R/write_CI_Calc_file.R
In erikerhardt/isogasex: Isotopic gas exchange using TDL and Licor input. Updated version of package tdllicor
#' write output section
#'
#' Write all observed and calculated values with BS CIs for all time points.
#'
#' @param val xxxPARAMxxx
#' @param TDL_cycle xxxPARAMxxx
#' @param output_CI_Calc_fn xxxPARAMxxx
#' @param output_CI_Calc_last_fn xxxPARAMxxx
#'
#' @return val$write xxxRETURNxxx
#'
write_CI_Calc_file <-
function# write_output section
### Write all observed and calculated values with BS CIs for all time points.
(val
###
, TDL_cycle
###
, output_CI_Calc_fn
###
, output_CI_Calc_last_fn
###
)
{
val$write$CI_Calc <- paste(
"date"
,"time"
,"site"
,"site_name"
,"first_ind"
,"ind"
,"gain_12C_CI_L" ,"gain_12C_CI_U" #,"gain_12C"
,"gain_13C_CI_L" ,"gain_13C_CI_U" #,"gain_13C"
,"offset_12C_CI_L" ,"offset_12C_CI_U" #,"offset_12C"
,"offset_13C_CI_L" ,"offset_13C_CI_U" #,"offset_13C"
,"reference_12Ce_CI_L" ,"reference_12Ce_CI_U" #,"reference_12Ce"
,"reference_13Ce_CI_L" ,"reference_13Ce_CI_U" #,"reference_13Ce"
,"chamber_12Co_CI_L" ,"chamber_12Co_CI_U" #,"chamber_12Co"
,"chamber_13Co_CI_L" ,"chamber_13Co_CI_U" #,"chamber_13Co"
,"reference_TotalCe_CI_L" ,"reference_TotalCe_CI_U" #,"reference_TotalCe"
,"chamber_TotalCo_CI_L" ,"chamber_TotalCo_CI_U" #,"chamber_TotalCo"
,"chamber_reference_Total_diff_CeCo_CI_L" ,"chamber_reference_Total_diff_CeCo_CI_U" #,"chamber_reference_Total_diff_CeCo"
,"chamber_reference_12_diff_CeCo_CI_L" ,"chamber_reference_12_diff_CeCo_CI_U" #,"chamber_reference_12_diff_CeCo"
,"chamber_reference_13_diff_CeCo_CI_L" ,"chamber_reference_13_diff_CeCo_CI_U" #,"chamber_reference_13_diff_CeCo"
,"xi_CI_L" ,"xi_CI_U" #,"xi"
#,"flow_adjusted_CI_L" ,"flow_adjusted_CI_U" #,"flow_adjusted" # 9/5/2012
,"TDL_A_photosynthesis_CI_L" ,"TDL_A_photosynthesis_CI_U" #,"TDL_A_photosynthesis"
,"TDL_12A_photosynthesis_CI_L" ,"TDL_12A_photosynthesis_CI_U" #,"TDL_12A_photosynthesis"
,"TDL_13A_photosynthesis_CI_L" ,"TDL_13A_photosynthesis_CI_U" #,"TDL_13A_photosynthesis"
,"Licor_A_photosynthesis_CI_L" ,"Licor_A_photosynthesis_CI_U" #,"Licor_A_photosynthesis"
,"Delta_from_ratios_in_out_CI_L" ,"Delta_from_ratios_in_out_CI_U" #,"Delta_from_ratios_in_out"
,"Delta_from_A_ratio_CI_L" ,"Delta_from_A_ratio_CI_U" #,"Delta_from_A_ratio"
,"VPD_CI_L" ,"VPD_CI_U" #,"VPD"
,"E_transpiration_CI_L" ,"E_transpiration_CI_U" #,"E_transpiration"
,"leaf_temp_CI_L" ,"leaf_temp_CI_U" #,"leaf_temp"
,"air_temp_CI_L" ,"air_temp_CI_U" #,"air_temp"
,"light_in_CI_L" ,"light_in_CI_U" #,"light_in"
,"light_out_CI_L" ,"light_out_CI_U" #,"light_out"
,"reference_delta_e_CI_L" ,"reference_delta_e_CI_U" #,"reference_delta_e"
,"chamber_delta_o_CI_L" ,"chamber_delta_o_CI_U" #,"chamber_delta_o"
,"chamber_reference_delta_diff_CoCe_CI_L" ,"chamber_reference_delta_diff_CoCe_CI_U" #,"chamber_reference_delta_diff_CoCe"
,"Delta_obs_CI_L" ,"Delta_obs_CI_U" #,"Delta_obs"
,"Delta_obs_permil_CI_L" ,"Delta_obs_permil_CI_U" #,"Delta_obs_permil"
,"delta_13C_Assim_CI_L" ,"delta_13C_Assim_CI_U" #,"delta_13C_Assim"
,"p_CI_L" ,"p_CI_U" #,"p"
,"delta_13C_Resp_CI_L" ,"delta_13C_Resp_CI_U" #,"delta_13C_Resp"
,"chamber_TotalCa_CI_L" ,"chamber_TotalCa_CI_U" #,"chamber_TotalCa"
,"chamber_12Ca_CI_L" ,"chamber_12Ca_CI_U" #,"chamber_12Ca"
,"chamber_13Ca_CI_L" ,"chamber_13Ca_CI_U" #,"chamber_13Ca"
,"chamber_TotalCs_CI_L" ,"chamber_TotalCs_CI_U" #,"chamber_TotalCs"
,"chamber_12Cs_CI_L" ,"chamber_12Cs_CI_U" #,"chamber_12Cs"
,"chamber_13Cs_CI_L" ,"chamber_13Cs_CI_U" #,"chamber_13Cs"
,"chamber_Totalpa_CI_L" ,"chamber_Totalpa_CI_U" #,"chamber_Totalpa"
,"chamber_12pa_CI_L" ,"chamber_12pa_CI_U" #,"chamber_12pa"
,"chamber_13pa_CI_L" ,"chamber_13pa_CI_U" #,"chamber_13pa"
,"chamber_Totalps_CI_L" ,"chamber_Totalps_CI_U" #,"chamber_Totalps"
,"chamber_12ps_CI_L" ,"chamber_12ps_CI_U" #,"chamber_12ps"
,"chamber_13ps_CI_L" ,"chamber_13ps_CI_U" #,"chamber_13ps"
,"chamber_Totalgbw_CI_L" ,"chamber_Totalgbw_CI_U" #,"chamber_Totalgbw"
,"chamber_Totalgbc_CI_L" ,"chamber_Totalgbc_CI_U" #,"chamber_Totalgbc"
,"chamber_12gbc_CI_L" ,"chamber_12gbc_CI_U" #,"chamber_12gbc"
,"chamber_13gbc_CI_L" ,"chamber_13gbc_CI_U" #,"chamber_13gbc"
,"chamber_Totalgsw_CI_L" ,"chamber_Totalgsw_CI_U" #,"chamber_Totalgsw"
,"chamber_Totalgsc_CI_L" ,"chamber_Totalgsc_CI_U" #,"chamber_Totalgsc"
,"chamber_12gsc_CI_L" ,"chamber_12gsc_CI_U" #,"chamber_12gsc"
,"chamber_13gsc_CI_L" ,"chamber_13gsc_CI_U" #,"chamber_13gsc"
,"chamber_Totalgtc_CI_L" ,"chamber_Totalgtc_CI_U" #,"chamber_Totalgtc"
,"chamber_12gtc_CI_L" ,"chamber_12gtc_CI_U" #,"chamber_12gtc"
,"chamber_13gtc_CI_L" ,"chamber_13gtc_CI_U" #,"chamber_13gtc"
,"chamber_TotalCi_CI_L" ,"chamber_TotalCi_CI_U" #,"chamber_TotalCi"
,"chamber_12Ci_CI_L" ,"chamber_12Ci_CI_U" #,"chamber_12Ci"
,"chamber_13Ci_CI_L" ,"chamber_13Ci_CI_U" #,"chamber_13Ci"
,"chamber_Totalpi_CI_L" ,"chamber_Totalpi_CI_U" #,"chamber_Totalpi"
,"chamber_12pi_CI_L" ,"chamber_12pi_CI_U" #,"chamber_12pi"
,"chamber_13pi_CI_L" ,"chamber_13pi_CI_U" #,"chamber_13pi"
,"chamber_Totalpi_pa_CI_L" ,"chamber_Totalpi_pa_CI_U" #,"chamber_Totalpi_pa"
,"chamber_Delta_i_simple_for_gm_CI_L" ,"chamber_Delta_i_simple_for_gm_CI_U" #,"chamber_Delta_i_simple_for_gm"
,"chamber_Delta_i_simple_for_modeling_CI_L" ,"chamber_Delta_i_simple_for_modeling_CI_U" #,"chamber_Delta_i_simple_for_modeling"
,"chamber_Delta_i_complex_for_gm_CI_L" ,"chamber_Delta_i_complex_for_gm_CI_U" #,"chamber_Delta_i_complex_for_gm"
,"chamber_Delta_i_simple_for_gm_Delta_obs_CI_L" ,"chamber_Delta_i_simple_for_gm_Delta_obs_CI_U" #,"chamber_Delta_i_simple_for_gm_Delta_obs"
,"chamber_Delta_i_complex_for_gm_Delta_obs_CI_L" ,"chamber_Delta_i_complex_for_gm_Delta_obs_CI_U" #,"chamber_Delta_i_complex_for_gm_Delta_obs"
