Cleans the raw data extracted from the Cary 5000 UV-Vis-IR spectrophotometer, ensuring an organized dataset for analysis. During the process, duplicate columns containing wavelength are removed to avoid redundancy. Samples with missing data are also eliminated, ensuring that only complete measurements are retained. Additionally, the columns are reordered based on the sample names, making it easier to interpret and manipulate the data. The wavelength column is placed as the first column, followed by the sample columns.
Usage
clean_sheet_cary(
data = data,
prefix = NULL,
name_wave = "Wave",
range_wave = c(380, 2500),
nm_step = 0.5
)Arguments
- data
A data.frame containing the wavelength and reflectance values. It should be obtained directly from the export of a CSV file.
- prefix
Indicates the prefix for columns where there is no sample. It is usually predefined as
xor..- name_wave
Indicates the name of the wavelength column. The default is 'wave'.
- range_wave
Is the wavelength range used. The default is from 380 nm to 2500 nm.
- nm_step
The increment in nanometers between consecutive wavelength readings. This defines the resolution of the measurements. The default value is 0.5 nm.
Examples
# example code
library(OxSR)
data(data_cary)
clean_sheet_cary(data_cary, prefix = "x")
#> # A tibble: 4,241 × 26
#> wavelength_nm a1 a2 a3 a4 a5 a6 a7 a8 a9 a10
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 2500 37.0 49.2 41.3 65.1 63.1 45.6 46.7 47.2 45.9 49.3
#> 2 2500. 36.0 48.8 40.5 64.6 62.1 45.8 47.1 44.9 45.5 51.7
#> 3 2499 36.0 47.8 42.1 64.8 61.8 46.4 44.7 45.8 45.1 48.8
#> 4 2498. 38.5 49.6 41.3 64.7 62.6 46.2 46.2 44.9 48.2 50.8
#> 5 2498 36.4 48.8 40.5 65.4 62.3 46.4 45.8 44.9 46.4 50.7
#> 6 2498. 35.5 47.4 39.3 64.7 62.8 47.5 45.4 43.9 46.6 49.8
#> 7 2497 37.5 49.1 40.5 66.3 61.4 47.5 47.2 45.5 47.0 52.3
#> 8 2496. 37.5 49.6 41.2 66.2 62.8 46.3 44.0 46.0 46.4 49.4
#> 9 2496 38.0 48.1 40.3 65.1 61.2 47.2 46.3 44.5 44.9 49.9
#> 10 2496. 36.0 48.1 40.4 63.1 60.8 47.4 45.3 45.7 46.4 50.6
#> # ℹ 4,231 more rows
#> # ℹ 15 more variables: a11 <dbl>, a12 <dbl>, a13 <dbl>, a14 <dbl>, a15 <dbl>,
#> # a16 <dbl>, a17 <dbl>, a18 <dbl>, a19 <dbl>, a20 <dbl>, a21 <dbl>,
#> # a22 <dbl>, a23 <dbl>, a24 <dbl>, a26 <dbl>
# With pipe
data_cary |> clean_sheet_cary(prefix = "x")
#> # A tibble: 4,241 × 26
#> wavelength_nm a1 a2 a3 a4 a5 a6 a7 a8 a9 a10
#> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 2500 37.0 49.2 41.3 65.1 63.1 45.6 46.7 47.2 45.9 49.3
#> 2 2500. 36.0 48.8 40.5 64.6 62.1 45.8 47.1 44.9 45.5 51.7
#> 3 2499 36.0 47.8 42.1 64.8 61.8 46.4 44.7 45.8 45.1 48.8
#> 4 2498. 38.5 49.6 41.3 64.7 62.6 46.2 46.2 44.9 48.2 50.8
#> 5 2498 36.4 48.8 40.5 65.4 62.3 46.4 45.8 44.9 46.4 50.7
#> 6 2498. 35.5 47.4 39.3 64.7 62.8 47.5 45.4 43.9 46.6 49.8
#> 7 2497 37.5 49.1 40.5 66.3 61.4 47.5 47.2 45.5 47.0 52.3
#> 8 2496. 37.5 49.6 41.2 66.2 62.8 46.3 44.0 46.0 46.4 49.4
#> 9 2496 38.0 48.1 40.3 65.1 61.2 47.2 46.3 44.5 44.9 49.9
#> 10 2496. 36.0 48.1 40.4 63.1 60.8 47.4 45.3 45.7 46.4 50.6
#> # ℹ 4,231 more rows
#> # ℹ 15 more variables: a11 <dbl>, a12 <dbl>, a13 <dbl>, a14 <dbl>, a15 <dbl>,
#> # a16 <dbl>, a17 <dbl>, a18 <dbl>, a19 <dbl>, a20 <dbl>, a21 <dbl>,
#> # a22 <dbl>, a23 <dbl>, a24 <dbl>, a26 <dbl>