tests/testthat/_snaps/import_instrument_data.md
In JamesHucklesby/vascr: Process Biological Impedance Sensing Data
Can import and ECIS file
Code
ecis_import(raw = w16)
Message
i Starting import
i Importing raw data
i Reading file
i Extracting data
i Lengthening the dataset
Condition
Warning:
Expected 2 pieces. Additional pieces discarded in 2 rows [1, 2].
Message
i Generating other physical quantaties
i Cleaning up
v Import complete
Output
# A tibble: 880 x 8
Time Well Frequency Unit Value Instrument Excluded Sample
<dbl> <chr> <dbl> <fct> <dbl> <chr> <chr> <chr>
1 0.000688 A01 1000 R 1508. ECIS no NA
2 0.000688 A01 125 R 22828. ECIS no NA
3 0.000688 A01 16000 R 1006. ECIS no NA
4 0.000688 A01 2000 R 1186. ECIS no NA
5 0.000688 A01 250 R 6776. ECIS no NA
6 0.000688 A01 32000 R 995. ECIS no NA
7 0.000688 A01 4000 R 1076. ECIS no NA
8 0.000688 A01 500 R 2556. ECIS no NA
9 0.000688 A01 62 R 82275. ECIS no NA
10 0.000688 A01 64000 R 996. ECIS no NA
# i 870 more rows
Code
ecis_import(model = empty)
Message
i Starting import
i Importing model data
i Reading file into R
i Extracting useful data
! No data imported, check the modeled data you are trying to import is correctly specified and an intact file
i Renaming units
i Naming dataset
i Creating long dataframe
i Finishing up
v Import complete
Output
# A tibble: 0 x 8
# i 8 variables: Time <???>, Unit <???>, Well <???>, Value <???>,
# Frequency <???>, Instrument <???>, Excluded <chr>, Sample <chr>
Code
ecis_import(raw, modeled, experimentname = "TEST")
Message
i Starting import
i Importing raw data
i Reading file
i Extracting data
i Lengthening the dataset
i Generating other physical quantaties
i Cleaning up
i Importing model data
i Reading file into R
i Extracting useful data
i Renaming units
i Naming dataset
i Creating long dataframe
i Finishing up
v Import complete
Output
# A tibble: 14,400 x 9
Time Well Frequency Unit Value Instrument Experiment Excluded Sample
<dbl> <chr> <dbl> <fct> <dbl> <chr> <chr> <chr> <chr>
1 0 A01 1000 R 394. ECIS TEST no NA
2 0 A01 16000 R 223. ECIS TEST no NA
3 0 A01 2000 R 316. ECIS TEST no NA
4 0 A01 250 R 824. ECIS TEST no NA
5 0 A01 32000 R 212. ECIS TEST no NA
6 0 A01 4000 R 267. ECIS TEST no NA
7 0 A01 500 R 533. ECIS TEST no NA
8 0 A01 64000 R 205. ECIS TEST no NA
9 0 A01 8000 R 240. ECIS TEST no NA
10 0 B01 1000 R 388. ECIS TEST no NA
# i 14,390 more rows
Can import cellZScope file
Code
cellzscope_import(raw, model, "test")
Output
# A tibble: 88,288 x 8
Time Unit Well Value Experiment Frequency Instrument Sample
<dbl> <chr> <chr> <dbl> <chr> <dbl> <chr> <chr>
1 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A01 NA test 0 cellZscope " 80,00~
2 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A02 46.8 test 0 cellZscope " 80,00~
3 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A04 42.9 test 0 cellZscope " 20,00~
4 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A05 NA test 0 cellZscope " 20,00~
5 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B01 NA test 0 cellZscope " 80,00~
6 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B02 NA test 0 cellZscope " 80,00~
7 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B04 NA test 0 cellZscope " 20,00~
8 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B05 NA test 0 cellZscope " 20,00~
9 1.3 CPE_A(sⁿ⁻¹·µF/cm²) A01 46.1 test 0 cellZscope " 80,00~
10 1.3 CPE_A(sⁿ⁻¹·µF/cm²) A02 51.8 test 0 cellZscope " 80,00~
# i 88,278 more rows
Code
cellzscope_import(raw, model)
Output
# A tibble: 88,288 x 8
Time Unit Well Value Experiment Frequency Instrument Sample
<dbl> <chr> <chr> <dbl> <chr> <dbl> <chr> <chr>
1 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A01 NA zscopemodel~ 0 cellZscope " 80,~
2 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A02 46.8 zscopemodel~ 0 cellZscope " 80,~
3 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A04 42.9 zscopemodel~ 0 cellZscope " 20,~
4 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A05 NA zscopemodel~ 0 cellZscope " 20,~
5 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B01 NA zscopemodel~ 0 cellZscope " 80,~
6 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B02 NA zscopemodel~ 0 cellZscope " 80,~
7 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B04 NA zscopemodel~ 0 cellZscope " 20,~
8 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B05 NA zscopemodel~ 0 cellZscope " 20,~