,"chamber_Totalgm_point_simple_CI_L" ,"chamber_Totalgm_point_simple_CI_U" #,"chamber_Totalgm_point_simple"
,"chamber_12gm_point_simple_CI_L" ,"chamber_12gm_point_simple_CI_U" #,"chamber_12gm_point_simple"
,"chamber_13gm_point_simple_CI_L" ,"chamber_13gm_point_simple_CI_U" #,"chamber_13gm_point_simple"
,"chamber_Totalgm_point_complex_CI_L" ,"chamber_Totalgm_point_complex_CI.U" #,"chamber_Totalgm_point_complex"
,"chamber_Totalgm_to_use_CI_L" ,"chamber_Totalgm_to_use_CI_U" #,"chamber_Totalgm_to_use"
,"chamber_Totalpc_using_gm_CI_L" ,"chamber_Totalpc_using_gm_CI_U" #,"chamber_Totalpc_using_gm"
,"chamber_12pc_using_gm_CI_L" ,"chamber_12pc_using_gm_CI_U" #,"chamber_12pc_using_gm"
,"chamber_13pc_using_gm_CI_L" ,"chamber_13pc_using_gm_CI_U" #,"chamber_13pc_using_gm"
,"chamber_Totalpc_using_simple_Delta_for_gm_CI_L" ,"chamber_Totalpc_using_simple_Delta_for_gm_CI_U" #,"chamber_Totalpc_using_simple_Delta_for_gm"
,"chamber_Totalpc_using_simple_Delta_for_modeling_CI_L" ,"chamber_Totalpc_using_simple_Delta_for_modeling_CI_U" #,"chamber_Totalpc_using_simple_Delta_for_modeling"
,"chamber_Totalpc_using_complex_Delta_no_decarboxylation_CI_L" ,"chamber_Totalpc_using_complex_Delta_no_decarboxylation_CI_U" #,"chamber_Totalpc_using_complex_Delta_no_decarboxylation"
,"chamber_Totalpc_using_complex_Delta_full_model_CI_L" ,"chamber_Totalpc_using_complex_Delta_full_model_CI_U" #,"chamber_Totalpc_using_complex_Delta_full_model"
,"chamber_Totalpc_to_use_CI_L" ,"chamber_Totalpc_to_use_CI_U" #,"chamber_Totalpc_to_use"
,"chamber_TotalCc_CI_L" ,"chamber_TotalCc_CI_U" #,"chamber_TotalCc"
,"chamber_12Cc_CI_L" ,"chamber_12Cc_CI_U" #,"chamber_12Cc"
,"chamber_13Cc_CI_L" ,"chamber_13Cc_CI_U" #,"chamber_13Cc"
,"Licor_flow_uin_CI_L" ,"Licor_flow_uin_CI_U" #,"Licor_flow_uin"
,"Licor_H2OR_xin_CI_L" ,"Licor_H2OR_xin_CI_U" #,"Licor_H2OR_xin"
,"Licor_La_CI_L" ,"Licor_La_CI_U" #,"Licor_La"
,"Licor_Atm_press_CI_L" ,"Licor_Atm_press_CI_U" #,"Licor_Atm_press"
,"Licor_gsc_CI_L" ,"Licor_gsc_CI_U" #,"Licor_gsc"
,"Licor_Ci_CI_L" ,"Licor_Ci_CI_U" #,"Licor_Ci"
,"Licor_StmRat_CI_L" ,"Licor_StmRat_CI_U" #,"Licor_StmRat"
,"Licor_gbw_CI_L" ,"Licor_gbw_CI_U" #,"Licor_gbw"
,"Licor_temp_block_CI_L" ,"Licor_temp_block_CI_U" #,"Licor_temp_block"
,"Licor_Ce_CI_L" ,"Licor_Ce_CI_U" #,"Licor_Ce"
,"Licor_Co_CI_L" ,"Licor_Co_CI_U" #,"Licor_Co"
,"Licor_xout_CI_L" ,"Licor_xout_CI_U" #,"Licor_xout"
,"Licor_rh_ref" ,"Licor_rh_ref" #,"Licor_rh_ref"
,"Licor_rh_sam_CI_L" ,"Licor_rh_sam_CI_U" #,"Licor_rh_sam"
,"Licor_CsMch_CI_L" ,"Licor_CsMch_CI_U" #,"Licor_CsMch"
,"Licor_HsMch_CI_L" ,"Licor_HsMch_CI_U" #,"Licor_HsMch"
,"Licor_StableF_CI_L" ,"Licor_StableF_CI_U" #,"Licor_StableF"
,"Licor_Status_CI_L" ,"Licor_Status_CI_U" #,"Licor_Status"
# typically not used
#,"VpdA_CI_L" ,"VpdA_CI_U" #,"VpdA"
#,"Ci_Ca_CI_L" ,"Ci_Ca_CI_U" #,"Ci_Ca"
#,"pi_CI_L" ,"pi_CI_U" #,"pi"
#,"uc_20_mV_CI_L" ,"uc_20_mV_CI_U" #,"uc_20_mV"
#,"uc_21_mV_CI_L" ,"uc_21_mV_CI_U" #,"uc_21_mV"
#,"U_S_CI_L" ,"U_S_CI_U" #,"U_S"
#,"Trans_CI_L" ,"Trans_CI_U" #,"Trans"
#,"CndCO2_CI_L" ,"CndCO2_CI_U" #,"CndCO2"
#,"Ref_mV_CI_L" ,"Ref_mV_CI_U" #,"Ref_mV"
#,"xTemp1_CI_L" ,"xTemp1_CI_U" #,"xTemp1"
#,"xTemp2_CI_L" ,"xTemp2_CI_U" #,"xTemp2"
, sep=",");
for (i_time in 1:val$sum$TDL$n) {
val$write$CI_Calc <-
rbind( val$write$CI_Calc
,paste(
format(val$sum$TDL$time[i_time],format="%Y-%m-%d")
,val$sum$TDL$site[i_time]
,TDL_cycle$table_name[(TDL_cycle$table[,1] == val$sum$TDL$site[i_time])]
,val$sum$TDL$first_ind[i_time]
,val$sum$TDL$ind[i_time]
,val$calc$CI$gain_12C[i_time,1] ,val$calc$CI$gain_12C[i_time,2] #,val$calc$sum$gain_12C[i_time]
,val$calc$CI$gain_13C[i_time,1] ,val$calc$CI$gain_13C[i_time,2] #,val$calc$sum$gain_13C[i_time]
,val$calc$CI$offset_12C[i_time,1] ,val$calc$CI$offset_12C[i_time,2] #,val$calc$sum$offset_12C[i_time]
,val$calc$CI$offset_13C[i_time,1] ,val$calc$CI$offset_13C[i_time,2] #,val$calc$sum$offset_13C[i_time]
,val$calc$CI$reference_12Ce[i_time,1] ,val$calc$CI$reference_12Ce[i_time,2] #,val$calc$sum$reference_12Ce[i_time]
,val$calc$CI$reference_13Ce[i_time,1] ,val$calc$CI$reference_13Ce[i_time,2] #,val$calc$sum$reference_13Ce[i_time]
,val$calc$CI$chamber_12Co[i_time,1] ,val$calc$CI$chamber_12Co[i_time,2] #,val$calc$sum$chamber_12Co[i_time]
,val$calc$CI$chamber_13Co[i_time,1] ,val$calc$CI$chamber_13Co[i_time,2] #,val$calc$sum$chamber_13Co[i_time]
,val$calc$CI$reference_TotalCe[i_time,1] ,val$calc$CI$reference_TotalCe[i_time,2] #,val$calc$sum$reference_TotalCe[i_time]
,val$calc$CI$chamber_TotalCo[i_time,1] ,val$calc$CI$chamber_TotalCo[i_time,2] #,val$calc$sum$chamber_TotalCo[i_time]
,val$calc$CI$chamber_reference_Total_diff_CeCo[i_time,1] ,val$calc$CI$chamber_reference_Total_diff_CeCo[i_time,2] #,val$calc$sum$chamber_reference_Total_diff_CeCo[i_time]
,val$calc$CI$chamber_reference_12_diff_CeCo[i_time,1] ,val$calc$CI$chamber_reference_12_diff_CeCo[i_time,2] #,val$calc$sum$chamber_reference_12_diff_CeCo[i_time]
,val$calc$CI$chamber_reference_13_diff_CeCo[i_time,1] ,val$calc$CI$chamber_reference_13_diff_CeCo[i_time,2] #,val$calc$sum$chamber_reference_13_diff_CeCo[i_time]
,val$calc$CI$xi[i_time,1] ,val$calc$CI$xi[i_time,2] #,val$calc$sum$xi[i_time]
#,val$calc$CI$flow_adjusted[i_time,1] ,val$calc$CI$flow_adjusted[i_time,2] #,val$calc$sum$flow_adjusted[i_time] # 9/5/2012
,val$calc$CI$TDL_A_photosynthesis[i_time,1] ,val$calc$CI$TDL_A_photosynthesis[i_time,2] #,val$calc$sum$TDL_A_photosynthesis[i_time]
,val$calc$CI$TDL_12A_photosynthesis[i_time,1] ,val$calc$CI$TDL_12A_photosynthesis[i_time,2] #,val$calc$sum$TDL_12A_photosynthesis[i_time]
,val$calc$CI$TDL_13A_photosynthesis[i_time,1] ,val$calc$CI$TDL_13A_photosynthesis[i_time,2] #,val$calc$sum$TDL_13A_photosynthesis[i_time]
