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1 Context and Purpose of this Brief

This document concentrates our analysis around soil helath indicators. Our main intentios are measuring impact of soil helath over our crop quality variables, assesment of the potential of this variables to add predictive power to our machine learning models and summarising and testing the effects of management practices over soil health indicators.

1.0.0.1 Crop Nutritional Density Variables

Crop Nutritional Density Variables
Nutritional
Antioxidants
Polyphenols
Proteins

1.0.1 Soil Health Variables

Soil Health Variables
Soil
organic_carbon_percentage_10cm
organic_carbon_percentage_20cm
PH_soil_10cm
PH_soil_20cm
respiration_soil_10cm
respiration_soil_20cm
respiration_soil_10cm
respiration_soil_20cm
  • The following table is available as a CSV file for manipulation, filename ./BFA-Soil-Extremes-Table.csv.
Position values and some dispersion measures for main analytes.
0cm-10cm
10cm-20cm
Type median_10cm_organic_carbon_percentage median_10cm_respiration_soil max_10cm_organic_carbon_percentage max_10cm_respiration_soil min_10cm_organic_carbon_percentage min_10cm_respiration_soil range_10cm_organic_carbon_percentage range_10cm_respiration_soil sd_10cm_organic_carbon_percentage sd_10cm_respiration_soil ratio_10cm_organic_carbon_percentage ratio_10cm_respiration_soil median_20cm_organic_carbon_percentage median_20cm_respiration_soil max_20cm_organic_carbon_percentage max_20cm_respiration_soil min_20cm_organic_carbon_percentage min_20cm_respiration_soil range_20cm_organic_carbon_percentage range_20cm_respiration_soil sd_20cm_organic_carbon_percentage sd_20cm_respiration_soil ratio_20cm_organic_carbon_percentage ratio_20cm_respiration_soil
oats 2.47 19.48 17.67 55.86 0.00 6.72 17.67 49.14 3.784392 11.16015 Inf 8.31250 2.31 14.75 17.18 35.17 1.12 3.75 16.06 31.42 3.557969 7.93948 15.339286 9.378667
wheat 3.29 20.91 7.27 47.81 1.15 4.52 6.12 43.29 1.178903 10.92112 6.321739 10.57743 2.72 12.02 6.94 36.41 0.99 3.30 5.95 33.11 1.222260 7.38056 7.010101 11.033333

1.1 Methodologies

We’ve performed an extensive medians comparisons in the past for crop nutritional quality indicators ( antioxidants, polyphenols and brix ). Methods, code implementations and a detailed guide on how we are interpreting results are all detailed on a previous brief available on the same site where this one is offered, 2019 Survey, Quality Relationships Analysis.

The predictive potential and impact of soil health indicators over nutritional density indicators will be measured by a non parametrical measure of correlation, Spearman’s Rank Correlation Coefficient, in line with the rank tests employed for median shifts on our Quality Relationships synthesis tables.

1.2 Boxplots for Soil Health Variables Over Climate Regions

2 Cuantification of Soil Quality Variables over Produce Quality Variables

As stated, we are measuring correlation between soil and nutritional variables for each crop. Two linear regressions will be adjusted for each crop, explaining a nutritional variable with all six soil variables.

On a first step, a first linear model is adjusted for all the explicative variables and all data points available. Then an \(\alpha\) trimming is performed for the \(15%\) biggest residuals and a second model is adjusted with this high residuals trimmmed dataset.

We don’t expect such a simple regression to yield a complete prediction of this variables, which have proven remarkably complex to predict in a regressive context. Good \(R^2\) results will inform that this variables are good material to increase the predictive power of our current complex models, like Random Forests which already employ spectrometry, regions, varieties, etc.

2.1 Fit Quality on Each Crop and Variable

  • Trimmed models are thos were an alfa trimming has been performed: after a first run, the 15% worst residual samples are removed and a new model is trained over the clean dataset.
  • The F Test p value is offered for both models.
  • The T test p values are offered just for the trimmed models. No Bonferroni correction has been applied, so the reader should bear in mind that for 6 variables to give the desired confidence, the threshold p value should be divided by 6 ( that is, to satisfy a level 0.05 we need to see 0.083 on the t test ).
Crop Nutritional Density Variables
Crop Variable Samples R2 F test p-value trimmed R2 F test p-value, trimmed t test p.val (Intercept) t test p.val PH_soil_10cm t test p.val PH_soil_20cm t test p.val respiration_soil_10cm t test p.val respiration_soil_20cm t test p.val organic_carbon_percentage_10cm t test p.val organic_carbon_percentage_20cm coefficient_Intercept coefficient_PH_10cm coefficient_PH_20cm coefficient_respiration_10cm coefficient_respiration_20cm coefficient_carbon_10cm coefficient_carbon_20cm
oats Antioxidants 110 0.3237056 0.0000000 0.5304825 0.0000000 0.0000 0.0000 0.1292 0.0079 0.0487 0.6188 0.0232 23544.40 -4896.85 1032.36 26.60 29.78 -32.74 167.49
oats Polyphenols 110 0.2213846 0.0000149 0.4936021 0.0000000 0.0000 0.0000 0.0364 0.0046 0.5333 0.6571 0.0100 386.66 -82.52 31.18 0.63 0.21 -0.61 3.94
wheat Polyphenols 156 0.0593321 0.0187955 0.1953265 0.0000083 0.0347 0.1301 0.7720 0.0800 0.0326 0.0010 0.2591 279.38 -32.29 -5.38 0.44 -0.91 12.47 -3.57
oats Proteins 110 0.1042241 0.0076261 0.1731663 0.0009213 0.7672 0.0335 0.0001 0.1790 0.7054 0.0015 0.0024 -1.74 -3.14 5.40 -0.02 -0.01 0.42 -0.42
wheat Proteins 156 0.0581945 0.0201620 0.0931013 0.0053923 0.9654 0.7534 0.5215 0.0088 0.1919 0.2600 0.4511 -0.46 0.55 0.94 0.05 0.04 -0.32 -0.18
wheat Antioxidants 156 0.0074932 0.3120372 0.0362460 0.1001291 0.6498 0.0893 0.2137 0.2740 0.0250 0.4899 0.1031 3739.13 -2084.70 1901.64 15.82 -47.45 -139.87 292.13

2.1.1 Residuals Graphics for the Most Promissing Regressions

2.1.1.1 Antioxidants on Oats

2.2 Random Forest Regressions

This random forest models are cross validated and include several other variables sets, to help better compare the importance of our soil predictors in comparison with other available information, which in this case is the hand spectrometer scans.