9 1.3 CPE_A(sⁿ⁻¹·µF/cm²) A01 46.1 zscopemodel~ 0 cellZscope " 80,~
10 1.3 CPE_A(sⁿ⁻¹·µF/cm²) A02 51.8 zscopemodel~ 0 cellZscope " 80,~
# i 88,278 more rows
Can import xCELLigence file
Code
import_xcelligence(rawdata = rawdata, "TEST7")
Output
# A tibble: 6,336 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <chr> <dbl> <chr> <chr> <dbl> <chr> <chr> <int>
1 0 CI 1 A01 HCMVEC80000 10000 TEST7 xCELLigence 1
2 0 CI 1 A02 HCMVEC80000 10000 TEST7 xCELLigence 1
3 0 CI 1 A03 HCMVEC80000 10000 TEST7 xCELLigence 1
4 1.54 CI 3.59 A01 HCMVEC80000 10000 TEST7 xCELLigence 1
5 1.54 CI 3.56 A02 HCMVEC80000 10000 TEST7 xCELLigence 1
6 1.54 CI 3.72 A03 HCMVEC80000 10000 TEST7 xCELLigence 1
7 3.21 CI 3.51 A01 HCMVEC80000 10000 TEST7 xCELLigence 1
8 3.21 CI 3.48 A02 HCMVEC80000 10000 TEST7 xCELLigence 1
9 3.21 CI 3.48 A03 HCMVEC80000 10000 TEST7 xCELLigence 1
10 4.87 CI 3.39 A01 HCMVEC80000 10000 TEST7 xCELLigence 1
# i 6,326 more rows
# i 1 more variable: Excluded <chr>
Code
import_xcelligence(rawdata = rawdata)
Output
# A tibble: 6,336 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <chr> <dbl> <chr> <chr> <dbl> <chr> <chr> <int>
1 0 CI 1 A01 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
2 0 CI 1 A02 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
3 0 CI 1 A03 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
4 1.54 CI 3.59 A01 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
5 1.54 CI 3.56 A02 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
6 1.54 CI 3.72 A03 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
7 3.21 CI 3.51 A01 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
8 3.21 CI 3.48 A02 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
9 3.21 CI 3.48 A03 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
10 4.87 CI 3.39 A01 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
# i 6,326 more rows
# i 1 more variable: Excluded <chr>
ERROR - file could not be duplicated to be opened. Ensure you have write capabilities in the new folder, and the file TEMPMDBFORIMPORT.mdb does not exist. Also check that the plt file is not open when you run this command
JamesHucklesby/vascr documentation built on July 16, 2025, 8:16 p.m.
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Can import and ECIS file
Code
ecis_import(raw = w16)
Message
i Starting import
i Importing raw data
i Reading file
i Extracting data
i Lengthening the dataset
Condition
Warning:
Expected 2 pieces. Additional pieces discarded in 2 rows [1, 2].
Message
i Generating other physical quantaties
i Cleaning up
v Import complete
Output
# A tibble: 880 x 8
Time Well Frequency Unit Value Instrument Excluded Sample
<dbl> <chr> <dbl> <fct> <dbl> <chr> <chr> <chr>
1 0.000688 A01 1000 R 1508. ECIS no NA
2 0.000688 A01 125 R 22828. ECIS no NA
3 0.000688 A01 16000 R 1006. ECIS no NA
4 0.000688 A01 2000 R 1186. ECIS no NA
5 0.000688 A01 250 R 6776. ECIS no NA
6 0.000688 A01 32000 R 995. ECIS no NA
7 0.000688 A01 4000 R 1076. ECIS no NA
8 0.000688 A01 500 R 2556. ECIS no NA
9 0.000688 A01 62 R 82275. ECIS no NA
10 0.000688 A01 64000 R 996. ECIS no NA
# i 870 more rows
Code
ecis_import(model = empty)
Message
i Starting import
i Importing model data
i Reading file into R
i Extracting useful data
! No data imported, check the modeled data you are trying to import is correctly specified and an intact file
i Renaming units
i Naming dataset
i Creating long dataframe
i Finishing up
v Import complete
Output
# A tibble: 0 x 8
# i 8 variables: Time <???>, Unit <???>, Well <???>, Value <???>,
# Frequency <???>, Instrument <???>, Excluded <chr>, Sample <chr>
Code
ecis_import(raw, modeled, experimentname = "TEST")
Message
i Starting import
i Importing raw data
i Reading file
i Extracting data
i Lengthening the dataset
i Generating other physical quantaties
i Cleaning up
i Importing model data
i Reading file into R
i Extracting useful data
i Renaming units
i Naming dataset
i Creating long dataframe
i Finishing up
v Import complete
Output
# A tibble: 14,400 x 9
Time Well Frequency Unit Value Instrument Experiment Excluded Sample
<dbl> <chr> <dbl> <fct> <dbl> <chr> <chr> <chr> <chr>
1 0 A01 1000 R 394. ECIS TEST no NA
2 0 A01 16000 R 223. ECIS TEST no NA
3 0 A01 2000 R 316. ECIS TEST no NA
4 0 A01 250 R 824. ECIS TEST no NA
5 0 A01 32000 R 212. ECIS TEST no NA
6 0 A01 4000 R 267. ECIS TEST no NA