,val$calc$CI$Licor_A_photosynthesis[i_time,1] ,val$calc$CI$Licor_A_photosynthesis[i_time,2] #,val$calc$sum$Licor_A_photosynthesis[i_time]
,val$calc$CI$Delta_from_ratios_in_out[i_time,1] ,val$calc$CI$Delta_from_ratios_in_out[i_time,2] #,val$calc$sum$Delta_from_ratios_in_out[i_time]
,val$calc$CI$Delta_from_A_ratio[i_time,1] ,val$calc$CI$Delta_from_A_ratio[i_time,2] #,val$calc$sum$Delta_from_A_ratio[i_time]
,val$calc$CI$VPD[i_time,1] ,val$calc$CI$VPD[i_time,2] #,val$calc$sum$VPD[i_time]
,val$calc$CI$E_transpiration[i_time,1] ,val$calc$CI$E_transpiration[i_time,2] #,val$calc$sum$E_transpiration[i_time]
,val$calc$CI$leaf_temp[i_time,1] ,val$calc$CI$leaf_temp[i_time,2] #,val$calc$sum$leaf_temp[i_time]
,val$calc$CI$air_temp[i_time,1] ,val$calc$CI$air_temp[i_time,2] #,val$calc$sum$air_temp[i_time]
,val$calc$CI$light_in[i_time,1] ,val$calc$CI$light_in[i_time,2] #,val$calc$sum$light_in[i_time]
,val$calc$CI$light_out[i_time,1] ,val$calc$CI$light_out[i_time,2] #,val$calc$sum$light_out[i_time]
,val$calc$CI$reference_delta_e[i_time,1] ,val$calc$CI$reference_delta_e[i_time,2] #,val$calc$sum$reference_delta_e[i_time]
,val$calc$CI$chamber_delta_o[i_time,1] ,val$calc$CI$chamber_delta_o[i_time,2] #,val$calc$sum$chamber_delta_o[i_time]
,val$calc$CI$chamber_reference_delta_diff_CoCe[i_time,1] ,val$calc$CI$chamber_reference_delta_diff_CoCe[i_time,2] #,val$calc$sum$chamber_reference_delta_diff_CoCe[i_time]
,val$calc$CI$Delta_obs[i_time,1] ,val$calc$CI$Delta_obs[i_time,2] #,val$calc$sum$Delta_obs[i_time]
,val$calc$CI$Delta_obs_permil[i_time,1] ,val$calc$CI$Delta_obs_permil[i_time,2] #,val$calc$sum$Delta_obs_permil[i_time]
,val$calc$CI$delta_13C_Assim[i_time,1] ,val$calc$CI$delta_13C_Assim[i_time,2] #,val$calc$sum$delta_13C_Assim[i_time]
,val$calc$CI$p[i_time,1] ,val$calc$CI$p[i_time,2] #,val$calc$sum$p[i_time]
,val$calc$CI$delta_13C_Resp[i_time,1] ,val$calc$CI$delta_13C_Resp[i_time,2] #,val$calc$sum$delta_13C_Resp[i_time]
,val$calc$CI$chamber_TotalCa[i_time,1] ,val$calc$CI$chamber_TotalCa[i_time,2] #,val$calc$sum$chamber_TotalCa[i_time]
,val$calc$CI$chamber_12Ca[i_time,1] ,val$calc$CI$chamber_12Ca[i_time,2] #,val$calc$sum$chamber_12Ca[i_time]
,val$calc$CI$chamber_13Ca[i_time,1] ,val$calc$CI$chamber_13Ca[i_time,2] #,val$calc$sum$chamber_13Ca[i_time]
,val$calc$CI$chamber_TotalCs[i_time,1] ,val$calc$CI$chamber_TotalCs[i_time,2] #,val$calc$sum$chamber_TotalCs[i_time]
,val$calc$CI$chamber_12Cs[i_time,1] ,val$calc$CI$chamber_12Cs[i_time,2] #,val$calc$sum$chamber_12Cs[i_time]
,val$calc$CI$chamber_13Cs[i_time,1] ,val$calc$CI$chamber_13Cs[i_time,2] #,val$calc$sum$chamber_13Cs[i_time]
,val$calc$CI$chamber_Totalpa[i_time,1] ,val$calc$CI$chamber_Totalpa[i_time,2] #,val$calc$sum$chamber_Totalpa[i_time]
,val$calc$CI$chamber_12pa[i_time,1] ,val$calc$CI$chamber_12pa[i_time,2] #,val$calc$sum$chamber_12pa[i_time]
,val$calc$CI$chamber_13pa[i_time,1] ,val$calc$CI$chamber_13pa[i_time,2] #,val$calc$sum$chamber_13pa[i_time]
,val$calc$CI$chamber_Totalps[i_time,1] ,val$calc$CI$chamber_Totalps[i_time,2] #,val$calc$sum$chamber_Totalps[i_time]
,val$calc$CI$chamber_12ps[i_time,1] ,val$calc$CI$chamber_12ps[i_time,2] #,val$calc$sum$chamber_12ps[i_time]
,val$calc$CI$chamber_13ps[i_time,1] ,val$calc$CI$chamber_13ps[i_time,2] #,val$calc$sum$chamber_13ps[i_time]
,val$calc$CI$chamber_Totalgbw[i_time,1] ,val$calc$CI$chamber_Totalgbw[i_time,2] #,val$calc$sum$chamber_Totalgbw[i_time]
,val$calc$CI$chamber_Totalgbc[i_time,1] ,val$calc$CI$chamber_Totalgbc[i_time,2] #,val$calc$sum$chamber_Totalgbc[i_time]
,val$calc$CI$chamber_12gbc[i_time,1] ,val$calc$CI$chamber_12gbc[i_time,2] #,val$calc$sum$chamber_12gbc[i_time]
,val$calc$CI$chamber_13gbc[i_time,1] ,val$calc$CI$chamber_13gbc[i_time,2] #,val$calc$sum$chamber_13gbc[i_time]
,val$calc$CI$chamber_Totalgsw[i_time,1] ,val$calc$CI$chamber_Totalgsw[i_time,2] #,val$calc$sum$chamber_Totalgsw[i_time]
,val$calc$CI$chamber_Totalgsc[i_time,1] ,val$calc$CI$chamber_Totalgsc[i_time,2] #,val$calc$sum$chamber_Totalgsc[i_time]
,val$calc$CI$chamber_12gsc[i_time,1] ,val$calc$CI$chamber_12gsc[i_time,2] #,val$calc$sum$chamber_12gsc[i_time]
,val$calc$CI$chamber_13gsc[i_time,1] ,val$calc$CI$chamber_13gsc[i_time,2] #,val$calc$sum$chamber_13gsc[i_time]
,val$calc$CI$chamber_Totalgtc[i_time,1] ,val$calc$CI$chamber_Totalgtc[i_time,2] #,val$calc$sum$chamber_Totalgtc[i_time]
,val$calc$CI$chamber_12gtc[i_time,1] ,val$calc$CI$chamber_12gtc[i_time,2] #,val$calc$sum$chamber_12gtc[i_time]
,val$calc$CI$chamber_13gtc[i_time,1] ,val$calc$CI$chamber_13gtc[i_time,2] #,val$calc$sum$chamber_13gtc[i_time]
,val$calc$CI$chamber_TotalCi[i_time,1] ,val$calc$CI$chamber_TotalCi[i_time,2] #,val$calc$sum$chamber_TotalCi[i_time]
,val$calc$CI$chamber_12Ci[i_time,1] ,val$calc$CI$chamber_12Ci[i_time,2] #,val$calc$sum$chamber_12Ci[i_time]
,val$calc$CI$chamber_13Ci[i_time,1] ,val$calc$CI$chamber_13Ci[i_time,2] #,val$calc$sum$chamber_13Ci[i_time]
,val$calc$CI$chamber_Totalpi[i_time,1] ,val$calc$CI$chamber_Totalpi[i_time,2] #,val$calc$sum$chamber_Totalpi[i_time]
,val$calc$CI$chamber_12pi[i_time,1] ,val$calc$CI$chamber_12pi[i_time,2] #,val$calc$sum$chamber_12pi[i_time]
,val$calc$CI$chamber_13pi[i_time,1] ,val$calc$CI$chamber_13pi[i_time,2] #,val$calc$sum$chamber_13pi[i_time]
,val$calc$CI$chamber_Totalpi_pa[i_time,1] ,val$calc$CI$chamber_Totalpi_pa[i_time,2] #,val$calc$sum$chamber_Totalpi_pa[i_time]
,val$calc$CI$chamber_Delta_i_simple_for_gm[i_time,1] ,val$calc$CI$chamber_Delta_i_simple_for_gm[i_time,2] #,val$calc$sum$chamber_Delta_i_simple_for_gm[i_time]
,val$calc$CI$chamber_Delta_i_simple_for_modeling[i_time,1] ,val$calc$CI$chamber_Delta_i_simple_for_modeling[i_time,2] #,val$calc$sum$chamber_Delta_i_simple_for_modeling[i_time]
,val$calc$CI$chamber_Delta_i_complex_for_gm[i_time,1] ,val$calc$CI$chamber_Delta_i_complex_for_gm[i_time,2] #,val$calc$sum$chamber_Delta_i_complex_for_gm[i_time]
