Calculate Change in VFA g/l with time

Recalculate the data into grams per litre - convert to molar: 1 millimolar to molar = 0.001 molar - multiply by the molecular weight of each VFA Calculate the percent representation of each VFA, by mM and by weight
3mmaRand · Apr 4, 2024 · 82e6186 · 82e6186
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diff --git a/omics/kelly/Octanoic VFA_inverse model example.xlsx b/omics/kelly/Octanoic VFA_inverse model example.xlsx
diff --git a/omics/kelly/data-raw/ph.csv b/omics/kelly/data-raw/ph.csv
@@ -0,0 +1,130 @@
+Feedstock,Replicate,Time (hours),pH
+N/A,1,-1,7.72
+N/A,2,-1,7.73
+N/A,3,-1,7.71
+N/A,4,-1,7.73
+Casein,1,0,7.70
+Casein,2,0,7.71
+Casein,3,0,7.64
+Casein,4,0,7.67
+Casein,1,3,7.87
+Casein,2,3,7.74
+Casein,3,3,7.86
+Casein,4,3,7.97
+Casein,1,6,7.71
+Casein,2,6,7.74
+Casein,3,6,7.75
+Casein,4,6,7.69
+Casein,1,24,7.95
+Casein,2,24,7.93
+Casein,3,24,7.94
+Casein,4,24,7.89
+Casein,1,48,8.02
+Casein,2,48,7.93
+Casein,3,48,7.96
+Casein,4,48,7.94
+Casein,1,54,7.96
+Casein,2,54,7.91
+Casein,3,54,7.90
+Casein,4,54,7.93
+Casein,1,72,7.87
+Casein,2,72,7.89
+Casein,3,72,7.89
+Casein,4,72,7.90
+Casein,1,96,7.96
+Casein,2,96,8.01
+Casein,3,96,7.98
+Casein,4,96,7.95
+Casein,1,168,7.92
+Casein,2,168,7.90
+Casein,3,168,7.93
+Casein,4,168,7.93
+Casein,1,192,7.90
+Casein,2,192,7.97
+Casein,3,192,7.98
+Casein,4,192,8.00
+Keratin,1,0,7.57
+Keratin,2,0,7.72
+Keratin,3,0,7.41
+Keratin,4,0,7.56
+Keratin,1,3,n/a
+Keratin,2,3,n/a
+Keratin,3,3,n/a
+Keratin,4,3,n/a
+Keratin,1,6,7.64
+Keratin,2,6,7.82
+Keratin,3,6,7.73
+Keratin,4,6,7.7
+Keratin,1,24,8.12
+Keratin,2,24,7.99
+Keratin,3,24,7.77
+Keratin,4,24,7.92
+Keratin,1,48,8.02
+Keratin,2,48,7.93
+Keratin,3,48,8.02
+Keratin,4,48,7.88
+Keratin,1,54,7.86
+Keratin,2,54,7.87
+Keratin,3,54,7.8
+Keratin,4,54,7.82
+Keratin,1,72,7.8
+Keratin,2,72,7.81
+Keratin,3,72,7.82
+Keratin,4,72,7.8
+Keratin,1,96,8.02
+Keratin,2,96,7.97
+Keratin,3,96,8.04
+Keratin,4,96,8.12
+Keratin,1,168,7.87
+Keratin,2,168,7.98
+Keratin,3,168,8.03
+Keratin,4,168,7.96
+Keratin,1,192,7.88
+Keratin,2,192,7.69
+Keratin,3,192,7.78
+Keratin,4,192,7.85
+Acetate,1,0,7.83
+Acetate,2,0,7.85
+Acetate,3,0,7.81
+Acetate,1,3,7.69
+Acetate,2,3,7.67
+Acetate,3,3,7.71
+Acetate,1,6,7.75
+Acetate,2,6,7.74
+Acetate,3,6,7.76
+Acetate,1,24,7.93
+Acetate,2,24,7.95