2.2.1 Datasets

composition of datasets
name variables
set1 organic_carbon_percentage_10cm, organic_carbon_percentage_20cm, PH_soil_10cm , PH_soil_20cm , respiration_soil_10cm , respiration_soil_20cm
set2 organic_carbon_percentage_10cm, organic_carbon_percentage_20cm, PH_soil_10cm , PH_soil_20cm , respiration_soil_10cm , respiration_soil_20cm
set3 organic_carbon_percentage_10cm, organic_carbon_percentage_20cm, PH_soil_10cm , PH_soil_20cm , respiration_soil_10cm , respiration_soil_20cm
set4 organic_carbon_percentage_10cm, organic_carbon_percentage_20cm, PH_soil_10cm , PH_soil_20cm , respiration_soil_10cm , respiration_soil_20cm

2.2.2 Observed Results

Random Forest Models on Soil and Scans
explained species dataset cvRsquared mtry N
Antioxidants oats set4 0.5922025 13 62
Antioxidants oats set2 0.7474786 18 62
Antioxidants oats set3 0.8130643 1 62
Antioxidants oats set1 0.8998767 3 62
Polyphenols oats set4 0.6560193 1 62
Polyphenols oats set1 0.7289460 1 62
Polyphenols oats set2 0.7441049 1 62
Polyphenols oats set3 0.7510898 4 62
Proteins oats set3 0.2978997 4 62
Proteins oats set2 0.5258622 37 62
Proteins oats set4 0.6164505 39 62
Proteins oats set1 0.7746392 7 62
Antioxidants wheat set4 0.3057721 1 108
Antioxidants wheat set1 0.4259567 2 108
Antioxidants wheat set3 0.5601010 2 108
Antioxidants wheat set2 0.5866954 2 108
Polyphenols wheat set3 0.3720503 35 108
Polyphenols wheat set2 0.3910017 3 108
Polyphenols wheat set4 0.5436691 18 108
Polyphenols wheat set1 0.5929456 1 108
Proteins wheat set2 0.3319374 29 108
Proteins wheat set4 0.5075490 34 108
Proteins wheat set3 0.5555066 2 108
Proteins wheat set1 0.5760422 36 108

2.2.2.1 Quality of fit plots for all Random Forest Regressions on Soil Health

3 Quality Relationship Tables

We offer separatedly the synthesis of this tables on the same site were this brief is available, showing the shifts as percentages of deviation over the median and the sample sizes.

This variables have shown interesting behaviours. As we are not accounting for the crop factor, populations are robust for most evaluated practices, and most of them have shown shifts that our test could detect as significant.

Tables offered below are much deeper so the recommended procedure is searching for interesting data on the synthesis tables, and then getting a deeper insight by looking at the complete summaries.

Besites the medians shift analysis, we’ve performed a much more informal summary for the frequency of factors on certaing percentiles. The intuitive idea behind this procedure is that if the frequency of Practice X over the whole dataset is \(30%\) but while looking at the “10%” biggest values for the vaiable it doubles to \(60%\), it is probably concentrated among the most succesfull crops. There are tables for the best and worst percentiles showing this behaviour.

It’s main advantage is that it spares the reader looking at the enormuos amount of graphics that would have been involved in comparint all these factors for each of the three variables and that it shows patterns even while not detected as relevant by the test, could be interesting for certain investigators or worth an additional exploration.

3.1 Percentual Shift Over the Median Value for Farm Practices

3.1.1 p.values Code Key

p Values Color Scale
Chances of 0 real shift, when observed is Positive Chances of 0 real Shift, when observed is Negative
Less than 10% Less than 10%
Between 10% and 50% Between 10% and 50%
50% or more% 50% or more

3.1.2 Tables

Percent of Variation over Median Value
Factor Organic Carbon Percentage 10cm Ph Soil 10cm Respiration Soil 10cm Organic Carbon Percentage 20cm Ph Soil 20cm Respiration Soil 20cm
Certified Organic 0.93 0 49.38 18.85 0 85.52
Covercrops -17.88 0 0.79 -17.25 0 -0.86
Organic -25.14 0 -9.21 -20.77 0 -7.76
Regenerative -25.98 0 -6.16 -23.64 0 -4.96
Transitioning -24.86 0 -10.78 -21.4 0 -11.93

3.2 Percentual Shift Over the Median for Soil Amendments

Percent of Variation over Median Value
Factor Organic Carbon Percentage 10cm Ph Soil 10cm Respiration Soil 10cm Organic Carbon Percentage 20cm Ph Soil 20cm Respiration Soil 20cm
Organic Amendment 20.4 0 1.71 12.21 0 -10.68
Synth Fertilizer 8.85 0 -19.72 -3.23 0 -29.23

3.3 Percentual Shift Over the Median for Tillage Intensity

Percent of Variation over Median Value
Factor Organic Carbon Percentage 10cm Ph Soil 10cm Respiration Soil 10cm Organic Carbon Percentage 20cm Ph Soil 20cm Respiration Soil 20cm
Heavy Tillage -26.27 0 13.58 -25.62 0 12.49
Light Tillage -20.72 0 4.74 -7.99 0 21.51

3.4 Quality Replationships for PH at 10cm

3.4.1 Median Shifts

Farm Practices: Position Measures and Median Comparisons with the ‘none’ category
factor mean median N explained observedUIDs observedUIDsY HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 5.543421 5.50 76 PH_soil_10cm 24 24 [5.8,5.9] 5.8 5.9 0.0069266 5.899998 TRUE NA
covercrops 5.648235 5.50 85 PH_soil_10cm 23 0 [0,0] 0.0 0.0 0.0000281 NA TRUE 6.30e-05
organic 5.615116 5.50 172 PH_soil_10cm 53 0 [0,0] 0.0 0.0 0.0003511 NA TRUE 4.44e-05
regenerative 5.597183 5.50 142 PH_soil_10cm 46 0 [0,0] 0.0 0.0 0.0048907 NA TRUE 2.63e-05
transitioning 5.600000 5.50 171 PH_soil_10cm 51 0 [0,0] 0.0 0.0 0.0034726 NA TRUE 2.65e-05
certified_organic 5.650000 5.65 12 PH_soil_10cm 4 0 [0,0.3] 0.0 0.3 0.3837338 NA FALSE 3.19e-05
Amendments: Position Measures and Median Comparisons with the ‘none’ category.
factor mean median N explained observedUIDsY observedUIDs HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 5.647273 5.5 110 PH_soil_10cm 33 33 [5.8,5.8] 5.8 5.8 0.0000000 5.8 TRUE NA
synth_fertilizer 5.547500 5.5 120 PH_soil_10cm 0 40 [0,0] 0.0 0.0 0.0000002 NA TRUE -1.80e-05
organic_amendment 5.563380 5.5 71 PH_soil_10cm 0 21 [0,0] 0.0 0.0 0.0003653 NA TRUE -3.46e-05

3.4.2 Density Variation on Certain Percentiles

On this tables, we attempt to find interesting patterns to explain atypicals and hopefully all variance for a given variable.