,val$calc$CI$chamber_Delta_i_simple_for_gm_Delta_obs[i_time,1] ,val$calc$CI$chamber_Delta_i_simple_for_gm_Delta_obs[i_time,2] #,val$calc$sum$chamber_Delta_i_simple_for_gm_Delta_obs[i_time]
,val$calc$CI$chamber_Delta_i_complex_for_gm_Delta_obs[i_time,1] ,val$calc$CI$chamber_Delta_i_complex_for_gm_Delta_obs[i_time,2] #,val$calc$sum$chamber_Delta_i_complex_for_gm_Delta_obs[i_time]
,val$calc$CI$chamber_Totalgm_point_simple[i_time,1] ,val$calc$CI$chamber_Totalgm_point_simple[i_time,2] #,val$calc$sum$chamber_Totalgm_point_simple[i_time]
,val$calc$CI$chamber_12gm_point_simple[i_time,1] ,val$calc$CI$chamber_12gm_point_simple[i_time,2] #,val$calc$sum$chamber_12gm_point_simple[i_time]
,val$calc$CI$chamber_13gm_point_simple[i_time,1] ,val$calc$CI$chamber_13gm_point_simple[i_time,2] #,val$calc$sum$chamber_13gm_point_simple[i_time]
,val$calc$CI$chamber_Totalgm_point_complex[i_time,1] ,val$calc$CI$chamber_Totalgm_point_complex[i_time,2] #,val$calc$sum$chamber_Totalgm_point_complex[i_time]
,val$calc$CI$chamber_Totalgm_to_use[i_time,1] ,val$calc$CI$chamber_Totalgm_to_use[i_time,2] #,val$calc$sum$chamber_Totalgm_to_use[i_time]
,val$calc$CI$chamber_Totalpc_using_gm[i_time,1] ,val$calc$CI$chamber_Totalpc_using_gm[i_time,2] #,val$calc$sum$chamber_Totalpc_using_gm[i_time]
,val$calc$CI$chamber_12pc_using_gm[i_time,1] ,val$calc$CI$chamber_12pc_using_gm[i_time,2] #,val$calc$sum$chamber_12pc_using_gm[i_time]
,val$calc$CI$chamber_13pc_using_gm[i_time,1] ,val$calc$CI$chamber_13pc_using_gm[i_time,2] #,val$calc$sum$chamber_13pc_using_gm[i_time]
,val$calc$CI$chamber_Totalpc_using_simple_Delta_for_gm[i_time,1] ,val$calc$CI$chamber_Totalpc_using_simple_Delta_for_gm[i_time,2] #,val$calc$sum$chamber_Totalpc_using_simple_Delta_for_gm[i_time]
,val$calc$CI$chamber_Totalpc_using_simple_Delta_for_modeling[i_time,1] ,val$calc$CI$chamber_Totalpc_using_simple_Delta_for_modeling[i_time,2] #,val$calc$sum$chamber_Totalpc_using_simple_Delta_for_modeling[i_time]
,val$calc$CI$chamber_Totalpc_using_complex_Delta_no_decarboxylation[i_time,1] ,val$calc$CI$chamber_Totalpc_using_complex_Delta_no_decarboxylation[i_time,2] #,val$calc$sum$chamber_Totalpc_using_complex_Delta_no_decarboxylation[i_time]
,val$calc$CI$chamber_Totalpc_using_complex_Delta_full_model[i_time,1] ,val$calc$CI$chamber_Totalpc_using_complex_Delta_full_model[i_time,2] #,val$calc$sum$chamber_Totalpc_using_complex_Delta_full_model[i_time]
,val$calc$CI$chamber_Totalpc_to_use[i_time,1] ,val$calc$CI$chamber_Totalpc_to_use[i_time,2] #,val$calc$sum$chamber_Totalpc_to_use[i_time]
,val$calc$CI$chamber_TotalCc[i_time,1] ,val$calc$CI$chamber_TotalCc[i_time,2] #,val$calc$sum$chamber_TotalCc[i_time]
,val$calc$CI$chamber_12Cc[i_time,1] ,val$calc$CI$chamber_12Cc[i_time,2] #,val$calc$sum$chamber_12Cc[i_time]
,val$calc$CI$chamber_13Cc[i_time,1] ,val$calc$CI$chamber_13Cc[i_time,2] #,val$calc$sum$chamber_13Cc[i_time]
,val$calc$CI$Licor_flow_uin[i_time,1] ,val$calc$CI$Licor_flow_uin[i_time,2] #,val$calc$sum$Licor_flow_uin[i_time]
,val$calc$CI$Licor_H2OR_xin[i_time,1] ,val$calc$CI$Licor_H2OR_xin[i_time,2] #,val$calc$sum$Licor_H2OR_xin[i_time]
,val$calc$CI$Licor_La[i_time,1] ,val$calc$CI$Licor_La[i_time,2] #,val$calc$sum$Licor_La[i_time]
,val$calc$CI$Licor_Atm_press[i_time,1] ,val$calc$CI$Licor_Atm_press[i_time,2] #,"Licor_Atm_press[i_time]
,val$calc$CI$Licor_gsc_CI_L[i_time,1] ,val$calc$CI$Licor_gsc_CI_U[i_time,2] #,"Licor_gsc"
,val$calc$CI$Licor_Ci_CI_L[i_time,1] ,val$calc$CI$Licor_Ci_CI_U[i_time,2] #,"Licor_Ci"
,val$calc$CI$Licor_StmRat_CI_L[i_time,1] ,val$calc$CI$Licor_StmRat_CI_U[i_time,2] #,"Licor_StmRat"
,val$calc$CI$Licor_gbw_CI_L[i_time,1] ,val$calc$CI$Licor_gbw_CI_U[i_time,2] #,"Licor_gbw"
,val$calc$CI$Licor_temp_block_CI_L[i_time,1] ,val$calc$CI$Licor_temp_block_CI_U[i_time,2] #,"Licor_temp_block"
,val$calc$CI$Licor_Ce_CI_L[i_time,1] ,val$calc$CI$Licor_Ce_CI_U[i_time,2] #,"Licor_Ce"
,val$calc$CI$Licor_Co_CI_L[i_time,1] ,val$calc$CI$Licor_Co_CI_U[i_time,2] #,"Licor_Co"
,val$calc$CI$Licor_xout[i_time,1] ,val$calc$CI$Licor_xout[i_time,2] #,"Licor_xout"
,val$calc$CI$Licor_rh_ref[i_time,1] ,val$calc$CI$Licor_rh_ref[i_time,2] #,"Licor_rh_ref"
,val$calc$CI$Licor_rh_sam_CI_L[i_time,1] ,val$calc$CI$Licor_rh_sam_CI_U[i_time,2] #,"Licor_rh_sam"
,val$calc$CI$Licor_CsMch_CI_L[i_time,1] ,val$calc$CI$Licor_CsMch_CI_U[i_time,2] #,"Licor_CsMch"
,val$calc$CI$Licor_HsMch_CI_L[i_time,1] ,val$calc$CI$Licor_HsMch_CI_U[i_time,2] #,"Licor_HsMch"
,val$calc$CI$Licor_StableF_CI_L[i_time,1] ,val$calc$CI$Licor_StableF_CI_U[i_time,2] #,"Licor_StableF"
,val$calc$CI$Licor_Status_CI_L[i_time,1] ,val$calc$CI$Licor_Status_CI_U[i_time,2] #,"Licor_Status"
, sep=",")
)
}
write(val$write$CI_Calc, file=output_CI_Calc_fn, append=FALSE);#, colnames=FALSE, row.names=FALSE)
# last file, last measurement of each cycle file, remove rows that are not last measurements
n <- val$sum$TDL$n;
sites <- val$sum$TDL$site;
last_sites <- rep(0,n);
for (i_site in 1:n) {
# if last record, then last by definition
if (i_site == n) { last_sites[i_site] <- i_site; }
else {
# if current different from next, then last
if (sites[i_site] != sites[i_site+1]) { last_sites[i_site] <- i_site; }
}
}
last_sites <- last_sites[last_sites > 0]; # include only last sites
last_sites <- c(1,last_sites+1); # include header row
val$write$CI_Calc_last <- val$write$CI_Calc[last_sites];
write(val$write$CI_Calc, file=output_CI_Calc_fn, append=FALSE);#, colnames=FALSE, row.names=FALSE)
write(val$write$CI_Calc_last, file=output_CI_Calc_last_fn, append=FALSE);#, colnames=FALSE, row.names=FALSE)
return( val$write );
### val$write
}
erikerhardt/isogasex documentation built on July 16, 2019, 5:25 a.m.