+Acetate,3,24,7.96
+Acetate,1,48,7.75
+Acetate,2,48,7.77
+Acetate,3,48,7.77
+Hexanoate,1,0,7.85
+Hexanoate,2,0,7.85
+Hexanoate,3,0,7.85
+Hexanoate,1,3,7.75
+Hexanoate,2,3,7.79
+Hexanoate,3,3,7.80
+Hexanoate,1,6,7.71
+Hexanoate,2,6,7.78
+Hexanoate,3,6,7.76
+Hexanoate,1,24,7.92
+Hexanoate,2,24,7.84
+Hexanoate,3,24,7.92
+Hexanoate,1,48,7.92
+Hexanoate,2,48,7.85
+Hexanoate,3,48,7.93
+Decanoate,1,0,7.73
+Decanoate,2,0,7.66
+Decanoate,3,0,7.69
+Decanoate,1,3,7.88
+Decanoate,2,3,7.79
+Decanoate,3,3,7.80
+Decanoate,1,6,7.71
+Decanoate,2,6,7.76
+Decanoate,3,6,7.74
+Decanoate ,1,24,7.71
+Decanoate ,2,24,7.00
+Decanoate,3,24,7.73
+Decanoate,1,48,7.61
+Decanoate,2,48,7.68
+Decanoate ,3,48,7.65
diff --git a/omics/kelly/data-raw/vfa2.csv b/omics/kelly/data-raw/vfa2.csv
@@ -0,0 +1,171 @@
+Set number,replicate,Treatment,Time day,Acetate,Propanoate,Isobutyrate,Butyrate,Isopentanoate,Pentanoate,Isohexanoate,Hexanoate
+2,1,Acetate,1,10.9,0,0,0,0,0,0,0
+2,2,Acetate,1,11.2,0,0,0,0,0,0,0
+2,3,Acetate,1,12.8,0,0,0,0,0,0,0
+2,1,Acetate,2,5.6,0,0,0,0,0,0,0
+2,2,Acetate,2,5.3,0,0,0,0,0,0,0
+2,3,Acetate,2,6.1,0,0,0,0,0,0,0
+2,1,Acetate,3,1.2,0,0,0,0,0,0,0
+2,2,Acetate,3,0.9,0,0,0,0,0,0,0
+2,3,Acetate,3,1.1,0,0,0,0,0,0,0
+2,1,Acetate,4,0.1,0,0,0,0,0,0,0
+2,2,Acetate,4,0,0,0,0,0,0,0,0
+2,3,Acetate,4,0,0,0,0,0,0,0,0
+2,1,Acetate,5,0,0,0,0,0,0,0,0
+2,2,Acetate,5,0,0,0,0,0,0,0,0
+2,3,Acetate,5,0,0,0,0,0,0,0,0
+2,1,Acetate,6,11.8,0,0,0,0,0,0,0
+2,2,Acetate,6,11.2,0,0,0,0,0,0,0
+2,3,Acetate,6,12,0,0,0,0,0,0,0
+2,1,Acetate,7,4.9,0,0,0,0,0,0,0
+2,2,Acetate,7,4.3,0,0,0,0,0,0,0
+2,3,Acetate,7,4.8,0,0,0,0,0,0,0
+2,1,Acetate,8,0.3,0,0,0,0,0,0,0
+2,2,Acetate,8,0.5,0,0,0,0,0,0,0
+2,3,Acetate,8,0.9,0,0,0,0,0,0,0
+2,1,Acetate,9,0,0,0,0,0,0,0,0
+2,2,Acetate,9,0,0,0,0,0,0,0,0
+2,3,Acetate,9,0,0,0,0,0,0,0,0
+2,1,Acetate,10,0,0,0,0,0,0,0,0
+2,2,Acetate,10,0,0,0,0,0,0,0,0
+2,3,Acetate,10,0,0,0,0,0,0,0,0
+2,1,Hexanoic,1,0,0,0,0,0,0,0,4.8
+2,2,Hexanoic,1,0,0,0,0,0,0,0,5.2
+2,3,Hexanoic,1,0,0,0,0,0,0,0,5.3
+2,1,Hexanoic,2,0,0,0,0,0,0,0,4
+2,2,Hexanoic,2,0,0,0,0,0,0,0,4.2
+2,3,Hexanoic,2,0,0,0,0,0,0,0,4.5
+2,1,Hexanoic,3,2.4,0,0,0,0,0,0,2.3
+2,2,Hexanoic,3,2.7,0,0,0,0,0,0,2.6
+2,3,Hexanoic,3,1.9,0,0,0,0,0,0,2.4
+2,1,Hexanoic,4,1,0,0,0,0,0,0,0
+2,2,Hexanoic,4,1.2,0,0,0,0,0,0,0
+2,3,Hexanoic,4,0.9,0,0,0,0,0,0,0