We’ve already looked at these tables in detail on the Quality Relationships brief for produce: we are comparing how frequent is to find a certain quality for the full dataset and for a certain quantile, implying that if a certain attribute is more usual between the points on an extreme, it is worth checking if it is influential over the variable and explains the outlyingness of some values.

Presence on the Last Decile for Every Practice
factor frequency[0.9,1] total[0.9,1] frequency[0,1] total[0,1] reason
none 0.2307692 3 0.0540541 6 4.2692308
covercrops 0.5384615 7 0.2522523 28 2.1346154
tillage.heavy_tillage 0.6153846 8 0.3783784 42 1.6263736
seed_treatment.biological 0.3846154 5 0.2972973 33 1.2937063
amendments.synth_fertilizer 0.3846154 5 0.3243243 36 1.1858974
companion_cropping.none 0.6153846 8 0.5585586 62 1.1017370
land_prep.tillage 0.8461538 11 0.8468468 94 0.9991817
amendments.none 0.4615385 6 0.4864865 54 0.9487179
companion_cropping.used 0.3846154 5 0.4414414 49 0.8712716
amendments.organic_amendment 0.1538462 2 0.1891892 21 0.8131868
transitioning 0.6153846 8 0.8378378 93 0.7344913
organic 0.6153846 8 0.8738739 97 0.7042030
seed_treatment.none 0.3846154 5 0.5585586 62 0.6885856
regenerative 0.3846154 5 0.7117117 79 0.5404090
tillage.light_tillage 0.2307692 3 0.4684685 52 0.4926036
certified_organic 0.0000000 0 0.0270270 3 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0270270 3 0.0000000
Presence on the Last Quartile for Every Practice
factor frequency[0.75,1] total[0.75,1] frequency[0,1] total[0,1] reason
certified_organic 0.0689655 2 0.0270270 3 2.5517241
covercrops 0.4827586 14 0.2522523 28 1.9137931
none 0.1034483 3 0.0540541 6 1.9137931
companion_cropping.used 0.6206897 18 0.4414414 49 1.4060521
amendments.none 0.6551724 19 0.4864865 54 1.3467433
tillage.heavy_tillage 0.4827586 14 0.3783784 42 1.2758621
seed_treatment.none 0.5517241 16 0.5585586 62 0.9877642
land_prep.tillage 0.8275862 24 0.8468468 94 0.9772561
organic 0.7931034 23 0.8738739 97 0.9075720
seed_treatment.biological 0.2413793 7 0.2972973 33 0.8119122
transitioning 0.6551724 19 0.8378378 93 0.7819800
amendments.synth_fertilizer 0.2413793 7 0.3243243 36 0.7442529
tillage.light_tillage 0.3448276 10 0.4684685 52 0.7360743
regenerative 0.5172414 15 0.7117117 79 0.7267569
companion_cropping.none 0.3793103 11 0.5585586 62 0.6790879
amendments.organic_amendment 0.1034483 3 0.1891892 21 0.5467980
seed_treatment.fungicide 0.0000000 0 0.0270270 3 0.0000000
Presence on the Worst 15% for Every Practice
factor frequency[0,0.15] total[0,0.15] frequency[0,1] total[0,1] reason
seed_treatment.fungicide 0.0588235 1 0.0270270 3 2.1764706
amendments.organic_amendment 0.2941176 5 0.1891892 21 1.5546218
companion_cropping.used 0.5294118 9 0.4414414 49 1.1992797
seed_treatment.none 0.6470588 11 0.5585586 62 1.1584440
tillage.light_tillage 0.5294118 9 0.4684685 52 1.1300905
land_prep.tillage 0.9411765 16 0.8468468 94 1.1113892
amendments.none 0.5294118 9 0.4864865 54 1.0882353
tillage.heavy_tillage 0.4117647 7 0.3783784 42 1.0882353
none 0.0588235 1 0.0540541 6 1.0882353
covercrops 0.2352941 4 0.2522523 28 0.9327731
transitioning 0.7647059 13 0.8378378 93 0.9127135
regenerative 0.6470588 11 0.7117117 79 0.9091586
organic 0.7647059 13 0.8738739 97 0.8750758
companion_cropping.none 0.4705882 8 0.5585586 62 0.8425047
amendments.synth_fertilizer 0.1764706 3 0.3243243 36 0.5441176
seed_treatment.biological 0.1176471 2 0.2972973 33 0.3957219
certified_organic 0.0000000 0 0.0270270 3 0.0000000

3.5 Quality Replationships for PH at 20cm

3.5.1 Median Shifts

Farm Practices: Position Measures and Median Comparisons with the ‘none’ category
factor mean median N explained observedUIDs observedUIDsY HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 5.564865 5.5 74 PH_soil_20cm 24 24 [5.8,6] 5.8 6 0.0014962 5.800056 TRUE NA
covercrops 5.581176 5.5 85 PH_soil_20cm 23 0 [0,0] 0.0 0 0.6879615 NA FALSE 9.90e-06
organic 5.576744 5.5 172 PH_soil_20cm 53 0 [0,0] 0.0 0 0.4861727 NA FALSE 3.40e-06
regenerative 5.573944 5.5 142 PH_soil_20cm 46 0 [0,0] 0.0 0 0.5835215 NA FALSE 4.38e-05
transitioning 5.573684 5.5 171 PH_soil_20cm 51 0 [0,0] 0.0 0 0.4981619 NA FALSE 1.48e-05
certified_organic 5.500000 5.5 12 PH_soil_20cm 4 0 [0,0] 0.0 0 0.1384629 NA FALSE 0.00e+00
Amendments: Position Measures and Median Comparisons with the ‘none’ category.
factor mean median N explained observedUIDsY observedUIDs HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 5.587273 5.5 110 PH_soil_20cm 33 33 [5.8,5.9] 5.8 5.9 0.0000104 5.89992 TRUE NA
synth_fertilizer 5.567500 5.5 120 PH_soil_20cm 0 40 [0,0] 0.0 0.0 0.4141736 NA FALSE -5.74e-05
organic_amendment 5.595652 5.5 69 PH_soil_20cm 0 21 [0,0] 0.0 0.0 0.7630738 NA FALSE 5.20e-06

3.5.2 Density Variation on Certain Percentiles

On this tables, we attempt to find interesting patterns to explain atypicals and hopefully all variance for a given variable.

