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Ignore or remove NA intensities

Source: R/manage_na.R
manage_na.Rd

Sometimes you want to keep or remove NA values in intensities to allow for spectra with varying shapes to be analyzed together or maintained in a single Open Specy object.

Usage

manage_na(x, ...)

# Default S3 method
manage_na(x, lead_tail_only = TRUE, ig = c(NA), ...)

# S3 method for class 'OpenSpecy'
manage_na(x, lead_tail_only = TRUE, ig = c(NA), fun, type = "ignore", ...)

Arguments

x

a numeric vector or an R OpenSpecy object.

lead_tail_only

logical whether to only look at leading adn tailing values.

ig

character vector, values to ignore.

fun

the name of the function you want run, this is only used if the "ignore" type is chosen.

type

character of either "ignore" or "remove".

...

further arguments passed to fun.

Value

manage_na() return logical vectors of NA locations (if vector provided) or an OpenSpecy object with ignored or removed NA values.

See also

OpenSpecy object to be matched with a reference library fill_spec() can be used to fill NA values in Open Specy objects. restrict_range() can be used to restrict spectral ranges in other ways than removing NAs.

Author

Win Cowger, Zacharias Steinmetz

Examples

manage_na(c(NA, -1, NA, 1, 10))
#> [1]  TRUE FALSE FALSE FALSE FALSE
manage_na(c(NA, -1, NA, 1, 10), lead_tail_only = FALSE)
#> [1]  TRUE FALSE  TRUE FALSE FALSE
manage_na(c(NA, 0, NA, 1, 10), lead_tail_only = FALSE, ig = c(NA,0))
#> [1]  TRUE  TRUE  TRUE FALSE FALSE
data(raman_hdpe)
raman_hdpe$spectra[[1]][1:10] <- NA

#would normally return all NA without na.rm = TRUE but doesn't here.
manage_na(raman_hdpe, fun = make_rel)
#>      wavenumber  intensity
#>           <num>      <num>
#>   1:    301.040         NA
#>   2:    304.632         NA
#>   3:    308.221         NA
#>   4:    311.810         NA
#>   5:    315.398         NA
#>  ---                      
#> 960:   3187.990 0.03870968
#> 961:   3190.520 0.03870968
#> 962:   3193.060 0.04387097
#> 963:   3195.590 0.04387097
#> 964:   3198.120 0.03354839
#> 
#> $metadata
#>        x     y  user_name spectrum_type spectrum_identity      organization
#>    <int> <int>     <char>        <char>            <char>            <char>
#> 1:     1     1 Win Cowger         Raman              HDPE Horiba Scientific
#>     license                                                        session_id
#>      <char>                                                            <char>
#> 1: CC BY-NC 5728ddde4f649fd71f6f487fc5ad8d80/dc85257201307a131e71d9ec24aaccbf
#>                             file_id
#>                              <char>
#> 1: cb06ce2846b119d932fb6696479a445b

#will remove the first 10 values we set to NA
manage_na(raman_hdpe, type = "remove")
#>      wavenumber intensity
#>           <num>     <int>
#>   1:    336.889        48
#>   2:    340.467        44
#>   3:    344.042        49
#>   4:    347.618        52
#>   5:    351.190        48
#>  ---                     
#> 950:   3187.990        71
#> 951:   3190.520        71
#> 952:   3193.060        75
#> 953:   3195.590        75
#> 954:   3198.120        67
#> 
#> $metadata
#>        x     y  user_name spectrum_type spectrum_identity      organization
#>    <int> <int>     <char>        <char>            <char>            <char>
#> 1:     1     1 Win Cowger         Raman              HDPE Horiba Scientific
#>     license                                                        session_id
#>      <char>                                                            <char>
#> 1: CC BY-NC 5728ddde4f649fd71f6f487fc5ad8d80/dc85257201307a131e71d9ec24aaccbf
#>                             file_id    col_id
#>                              <char>    <char>
#> 1: cb06ce2846b119d932fb6696479a445b intensity