+2,1,Hexanoic,5,0,0,0,0,0,0,0,0
+2,2,Hexanoic,5,0,0,0,0,0,0,0,0
+2,3,Hexanoic,5,0,0,0,0,0,0,0,0
+2,1,Hexanoic,6,0.5,0,0,0,0,0,0,4.2
+2,2,Hexanoic,6,0.3,0,0,0,0,0,0,4.1
+2,3,Hexanoic,6,0.6,0,0,0,0,0,0,3.9
+2,1,Hexanoic,7,2.1,0,0,0,0,0,0,3.6
+2,2,Hexanoic,7,2.4,0,0,0,0,0,0,3.2
+2,3,Hexanoic,7,2.7,0,0,0,0,0,0,3.5
+2,1,Hexanoic,8,1.2,0,0,0,0,0,0,1.3
+2,2,Hexanoic,8,1.5,0,0,0,0,0,0,1.1
+2,3,Hexanoic,8,1.3,0,0,0,0,0,0,1.6
+2,1,Hexanoic,9,0.2,0,0,0,0,0,0,0
+2,2,Hexanoic,9,0.6,0,0,0,0,0,0,0
+2,3,Hexanoic,9,0.1,0,0,0,0,0,0,0
+2,1,Hexanoic,10,0,0,0,0,0,0,0,0
+2,2,Hexanoic,10,0,0,0,0,0,0,0,0
+2,3,Hexanoic,10,0,0,0,0,0,0,0,0
+2,1,Decanoic,1,0,0,0,0,0,0,0,0
+2,2,Decanoic,1,0,0,0,0,0,0,0,0
+2,3,Decanoic,1,0,0,0,0,0,0,0,0
+2,1,Decanoic,2,0,0,0,0,0,0,0,0
+2,2,Decanoic,2,0,0,0,0,0,0,0,0
+2,3,Decanoic,2,0,0,0,0,0,0,0,0
+2,1,Decanoic,3,0.3,0,0,0,0,0,0,0.1
+2,2,Decanoic,3,0.4,0,0,0,0,0,0,0
+2,3,Decanoic,3,0.5,0,0,0,0,0,0,0.2
+2,1,Decanoic,4,3,0,0,0,0,0,0,0.8
+2,2,Decanoic,4,3.2,0,0,0,0,0,0,0.9
+2,3,Decanoic,4,4,0,0,0,0,0,0,1.1
+2,1,Decanoic,5,1.1,0,0,0,0,0,0,0
+2,2,Decanoic,5,1.3,0,0,0,0,0,0,0
+2,3,Decanoic,5,0.8,0,0,0,0,0,0,0
+2,1,Decanoic,6,0,0,0,0,0,0,0,0
+2,2,Decanoic,6,0,0,0,0,0,0,0,0
+2,3,Decanoic,6,0,0,0,0,0,0,0,0
+2,1,Decanoic,7,0,0,0,0,0,0,0,0
+2,2,Decanoic,7,0,0,0,0,0,0,0,0
+2,3,Decanoic,7,0,0,0,0,0,0,0,0
+2,1,Decanoic,8,0.6,0,0,0,0,0,0,0.1
+2,2,Decanoic,8,0.9,0,0,0,0,0,0,0.1
+2,3,Decanoic,8,0.8,0,0,0,0,0,0,0.3
+2,1,Decanoic,9,3.7,0,0,0,0,0,0,1.3
+2,2,Decanoic,9,4.1,0,0,0,0,0,0,1.7
+2,3,Decanoic,9,3.9,0,0,0,0,0,0,1.5
+2,1,Decanoic,10,0.9,0,0,0,0,0,0,0
+2,2,Decanoic,10,0.6,0,0,0,0,0,0,0
+2,3,Decanoic,10,0.4,0,0,0,0,0,0,0
+1,1,Casein,1,0,0,0,0,0,0,0,0
+1,2,Casein,1,0,0,0,0,0,0,0,0
+1,3,Casein,1,0,0,0,0,0,0,0,0
+1,4,Casein,1,0,0,0,0,0,0,0,0
+1,1,Casein,2,0,0,0,0,0,0,0,0
+1,2,Casein,2,0,0,0,0,0,0,0,0
+1,3,Casein,2,0,0,0,0,0,0,0,0
+1,4,Casein,2,0,0,0,0,0,0,0,0
+1,1,Casein,3,0,0,0,0,0,0,0,0
+1,2,Casein,3,0,0,0,0,0,0,0,0
+1,3,Casein,3,0,0,0,0,0,0,0,0
+1,4,Casein,3,0,0,0,0,0,0,0,0
+1,1,Casein,4,0,0,0,0,0,0,0,0
+1,2,Casein,4,0,0,0,0,0,0,0,0
+1,3,Casein,4,0,0,0,0,0,0,0,0
+1,4,Casein,4,0,0,0,0,0,0,0,0
+1,1,Casein,5,4.3,1.2,2,4.1,0.3,1,3,5.1
+1,2,Casein,5,3.9,1.4,1.7,3.8,0.2,1.1,2.8,4.8
+1,3,Casein,5,4.1,0.8,2.2,4,0.4,1.2,2.7,6
+1,4,Casein,5,4,1.3,2.1,4.2,0.3,1.3,3.1,5.5
+1,1,Casein,6,6.4,0.2,0.1,3.5,0,0.2,0.7,3.4