We’ve already looked at these tables in detail on the Quality Relationships brief for produce: we are comparing how frequent is to find a certain quality for the full dataset and for a certain quantile, implying that if a certain attribute is more usual between the points on an extreme, it is worth checking if it is influential over the variable and explains the outlyingness of some values.

Presence on the Last Decile for Every Practice
factor frequency[0.9,1] total[0.9,1] frequency[0,1] total[0,1] reason
none 0.2307692 3 0.0540541 6 4.2692308
covercrops 0.4615385 6 0.2522523 28 1.8296703
tillage.heavy_tillage 0.5384615 7 0.3783784 42 1.4230769
amendments.none 0.5384615 7 0.4864865 54 1.1068376
companion_cropping.used 0.4615385 6 0.4414414 49 1.0455259
seed_treatment.biological 0.3076923 4 0.2972973 33 1.0349650
land_prep.tillage 0.8461538 11 0.8468468 94 0.9991817
seed_treatment.none 0.5384615 7 0.5585586 62 0.9640199
companion_cropping.none 0.5384615 7 0.5585586 62 0.9640199
amendments.synth_fertilizer 0.3076923 4 0.3243243 36 0.9487179
amendments.organic_amendment 0.1538462 2 0.1891892 21 0.8131868
transitioning 0.6153846 8 0.8378378 93 0.7344913
organic 0.6153846 8 0.8738739 97 0.7042030
tillage.light_tillage 0.3076923 4 0.4684685 52 0.6568047
regenerative 0.4615385 6 0.7117117 79 0.6484907
certified_organic 0.0000000 0 0.0270270 3 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0270270 3 0.0000000
Presence on the Last Quartile for Every Practice
factor frequency[0.75,1] total[0.75,1] frequency[0,1] total[0,1] reason
none 0.2068966 6 0.0540541 6 3.8275862
tillage.light_tillage 0.5862069 17 0.4684685 52 1.2513263
covercrops 0.3103448 9 0.2522523 28 1.2302956
amendments.none 0.5517241 16 0.4864865 54 1.1340996
companion_cropping.used 0.4827586 14 0.4414414 49 1.0935961
land_prep.tillage 0.8965517 26 0.8468468 94 1.0586941
seed_treatment.none 0.5862069 17 0.5585586 62 1.0494994
seed_treatment.biological 0.3103448 9 0.2972973 33 1.0438871
amendments.synth_fertilizer 0.3103448 9 0.3243243 36 0.9568966
companion_cropping.none 0.5172414 15 0.5585586 62 0.9260289
transitioning 0.6896552 20 0.8378378 93 0.8231368
tillage.heavy_tillage 0.3103448 9 0.3783784 42 0.8201970
organic 0.6896552 20 0.8738739 97 0.7891930
regenerative 0.5517241 16 0.7117117 79 0.7752073
amendments.organic_amendment 0.1379310 4 0.1891892 21 0.7290640
certified_organic 0.0000000 0 0.0270270 3 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0270270 3 0.0000000
Presence on the Worst 15% for Every Practice
factor frequency[0,0.15] total[0,0.15] frequency[0,1] total[0,1] reason
seed_treatment.fungicide 0.0588235 1 0.0270270 3 2.1764706
companion_cropping.used 0.5882353 10 0.4414414 49 1.3325330
amendments.none 0.6470588 11 0.4864865 54 1.3300654
amendments.organic_amendment 0.2352941 4 0.1891892 21 1.2436975
tillage.heavy_tillage 0.4117647 7 0.3783784 42 1.0882353
seed_treatment.none 0.5882353 10 0.5585586 62 1.0531309
land_prep.tillage 0.8823529 15 0.8468468 94 1.0419274
tillage.light_tillage 0.4705882 8 0.4684685 52 1.0045249
transitioning 0.8235294 14 0.8378378 93 0.9829222
organic 0.8235294 14 0.8738739 97 0.9423893
covercrops 0.2352941 4 0.2522523 28 0.9327731
regenerative 0.6470588 11 0.7117117 79 0.9091586
companion_cropping.none 0.4117647 7 0.5585586 62 0.7371917
amendments.synth_fertilizer 0.1176471 2 0.3243243 36 0.3627451
seed_treatment.biological 0.0588235 1 0.2972973 33 0.1978610
none 0.0000000 0 0.0540541 6 0.0000000
certified_organic 0.0000000 0 0.0270270 3 0.0000000

3.6 Quality Replationships for respiration at 10cm

3.6.1 Median Shifts

Farm Practices: Position Measures and Median Comparisons with the ‘none’ category
factor mean median N explained observedUIDs observedUIDsY HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 23.27022 21.670 91 respiration_soil_10cm 29 29 [20.97,25.64] 20.97 25.64 0.2331702 22.90503 TRUE NA
covercrops 23.02294 21.880 85 respiration_soil_10cm 24 0 [-2.95,2.9] -2.95 2.90 0.9610339 NA FALSE 0.1799438
organic 21.38525 19.815 160 respiration_soil_10cm 51 0 [-4.52,0.82] -4.52 0.82 0.8685626 NA FALSE -2.1100425
regenerative 22.00263 21.210 133 respiration_soil_10cm 44 0 [-4.1,1.31] -4.10 1.31 0.5787002 NA FALSE -1.4100300
transitioning 20.70208 18.180 159 respiration_soil_10cm 49 0 [-5.09,-0.01] -5.09 -0.01 0.4965751 NA TRUE -2.4699699
certified_organic 33.61250 38.305 12 respiration_soil_10cm 4 0 [5.02,19.24] 5.02 19.24 0.2077866 NA TRUE 11.3099699
Amendments: Position Measures and Median Comparisons with the ‘none’ category.
factor mean median N explained observedUIDsY observedUIDs HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 23.76925 23.00 107 respiration_soil_10cm 33 33 [22.01,24.87] 22.01 24.87 0.6768711 23.43144 TRUE NA
synth_fertilizer 19.91955 16.40 132 respiration_soil_10cm 0 44 [-6.99,-2.49] -6.99 -2.49 0.2064026 NA TRUE -4.620035
organic_amendment 23.95956 23.25 68 respiration_soil_10cm 0 21 [-4.02,4.01] -4.02 4.01 0.9633709 NA FALSE 0.399991

3.6.2 Density Variation on Certain Percentiles

On this tables, we attempt to find interesting patterns to explain atypicals and hopefully all variance for a given variable.

We’ve already looked at these tables in detail on the Quality Relationships brief for produce: we are comparing how frequent is to find a certain quality for the full dataset and for a certain quantile, implying that if a certain attribute is more usual between the points on an extreme, it is worth checking if it is influential over the variable and explains the outlyingness of some values.

