2020-01-17 tc125 M1SS fails to find TAU/TOLD values in either input concentration dataset or flags dataset #158
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I noticed that in the flag dataset used for tc125 has additional parameters which is what is causing this error to occur when the flag dataset and the data dataset is merged by the computation: > names(flag_tc125)
[1] "PKDATAROWID" "FLGEXKEL" "FLGEXAUC" "FLGEXSDE" "FLGEXST" "PKRCOM" "PKPCOM" "FLGTIME" "TOLD1"
[10] "TOLD2" "TAU1" "TAU2" "SDEID" "TIME" "CEST_KEL" "CEST_INT" "CEST_EXT" "CEST_C0"
[19] "CEST_TLAST"
> flag_tc125 <- flag_tc125[!names(flag_tc125) %in% c("PKRCOM", "PKPCOM", "SDEID", "TIME", "CEST_KEL", "CEST_INT", "CEST_EXT", "CEST_C0", "CEST_TLAST")]
> res_tc125 <- openNCA::run_computation(data = data_tc125, map = map_tc125, flag = flag_tc125, parameterset = "PARAMETERLIST")
unit_conversion : Unit Class 1 (Time) time_col: TMAX TMAX1 TMAX2 TMIN TMIN1 TMIN2 TLAST TLAST1 TLAST2 TLAG KELTMLO KELTMHI THALF LASTTIME LASTTIME1 LASTTIME2 MRTLAST MRTLAST1 MRTLAST2 MRTEVIFO1 MRTEVIFO2 MRTEVIFP1 MRTEVIFP2 TAU1 TAU2 TOLD1 TOLD2 parameters are scaled from 1 to HR via scaling factor: 1
unit_conversion : Unit Class 3 (Dose) dose_col: DOSE1 parameters are scaled from 1 to MG via scaling factor: 0.001
unit_conversion : Unit Class 3 (Dose) dose_col: DOSE2 parameters are scaled from 1 to MG via scaling factor: 0.001
unit_conversion : Unit Class 4 (Volume) volume_col: VZFTAU1 VZFTAU2 parameters are scaled from ML to L via scaling factor: 0.001
unit_conversion : Unit Class 5 (Amount/Volume) conc_col: CMAX CMAX1 CMAX2 CMIN CMIN1 CMIN2 CLAST CLAST1 CLAST2 CTROUGH1 CTROUGH2 CTROUGHEND1 CTROUGHEND2 KELC0 CEST CAV1 CAV2 parameters are scaled from NG/ML to NG/ML via scaling factor: 1
unit_conversion : Unit Class 6 (1/Time) kel_col: KEL parameters are scaled from 1/HR to 1/HR via scaling factor: 1
unit_conversion : Unit Class 7 (Volume/Time) cl_col: CLFTAU1 CLFTAU2 parameters are scaled from ML/HR to L/HR via scaling factor: 0.001
unit_conversion : Unit Class 8: (Amount.Time/Volume) auc_col: AUCALL AUCLAST AUCLASTC AUCLAST1 AUCLAST2 AUCLASTC1 AUCLASTC2 AUC1 AUC2 AUC3 AUC4 AUC5 AUC6 AUC7 AUC8 AUC9 AUC10 AUC11 AUC12 AUC13 AUCINFO AUCINFO1 AUCINFO2 AUCINFOC AUCINFP AUCINFP1 AUCINFP2 AUCINFPC AUCTAU1 AUCTAU2 parameters are scaled from NG.HR/ML to NG.HR/ML via scaling factor: 1
unit_conversion : Unit Class 9: (Amount.Time.Time/Volume) aumc_col: AUMCLAST1 AUMCLAST2 AUMCINFO1 AUMCINFO2 AUMCINFP1 AUMCINFP2 AUMCTAU1 AUMCTAU2 parameters are scaled from NG.HR.HR/ML to NG.HR.HR/ML via scaling factor: 1
unit_conversion : Unit Class 12: ([Amount/Volume]/Amount) concdn_col: CMAXDN CMAXDN1 CMAXDN2 CMINDN CMINDN1 CMINDN2 parameters are scaled from NG/ML/MCG to NG/ML/MG via scaling factor: 1000
unit_conversion : Unit Class 14: (Volume/Body Weight) volumew_col: VZFTAUW1 VZFTAUW2 parameters are scaled from ML/LB to L/KG via scaling factor: 0.001
unit_conversion : Unit Class 15: (Volume/Time/Body Weight) clw_col: CLFTAUW1 CLFTAUW2 parameters are scaled from ML/HR/LB to ML/HR/KG via scaling factor: 1
Warning messages:
1: In openNCA::run_computation(data = data_tc125, map = map_tc125, :
'RETURNCOLS' values provided via 'map' are not used for this computation
2: In run_M1_SS_computation(data = merged_data, map = map_data, method = method, :
Flag 'FLGEMESIS' is not present in the dataset
3: In unit_conversion(data = data_data, map = map_data, result = computation_df, :
'AMOUNTU' #2# is not present in the dataset provided via 'map'
4: In unit_conversion(data = data_data, map = map_data, result = computation_df, :
'CONCU' and 'DOSEU' values provided via 'map' is not present in the dataset provided via 'data'
5: In unit_conversion(data = data_data, map = map_data, result = computation_df, :
'PKATPDU' and 'CONCU' #10# are not present in the dataset provided via 'map'
6: In unit_conversion(data = data_data, map = map_data, result = computation_df, :
'CONCU' and/or 'NORMBSU' and/or 'VOLUMENORMOUTPUTUNIT' value provided via 'map' is not valid for unit conversion
7: In unit_conversion(data = data_data, map = map_data, result = computation_df, :
'CONCU' and/or 'PKATPDU and/or 'NORMBSU' and/or 'TRUE' value provided via 'map' is not valid for unit conversionRemoving these columns from the flag dataset fixes the issue. Please let me know if this is an expectation from the tc125. |
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This appears to be a problem with the data provided by the application. This is being investigated through JIRA Issue #2210 |
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Can we confirm that this was a data problem and close this issue @TomTensfeldt? |
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With commit 824be9d, test of tc125 which is an M1SS model with TAU and TOLD stored in both the concentration and flags datasets fails to find the TAU and TOLD and crashes as a consequence.
This was identified by modifiying the run_computation.R routine to print the TAU and TOLD values just before the statement that is crashing. It apparently impacts assignment of DI#F.
tc125 is stored (along with a modified version of run_computation.R on the one drive location for reference and further testing.
error message without modification of run_computation.R
output with modified run_computation.R
mct values associated with TAU/TOLD
snippet of input concentration dataset, d
clearly shows TAU/TOLD values are provided
snippet of flags dataset
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