R Package Documentation
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#' write output section
#'
#' Write all observed and calculated values with BS CIs for all time points.
#'
#' @param val xxxPARAMxxx
#' @param TDL_cycle xxxPARAMxxx
#' @param output_CI_Calc_fn xxxPARAMxxx
#' @param output_CI_Calc_last_fn xxxPARAMxxx
#'
#' @return val$write xxxRETURNxxx
#'
write_CI_Calc_file <-
function# write_output section
### Write all observed and calculated values with BS CIs for all time points.
(val
###
, TDL_cycle
###
, output_CI_Calc_fn
###
, output_CI_Calc_last_fn
###
)
{
val$write$CI_Calc <- paste(
"date"
,"time"
,"site"
,"site_name"
,"first_ind"
,"ind"
,"gain_12C_CI_L" ,"gain_12C_CI_U" #,"gain_12C"
,"gain_13C_CI_L" ,"gain_13C_CI_U" #,"gain_13C"
,"offset_12C_CI_L" ,"offset_12C_CI_U" #,"offset_12C"
,"offset_13C_CI_L" ,"offset_13C_CI_U" #,"offset_13C"
,"reference_12Ce_CI_L" ,"reference_12Ce_CI_U" #,"reference_12Ce"
,"reference_13Ce_CI_L" ,"reference_13Ce_CI_U" #,"reference_13Ce"
,"chamber_12Co_CI_L" ,"chamber_12Co_CI_U" #,"chamber_12Co"
,"chamber_13Co_CI_L" ,"chamber_13Co_CI_U" #,"chamber_13Co"
,"reference_TotalCe_CI_L" ,"reference_TotalCe_CI_U" #,"reference_TotalCe"
,"chamber_TotalCo_CI_L" ,"chamber_TotalCo_CI_U" #,"chamber_TotalCo"
,"chamber_reference_Total_diff_CeCo_CI_L" ,"chamber_reference_Total_diff_CeCo_CI_U" #,"chamber_reference_Total_diff_CeCo"
,"chamber_reference_12_diff_CeCo_CI_L" ,"chamber_reference_12_diff_CeCo_CI_U" #,"chamber_reference_12_diff_CeCo"
,"chamber_reference_13_diff_CeCo_CI_L" ,"chamber_reference_13_diff_CeCo_CI_U" #,"chamber_reference_13_diff_CeCo"
,"xi_CI_L" ,"xi_CI_U" #,"xi"
#,"flow_adjusted_CI_L" ,"flow_adjusted_CI_U" #,"flow_adjusted" # 9/5/2012
,"TDL_A_photosynthesis_CI_L" ,"TDL_A_photosynthesis_CI_U" #,"TDL_A_photosynthesis"
,"TDL_12A_photosynthesis_CI_L" ,"TDL_12A_photosynthesis_CI_U" #,"TDL_12A_photosynthesis"
,"TDL_13A_photosynthesis_CI_L" ,"TDL_13A_photosynthesis_CI_U" #,"TDL_13A_photosynthesis"
,"Licor_A_photosynthesis_CI_L" ,"Licor_A_photosynthesis_CI_U" #,"Licor_A_photosynthesis"
,"Delta_from_ratios_in_out_CI_L" ,"Delta_from_ratios_in_out_CI_U" #,"Delta_from_ratios_in_out"
,"Delta_from_A_ratio_CI_L" ,"Delta_from_A_ratio_CI_U" #,"Delta_from_A_ratio"
,"VPD_CI_L" ,"VPD_CI_U" #,"VPD"
,"E_transpiration_CI_L" ,"E_transpiration_CI_U" #,"E_transpiration"
,"leaf_temp_CI_L" ,"leaf_temp_CI_U" #,"leaf_temp"
,"air_temp_CI_L" ,"air_temp_CI_U" #,"air_temp"
,"light_in_CI_L" ,"light_in_CI_U" #,"light_in"
,"light_out_CI_L" ,"light_out_CI_U" #,"light_out"
,"reference_delta_e_CI_L" ,"reference_delta_e_CI_U" #,"reference_delta_e"
,"chamber_delta_o_CI_L" ,"chamber_delta_o_CI_U" #,"chamber_delta_o"
,"chamber_reference_delta_diff_CoCe_CI_L" ,"chamber_reference_delta_diff_CoCe_CI_U" #,"chamber_reference_delta_diff_CoCe"
,"Delta_obs_CI_L" ,"Delta_obs_CI_U" #,"Delta_obs"
,"Delta_obs_permil_CI_L" ,"Delta_obs_permil_CI_U" #,"Delta_obs_permil"
,"delta_13C_Assim_CI_L" ,"delta_13C_Assim_CI_U" #,"delta_13C_Assim"
,"p_CI_L" ,"p_CI_U" #,"p"
,"delta_13C_Resp_CI_L" ,"delta_13C_Resp_CI_U" #,"delta_13C_Resp"
,"chamber_TotalCa_CI_L" ,"chamber_TotalCa_CI_U" #,"chamber_TotalCa"
,"chamber_12Ca_CI_L" ,"chamber_12Ca_CI_U" #,"chamber_12Ca"
,"chamber_13Ca_CI_L" ,"chamber_13Ca_CI_U" #,"chamber_13Ca"
,"chamber_TotalCs_CI_L" ,"chamber_TotalCs_CI_U" #,"chamber_TotalCs"
,"chamber_12Cs_CI_L" ,"chamber_12Cs_CI_U" #,"chamber_12Cs"
,"chamber_13Cs_CI_L" ,"chamber_13Cs_CI_U" #,"chamber_13Cs"
,"chamber_Totalpa_CI_L" ,"chamber_Totalpa_CI_U" #,"chamber_Totalpa"
,"chamber_12pa_CI_L" ,"chamber_12pa_CI_U" #,"chamber_12pa"
,"chamber_13pa_CI_L" ,"chamber_13pa_CI_U" #,"chamber_13pa"
,"chamber_Totalps_CI_L" ,"chamber_Totalps_CI_U" #,"chamber_Totalps"
,"chamber_12ps_CI_L" ,"chamber_12ps_CI_U" #,"chamber_12ps"
,"chamber_13ps_CI_L" ,"chamber_13ps_CI_U" #,"chamber_13ps"
,"chamber_Totalgbw_CI_L" ,"chamber_Totalgbw_CI_U" #,"chamber_Totalgbw"
,"chamber_Totalgbc_CI_L" ,"chamber_Totalgbc_CI_U" #,"chamber_Totalgbc"
,"chamber_12gbc_CI_L" ,"chamber_12gbc_CI_U" #,"chamber_12gbc"
,"chamber_13gbc_CI_L" ,"chamber_13gbc_CI_U" #,"chamber_13gbc"
,"chamber_Totalgsw_CI_L" ,"chamber_Totalgsw_CI_U" #,"chamber_Totalgsw"
,"chamber_Totalgsc_CI_L" ,"chamber_Totalgsc_CI_U" #,"chamber_Totalgsc"
,"chamber_12gsc_CI_L" ,"chamber_12gsc_CI_U" #,"chamber_12gsc"
,"chamber_13gsc_CI_L" ,"chamber_13gsc_CI_U" #,"chamber_13gsc"
,"chamber_Totalgtc_CI_L" ,"chamber_Totalgtc_CI_U" #,"chamber_Totalgtc"
,"chamber_12gtc_CI_L" ,"chamber_12gtc_CI_U" #,"chamber_12gtc"
,"chamber_13gtc_CI_L" ,"chamber_13gtc_CI_U" #,"chamber_13gtc"
,"chamber_TotalCi_CI_L" ,"chamber_TotalCi_CI_U" #,"chamber_TotalCi"
,"chamber_12Ci_CI_L" ,"chamber_12Ci_CI_U" #,"chamber_12Ci"
,"chamber_13Ci_CI_L" ,"chamber_13Ci_CI_U" #,"chamber_13Ci"
,"chamber_Totalpi_CI_L" ,"chamber_Totalpi_CI_U" #,"chamber_Totalpi"
,"chamber_12pi_CI_L" ,"chamber_12pi_CI_U" #,"chamber_12pi"
,"chamber_13pi_CI_L" ,"chamber_13pi_CI_U" #,"chamber_13pi"
,"chamber_Totalpi_pa_CI_L" ,"chamber_Totalpi_pa_CI_U" #,"chamber_Totalpi_pa"
,"chamber_Delta_i_simple_for_gm_CI_L" ,"chamber_Delta_i_simple_for_gm_CI_U" #,"chamber_Delta_i_simple_for_gm"
,"chamber_Delta_i_simple_for_modeling_CI_L" ,"chamber_Delta_i_simple_for_modeling_CI_U" #,"chamber_Delta_i_simple_for_modeling"
,"chamber_Delta_i_complex_for_gm_CI_L" ,"chamber_Delta_i_complex_for_gm_CI_U" #,"chamber_Delta_i_complex_for_gm"
,"chamber_Delta_i_simple_for_gm_Delta_obs_CI_L" ,"chamber_Delta_i_simple_for_gm_Delta_obs_CI_U" #,"chamber_Delta_i_simple_for_gm_Delta_obs"
,"chamber_Delta_i_complex_for_gm_Delta_obs_CI_L" ,"chamber_Delta_i_complex_for_gm_Delta_obs_CI_U" #,"chamber_Delta_i_complex_for_gm_Delta_obs"
,"chamber_Totalgm_point_simple_CI_L" ,"chamber_Totalgm_point_simple_CI_U" #,"chamber_Totalgm_point_simple"