Presence on the Last Decile for Every Practice
factor frequency[0.9,1] total[0.9,1] frequency[0,1] total[0,1] reason
amendments.organic_amendment 0.50 6 0.2000000 21 2.500000
companion_cropping.used 1.00 12 0.4380952 46 2.282609
covercrops 0.50 6 0.2666667 28 1.875000
tillage.heavy_tillage 0.50 6 0.3714286 39 1.346154
seed_treatment.none 0.75 9 0.5619048 59 1.334746
transitioning 1.00 12 0.8285714 87 1.206897
organic 1.00 12 0.8666667 91 1.153846
land_prep.tillage 1.00 12 0.8666667 91 1.153846
regenerative 0.75 9 0.6952381 73 1.078767
amendments.none 0.50 6 0.4857143 51 1.029412
tillage.light_tillage 0.50 6 0.4952381 52 1.009615
none 0.00 0 0.0571429 6 0.000000
certified_organic 0.00 0 0.0285714 3 0.000000
amendments.synth_fertilizer 0.00 0 0.3142857 33 0.000000
seed_treatment.biological 0.00 0 0.2857143 30 0.000000
seed_treatment.fungicide 0.00 0 0.0285714 3 0.000000
companion_cropping.none 0.00 0 0.5619048 59 0.000000
Presence on the Last Quartile for Every Practice
factor frequency[0.75,1] total[0.75,1] frequency[0,1] total[0,1] reason
covercrops 0.4642857 13 0.2666667 28 1.7410714
tillage.heavy_tillage 0.6071429 17 0.3714286 39 1.6346154
companion_cropping.used 0.6428571 18 0.4380952 46 1.4673913
amendments.organic_amendment 0.2500000 7 0.2000000 21 1.2500000
seed_treatment.biological 0.3214286 9 0.2857143 30 1.1250000
transitioning 0.9285714 26 0.8285714 87 1.1206897
organic 0.9642857 27 0.8666667 91 1.1126374
regenerative 0.7500000 21 0.6952381 73 1.0787671
land_prep.tillage 0.9285714 26 0.8666667 91 1.0714286
amendments.synth_fertilizer 0.3214286 9 0.3142857 33 1.0227273
amendments.none 0.4285714 12 0.4857143 51 0.8823529
seed_treatment.none 0.4285714 12 0.5619048 59 0.7627119
tillage.light_tillage 0.3214286 9 0.4952381 52 0.6490385
companion_cropping.none 0.3571429 10 0.5619048 59 0.6355932
none 0.0000000 0 0.0571429 6 0.0000000
certified_organic 0.0000000 0 0.0285714 3 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0285714 3 0.0000000
Presence on the Worst 15% for Every Practice
factor frequency[0,0.15] total[0,0.15] frequency[0,1] total[0,1] reason
amendments.organic_amendment 0.3750 6 0.2000000 21 1.8750000
tillage.light_tillage 0.8125 13 0.4952381 52 1.6406250
companion_cropping.none 0.8125 13 0.5619048 59 1.4459746
seed_treatment.none 0.7500 12 0.5619048 59 1.3347458
transitioning 1.0000 16 0.8285714 87 1.2068966
regenerative 0.8125 13 0.6952381 73 1.1686644
organic 1.0000 16 0.8666667 91 1.1538462
land_prep.tillage 0.8125 13 0.8666667 91 0.9375000
seed_treatment.biological 0.2500 4 0.2857143 30 0.8750000
amendments.synth_fertilizer 0.2500 4 0.3142857 33 0.7954545
amendments.none 0.3750 6 0.4857143 51 0.7720588
companion_cropping.used 0.1875 3 0.4380952 46 0.4279891
none 0.0000 0 0.0571429 6 0.0000000
covercrops 0.0000 0 0.2666667 28 0.0000000
certified_organic 0.0000 0 0.0285714 3 0.0000000
seed_treatment.fungicide 0.0000 0 0.0285714 3 0.0000000
tillage.heavy_tillage 0.0000 0 0.3714286 39 0.0000000

3.7 Quality Replationships for Soil Respiration at 20cm

3.7.1 Median Shifts

Farm Practices: Position Measures and Median Comparisons with the ‘none’ category
factor mean median N explained observedUIDs observedUIDsY HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 14.63022 13.100 89 respiration_soil_20cm 29 29 [12.77,15.15] 12.77 15.15 0.2156512 13.915 TRUE NA
covercrops 14.89568 12.280 88 respiration_soil_20cm 24 0 [-1.85,1.97] -1.85 1.97 0.4703933 NA FALSE -0.1200110
organic 13.94570 11.540 172 respiration_soil_20cm 53 0 [-2.58,0.48] -2.58 0.48 0.5722080 NA FALSE -1.0800608
regenerative 14.16134 11.945 142 respiration_soil_20cm 46 0 [-2.19,1.06] -2.19 1.06 0.6251179 NA FALSE -0.6899463
transitioning 13.07550 11.480 171 respiration_soil_20cm 51 0 [-3.14,-0.26] -3.14 -0.26 0.9688025 NA TRUE -1.6599691
certified_organic 25.41000 26.780 12 respiration_soil_20cm 4 0 [8.69,15.09] 8.69 15.09 0.3314417 NA TRUE 11.9000116
Amendments: Position Measures and Median Comparisons with the ‘none’ category.
factor mean median N explained observedUIDsY observedUIDs HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 16.97036 15.280 110 respiration_soil_20cm 33 33 [14.88,17.9] 14.88 17.90 0.1901434 16.28503 TRUE NA
synth_fertilizer 11.29217 9.885 138 respiration_soil_20cm 0 46 [-6.37,-3.16] -6.37 -3.16 0.5183152 NA TRUE -4.759987
organic_amendment 15.12478 14.720 69 respiration_soil_20cm 0 21 [-3.63,0.48] -3.63 0.48 0.3628288 NA FALSE -1.740012

3.7.2 Density Variation on Certain Percentiles

On this tables, we attempt to find interesting patterns to explain atypicals and hopefully all variance for a given variable.

We’ve already looked at these tables in detail on the Quality Relationships brief for produce: we are comparing how frequent is to find a certain quality for the full dataset and for a certain quantile, implying that if a certain attribute is more usual between the points on an extreme, it is worth checking if it is influential over the variable and explains the outlyingness of some values.

