This repo is accompanying the publication: “Computational fingerprinting workflow for environmental source tracking of microplastic based on representative additives”
Demo of each ML algorithms is shown below.
PLEASE FEEL FREE TO REPORT ANY BUGS TO ME @ [email protected]
You can include R code in the document as follows:
## Warning in as.Date(as.numeric(sampleinfo$`Collection Date (YYYY-MM-DD)`), : NAs
## introduced by coercion
## Loading required package: ggrepel
##
## Attaching package: 'PCAtools'
## The following objects are masked from 'package:stats':
##
## biplot, screeplot
## `summarise()` has grouped output by 'File'. You can override using the
## `.groups` argument.
## `summarise()` has grouped output by 'File'. You can override using the
## `.groups` argument.
##
## randomForestSRC 3.2.2
##
## Type rfsrc.news() to see new features, changes, and bug fixes.
##
##
## Attaching package: 'randomForestSRC'
## The following object is masked from 'package:purrr':
##
## partial
## Sample size: 47
## Frequency of class labels: 11, 3, 3, 5, 6, 13, 6
## Number of trees: 20000
## Forest terminal node size: 1
## Average no. of terminal nodes: 28.6001
## No. of variables tried at each split: 9
## Total no. of variables: 77
## Resampling used to grow trees: swr
## Resample size used to grow trees: 47
## Analysis: RF-C
## Family: class
## Splitting rule: auc *random*
## Number of random split points: 10
## (OOB) Brier score: 0.1070575
## (OOB) Normalized Brier score: 0.87430294
## (OOB) AUC: 0.54327247
## (OOB) Requested performance error: 0.55319149, 0.09090909, 1, 1, 1, 1, 0.15384615, 1
##
## Confusion matrix:
##
## predicted
## observed Balloons Food_Packaging_Waste
## Balloons 10 0
## Food_Packaging_Waste 1 0
## Mixed_Plastic_Waste 3 0
## Other 2 0
## Plastic_Bottles_and_Bottle_Caps 1 0
## Plastic_Cups 1 0
## Plastic_Drinking_Straws 1 0
## predicted
## observed Mixed_Plastic_Waste Other
## Balloons 0 0
## Food_Packaging_Waste 0 0
## Mixed_Plastic_Waste 0 0
## Other 0 0
## Plastic_Bottles_and_Bottle_Caps 0 0
## Plastic_Cups 0 0
## Plastic_Drinking_Straws 0 0
## predicted
## observed Plastic_Bottles_and_Bottle_Caps Plastic_Cups
## Balloons 0 1
## Food_Packaging_Waste 0 2
## Mixed_Plastic_Waste 0 0
## Other 0 3
## Plastic_Bottles_and_Bottle_Caps 0 5
## Plastic_Cups 0 11
## Plastic_Drinking_Straws 0 5
## predicted
## observed Plastic_Drinking_Straws class.error
## Balloons 0 0.0909
## Food_Packaging_Waste 0 1.0000
## Mixed_Plastic_Waste 0 1.0000
## Other 0 1.0000
## Plastic_Bottles_and_Bottle_Caps 0 1.0000
## Plastic_Cups 1 0.1538
## Plastic_Drinking_Straws 0 1.0000
##
## (OOB) Misclassification rate: 0.5531915
##
## all Balloons Food_Packaging_Waste Mixed_Plastic_Waste Other
## Type 0.0105 0.0207 0.0055 0.0130 0.0034
## PC8 0.0068 0.0222 0.0039 