.row[ .col-7[ .title[ ###Duke Farms Soil Organic Carbon Study. ] .subtitle[ #### <span style="color: red;">Duke Fields - Impact of land use and soil series on soil carbon stock</span> ##### Project update, 12 April 2021 ] .author[ ##### Daniel Gimenez, Professor.<br/>Stephanie Murphy, Dr.<br/>Ewan Oleghe, Dr. ] .affiliation[ ##### Department of Environmental Sciences <br> Rutgers, The State University of New Jersey ] ] .col-5[ .logo[ <!-- --> ] <br> <br> --- Slides:<br> 31 slides Data set:<br> [**CLICK HERE TO DOWNLOAD**](https://ewanoleghe.github.io/science/Data.txt) ] ] --- class: center, middle ### Part 1: Sampling --- ##### 1.1. Field Sampling -- ###### 1.1.1.) ... landuse <img src="map/df.png" width="70%" /> --- ###### 1.1.2.) ... and soil series <img src="map/sk1.png" width="75%" /> --- ##### 1.2.) ... using a grid <img src="map/sk2.png" width="70%" /> --- ###### 1.2.1.) ... with reular equalateral triangular spacing <img src="map/skeet.png" width="70%" /> Example: Shows 30 meters triangular sampling point laid over different soil series within a grid. --- ##### 1.2.2.) ... and random sampling <img src="map/sk2.png" width="70%" /> --- class: center, middle ### Part 2. Summary & Statistics --- ##### 2.1.) Total number of samples. ###### 2.1.1.) Grid sampling (Spatial dstribution of soil organic carbon) Landuse | n |<- | | Soil|series | | ->|Total ------------|-----|------|------|------|-------|------|------|------ | | PeoC | PenB |KkoC |KkoD |PeoB | RehB | Agriculture |333 |32 | 140 |143 |18 | - | - |333 Grassland |443 |56 | 201 |186 | - | - | - |443 Forest |206 | - | - | - | - |97 |109 |206 | Total |982 | - | - | - | - | - | - |982 -- ###### 2.1.2.) Random sampling (Vertical dstribution of soil organic carbon) Landuse | n |<-Soil|series| -> |Total ------------|-----|------|------|------|------- | | PeoC | PenB |KkoC | Agriculture |136 |41 | 44 |51 |136 Grassland |140 |42 | 45 |53 |140 Wetlands |60 | - | - | - |60 | Total |336 | - | - | - |336 --- ##### 2.2.) Grid sampling - Summary statistics ###### (2.2.1.) Grassland - Skeet shoot field ###### **Table 1:** Descriptive statistics of soil organic C (Total_C) concentration, nitrogen concentration (Total_N), and organic matter (OM). Values are based on n = 150 samples. Soil properties represent the top 15 cm of Duke Farm's grassland (skeet shoot field) soil. <!-- <font size="-2"> --> | | | | N | | | | | C | | | | | OM | | ------------|-----|------|---------|------|-----------------|--|------|--------|-----|------------------|--|-----|--------|-----|------- Soil series | n | Min | Median | Max | Mean | |Min | Median | Max | Mean | |Min | Median | Max | Mean KkoC |60 |0.108 | 0.170 |0.227 |0.172<sup>a</sup>| |0.975 |1.684 |2.360|1.673<sup>a </sup>| |1.681| 2.903 |4.069|2.885<sup>a</sup> PenB |65 |0.094 | 0.161 |0.310 |0.161<sup>a</sup>| |0.767 |1.556 |3.251|1.591<sup>a </sup>| |1.322| 2.683 |5.605|2.744<sup>a</sup> PeoC |25 |0.099 | 0.141 |0.189 |0.144<sup>b</sup>| |0.853 |1.364 |1.849|1.347<sup>b </sup>| |1.471| 2.352 |3.188|2.323<sup>b</sup> where N = Total Nitrogen, C = Total Carbon and OM = organic matter <!