Presence on the Last Decile for Every Practice
factor frequency[0.9,1] total[0.9,1] frequency[0,1] total[0,1] reason
companion_cropping.used 0.6153846 8 0.4414414 49 1.3940345
tillage.light_tillage 0.6153846 8 0.4684685 52 1.3136095
amendments.none 0.6153846 8 0.4864865 54 1.2649573
transitioning 1.0000000 13 0.8378378 93 1.1935484
organic 1.0000000 13 0.8738739 97 1.1443299
land_prep.tillage 0.8461538 11 0.8468468 94 0.9991817
covercrops 0.2307692 3 0.2522523 28 0.9148352
regenerative 0.6153846 8 0.7117117 79 0.8646543
amendments.organic_amendment 0.1538462 2 0.1891892 21 0.8131868
seed_treatment.biological 0.2307692 3 0.2972973 33 0.7762238
amendments.synth_fertilizer 0.2307692 3 0.3243243 36 0.7115385
seed_treatment.none 0.3846154 5 0.5585586 62 0.6885856
companion_cropping.none 0.3846154 5 0.5585586 62 0.6885856
tillage.heavy_tillage 0.2307692 3 0.3783784 42 0.6098901
none 0.0000000 0 0.0540541 6 0.0000000
certified_organic 0.0000000 0 0.0270270 3 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0270270 3 0.0000000
Presence on the Last Quartile for Every Practice
factor frequency[0.75,1] total[0.75,1] frequency[0,1] total[0,1] reason
companion_cropping.used 0.6896552 20 0.4414414 49 1.5622801
tillage.light_tillage 0.5862069 17 0.4684685 52 1.2513263
covercrops 0.3103448 9 0.2522523 28 1.2302956
amendments.none 0.5862069 17 0.4864865 54 1.2049808
amendments.organic_amendment 0.2068966 6 0.1891892 21 1.0935961
transitioning 0.8965517 26 0.8378378 93 1.0700779
organic 0.8965517 26 0.8738739 97 1.0259509
land_prep.tillage 0.7931034 23 0.8468468 94 0.9365371
seed_treatment.none 0.5172414 15 0.5585586 62 0.9260289
regenerative 0.6206897 18 0.7117117 79 0.8721082
seed_treatment.biological 0.2068966 6 0.2972973 33 0.6959248
amendments.synth_fertilizer 0.2068966 6 0.3243243 36 0.6379310
companion_cropping.none 0.3103448 9 0.5585586 62 0.5556174
tillage.heavy_tillage 0.2068966 6 0.3783784 42 0.5467980
none 0.0000000 0 0.0540541 6 0.0000000
certified_organic 0.0000000 0 0.0270270 3 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0270270 3 0.0000000
Presence on the Worst 15% for Every Practice
factor frequency[0,0.15] total[0,0.15] frequency[0,1] total[0,1] reason
amendments.organic_amendment 0.3529412 6 0.1891892 21 1.8655462
seed_treatment.none 1.0000000 17 0.5585586 62 1.7903226
tillage.light_tillage 0.7058824 12 0.4684685 52 1.5067873
companion_cropping.used 0.6470588 11 0.4414414 49 1.4657863
amendments.none 0.6470588 11 0.4864865 54 1.3300654
transitioning 1.0000000 17 0.8378378 93 1.1935484
land_prep.tillage 0.8823529 15 0.8468468 94 1.0419274
organic 0.8235294 14 0.8738739 97 0.9423893
regenerative 0.6470588 11 0.7117117 79 0.9091586
covercrops 0.1764706 3 0.2522523 28 0.6995798
companion_cropping.none 0.3529412 6 0.5585586 62 0.6318786
tillage.heavy_tillage 0.1764706 3 0.3783784 42 0.4663866
none 0.0000000 0 0.0540541 6 0.0000000
certified_organic 0.0000000 0 0.0270270 3 0.0000000
amendments.synth_fertilizer 0.0000000 0 0.3243243 36 0.0000000
seed_treatment.biological 0.0000000 0 0.2972973 33 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0270270 3 0.0000000

3.8 Quality Replationships for Carbon Mass Percentage at 10cm

3.8.1 Median Shifts

Farm Practices: Position Measures and Median Comparisons with the ‘none’ category
factor mean median N explained observedUIDs observedUIDsY HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 3.683143 3.355 70 organic_carbon_percentage_10cm 22 22 [3.3,3.91] 3.30 3.91 0.2124344 3.579985 TRUE NA
covercrops 3.071412 2.800 85 organic_carbon_percentage_10cm 23 0 [-0.93,-0.31] -0.93 -0.31 0.6517521 NA TRUE -0.6399866
organic 3.332952 2.480 166 organic_carbon_percentage_10cm 51 0 [-1.13,-0.65] -1.13 -0.65 0.8961876 NA TRUE -0.9000328
regenerative 3.426403 2.460 139 organic_carbon_percentage_10cm 45 0 [-1.2,-0.72] -1.20 -0.72 0.7334531 NA TRUE -0.9300274
transitioning 3.367818 2.480 165 organic_carbon_percentage_10cm 49 0 [-1.11,-0.64] -1.11 -0.64 0.9406161 NA TRUE -0.8900105
certified_organic 3.442500 3.430 12 organic_carbon_percentage_10cm 4 0 [-0.36,0.4] -0.36 0.40 0.8183086 NA FALSE 0.0331268
Amendments: Position Measures and Median Comparisons with the ‘none’ category.
factor mean median N explained observedUIDsY observedUIDs HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 3.018037 2.67 107 organic_carbon_percentage_10cm 32 32 [2.77,3.18] 2.77 3.18 0.0234882 2.989943 TRUE NA
synth_fertilizer 4.039211 2.96 114 organic_carbon_percentage_10cm 0 38 [0,0.5] 0.00 0.50 0.9003100 NA FALSE 0.2645370
organic_amendment 3.511765 3.51 68 organic_carbon_percentage_10cm 0 20 [0.24,0.89] 0.24 0.89 0.2195347 NA TRUE 0.6099816

3.8.2 Density Variation on Certain Percentiles

On this tables, we attempt to find interesting patterns to explain atypicals and hopefully all variance for a given variable.

We’ve already looked at these tables in detail on the Quality Relationships brief for produce: we are comparing how frequent is to find a certain quality for the full dataset and for a certain quantile, implying that if a certain attribute is more usual between the points on an extreme, it is worth checking if it is influential over the variable and explains the outlyingness of some values.