+1,2,Casein,6,6.2,0.3,0,3.2,0,0.3,0.8,3
+1,3,Casein,6,6.6,0.1,0,3.8,0,0.1,0.3,3.6
+1,4,Casein,6,5.8,0.2,0.3,3.4,0,0.1,1.1,3.1
+1,1,Casein,7,7.5,0,0,2.1,0,0,0,1.5
+1,2,Casein,7,7.9,0,0,1.6,0,0,0,1.9
+1,3,Casein,7,8.1,0,0,1.9,0,0,0,2.1
+1,4,Casein,7,7.3,0,0,2,0,0,0,1.2
+1,1,Casein,8,9,0,0,0.1,0,0,0,0.5
+1,2,Casein,8,9.7,0,0,0.3,0,0,0,0.3
+1,3,Casein,8,10.1,0,0,0.2,0,0,0,0.1
+1,4,Casein,8,8.9,0,0,0.1,0,0,0,0.5
+1,1,Casein,9,8.7,0.7,1.1,3.3,0,0.2,1.8,4.2
+1,2,Casein,9,7.9,0.6,1.3,3.1,0,0,2.1,4.7
+1,3,Casein,9,8.2,0.3,1,2.9,0,0.1,1.6,4.1
+1,4,Casein,9,8.1,0.9,1.4,3,0,0,2.2,4.5
+1,1,Casein,10,8.8,0.2,0,1.4,0,0,0.1,3.1
+1,2,Casein,10,8.3,0,0.1,1.2,0,0,0.3,2.6
+1,3,Casein,10,7.8,0.1,0,1.7,0,0,0,2.8
+1,4,Casein,10,8.5,0,0,1.1,0,0,0.1,2.3
+1,1,Keratin,1,0,0,0,0,0,0,0,0
+1,2,Keratin,1,0,0,0,0,0,0,0,0
+1,3,Keratin,1,0,0,0,0,0,0,0,0
+1,4,Keratin,1,0,0,0,0,0,0,0,0
+1,1,Keratin,2,0,0,0,0,0,0,0,0
+1,2,Keratin,2,0,0,0,0,0,0,0,0
+1,3,Keratin,2,0,0,0,0,0,0,0,0
+1,4,Keratin,2,0,0,0,0,0,0,0,0
+1,1,Keratin,3,0,0,0,0,0,0,0,0
+1,2,Keratin,3,0,0,0,0,0,0,0,0
+1,3,Keratin,3,0,0,0,0,0,0,0,0
+1,4,Keratin,3,0,0,0,0,0,0,0,0
+1,1,Keratin,4,0,0,0,0,0,0,0,0
+1,2,Keratin,4,0,0,0,0,0,0,0,0
+1,3,Keratin,4,0,0,0,0,0,0,0,0
+1,4,Keratin,4,0,0,0,0,0,0,0,0
+1,1,Keratin,5,0,0,0,0,0,0,0,0
+1,2,Keratin,5,0,0,0,0,0,0,0,0
+1,3,Keratin,5,0,0,0,0,0,0,0,0
+1,4,Keratin,5,0,0,0,0,0,0,0,0
+1,1,Keratin,6,2.1,0,0,0.3,0,0,0,0.4
+1,2,Keratin,6,2.4,0,0,0.4,0,0,0,0.2
+1,3,Keratin,6,1.7,0,0,0.2,0,0,0,0.5
+1,4,Keratin,6,2.5,0,0,0.1,0,0,0,0.3
+1,1,Keratin,7,5,0,0,3,0,0,0,1.4
+1,2,Keratin,7,5.6,0,0,4.2,0,0,0,1.6
+1,3,Keratin,7,4.7,0,0,4,0,0,0,1.2
+1,4,Keratin,7,5.2,0,0,2,0,0,0,1.5
+1,1,Keratin,8,7.1,5,2.6,0.2,4.4,3.7,1.2,3.1
+1,2,Keratin,8,7.3,4.8,2.2,0.4,4.2,3.5,1.4,3.5
+1,3,Keratin,8,6.9,4.9,2.4,0.3,3.8,3.4,0.7,3.2
+1,4,Keratin,8,7,5.3,2.3,0.1,2.9,4.1,1.1,3.3
+1,1,Keratin,9,9.8,5.3,0.4,0,6,5.2,0.1,3.3
+1,2,Keratin,9,10.1,5.4,0.3,0,6.3,4.9,0.3,3
+1,3,Keratin,9,9.6,5.3,0.3,0,6.2,5.1,0.2,2.9
+1,4,Keratin,9,9.9,5.7,0.2,0,5.9,5,0.1,2.8
+1,1,Keratin,10,10.1,5.2,0,0,5.3,6,0,3.4
+1,2,Keratin,10,9.7,5.3,0,0,5.2,6.1,0,3.6
+1,3,Keratin,10,9.9,3.8,0,0,5.5,7.3,0,3.2
+1,4,Keratin,10,10.3,5.9,0,0,5.6,6.4,0,3.5
diff --git a/omics/kelly/temp/example.R b/omics/kelly/temp/example.R
diff --git a/omics/kelly/temp/example.csv b/omics/kelly/temp/example.csv