "Leak" "LeakPct"
#> [45] "CorrFact" "CorrFactPct" "Fan" "DarkAdaptedID"
#> [49] "Qmax_d" "Fo" "Fm" "Fv/Fm"
#> [53] "A_dark" "LightAdaptedID" "Qmax" "Fs"
#> [57] "Fm'" "PhiPS2" "PS2/1" "Qabs_fs"
#> [61] "A_fs" "ETR" "PhiCO2" "NPQ"
#> [65] "alt..Fo'" "DarkPulseID" "Fmin" "Fo'"
#> [69] "Fv'/Fm'" "qP" "qN" "qP_Fo"
#> [73] "qN_Fo" "qL" "1-qL" "Qin"
#> [77] "Qabs" "alpha" "convert" "S"
#> [81] "K" "Geometry" "Custom" "UseDynamic"
#> [85] "TIME" "CO2_s" "CO2_r" "H2O_s"
#> [89] "H2O_r" "CO2_a" "H2O_a" "Flow"
#> [93] "Pa" "ΔPcham" "Tair" "Tleaf"
#> [97] "Tleaf2" "Offset" "Offset2" "Fan_speed"
#> [101] "Qamb_in" "Qamb_out" "Q" "f_red"
#> [105] "f_blue" "f_farred" "F" "Q_modavg"
#> [109] "F_dc" "Pc" "Tled" "TDigital"
#> [113] "TPreamp" "TPwrSpy" "TDrive" "Q_red"
#> [117] "Q_blue" "Q_farred" "TSPF" "state"
#> [121] "F_avg" "dF/dt" "dF_dc/dt" "F_dc_avg"
#> [125] "period" "time" "hhmmss" "co2_t"
#> [129] "h2o_t" "count" "co2_adj" "h2o_adj"
#> [133] "co2_match" "h2o_match" "co2_at" "h2o_at"
#> [137] "co2_cv" "h2o_cv" "MatchValveR" "MatchValveS"
#> [141] "MatchCO2" "MatchH2O" "cf_co2_a" "cf_co2_b"
#> [145] "cf_co2_c" "cf_co2_d" "cf_h2o_a" "cf_h2o_b"
#> [149] "cf_h2o_c" "cf_h2o_d" "co2_fit_low" "co2_fit_high"
#> [153] "h2o_fit_low" "h2o_fit_high" "co2_elapsed" "h2o_elapsed"
#> [157] "DIAG" "Flow_s" "Flow_r" "Txchg"
#> [161] "Tirga" "Tchopper" "Ts" "Tr"
#> [165] "CO2_%" "Desiccant_%" "Humidifier_%" "Txchg_sp"
#> [169] "CO2_r_sp" "H2O_r_sp" "SS_s" "SS_r"
#> [173] "data_tag"
head(aci$data_tag)
#> [1] "racirtest1" "racirtest1" "racirtest1" "racirtest1" "racirtest1"
#> [6] "racirtest1"
tail(aci$data_tag)
#> [1] "racirtest3" "racirtest3" "racirtest3" "racirtest3" "racirtest3"
#> [6] "racirtest3"when use custom tags, make sure the tags have the right order and right
length with what the list.files() shows
aci <- read_li6800_folder("inst/extdata/", tags = paste('test', 1:2))
aci[1:3, 1:6]
#> obs time elapsed date hhmmss averaging
#> 1 1 1617082892.5 0 20210330 13:41:32 13:41:32 2
#> 2 2 1617082895 2.5 20210330 13:41:35 13:41:35 2
#> 3 3 1617082896.5 4 20210330 13:41:36 13:41:36 2
names(aci)
#> [1] "obs" "time" "elapsed" "date"
#> [5] "hhmmss" "averaging" "TIME" "E"
#> [9] "Emm" "A" "Ca" "Ci"
#> [13] "Pci" "Pca" "gsw" "gbw"
#> [17] "gtw" "gtc" "Rabs" "TleafEB"
#> [21] "TleafCnd" "SVPleaf" "RHcham" "VPcham"
#> [25] "SVPcham" "VPDleaf" "LatHFlux" "SenHFlux"
#> [29] "NetTherm" "EBSum" "Asty" "Esty"
#> [33] "Adyn" "Crd" "Csd" "dCsd/dt"
#> [37] "αVc" "Edyn" "Hr" "Hs"
#> [41] "dHs/dt" "αVh" "Leak" "LeakPct"
#> [45] "CorrFact" "CorrFactPct" "Fan" "DarkAdaptedID"
#> [49] "Qmax_d" "Fo" "Fm" "Fv/Fm"
#> [53] "A_dark" "LightAdaptedID" "Qmax" "Fs"
#> [57] "Fm'" "PhiPS2" "PS2/1" "Qabs_fs"
#> [61] "A_fs" "ETR" "PhiCO2" "NPQ"
#> [65] "alt..Fo'" "DarkPulseID" "Fmin" "Fo'"
#> [69] "Fv'/Fm'" "qP" "qN" "qP_Fo"
#> [73] "qN_Fo" "qL" "1-qL" "Qin"
#> [77] "Qabs" "alpha" "convert" "S"
#> [81] "K" "Geometry" "Custom" "UseDynamic"
#> [85] "TIME" "CO2_s" "CO2_r" "H2O_s"
#> [89] "H2O_r" "CO2_a" "H2O_a" "Flow"
#> [93] "Pa" "ΔPcham" "Tair" "Tleaf"
#> [97] "Tleaf2" "Offset" "Offset2" "Fan_speed"
#> [101] "Qamb_in" "Qamb_out" "Q" "f_red"
#> [105] "f_blue" "f_farred" "F" "Q_modavg"
#> [109] "F_dc" "Pc" "Tled" "TDigital"
#> [113] "TPreamp" "TPwrSpy" "TDrive" "Q_red"
#> [117] "Q_blue" "Q_farred" "TSPF" "state"
#> [121] "F_avg" "dF/dt" "dF_dc/dt" "F_dc_avg"
#> [125] "period" "time" "hhmmss" "co2_t"
#> [129] "h2o_t" "count" "co2_adj" "h2o_adj"
#> [133] "co2_match" "h2o_match" "co2_at" "h2o_at"
#> [137] "co2_cv" "h2o_cv" "MatchValveR" "MatchValveS"
#> [141] "MatchCO2" "MatchH2O" "cf_co2_a" "cf_co2_b"
#> [145] "cf_co2_c" "cf_co2_d" "cf_h2o_a" "cf_h2o_b"
#> [149] "cf_h2o_c" "cf_h2o_d" "co2_fit_low" "co2_fit_high"
#> [153] "h2o_fit_low" "h2o_fit_high" "co2_elapsed" "h2o_elapsed"
#> [157] "DIAG" "Flow_s" "Flow_r" "Txchg"
#> [161] "Tirga" "Tchopper" "Ts" "Tr"
#> [165] "CO2_%" "Desiccant_%" "Humidifier_%" "Txchg_sp"
#> [169] "CO2_r_sp" "H2O_r_sp" "SS_s" "SS_r"
#> [173] "data_tag"
head(aci$data_tag)
#> [1] "test 1" "test 1" "test 1" "test 1" "test 1" "test 1"
tail(aci$data_tag)
#> [1] "test 2" "test 2" "test 2" "test 2" "test 2" "test 2"