Presence on the Last Decile for Every Practice
factor frequency[0.9,1] total[0.9,1] frequency[0,1] total[0,1] reason
seed_treatment.biological 0.75 9 0.2777778 30 2.7000000
amendments.synth_fertilizer 0.75 9 0.3055556 33 2.4545455
tillage.light_tillage 0.75 9 0.4814815 52 1.5576923
regenerative 1.00 12 0.7037037 76 1.4210526
companion_cropping.none 0.75 9 0.5462963 59 1.3728814
amendments.organic_amendment 0.25 3 0.1944444 21 1.2857143
transitioning 1.00 12 0.8333333 90 1.2000000
land_prep.tillage 1.00 12 0.8425926 91 1.1868132
organic 1.00 12 0.8703704 94 1.1489362
covercrops 0.25 3 0.2592593 28 0.9642857
tillage.heavy_tillage 0.25 3 0.3611111 39 0.6923077
companion_cropping.used 0.25 3 0.4537037 49 0.5510204
seed_treatment.none 0.25 3 0.5740741 62 0.4354839
none 0.00 0 0.0555556 6 0.0000000
certified_organic 0.00 0 0.0277778 3 0.0000000
amendments.none 0.00 0 0.5000000 54 0.0000000
seed_treatment.fungicide 0.00 0 0.0277778 3 0.0000000
Presence on the Last Quartile for Every Practice
factor frequency[0.75,1] total[0.75,1] frequency[0,1] total[0,1] reason
certified_organic 0.1071429 3 0.0277778 3 3.8571429
companion_cropping.used 0.6785714 19 0.4537037 49 1.4956268
tillage.light_tillage 0.6428571 18 0.4814815 52 1.3351648
seed_treatment.biological 0.3214286 9 0.2777778 30 1.1571429
amendments.none 0.5714286 16 0.5000000 54 1.1428571
land_prep.tillage 0.8928571 25 0.8425926 91 1.0596546
amendments.synth_fertilizer 0.3214286 9 0.3055556 33 1.0519481
transitioning 0.8571429 24 0.8333333 90 1.0285714
organic 0.8928571 25 0.8703704 94 1.0258359
covercrops 0.2500000 7 0.2592593 28 0.9642857
regenerative 0.6428571 18 0.7037037 76 0.9135338
seed_treatment.none 0.4642857 13 0.5740741 62 0.8087558
tillage.heavy_tillage 0.2500000 7 0.3611111 39 0.6923077
companion_cropping.none 0.3214286 9 0.5462963 59 0.5883777
amendments.organic_amendment 0.1071429 3 0.1944444 21 0.5510204
none 0.0000000 0 0.0555556 6 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0277778 3 0.0000000
Presence on the Worst 15% for Every Practice
factor frequency[0,0.15] total[0,0.15] frequency[0,1] total[0,1] reason
seed_treatment.biological 0.5294118 9 0.2777778 30 1.9058824
amendments.synth_fertilizer 0.5294118 9 0.3055556 33 1.7326203
companion_cropping.none 0.8235294 14 0.5462963 59 1.5074776
transitioning 1.0000000 17 0.8333333 90 1.2000000
regenerative 0.8235294 14 0.7037037 76 1.1702786
organic 1.0000000 17 0.8703704 94 1.1489362
tillage.light_tillage 0.4705882 8 0.4814815 52 0.9773756
tillage.heavy_tillage 0.3529412 6 0.3611111 39 0.9773756
land_prep.tillage 0.8235294 14 0.8425926 91 0.9773756
amendments.organic_amendment 0.1764706 3 0.1944444 21 0.9075630
seed_treatment.none 0.4705882 8 0.5740741 62 0.8197343
covercrops 0.1764706 3 0.2592593 28 0.6806723
amendments.none 0.2941176 5 0.5000000 54 0.5882353
companion_cropping.used 0.1764706 3 0.4537037 49 0.3889556
none 0.0000000 0 0.0555556 6 0.0000000
certified_organic 0.0000000 0 0.0277778 3 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0277778 3 0.0000000

3.9 Quality Replationships for Soil Carbon Mass Percentage at 20cm

3.9.1 Median Shifts

Farm Practices: Position Measures and Median Comparisons with the ‘none’ category
factor mean median N explained observedUIDs observedUIDsY HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 3.113380 2.88 71 organic_carbon_percentage_20cm 23 23 [2.88,3.33] 2.88 3.33 0.0939950 3.129989 TRUE NA
covercrops 2.677439 2.28 82 organic_carbon_percentage_20cm 22 0 [-0.79,-0.33] -0.79 -0.33 0.6434301 NA TRUE -0.5399155
organic 3.190930 2.19 172 organic_carbon_percentage_20cm 53 0 [-0.84,-0.44] -0.84 -0.44 0.7580231 NA TRUE -0.6499866
regenerative 3.244789 2.08 142 organic_carbon_percentage_20cm 46 0 [-0.96,-0.54] -0.96 -0.54 0.7067584 NA TRUE -0.7400067
transitioning 3.129357 2.16 171 organic_carbon_percentage_20cm 51 0 [-0.84,-0.46] -0.84 -0.46 0.6247533 NA TRUE -0.6699494
certified_organic 4.020000 3.25 12 organic_carbon_percentage_20cm 4 0 [0.09,0.91] 0.09 0.91 0.5382758 NA TRUE 0.5900220
Amendments: Position Measures and Median Comparisons with the ‘none’ category.
factor mean median N explained observedUIDsY observedUIDs HL Interval Medians Shift intervalMin intervalMax p.value HL Estimate isRelevant HL Median Shift Estimate
none 2.863727 2.500 110 organic_carbon_percentage_20cm 33 33 [2.59,2.97] 2.59 2.97 0.0103802 2.784971 TRUE NA
synth_fertilizer 3.624474 2.455 114 organic_carbon_percentage_20cm 0 38 [-0.33,0.16] -0.33 0.16 0.7112157 NA FALSE -0.0900485
organic_amendment 3.186812 3.020 69 organic_carbon_percentage_20cm 0 21 [0.02,0.7] 0.02 0.70 0.3714700 NA TRUE 0.3400368

3.9.2 Density Variation on Certain Percentiles

On this tables, we attempt to find interesting patterns to explain atypicals and hopefully all variance for a given variable.

We’ve already looked at these tables in detail on the Quality Relationships brief for produce: we are comparing how frequent is to find a certain quality for the full dataset and for a certain quantile, implying that if a certain attribute is more usual between the points on an extreme, it is worth checking if it is influential over the variable and explains the outlyingness of some values.

