Aggregate data based on grouping variables and a user-provided function

Source: R/aggregate_spectra.R

Use grouping variables to collapse spectral data.frame by mean or median. Recommended for use after filter_spectra

aggregate_spectra(df, grouping.colnames, reference.value.colname,
  agg.function)

Arguments

df

data.frame object containing one or multiple columns of grouping variables (must be consistent within each group), column of reference values (optional), and columns of spectra. Spectral column names must start with "X".

grouping.colnames

Names of columns to be used as grouping variables. Minimum 2 variables required. Default is c("trial", "plot").

reference.value.colname

Name of reference column to be aggregated along with spectra. Default is "reference"

agg.function

Name of function (string format) to be used for sample aggregation. Must be either "mean" or "median". Default is "mean".

Value

data.frame object df aggregated based on grouping column by agg.function

Author

Jenna Hershberger jmh579@cornell.edu

Examples

library(magrittr)
aggregated.test <- ikeogu.2017 %>%
  dplyr::select(-TCC) %>%
  na.omit() %>%
  aggregate_spectra(
    grouping.colnames = c("study.name"),
    reference.value.colname = "DMC.oven",
    agg.function = "mean"
  )
aggregated.test[1:5, 1:5]
#> # A tibble: 5 × 5
#>   study.name DMC.oven   X350   X351   X352
#>   <chr>         <dbl>  <dbl>  <dbl>  <dbl>
#> 1 C16Mcal        36.1  0.559  0.562  0.569
#> 2 C16Mval        36.4  0.545  0.549  0.552
#> 3 NA             NA   NA     NA     NA    
#> 4 NA             NA   NA     NA     NA    
#> 5 NA             NA   NA     NA     NA