0.0076 0.0002
## PC4 0.0053 0.0165 0.0001 0.0063 -0.0025
## PC2 0.0043 0.0049 0.0023 0.0024 -0.0006
## PC9 0.0038 0.0097 0.0015 -0.0025 0.0001
## PC16 0.0036 0.0084 0.0000 0.0003 0.0004
## PC19 0.0035 0.0124 0.0031 0.0068 0.0013
## PC43 0.0035 0.0084 0.0013 0.0133 0.0007
## PC5 0.0033 0.0115 0.0031 0.0037 -0.0015
## PC13 0.0033 0.0119 -0.0008 0.0026 -0.0009
## Plastic_Bottles_and_Bottle_Caps Plastic_Cups Plastic_Drinking_Straws
## Type 0.0091 0.0098 0.0007
## PC8 -0.0009 0.0031 -0.0002
## PC4 0.0066 -0.0010 0.0048
## PC2 0.0017 0.0089 0.0011
## PC9 0.0011 0.0042 0.0014
## PC16 -0.0003 0.0057 0.0000
## PC19 -0.0009 -0.0001 -0.0005
## PC43 -0.0012 -0.0014 0.0073
## PC5 0.0007 0.0014 -0.0013
## PC13 0.0049 0.0000 -0.0016
## [1] 0.5432725
## Sample size: 47
## Frequency of class labels: 11, 3, 3, 5, 6, 13, 6
## Number of trees: 20000
## Forest terminal node size: 1
## Average no. of terminal nodes: 28.6001
## No. of variables tried at each split: 9
## Total no. of variables: 77
## Resampling used to grow trees: swr
## Resample size used to grow trees: 47
## Analysis: RF-C
## Family: class
## Splitting rule: auc *random*
## Number of random split points: 10
## (OOB) Brier score: 0.1070575
## (OOB) Normalized Brier score: 0.87430294
## (OOB) AUC: 0.54327247
## (OOB) Requested performance error: 0.55319149, 0.09090909, 1, 1, 1, 1, 0.15384615, 1
##
## Confusion matrix:
##
## predicted
## observed Balloons Food_Packaging_Waste
## Balloons 10 0
## Food_Packaging_Waste 1 0
## Mixed_Plastic_Waste 3 0
## Other 2 0
## Plastic_Bottles_and_Bottle_Caps 1 0
## Plastic_Cups 1 0
## Plastic_Drinking_Straws 1 0
## predicted
## observed Mixed_Plastic_Waste Other
## Balloons 0 0
## Food_Packaging_Waste 0 0
## Mixed_Plastic_Waste 0 0
## Other 0 0
## Plastic_Bottles_and_Bottle_Caps 0 0
## Plastic_Cups 0 0
## Plastic_Drinking_Straws 0 0
## predicted
## observed Plastic_Bottles_and_Bottle_Caps Plastic_Cups
## Balloons 0 1
## Food_Packaging_Waste 0 2
## Mixed_Plastic_Waste 0 0
## Other 0 3
## Plastic_Bottles_and_Bottle_Caps 0 5
## Plastic_Cups 0 11
## Plastic_Drinking_Straws 0 5
## predicted
## observed Plastic_Drinking_Straws class.error
## Balloons 0 0.0909
## Food_Packaging_Waste 0 1.0000
## Mixed_Plastic_Waste 0 1.0000
## Other 0 1.0000
## Plastic_Bottles_and_Bottle_Caps 0 1.0000
## Plastic_Cups 1 0.1538
## Plastic_Drinking_Straws 0 1.0000
##
## (OOB) Misclassification rate: 0.5531915
##
## all Balloons Food_Packaging_Waste Mixed_Plastic_Waste Other
## Type 0.0105 0.0207 0.0055 0.0130 0.0034
## PC8 0.0068 0.0222 0.0039 0.0076 0.0002
## PC4 0.0053 0.0165 0.0001 0.0063 -0.0025
## PC2 0.0043 0.0049 0.0023 0.0024 -0.0006
## PC9 0.0038 0.0097 0.0015 -0.0025 0.0001
## PC16 0.0036 0.0084 0.0000 0.0003 0.0004
## PC19 0.0035 0.0124 0.0031 0.0068 0.0013
## PC43 0.0035 