Presence on the Last Decile for Every Practice
factor frequency[0.9,1] total[0.9,1] frequency[0,1] total[0,1] reason
seed_treatment.biological 0.9230769 12 0.2972973 33 3.1048951
amendments.synth_fertilizer 0.9230769 12 0.3243243 36 2.8461538
tillage.light_tillage 0.9230769 12 0.4684685 52 1.9704142
companion_cropping.none 0.9230769 12 0.5585586 62 1.6526055
regenerative 1.0000000 13 0.7117117 79 1.4050633
transitioning 1.0000000 13 0.8378378 93 1.1935484
land_prep.tillage 1.0000000 13 0.8468468 94 1.1808511
organic 1.0000000 13 0.8738739 97 1.1443299
amendments.organic_amendment 0.0769231 1 0.1891892 21 0.4065934
covercrops 0.0769231 1 0.2522523 28 0.3049451
tillage.heavy_tillage 0.0769231 1 0.3783784 42 0.2032967
companion_cropping.used 0.0769231 1 0.4414414 49 0.1742543
seed_treatment.none 0.0769231 1 0.5585586 62 0.1377171
none 0.0000000 0 0.0540541 6 0.0000000
certified_organic 0.0000000 0 0.0270270 3 0.0000000
amendments.none 0.0000000 0 0.4864865 54 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0270270 3 0.0000000
Presence on the Last Quartile for Every Practice
factor frequency[0.75,1] total[0.75,1] frequency[0,1] total[0,1] reason
tillage.light_tillage 0.7586207 22 0.4684685 52 1.6193634
seed_treatment.biological 0.4137931 12 0.2972973 33 1.3918495
amendments.synth_fertilizer 0.4137931 12 0.3243243 36 1.2758621
transitioning 0.9655172 28 0.8378378 93 1.1523915
companion_cropping.used 0.4827586 14 0.4414414 49 1.0935961
land_prep.tillage 0.8965517 26 0.8468468 94 1.0586941
organic 0.8965517 26 0.8738739 97 1.0259509
companion_cropping.none 0.5172414 15 0.5585586 62 0.9260289
amendments.none 0.4482759 13 0.4864865 54 0.9214559
regenerative 0.6206897 18 0.7117117 79 0.8721082
amendments.organic_amendment 0.1379310 4 0.1891892 21 0.7290640
seed_treatment.none 0.3793103 11 0.5585586 62 0.6790879
covercrops 0.1379310 4 0.2522523 28 0.5467980
tillage.heavy_tillage 0.1379310 4 0.3783784 42 0.3645320
none 0.0000000 0 0.0540541 6 0.0000000
certified_organic 0.0000000 0 0.0270270 3 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0270270 3 0.0000000
Presence on the Worst 15% for Every Practice
factor frequency[0,0.15] total[0,0.15] frequency[0,1] total[0,1] reason
seed_treatment.biological 0.4705882 8 0.2972973 33 1.5828877
companion_cropping.none 0.8235294 14 0.5585586 62 1.4743833
amendments.synth_fertilizer 0.4705882 8 0.3243243 36 1.4509804
regenerative 1.0000000 17 0.7117117 79 1.4050633
tillage.heavy_tillage 0.4705882 8 0.3783784 42 1.2436975
transitioning 1.0000000 17 0.8378378 93 1.1935484
organic 1.0000000 17 0.8738739 97 1.1443299
land_prep.tillage 0.8235294 14 0.8468468 94 0.9724656
seed_treatment.none 0.5294118 9 0.5585586 62 0.9478178
amendments.organic_amendment 0.1764706 3 0.1891892 21 0.9327731
tillage.light_tillage 0.3529412 6 0.4684685 52 0.7533937
amendments.none 0.3529412 6 0.4864865 54 0.7254902
covercrops 0.1764706 3 0.2522523 28 0.6995798
companion_cropping.used 0.1764706 3 0.4414414 49 0.3997599
none 0.0000000 0 0.0540541 6 0.0000000
certified_organic 0.0000000 0 0.0270270 3 0.0000000
seed_treatment.fungicide 0.0000000 0 0.0270270 3 0.0000000

4 Predicting Soil Organic Carbon Content

In an attempt of having as much reassurance as possible, both Linear Models and Random Forest Models have been trained for this experiment.

As it is to be expected when mixing diverse sets of variables which can’t be expected to seek for an intrinsical mathematical model such as a physical equation, random forest yields an increase in precission.

The behaviour of this increase in observed precission points to future enquiry paths about the informing power of each variable, especially considering the most powerful model replaces the 10 bionutrient meter scan variables by just climateRegion achieving an apparent improvement. This result is probably the result of an overfit over the climate region and probably shouldn’t be considered relevant. I wouldn’t attribute this to a mathematical overfit, but to an under representation of the internal variance of each climatic region, so a further check is also seeing how many actual locations represent each climatic region and how far from each other they are.

Overall, the prediction seems feasible but probably requires some further variables to be useful, besides the checks we considered above.

This experiment will without doubt benefit from a comparison with all the other soil samples we have, even considering that crop as factor for sure has a high influence on the results both a as a consequence of the physiological action of each species on it and because it is to be expected that the crop has been chosen because of preexisting qualities of the soil.

A proposed strategy to face the possible overfit over regions is to clusterize the residulas/actual vs. predicted plots and search for evident clusters.

4.1 Grain Soils

datasets composition
1-10cm 2-10cm 3-10cm 4-10cm 5-10cm 6-10cm 7-10cm 1-20cm 2-20cm 3-20cm 4-20cm 5-20cm 6-20cm 7-20cm
bionutrientMeter10cm bionutrientMeter10cm, scsMetadata10cm bionutrientMeter10cm, climateRegion, medFarmPractices bionutrientMeter10cm, scsMetadata10cm, climateRegion, medFarmPractices scsMetadata10cm, climateRegion, medFarmPractices scsMetadata10cm, climateRegion, medFarmPractices, PH_soil_10cm, respiration_soil_10cm scsMetadata10cm, scsMetadata20cm, climateRegion, medFarmPractices, PH_soil_10cm, PH_soil_20cm, respiration_soil_10cm, respiration_soil_20cm bionutrientMeter20cm bionutrientMeter20cm, scsMetadata20cm bionutrientMeter20cm, climateRegion, medFarmPractices bionutrientMeter20cm, scsMetadata20cm, climateRegion, medFarmPractices scsMetadata20cm, climateRegion, medFarmPractices, respiration_soil_20cm scsMetadata20cm, climateRegion, medFarmPractices, PH_soil_20cm scsMetadata10cm, scsMetadata20cm, climateRegion, medFarmPractices, PH_soil_10cm, PH_soil_20cm, respiration_soil_10cm, respiration_soil_20cm

4.2 Soil Models for All Crops

4.2.1 Organic content percentage at 10cm, model ‘2-10cm’

  • Saved as ./graphics/grainSoilHealRegressionModel210cm.png.

4.3 Depth as a variable

datasets composition
1-10cm 2-10cm 3-10cm 4-10cm 5-10cm 6-10cm 7-10cm
bionutrientMeter bionutrientMeter, scsMetadata bionutrientMeter, climateRegion, medFarmPractices bionutrientMeter, scsMetadata, climateRegion, medFarmPractices scsMetadata, climateRegion, medFarmPractices scsMetadata, climateRegion, medFarmPractices, PH_soil bionutrientMeter, scsMetadata, climateRegion, medFarmPractices, PH_soil

5 Agnostic on Depth Soil Model Review