,"chamber_12gm_point_simple_CI_L" ,"chamber_12gm_point_simple_CI_U" #,"chamber_12gm_point_simple"
,"chamber_13gm_point_simple_CI_L" ,"chamber_13gm_point_simple_CI_U" #,"chamber_13gm_point_simple"
,"chamber_Totalgm_point_complex_CI_L" ,"chamber_Totalgm_point_complex_CI.U" #,"chamber_Totalgm_point_complex"
,"chamber_Totalgm_to_use_CI_L" ,"chamber_Totalgm_to_use_CI_U" #,"chamber_Totalgm_to_use"
,"chamber_Totalpc_using_gm_CI_L" ,"chamber_Totalpc_using_gm_CI_U" #,"chamber_Totalpc_using_gm"
,"chamber_12pc_using_gm_CI_L" ,"chamber_12pc_using_gm_CI_U" #,"chamber_12pc_using_gm"
,"chamber_13pc_using_gm_CI_L" ,"chamber_13pc_using_gm_CI_U" #,"chamber_13pc_using_gm"
,"chamber_Totalpc_using_simple_Delta_for_gm_CI_L" ,"chamber_Totalpc_using_simple_Delta_for_gm_CI_U" #,"chamber_Totalpc_using_simple_Delta_for_gm"
,"chamber_Totalpc_using_simple_Delta_for_modeling_CI_L" ,"chamber_Totalpc_using_simple_Delta_for_modeling_CI_U" #,"chamber_Totalpc_using_simple_Delta_for_modeling"
,"chamber_Totalpc_using_complex_Delta_no_decarboxylation_CI_L" ,"chamber_Totalpc_using_complex_Delta_no_decarboxylation_CI_U" #,"chamber_Totalpc_using_complex_Delta_no_decarboxylation"
,"chamber_Totalpc_using_complex_Delta_full_model_CI_L" ,"chamber_Totalpc_using_complex_Delta_full_model_CI_U" #,"chamber_Totalpc_using_complex_Delta_full_model"
,"chamber_Totalpc_to_use_CI_L" ,"chamber_Totalpc_to_use_CI_U" #,"chamber_Totalpc_to_use"
,"chamber_TotalCc_CI_L" ,"chamber_TotalCc_CI_U" #,"chamber_TotalCc"
,"chamber_12Cc_CI_L" ,"chamber_12Cc_CI_U" #,"chamber_12Cc"
,"chamber_13Cc_CI_L" ,"chamber_13Cc_CI_U" #,"chamber_13Cc"
,"Licor_flow_uin_CI_L" ,"Licor_flow_uin_CI_U" #,"Licor_flow_uin"
,"Licor_H2OR_xin_CI_L" ,"Licor_H2OR_xin_CI_U" #,"Licor_H2OR_xin"
,"Licor_La_CI_L" ,"Licor_La_CI_U" #,"Licor_La"
,"Licor_Atm_press_CI_L" ,"Licor_Atm_press_CI_U" #,"Licor_Atm_press"
,"Licor_gsc_CI_L" ,"Licor_gsc_CI_U" #,"Licor_gsc"
,"Licor_Ci_CI_L" ,"Licor_Ci_CI_U" #,"Licor_Ci"
,"Licor_StmRat_CI_L" ,"Licor_StmRat_CI_U" #,"Licor_StmRat"
,"Licor_gbw_CI_L" ,"Licor_gbw_CI_U" #,"Licor_gbw"
,"Licor_temp_block_CI_L" ,"Licor_temp_block_CI_U" #,"Licor_temp_block"
,"Licor_Ce_CI_L" ,"Licor_Ce_CI_U" #,"Licor_Ce"
,"Licor_Co_CI_L" ,"Licor_Co_CI_U" #,"Licor_Co"
,"Licor_xout_CI_L" ,"Licor_xout_CI_U" #,"Licor_xout"
,"Licor_rh_ref" ,"Licor_rh_ref" #,"Licor_rh_ref"
,"Licor_rh_sam_CI_L" ,"Licor_rh_sam_CI_U" #,"Licor_rh_sam"
,"Licor_CsMch_CI_L" ,"Licor_CsMch_CI_U" #,"Licor_CsMch"
,"Licor_HsMch_CI_L" ,"Licor_HsMch_CI_U" #,"Licor_HsMch"
,"Licor_StableF_CI_L" ,"Licor_StableF_CI_U" #,"Licor_StableF"
,"Licor_Status_CI_L" ,"Licor_Status_CI_U" #,"Licor_Status"
# typically not used
#,"VpdA_CI_L" ,"VpdA_CI_U" #,"VpdA"
#,"Ci_Ca_CI_L" ,"Ci_Ca_CI_U" #,"Ci_Ca"
#,"pi_CI_L" ,"pi_CI_U" #,"pi"
#,"uc_20_mV_CI_L" ,"uc_20_mV_CI_U" #,"uc_20_mV"
#,"uc_21_mV_CI_L" ,"uc_21_mV_CI_U" #,"uc_21_mV"
#,"U_S_CI_L" ,"U_S_CI_U" #,"U_S"
#,"Trans_CI_L" ,"Trans_CI_U" #,"Trans"
#,"CndCO2_CI_L" ,"CndCO2_CI_U" #,"CndCO2"
#,"Ref_mV_CI_L" ,"Ref_mV_CI_U" #,"Ref_mV"
#,"xTemp1_CI_L" ,"xTemp1_CI_U" #,"xTemp1"
#,"xTemp2_CI_L" ,"xTemp2_CI_U" #,"xTemp2"
, sep=",");
for (i_time in 1:val$sum$TDL$n) {
val$write$CI_Calc <-
rbind( val$write$CI_Calc
,paste(
format(val$sum$TDL$time[i_time],format="%Y-%m-%d")
,val$sum$TDL$site[i_time]
,TDL_cycle$table_name[(TDL_cycle$table[,1] == val$sum$TDL$site[i_time])]
,val$sum$TDL$first_ind[i_time]
,val$sum$TDL$ind[i_time]
,val$calc$CI$gain_12C[i_time,1] ,val$calc$CI$gain_12C[i_time,2] #,val$calc$sum$gain_12C[i_time]
,val$calc$CI$gain_13C[i_time,1] ,val$calc$CI$gain_13C[i_time,2] #,val$calc$sum$gain_13C[i_time]
,val$calc$CI$offset_12C[i_time,1] ,val$calc$CI$offset_12C[i_time,2] #,val$calc$sum$offset_12C[i_time]
,val$calc$CI$offset_13C[i_time,1] ,val$calc$CI$offset_13C[i_time,2] #,val$calc$sum$offset_13C[i_time]
,val$calc$CI$reference_12Ce[i_time,1] ,val$calc$CI$reference_12Ce[i_time,2] #,val$calc$sum$reference_12Ce[i_time]
,val$calc$CI$reference_13Ce[i_time,1] ,val$calc$CI$reference_13Ce[i_time,2] #,val$calc$sum$reference_13Ce[i_time]
,val$calc$CI$chamber_12Co[i_time,1] ,val$calc$CI$chamber_12Co[i_time,2] #,val$calc$sum$chamber_12Co[i_time]
,val$calc$CI$chamber_13Co[i_time,1] ,val$calc$CI$chamber_13Co[i_time,2] #,val$calc$sum$chamber_13Co[i_time]
,val$calc$CI$reference_TotalCe[i_time,1] ,val$calc$CI$reference_TotalCe[i_time,2] #,val$calc$sum$reference_TotalCe[i_time]
,val$calc$CI$chamber_TotalCo[i_time,1] ,val$calc$CI$chamber_TotalCo[i_time,2] #,val$calc$sum$chamber_TotalCo[i_time]
,val$calc$CI$chamber_reference_Total_diff_CeCo[i_time,1] ,val$calc$CI$chamber_reference_Total_diff_CeCo[i_time,2] #,val$calc$sum$chamber_reference_Total_diff_CeCo[i_time]
,val$calc$CI$chamber_reference_12_diff_CeCo[i_time,1] ,val$calc$CI$chamber_reference_12_diff_CeCo[i_time,2] #,val$calc$sum$chamber_reference_12_diff_CeCo[i_time]
,val$calc$CI$chamber_reference_13_diff_CeCo[i_time,1] ,val$calc$CI$chamber_reference_13_diff_CeCo[i_time,2] #,val$calc$sum$chamber_reference_13_diff_CeCo[i_time]
,val$calc$CI$xi[i_time,1] ,val$calc$CI$xi[i_time,2] #,val$calc$sum$xi[i_time]
#,val$calc$CI$flow_adjusted[i_time,1] ,val$calc$CI$flow_adjusted[i_time,2] #,val$calc$sum$flow_adjusted[i_time] # 9/5/2012
,val$calc$CI$TDL_A_photosynthesis[i_time,1] ,val$calc$CI$TDL_A_photosynthesis[i_time,2] #,val$calc$sum$TDL_A_photosynthesis[i_time]
,val$calc$CI$TDL_12A_photosynthesis[i_time,1] ,val$calc$CI$TDL_12A_photosynthesis[i_time,2] #,val$calc$sum$TDL_12A_photosynthesis[i_time]
,val$calc$CI$TDL_13A_photosynthesis[i_time,1] ,val$calc$CI$TDL_13A_photosynthesis[i_time,2] #,val$calc$sum$TDL_13A_photosynthesis[i_time]
,val$calc$CI$Licor_A_photosynthesis[i_time,1] ,val$calc$CI$Licor_A_photosynthesis[i_time,2] #,val$calc$sum$Licor_A_photosynthesis[i_time]