0.0084 0.0013 0.0133 0.0007
## PC5 0.0033 0.0115 0.0031 0.0037 -0.0015
## PC13 0.0033 0.0119 -0.0008 0.0026 -0.0009
## Plastic_Bottles_and_Bottle_Caps Plastic_Cups Plastic_Drinking_Straws
## Type 0.0091 0.0098 0.0007
## PC8 -0.0009 0.0031 -0.0002
## PC4 0.0066 -0.0010 0.0048
## PC2 0.0017 0.0089 0.0011
## PC9 0.0011 0.0042 0.0014
## PC16 -0.0003 0.0057 0.0000
## PC19 -0.0009 -0.0001 -0.0005
## PC43 -0.0012 -0.0014 0.0073
## PC5 0.0007 0.0014 -0.0013
## PC13 0.0049 0.0000 -0.0016
## [1] 0.5432725
## Sample size: 47
## Frequency of class labels: 11, 3, 3, 5, 6, 13, 6
## Number of trees: 20000
## Forest terminal node size: 1
## Average no. of terminal nodes: 28.6001
## No. of variables tried at each split: 9
## Total no. of variables: 77
## Resampling used to grow trees: swr
## Resample size used to grow trees: 47
## Analysis: RF-C
## Family: class
## Splitting rule: auc *random*
## Number of random split points: 10
## (OOB) Brier score: 0.1070575
## (OOB) Normalized Brier score: 0.87430294
## (OOB) AUC: 0.54327247
## (OOB) Requested performance error: 0.55319149, 0.09090909, 1, 1, 1, 1, 0.15384615, 1
##
## Confusion matrix:
##
## predicted
## observed Balloons Food_Packaging_Waste
## Balloons 10 0
## Food_Packaging_Waste 1 0
## Mixed_Plastic_Waste 3 0
## Other 2 0
## Plastic_Bottles_and_Bottle_Caps 1 0
## Plastic_Cups 1 0
## Plastic_Drinking_Straws 1 0
## predicted
## observed Mixed_Plastic_Waste Other
## Balloons 0 0
## Food_Packaging_Waste 0 0
## Mixed_Plastic_Waste 0 0
## Other 0 0
## Plastic_Bottles_and_Bottle_Caps 0 0
## Plastic_Cups 0 0
## Plastic_Drinking_Straws 0 0
## predicted
## observed Plastic_Bottles_and_Bottle_Caps Plastic_Cups
## Balloons 0 1
## Food_Packaging_Waste 0 2
## Mixed_Plastic_Waste 0 0
## Other 0 3
## Plastic_Bottles_and_Bottle_Caps 0 5
## Plastic_Cups 0 11
## Plastic_Drinking_Straws 0 5
## predicted
## observed Plastic_Drinking_Straws class.error
## Balloons 0 0.0909
## Food_Packaging_Waste 0 1.0000
## Mixed_Plastic_Waste 0 1.0000
## Other 0 1.0000
## Plastic_Bottles_and_Bottle_Caps 0 1.0000
## Plastic_Cups 1 0.1538
## Plastic_Drinking_Straws 0 1.0000
##
## (OOB) Misclassification rate: 0.5531915
##
## all Balloons Food_Packaging_Waste Mixed_Plastic_Waste Other
## Type 0.0105 0.0207 0.0055 0.0130 0.0034
## PC8 0.0068 0.0222 0.0039 0.0076 0.0002
## PC4 0.0053 0.0165 0.0001 0.0063 -0.0025
## PC2 0.0043 0.0049 0.0023 0.0024 -0.0006
## PC9 0.0038 0.0097 0.0015 -0.0025 0.0001
## PC16 0.0036 0.0084 0.0000 0.0003 0.0004
## PC19 0.0035 0.0124 0.0031 0.0068 0.0013
## PC43 0.0035 0.0084 0.0013 0.0133 0.0007
## PC5 0.0033 0.0115 0.0031 0.0037 -0.0015
## PC13 0.0033 0.0119 -0.0008 0.0026 -0.0009
## Plastic_Bottles_and_Bottle_Caps Plastic_Cups Plastic_Drinking_Straws
## Type 0.0091 0.0098 0.0007
## PC8 -0.0009 0.0031 -0.0002