7 0 A01 500 R 533. ECIS TEST no NA
8 0 A01 64000 R 205. ECIS TEST no NA
9 0 A01 8000 R 240. ECIS TEST no NA
10 0 B01 1000 R 388. ECIS TEST no NA
# i 14,390 more rows
Can import cellZScope file
Code
cellzscope_import(raw, model, "test")
Output
# A tibble: 88,288 x 8
Time Unit Well Value Experiment Frequency Instrument Sample
<dbl> <chr> <chr> <dbl> <chr> <dbl> <chr> <chr>
1 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A01 NA test 0 cellZscope " 80,00~
2 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A02 46.8 test 0 cellZscope " 80,00~
3 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A04 42.9 test 0 cellZscope " 20,00~
4 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A05 NA test 0 cellZscope " 20,00~
5 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B01 NA test 0 cellZscope " 80,00~
6 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B02 NA test 0 cellZscope " 80,00~
7 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B04 NA test 0 cellZscope " 20,00~
8 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B05 NA test 0 cellZscope " 20,00~
9 1.3 CPE_A(sⁿ⁻¹·µF/cm²) A01 46.1 test 0 cellZscope " 80,00~
10 1.3 CPE_A(sⁿ⁻¹·µF/cm²) A02 51.8 test 0 cellZscope " 80,00~
# i 88,278 more rows
Code
cellzscope_import(raw, model)
Output
# A tibble: 88,288 x 8
Time Unit Well Value Experiment Frequency Instrument Sample
<dbl> <chr> <chr> <dbl> <chr> <dbl> <chr> <chr>
1 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A01 NA zscopemodel~ 0 cellZscope " 80,~
2 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A02 46.8 zscopemodel~ 0 cellZscope " 80,~
3 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A04 42.9 zscopemodel~ 0 cellZscope " 20,~
4 0.03 CPE_A(sⁿ⁻¹·µF/cm²) A05 NA zscopemodel~ 0 cellZscope " 20,~
5 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B01 NA zscopemodel~ 0 cellZscope " 80,~
6 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B02 NA zscopemodel~ 0 cellZscope " 80,~
7 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B04 NA zscopemodel~ 0 cellZscope " 20,~
8 0.03 CPE_A(sⁿ⁻¹·µF/cm²) B05 NA zscopemodel~ 0 cellZscope " 20,~
9 1.3 CPE_A(sⁿ⁻¹·µF/cm²) A01 46.1 zscopemodel~ 0 cellZscope " 80,~
10 1.3 CPE_A(sⁿ⁻¹·µF/cm²) A02 51.8 zscopemodel~ 0 cellZscope " 80,~
# i 88,278 more rows
Can import xCELLigence file
Code
import_xcelligence(rawdata = rawdata, "TEST7")
Output
# A tibble: 6,336 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <chr> <dbl> <chr> <chr> <dbl> <chr> <chr> <int>
1 0 CI 1 A01 HCMVEC80000 10000 TEST7 xCELLigence 1
2 0 CI 1 A02 HCMVEC80000 10000 TEST7 xCELLigence 1
3 0 CI 1 A03 HCMVEC80000 10000 TEST7 xCELLigence 1
4 1.54 CI 3.59 A01 HCMVEC80000 10000 TEST7 xCELLigence 1
5 1.54 CI 3.56 A02 HCMVEC80000 10000 TEST7 xCELLigence 1
6 1.54 CI 3.72 A03 HCMVEC80000 10000 TEST7 xCELLigence 1
7 3.21 CI 3.51 A01 HCMVEC80000 10000 TEST7 xCELLigence 1
8 3.21 CI 3.48 A02 HCMVEC80000 10000 TEST7 xCELLigence 1
9 3.21 CI 3.48 A03 HCMVEC80000 10000 TEST7 xCELLigence 1
10 4.87 CI 3.39 A01 HCMVEC80000 10000 TEST7 xCELLigence 1
# i 6,326 more rows
# i 1 more variable: Excluded <chr>
Code
import_xcelligence(rawdata = rawdata)
Output
# A tibble: 6,336 x 10
Time Unit Value Well Sample Frequency Experiment Instrument SampleID
<dbl> <chr> <dbl> <chr> <chr> <dbl> <chr> <chr> <int>
1 0 CI 1 A01 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
2 0 CI 1 A02 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
3 0 CI 1 A03 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
4 1.54 CI 3.59 A01 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
5 1.54 CI 3.56 A02 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
6 1.54 CI 3.72 A03 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
7 3.21 CI 3.51 A01 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
8 3.21 CI 3.48 A02 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
9 3.21 CI 3.48 A03 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
10 4.87 CI 3.39 A01 HCMVEC80000 10000 TEMPMDBFOR~ xCELLigen~ 1
# i 6,326 more rows
# i 1 more variable: Excluded <chr>
ERROR - file could not be duplicated to be opened. Ensure you have write capabilities in the new folder, and the file TEMPMDBFORIMPORT.mdb does not exist. Also check that the plt file is not open when you run this command
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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