,val$calc$CI$Delta_from_ratios_in_out[i_time,1] ,val$calc$CI$Delta_from_ratios_in_out[i_time,2] #,val$calc$sum$Delta_from_ratios_in_out[i_time]
,val$calc$CI$Delta_from_A_ratio[i_time,1] ,val$calc$CI$Delta_from_A_ratio[i_time,2] #,val$calc$sum$Delta_from_A_ratio[i_time]
,val$calc$CI$VPD[i_time,1] ,val$calc$CI$VPD[i_time,2] #,val$calc$sum$VPD[i_time]
,val$calc$CI$E_transpiration[i_time,1] ,val$calc$CI$E_transpiration[i_time,2] #,val$calc$sum$E_transpiration[i_time]
,val$calc$CI$leaf_temp[i_time,1] ,val$calc$CI$leaf_temp[i_time,2] #,val$calc$sum$leaf_temp[i_time]
,val$calc$CI$air_temp[i_time,1] ,val$calc$CI$air_temp[i_time,2] #,val$calc$sum$air_temp[i_time]
,val$calc$CI$light_in[i_time,1] ,val$calc$CI$light_in[i_time,2] #,val$calc$sum$light_in[i_time]
,val$calc$CI$light_out[i_time,1] ,val$calc$CI$light_out[i_time,2] #,val$calc$sum$light_out[i_time]
,val$calc$CI$reference_delta_e[i_time,1] ,val$calc$CI$reference_delta_e[i_time,2] #,val$calc$sum$reference_delta_e[i_time]
,val$calc$CI$chamber_delta_o[i_time,1] ,val$calc$CI$chamber_delta_o[i_time,2] #,val$calc$sum$chamber_delta_o[i_time]
,val$calc$CI$chamber_reference_delta_diff_CoCe[i_time,1] ,val$calc$CI$chamber_reference_delta_diff_CoCe[i_time,2] #,val$calc$sum$chamber_reference_delta_diff_CoCe[i_time]
,val$calc$CI$Delta_obs[i_time,1] ,val$calc$CI$Delta_obs[i_time,2] #,val$calc$sum$Delta_obs[i_time]
,val$calc$CI$Delta_obs_permil[i_time,1] ,val$calc$CI$Delta_obs_permil[i_time,2] #,val$calc$sum$Delta_obs_permil[i_time]
,val$calc$CI$delta_13C_Assim[i_time,1] ,val$calc$CI$delta_13C_Assim[i_time,2] #,val$calc$sum$delta_13C_Assim[i_time]
,val$calc$CI$p[i_time,1] ,val$calc$CI$p[i_time,2] #,val$calc$sum$p[i_time]
,val$calc$CI$delta_13C_Resp[i_time,1] ,val$calc$CI$delta_13C_Resp[i_time,2] #,val$calc$sum$delta_13C_Resp[i_time]
,val$calc$CI$chamber_TotalCa[i_time,1] ,val$calc$CI$chamber_TotalCa[i_time,2] #,val$calc$sum$chamber_TotalCa[i_time]
,val$calc$CI$chamber_12Ca[i_time,1] ,val$calc$CI$chamber_12Ca[i_time,2] #,val$calc$sum$chamber_12Ca[i_time]
,val$calc$CI$chamber_13Ca[i_time,1] ,val$calc$CI$chamber_13Ca[i_time,2] #,val$calc$sum$chamber_13Ca[i_time]
,val$calc$CI$chamber_TotalCs[i_time,1] ,val$calc$CI$chamber_TotalCs[i_time,2] #,val$calc$sum$chamber_TotalCs[i_time]
,val$calc$CI$chamber_12Cs[i_time,1] ,val$calc$CI$chamber_12Cs[i_time,2] #,val$calc$sum$chamber_12Cs[i_time]
,val$calc$CI$chamber_13Cs[i_time,1] ,val$calc$CI$chamber_13Cs[i_time,2] #,val$calc$sum$chamber_13Cs[i_time]
,val$calc$CI$chamber_Totalpa[i_time,1] ,val$calc$CI$chamber_Totalpa[i_time,2] #,val$calc$sum$chamber_Totalpa[i_time]
,val$calc$CI$chamber_12pa[i_time,1] ,val$calc$CI$chamber_12pa[i_time,2] #,val$calc$sum$chamber_12pa[i_time]
,val$calc$CI$chamber_13pa[i_time,1] ,val$calc$CI$chamber_13pa[i_time,2] #,val$calc$sum$chamber_13pa[i_time]
,val$calc$CI$chamber_Totalps[i_time,1] ,val$calc$CI$chamber_Totalps[i_time,2] #,val$calc$sum$chamber_Totalps[i_time]
,val$calc$CI$chamber_12ps[i_time,1] ,val$calc$CI$chamber_12ps[i_time,2] #,val$calc$sum$chamber_12ps[i_time]
,val$calc$CI$chamber_13ps[i_time,1] ,val$calc$CI$chamber_13ps[i_time,2] #,val$calc$sum$chamber_13ps[i_time]
,val$calc$CI$chamber_Totalgbw[i_time,1] ,val$calc$CI$chamber_Totalgbw[i_time,2] #,val$calc$sum$chamber_Totalgbw[i_time]
,val$calc$CI$chamber_Totalgbc[i_time,1] ,val$calc$CI$chamber_Totalgbc[i_time,2] #,val$calc$sum$chamber_Totalgbc[i_time]
,val$calc$CI$chamber_12gbc[i_time,1] ,val$calc$CI$chamber_12gbc[i_time,2] #,val$calc$sum$chamber_12gbc[i_time]
,val$calc$CI$chamber_13gbc[i_time,1] ,val$calc$CI$chamber_13gbc[i_time,2] #,val$calc$sum$chamber_13gbc[i_time]
,val$calc$CI$chamber_Totalgsw[i_time,1] ,val$calc$CI$chamber_Totalgsw[i_time,2] #,val$calc$sum$chamber_Totalgsw[i_time]
,val$calc$CI$chamber_Totalgsc[i_time,1] ,val$calc$CI$chamber_Totalgsc[i_time,2] #,val$calc$sum$chamber_Totalgsc[i_time]
,val$calc$CI$chamber_12gsc[i_time,1] ,val$calc$CI$chamber_12gsc[i_time,2] #,val$calc$sum$chamber_12gsc[i_time]
,val$calc$CI$chamber_13gsc[i_time,1] ,val$calc$CI$chamber_13gsc[i_time,2] #,val$calc$sum$chamber_13gsc[i_time]
,val$calc$CI$chamber_Totalgtc[i_time,1] ,val$calc$CI$chamber_Totalgtc[i_time,2] #,val$calc$sum$chamber_Totalgtc[i_time]
,val$calc$CI$chamber_12gtc[i_time,1] ,val$calc$CI$chamber_12gtc[i_time,2] #,val$calc$sum$chamber_12gtc[i_time]
,val$calc$CI$chamber_13gtc[i_time,1] ,val$calc$CI$chamber_13gtc[i_time,2] #,val$calc$sum$chamber_13gtc[i_time]
,val$calc$CI$chamber_TotalCi[i_time,1] ,val$calc$CI$chamber_TotalCi[i_time,2] #,val$calc$sum$chamber_TotalCi[i_time]
,val$calc$CI$chamber_12Ci[i_time,1] ,val$calc$CI$chamber_12Ci[i_time,2] #,val$calc$sum$chamber_12Ci[i_time]
,val$calc$CI$chamber_13Ci[i_time,1] ,val$calc$CI$chamber_13Ci[i_time,2] #,val$calc$sum$chamber_13Ci[i_time]
,val$calc$CI$chamber_Totalpi[i_time,1] ,val$calc$CI$chamber_Totalpi[i_time,2] #,val$calc$sum$chamber_Totalpi[i_time]
,val$calc$CI$chamber_12pi[i_time,1] ,val$calc$CI$chamber_12pi[i_time,2] #,val$calc$sum$chamber_12pi[i_time]
,val$calc$CI$chamber_13pi[i_time,1] ,val$calc$CI$chamber_13pi[i_time,2] #,val$calc$sum$chamber_13pi[i_time]
,val$calc$CI$chamber_Totalpi_pa[i_time,1] ,val$calc$CI$chamber_Totalpi_pa[i_time,2] #,val$calc$sum$chamber_Totalpi_pa[i_time]
,val$calc$CI$chamber_Delta_i_simple_for_gm[i_time,1] ,val$calc$CI$chamber_Delta_i_simple_for_gm[i_time,2] #,val$calc$sum$chamber_Delta_i_simple_for_gm[i_time]
,val$calc$CI$chamber_Delta_i_simple_for_modeling[i_time,1] ,val$calc$CI$chamber_Delta_i_simple_for_modeling[i_time,2] #,val$calc$sum$chamber_Delta_i_simple_for_modeling[i_time]
,val$calc$CI$chamber_Delta_i_complex_for_gm[i_time,1] ,val$calc$CI$chamber_Delta_i_complex_for_gm[i_time,2] #,val$calc$sum$chamber_Delta_i_complex_for_gm[i_time]