## PC4 0.0066 -0.0010 0.0048
## PC2 0.0017 0.0089 0.0011
## PC9 0.0011 0.0042 0.0014
## PC16 -0.0003 0.0057 0.0000
## PC19 -0.0009 -0.0001 -0.0005
## PC43 -0.0012 -0.0014 0.0073
## PC5 0.0007 0.0014 -0.0013
## PC13 0.0049 0.0000 -0.0016
## [1] 0.5432725
## Sample size: 21
## Frequency of class labels: 3, 3, 3, 3, 3, 3, 3
## Number of trees: 20000
## Forest terminal node size: 1
## Average no. of terminal nodes: 13.105
## No. of variables tried at each split: 9
## Total no. of variables: 77
## Resampling used to grow trees: swr
## Resample size used to grow trees: 21
## Analysis: RF-C
## Family: class
## Splitting rule: auc *random*
## Number of random split points: 10
## (OOB) Brier score: 0.13184216
## (OOB) Normalized Brier score: 1.076711
## (OOB) AUC: 0.27513228
## (OOB) Requested performance error: 1, 1, 1, 1, 1, 1, 1, 1
##
## Confusion matrix:
##
## predicted
## observed Balloons Food_Packaging_Waste
## Balloons 0 0
## Food_Packaging_Waste 0 0
## Mixed_Plastic_Waste 1 0
## Other 1 1
## Plastic_Bottles_and_Bottle_Caps 1 0
## Plastic_Cups 1 0
## Plastic_Drinking_Straws 0 0
## predicted
## observed Mixed_Plastic_Waste Other
## Balloons 2 1
## Food_Packaging_Waste 1 2
## Mixed_Plastic_Waste 0 2
## Other 1 0
## Plastic_Bottles_and_Bottle_Caps 1 1
## Plastic_Cups 0 2
## Plastic_Drinking_Straws 2 1
## predicted
## observed Plastic_Bottles_and_Bottle_Caps Plastic_Cups
## Balloons 0 0
## Food_Packaging_Waste 0 0
## Mixed_Plastic_Waste 0 0
## Other 0 0
## Plastic_Bottles_and_Bottle_Caps 0 0
## Plastic_Cups 0 0
## Plastic_Drinking_Straws 0 0
## predicted
## observed Plastic_Drinking_Straws class.error
## Balloons 0 1
## Food_Packaging_Waste 0 1
## Mixed_Plastic_Waste 0 1
## Other 0 1
## Plastic_Bottles_and_Bottle_Caps 0 1
## Plastic_Cups 0 1
## Plastic_Drinking_Straws 0 1
##
## (OOB) Misclassification rate: 1
##
## all Balloons Food_Packaging_Waste Mixed_Plastic_Waste Other
## PC7 0.0047 0.0056 0.0051 0.0034 0.0076
## PC25 0.0045 0.0045 0.0029 -0.0006 0.0046
## Type 0.0034 0.0092 0.0025 0.0050 -0.0041
## PC26 0.0023 0.0067 -0.0014 0.0014 -0.0001
## PC10 0.0020 -0.0005 -0.0013 0.0118 0.0020
## PC17 0.0013 0.0020 0.0040 -0.0025 -0.0039
## PC65 0.0012 -0.0016 -0.0006 -0.0005 0.0010
## PC56 0.0011 -0.0014 0.0091 -0.0023 0.0029
## PC31 0.0011 0.0032 -0.0006 0.0041 -0.0030
## PC35 0.0011 0.0011 -0.0005 0.0040 0.0014
## Plastic_Bottles_and_Bottle_Caps Plastic_Cups Plastic_Drinking_Straws
## PC7 0.0019 0.0027 0.0041
## PC25 0.0081 0.0054 0.0039
## Type 0.0033 0.0070 0.0003
## PC26 0.0027 0.0021 0.0038
## PC10 0.0005 0.0022 -0.0007
## PC17 0.0028 0.0053 0.0008
## PC65 0.0018 0.0081 -0.0003
## PC56 0.0019 -0.0010 -0.0014
## PC31 0.0019 0.0030 -0.0006
## PC35 -0.0006 0.0033 -0.0010
## [1] 0.2751323
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