aggregate chapter graphs
James Lin
3/30/2021
Set up
1) Load packages
2) Import data
3) Data Wrangling
4) Theme James
20 min Aggregate Graphs
Aggregate function
0-5 cm 20 minutes
5-10 cm 20 minutes
10-15 cm 20 minutes
15-25 cm 20 minutes
5 min Aggregate Graphs
Aggregate function
0-5 cm 5 minutes
5-10 cm 20 minutes
10-15 cm 20 minutes
15-25 cm 20 minutes
NRCS Aggregate Graphs
Aggregate function
0-5 cm 5 minutes
5-10 cm 20 minutes
10-15 cm 20 minutes
15-25 cm 20 minutes
Methods Comparison
20mwd and 5mwd Scatter plots
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## Warning: Removed 82 rows containing non-finite values (stat_smooth).## Warning: Removed 82 rows containing missing values (geom_point).
## Warning: Removed 82 rows containing non-finite values (stat_smooth).
## Warning: Removed 82 rows containing missing values (geom_point).
dont need for 20 mwd and 5 mwd #```{r} #Don’t need
#one graph group by treatment
#soils %>% ggplot(aes(x=x20mwd, y= x5mwd, color=treatment, shape=treatment))+ geom_point(size=1)+ labs(x=“20 minute method”, y=“5 minute method”, title=“Correlation between 20 minute Mean Weight Diameter vs 5 minute MWD”) + theme_classic()+ geom_smooth(method=“lm”, se=FALSE)
#group by treatment
#soils %>% ggplot(aes(x=x20mwd, y= x5mwd))+ facet_wrap(~treatment)+ labs(x=“20 minute method”, y=“5 minute method”, title=“Correlation between 20 minute Mean Weight Diameter vs 5 minute MWD”) + theme_classic()+ geom_smooth(method=“lm”, se=FALSE, color= “black”) + geom_point(size=.5)
#group by horizon
#soils %>% ggplot(aes(x=x20mwd, y= x5mwd))+ facet_wrap(~horizon)+ labs(x=“20 minute method”, y=“5 minute method”, title=“Correlation between 20 minute Mean Weight Diameter vs 5 minute MWD”) + theme_classic()+ geom_smooth(method=“lm”, se=FALSE, color= “black”) + geom_point(size=.5)
## 20mwd and NRCS Scatter plots
Warning: Removed 27 rows containing non-finite values (stat_smooth).
Warning: Removed 27 rows containing missing values (geom_point).
<img src="version-2-nrcs-agg-graphs_files/figure-html/unnamed-chunk-21-1.png" width="672" />
Warning: Removed 27 rows containing non-finite values (stat_smooth).
Warning: Removed 27 rows containing missing values (geom_point).
<img src="version-2-nrcs-agg-graphs_files/figure-html/unnamed-chunk-21-2.png" width="672" />
Warning: Removed 27 rows containing non-finite values (stat_smooth).
Warning: Removed 27 rows containing missing values (geom_point).
<img src="version-2-nrcs-agg-graphs_files/figure-html/unnamed-chunk-21-3.png" width="672" />
Dont need - 20 mwd and nrcs
#```{r}
#one graph group by treatment
soils %>%
ggplot(aes(x=x20mwd, y= nagg, color=treatment, shape=treatment))+
geom_point(size=1)+
labs(x="20 minute method",
y="NRCS hand method",
title="Correlation between 20 minute Mean Weight Diameter vs NRCS Hand Method") +
theme_classic()+
geom_smooth(method="lm", se=FALSE)
#group by treatment
soils %>%
ggplot(aes(x=x20mwd, y= nagg))+
facet_wrap(~treatment)+
labs(x="20 minute method",
y="NRCS hand method",
title="Correlation between 20 minute Mean Weight Diameter vs NRCS Hand Method") +
theme_classic()+
geom_smooth(method="lm", se=FALSE, color= "black") +
geom_point(size=.5)
#group by horizon
soils %>%
ggplot(aes(x=x20mwd, y= nagg))+
facet_wrap(~horizon)+
labs(x="20 minute method",
y="NRCS hand method",
title="Correlation between 20 minute Mean Weight Diameter vs NRCS Hand Method") +
theme_classic()+
geom_smooth(method="lm", se=FALSE, color= "black") +
geom_point(size=.5)MWD Bland-Altman plots
## Warning: package 'BlandAltmanLeh' was built under R version 4.0.4## Warning: Removed 27 rows containing missing values (geom_point).
## Warning in plot.window(...): "na.rm" is not a graphical parameter## Warning in plot.xy(xy, type, ...): "na.rm" is not a graphical parameter## Warning in axis(side = side, at = at, labels = labels, ...): "na.rm" is not a
## graphical parameter
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## NULL## Warning: Removed 82 rows containing missing values (geom_point).
## NULL##
## Call:
## lm(formula = x5mwd ~ x20mwd, data = soils)
##
## Residuals:
## Min 1Q Median 3Q Max
## -1.80093 -0.29022 -0.04859 0.24176 1.69966
##
## Coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) 0.47061 0.08500 5.537 1.44e-07 ***
## x20mwd 0.77571 0.07821 9.918 < 2e-16 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Residual standard error: 0.5337 on 142 degrees of freedom
## (82 observations deleted due to missingness)
## Multiple R-squared: 0.4092, Adjusted R-squared: 0.4051
## F-statistic: 98.37 on 1 and 142 DF, p-value: < 2.2e-16