,val$calc$CI$chamber_Delta_i_simple_for_gm_Delta_obs[i_time,1] ,val$calc$CI$chamber_Delta_i_simple_for_gm_Delta_obs[i_time,2] #,val$calc$sum$chamber_Delta_i_simple_for_gm_Delta_obs[i_time]
,val$calc$CI$chamber_Delta_i_complex_for_gm_Delta_obs[i_time,1] ,val$calc$CI$chamber_Delta_i_complex_for_gm_Delta_obs[i_time,2] #,val$calc$sum$chamber_Delta_i_complex_for_gm_Delta_obs[i_time]
,val$calc$CI$chamber_Totalgm_point_simple[i_time,1] ,val$calc$CI$chamber_Totalgm_point_simple[i_time,2] #,val$calc$sum$chamber_Totalgm_point_simple[i_time]
,val$calc$CI$chamber_12gm_point_simple[i_time,1] ,val$calc$CI$chamber_12gm_point_simple[i_time,2] #,val$calc$sum$chamber_12gm_point_simple[i_time]
,val$calc$CI$chamber_13gm_point_simple[i_time,1] ,val$calc$CI$chamber_13gm_point_simple[i_time,2] #,val$calc$sum$chamber_13gm_point_simple[i_time]
,val$calc$CI$chamber_Totalgm_point_complex[i_time,1] ,val$calc$CI$chamber_Totalgm_point_complex[i_time,2] #,val$calc$sum$chamber_Totalgm_point_complex[i_time]
,val$calc$CI$chamber_Totalgm_to_use[i_time,1] ,val$calc$CI$chamber_Totalgm_to_use[i_time,2] #,val$calc$sum$chamber_Totalgm_to_use[i_time]
,val$calc$CI$chamber_Totalpc_using_gm[i_time,1] ,val$calc$CI$chamber_Totalpc_using_gm[i_time,2] #,val$calc$sum$chamber_Totalpc_using_gm[i_time]
,val$calc$CI$chamber_12pc_using_gm[i_time,1] ,val$calc$CI$chamber_12pc_using_gm[i_time,2] #,val$calc$sum$chamber_12pc_using_gm[i_time]
,val$calc$CI$chamber_13pc_using_gm[i_time,1] ,val$calc$CI$chamber_13pc_using_gm[i_time,2] #,val$calc$sum$chamber_13pc_using_gm[i_time]
,val$calc$CI$chamber_Totalpc_using_simple_Delta_for_gm[i_time,1] ,val$calc$CI$chamber_Totalpc_using_simple_Delta_for_gm[i_time,2] #,val$calc$sum$chamber_Totalpc_using_simple_Delta_for_gm[i_time]
,val$calc$CI$chamber_Totalpc_using_simple_Delta_for_modeling[i_time,1] ,val$calc$CI$chamber_Totalpc_using_simple_Delta_for_modeling[i_time,2] #,val$calc$sum$chamber_Totalpc_using_simple_Delta_for_modeling[i_time]
,val$calc$CI$chamber_Totalpc_using_complex_Delta_no_decarboxylation[i_time,1] ,val$calc$CI$chamber_Totalpc_using_complex_Delta_no_decarboxylation[i_time,2] #,val$calc$sum$chamber_Totalpc_using_complex_Delta_no_decarboxylation[i_time]
,val$calc$CI$chamber_Totalpc_using_complex_Delta_full_model[i_time,1] ,val$calc$CI$chamber_Totalpc_using_complex_Delta_full_model[i_time,2] #,val$calc$sum$chamber_Totalpc_using_complex_Delta_full_model[i_time]
,val$calc$CI$chamber_Totalpc_to_use[i_time,1] ,val$calc$CI$chamber_Totalpc_to_use[i_time,2] #,val$calc$sum$chamber_Totalpc_to_use[i_time]
,val$calc$CI$chamber_TotalCc[i_time,1] ,val$calc$CI$chamber_TotalCc[i_time,2] #,val$calc$sum$chamber_TotalCc[i_time]
,val$calc$CI$chamber_12Cc[i_time,1] ,val$calc$CI$chamber_12Cc[i_time,2] #,val$calc$sum$chamber_12Cc[i_time]
,val$calc$CI$chamber_13Cc[i_time,1] ,val$calc$CI$chamber_13Cc[i_time,2] #,val$calc$sum$chamber_13Cc[i_time]
,val$calc$CI$Licor_flow_uin[i_time,1] ,val$calc$CI$Licor_flow_uin[i_time,2] #,val$calc$sum$Licor_flow_uin[i_time]
,val$calc$CI$Licor_H2OR_xin[i_time,1] ,val$calc$CI$Licor_H2OR_xin[i_time,2] #,val$calc$sum$Licor_H2OR_xin[i_time]
,val$calc$CI$Licor_La[i_time,1] ,val$calc$CI$Licor_La[i_time,2] #,val$calc$sum$Licor_La[i_time]
,val$calc$CI$Licor_Atm_press[i_time,1] ,val$calc$CI$Licor_Atm_press[i_time,2] #,"Licor_Atm_press[i_time]
,val$calc$CI$Licor_gsc_CI_L[i_time,1] ,val$calc$CI$Licor_gsc_CI_U[i_time,2] #,"Licor_gsc"
,val$calc$CI$Licor_Ci_CI_L[i_time,1] ,val$calc$CI$Licor_Ci_CI_U[i_time,2] #,"Licor_Ci"
,val$calc$CI$Licor_StmRat_CI_L[i_time,1] ,val$calc$CI$Licor_StmRat_CI_U[i_time,2] #,"Licor_StmRat"
,val$calc$CI$Licor_gbw_CI_L[i_time,1] ,val$calc$CI$Licor_gbw_CI_U[i_time,2] #,"Licor_gbw"
,val$calc$CI$Licor_temp_block_CI_L[i_time,1] ,val$calc$CI$Licor_temp_block_CI_U[i_time,2] #,"Licor_temp_block"
,val$calc$CI$Licor_Ce_CI_L[i_time,1] ,val$calc$CI$Licor_Ce_CI_U[i_time,2] #,"Licor_Ce"
,val$calc$CI$Licor_Co_CI_L[i_time,1] ,val$calc$CI$Licor_Co_CI_U[i_time,2] #,"Licor_Co"
,val$calc$CI$Licor_xout[i_time,1] ,val$calc$CI$Licor_xout[i_time,2] #,"Licor_xout"
,val$calc$CI$Licor_rh_ref[i_time,1] ,val$calc$CI$Licor_rh_ref[i_time,2] #,"Licor_rh_ref"
,val$calc$CI$Licor_rh_sam_CI_L[i_time,1] ,val$calc$CI$Licor_rh_sam_CI_U[i_time,2] #,"Licor_rh_sam"
,val$calc$CI$Licor_CsMch_CI_L[i_time,1] ,val$calc$CI$Licor_CsMch_CI_U[i_time,2] #,"Licor_CsMch"
,val$calc$CI$Licor_HsMch_CI_L[i_time,1] ,val$calc$CI$Licor_HsMch_CI_U[i_time,2] #,"Licor_HsMch"
,val$calc$CI$Licor_StableF_CI_L[i_time,1] ,val$calc$CI$Licor_StableF_CI_U[i_time,2] #,"Licor_StableF"
,val$calc$CI$Licor_Status_CI_L[i_time,1] ,val$calc$CI$Licor_Status_CI_U[i_time,2] #,"Licor_Status"
, sep=",")
)
}
write(val$write$CI_Calc, file=output_CI_Calc_fn, append=FALSE);#, colnames=FALSE, row.names=FALSE)
# last file, last measurement of each cycle file, remove rows that are not last measurements
n <- val$sum$TDL$n;
sites <- val$sum$TDL$site;
last_sites <- rep(0,n);
for (i_site in 1:n) {
# if last record, then last by definition
if (i_site == n) { last_sites[i_site] <- i_site; }
else {
# if current different from next, then last
if (sites[i_site] != sites[i_site+1]) { last_sites[i_site] <- i_site; }
}
}
last_sites <- last_sites[last_sites > 0]; # include only last sites
last_sites <- c(1,last_sites+1); # include header row
val$write$CI_Calc_last <- val$write$CI_Calc[last_sites];
write(val$write$CI_Calc, file=output_CI_Calc_fn, append=FALSE);#, colnames=FALSE, row.names=FALSE)
write(val$write$CI_Calc_last, file=output_CI_Calc_last_fn, append=FALSE);#, colnames=FALSE, row.names=FALSE)
return( val$write );
### val$write
}
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