-- </font> --> --- ###### (2.2.2.) Agriculture - Grazed field ###### **Table 2:** Descriptive statistics of soil organic C (Total_C) concentration, nitrogen concentration (Total_N), and organic matter (OM). Values are based on n = 150 samples. Soil properties represent the top 15 cm of Duke Farm's agriculture (grazed field) soil | | | |N | | | | | C | | | | | OM | | ------------|-----|------|---------|------|-------|--|-----|--------|-----|-------|--|-----|--------|-----|------- Soil series | n | Min | Median | Max | Mean | |Min | Median | Max | Mean | |Min | Median | Max | Mean KkoC |25 |0.100 | 0.180 |0.310 |0.188 | |0.990|1.800 |3.120|1.874 | |1.700| 3.100 |5.380|3.220 KkoD |13 |0.130 | 0.220 |0.390 |0.231 | |1.240|2.180 |4.050|2.317 | |2.140| 3.760 |6.970|3.992 PenB |36 |0.060 | 0.205 |0.310 |0.192 | |0.250|2.150 |3.520|1.952 | |0.420| 3.705 |6.070|3.366 PeoC |26 |0.120 | 0.210 |0.390 |0.218 | |1.260|2.090 |3.800|2.199 | |2.170| 3.600 |6.540|3.790 where N = Total Nitrogen, C = Total Carbon and OM = organic matter --- ###### (2.2.3.) Forest ###### **Table 3:** Descriptive statistics of soil organic C (Total_C) concentration, nitrogen concentration (Total_N), and organic matter (OM). Values are based on the 1st sample set (n = 50). Soil properties represent the top 15 cm of Duke Farm's agriculture (xxxx forest) soil | | | |N | | | | | C | | | | | OM | | ------------|-----|------|---------|------|-------|--|-----|--------|-----|-------|--|-----|--------|------|------- Soil series | n | Min | Median | Max | Mean | |Min | Median | Max | Mean | |Min | Median | Max | Mean PeoB |21 |0.082 | 0.266 |0.496 |0.272 | |0.897|3.739 |7.422|3.986 | |1.547| 6.447 |12.797|6.872 RehB |29 |0.055 | 0.259 |0.430 |0.246 | |0.429|3.654 |6.696|3.482 | |0.740| 6.300 |11.545|6.004 where N = Total Nitrogen, C = Total Carbon and OM = organic matter --- ###### **Table 2:** Analysis of variance for soil organic C (Total_C) concentration, nitrogen concentration (Total_N), and organic matter (OM) for Duke Farm's grassland (skeet shoot field) soil n = 150. Parameters| |df |Sum Sq|Mean Sq|F value|Pr(>F) ----------|----------|----|------|-------|-------|------- Total_C |S_Series |2 |1.881 | 0.940 |7.492 |0.001*** | |Residuals |147 |18.450| 0.126 |- |- | Total_N |S_Series |2 |0.014 |0.007 |7.481 |0.001*** | |Residuals |147 |0.137 |0.001 |- | - | OM |S_Series |2 |5.590 |2.795 |7.492 |0.001*** | |Residuals |147 |54.845|0.373 |- | - --- ###### 2.3.) Grassland - Skeet shoot field **ANOVA of sampling distance and soil effects on Total_C:** ``` ## Df Sum Sq Mean Sq F value Pr(>F) ## distance 2 0.286 0.1428 1.200 0.304345 ## S_Series 2 1.969 0.9843 8.271 0.000401 *** ## distance:S_Series 4 1.296 0.3239 2.722 0.031969 * ## Residuals 141 16.781 0.1190 ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ``` ###### 2.4.) Grassland - Skeet shoot field **ANOVA for soil series:** ``` ## Df Sum Sq Mean Sq F value Pr(>F) ## S_Series 2 1.881 0.9403 7.492 0.000798 *** ## Residuals 147 18.450 0.1255 ## --- ## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 ``` --- ###### 2.5.) Grassland - Skeet shoot field **POSTHOC TEST:** .pull-left[ ``` ## ## Study: IMPACT OF SOIL SERIES ON CARBON CONTENT ## ## HSD Test for Total_C ## ## Mean Square Error: 0.1190116 ## ## S_Series, means ## ## Total_C std r Min Max ## KkoC 1.673217 0.3278467 60 0.975 2.360 ## PenB 1.591369 0.4033851 65 0.767 3.251 ## PeoC 1.347400 0.2657072 25 0.853 1.849 ## ## Alpha: 0.05 ; DF Error: 141 ## Critical Value of Studentized Range: 3.349881 ## ## Groups according to probability of means differences and alpha level( 0.05 ) ## ## Treatments with the same letter are not significantly different. ## ## Total_C groups ## KkoC 1.673217 a ## PenB 1.591369 a ## PeoC 1.347400 b ``` ] .pull-right[ ###### b.) Soil series: **Mean ranking - Grassland** <!