R_Scripts/Comparing_Spectra_Directly.md

In John-R-Wallace-NOAA/FishNIRS: NIRS on fish structures.

 # Determine the columns that contain the spectra.  Here the spectra columns range from 2 - 1155, with the metadata start in column 1156.
 Sable_2017_2019[1:4, c(1:4, 1153:1157)] 
                          filenames     12490     12482     12474      3610      3603      3595 age_structure_id   Barcode
 1 SABLEFISH_COMBO201701203A_2_OD1.0 0.4218516 0.4214812 0.4218767 0.6086814 0.6070352 0.6034645 102118142-SABL-O 102118142
 2 SABLEFISH_COMBO201701203A_3_OD1.0 0.4033358 0.4044081 0.4050675 0.6221674 0.6203897 0.6174445 102118143-SABL-O 102118143
 3 SABLEFISH_COMBO201701203A_6_OD1.0 0.4066261 0.4073936 0.4081993 0.6152601 0.6138538 0.6109281 102118146-SABL-O 102118146
 4 SABLEFISH_COMBO201701203A_7_OD1.0 0.3954711 0.3966139 0.3982748 0.6274921 0.6246090 0.6208161 102118147-SABL-O 102118147


 # Using the TMA (Traditional Method of Aging) column, find file names that were aged to be 1 year old:
 Sable_2017_2019[Sable_2017_2019$TMA == 1 & !is.na(Sable_2017_2019$TMA), ][1:3, c('filenames', 'TMA', '12490', '12482', '12474', '12467')]
                            filenames TMA     12490     12482     12474     12467
 1   SABLEFISH_COMBO201701203A_2_OD1.0   1 0.4218516 0.4214812 0.4218767 0.4225301
 10 SABLEFISH_COMBO201701203A_14_OD1.0   1 0.4180041 0.4192649 0.4201036 0.4197980
 11 SABLEFISH_COMBO201701203A_15_OD1.0   1 0.4216180 0.4224118 0.4230497 0.4232008


 # Save 3 vectors of spectra from the age 1 Sablefish
 (Otie_1A <- Sable_2017_2019[Sable_2017_2019$filenames == 'SABLEFISH_COMBO201701203A_2_OD1.0', 2:1155])[1:10]
 Otie_1B <- Sable_2017_2019[Sable_2017_2019$filenames == 'SABLEFISH_COMBO201701203A_15_OD1.0', 2:1155]
 Otie_1C <- Sable_2017_2019[Sable_2017_2019$filenames == 'SABLEFISH_COMBO201701203A_14_OD1.0', 2:1155]


 # Find the sum of the absolute differences for the 3 vectors. (We don't want correlation or R-squared here, since vectors of numbers can be correlated but separated by a delta.)
 sum(abs(Otie_1A - Otie_1A))
 [1] 0

 sum(abs(Otie_1A - Otie_1B))
 [1] 3.286354

 sum(abs(Otie_1A - Otie_1C))
 [1] 1.284246

 sum(abs(Otie_1B - Otie_1C))
 [1] 3.727268


 # Do the same for Sablefish with a TMA of 5 
 Sable_2017_2019[Sable_2017_2019$TMA == 5 & !is.na(Sable_2017_2019$TMA), ][1:3, c('filenames', 'TMA', '12490', '12482', '12474', '12467')]
                              filenames TMA     12490     12482     12474     12467
 127 SABLEFISH_COMBO201701203A_171_OD1.0   5 0.3976701 0.3984869 0.3992108 0.3992122
 173 SABLEFISH_COMBO201701203A_231_OD1.0   5 0.3994965 0.4003064 0.4008479 0.4011689
 238 SABLEFISH_COMBO201701203A_324_OD1.0   5 0.4164396 0.4172910 0.4182080 0.4181522

 # Note that sum of the absolute differences is large between the age 5 fish and the age 1 fish.
 Otie_5A <- Sable_2017_2019[Sable_2017_2019$filenames == 'SABLEFISH_COMBO201701203A_171_OD1.0', 2:1155]
 sum(abs(Otie_1A - Otie_5A))
 [1] 34.17674

 Otie_5B <- Sable_2017_2019[Sable_2017_2019$filenames == 'SABLEFISH_COMBO201701203A_231_OD1.0', 2:1155]
 sum(abs(Otie_1A - Otie_5B))
 [1] 30.20351


 # The difference between the age 5 fish is smaller
 sum(abs(Otie_5A - Otie_5B))
 [1] 5.259298


 # Try the same with age 10 Sablefish
 Sable_2017_2019[Sable_2017_2019$TMA == 10 & !is.na(Sable_2017_2019$TMA), ][1:3, c('filenames', 'TMA', '12490', '12482', '12474', '12467')]
                               filenames TMA     12490     12482     12474     12467
 80  SABLEFISH_COMBO201701203A_115_OD1.0  10 0.3888220 0.3894408 0.3902158 0.3910199
 81  SABLEFISH_COMBO201701203A_116_OD1.0  10 0.3894672 0.3900470 0.3902689 0.3904091
 115 SABLEFISH_COMBO201701203A_157_OD1.0  10 0.4037862 0.4047136 0.4055516 0.4060116

 # Large difference
 Otie_10A <- Sable_2017_2019[Sable_2017_2019$filenames == 'SABLEFISH_COMBO201701203A_115_OD1.0', 2:1155]
 sum(abs(Otie_1A - Otie_10A))
 [1] 38.48886

 Otie_10B <- Sable_2017_2019[Sable_2017_2019$filenames == 'SABLEFISH_COMBO201701203A_116_OD1.0', 2:1155]
 sum(abs(Otie_1A - Otie_10B))
 [1] 37.40644

 # Small difference
 sum(abs(Otie_10A - Otie_10B))
 [1] 1.614045


 # Difference for age 5 vs. age 10
 sum(abs(Otie_5A - Otie_10A))
 [1] 4.581376

 sum(abs(Otie_5B - Otie_10B))
 [1] 8.75515

John-R-Wallace-NOAA/FishNIRS documentation built on April 12, 2025, 12:59 a.m.