-- --> ] --- ###### 2.6.) Spatial plot of soil organic carbon concentration .pull-left[ ##### Grassland <!-- --> ] .pull-right[ ##### Agriculture <!-- --> ] --- class: center, middle ### Part 3. Spatial Study --- ###### 3.1.) **Compute undirected (isotropic) empirical semivariogram** ###### 3.1a.) R codes to calculation number of pairs for undirected (isotropic) empirical semivariogram ````markdown ```{r setup, include=FALSE} # Group by landuse - subset skeetSub = subset(mData, landuse== "Grassland"); grazedSub = subset(mData, landuse== "Agriculture"); *library(gstat) *var1 <- variogram(Total_C ~ 1, ~x.axis + y.axis, cutoff = 480, width = 55, data = skeetSub) *var2 <- variogram(Total_C ~ 1, ~x.axis + y.axis, cutoff = 480, width = 55, data = grazedSub) ``` --- ###### 3.1b.) **Compute undirected (isotropic) empirical semivariogram** .pull-left[ ###### Grassland <!-- --> ] .pull-right[ ##### Agriculture <!-- --> ] ###### **Figure 1:** Undirected semivariogram of Total_C for Grassland and Agriculture fields. --- ###### 3.2.) compute semivariogram model based on the empiral semivariogram** ###### 3.2a.) show nugget, psill and range of the semivariogram (EXP) model .pull-left[ ###### Grassland ``` ## model psill range ## 1 Nug 0.03152633 0.00000 ## 2 Exp 0.11313418 23.47788 ``` ###### (weighted) sum of squared errors of the fitted model ``` ## [1] 3.25204 ``` ] .pull-right[ ###### Agriculture ``` ## model psill range ## 1 Nug 0.09366273 0.00000 ## 2 Exp 0.34809411 39.03366 ``` ###### (weighted) sum of squared errors of the fitted model ``` ## [1] 4.962368 ``` ] --- <!-- --- #fit plot --> ###### 3.3.) Fit of theoretical semivariograms to those empirical semivariograms .pull-left[ ###### Grassland <!-- --> ] .pull-right[ ###### Agriculture -replace with grazed <!-- --> ] --- <!-- CONVERT THE DATAFRAME TO SPATIAL POINTS --> <!-- --- # Create Kriging map for experimental area --> ###### 3.4.) Scatterplot plot of total carbon concentration .pull-left[ ###### Grassland <!-- --> ] .pull-right[ ###### Agriculture <!-- --> ] ``` ## [using ordinary kriging] ``` ``` ## [using ordinary kriging] ``` --- ###### 3.5.) Kriging & Predict carbon content for each field ###### 3.5a.) using ordinary kriging .pull-left[ ###### Grassland <!-- --> ] .pull-right[ ###### Agriculture <!-- --> ] --- class: center, middle ### Part 4. Elevation & Maps --- ###### 4.1.) **Relationship between elevation and total organic carbon** .pull-left[ ###### Grassland <!-- --> ] .pull-right[ ##### Agriculture <!-- --> ] --- ###### 4.2.) **Relationship between elevation and total nitrogen** .pull-left[ ###### Grassland <!-- --> ] .pull-right[ ##### Agriculture <!-- --> ] --- ###### 4.3.) **Relationship between elevation and organic matter** .pull-left[ ###### Grassland <!-- --> ] .pull-right[ ##### Agriculture <!-- --> ] --- ###### Map: Grassland <!-- # EXTRACT POINTS EITH ELEVATION DATA --> <div id="htmlwidget-ea1158703cd21b32f2d9" style="width:1008px;height:540px;" class="leaflet html-widget"></div> <script type="application/json" 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That's all for today