fishdrought.tex

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\hypersetup{
  pdftitle={Fish multi-yeardrought},
  pdfauthor={Rosemary Hartman},
  hidelinks,
  pdfcreator={LaTeX via pandoc}}

\title{Fish multi-yeardrought}
\author{Rosemary Hartman}
\date{2023-01-17}

\begin{document}
\maketitle

\hypertarget{fish---multiple-drought-years}{%
\subsection{Fish - multiple drought
years}\label{fish---multiple-drought-years}}

I categorized drought years into year `0' (wet years), `1' (single dry
year or first year of drought), `2' (Second year of drought) and `3+'
(third or more year of drought. )

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-1-1.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-1-2.pdf}

Then I ran statistics. For POD species i included both ``year of
drought'' and ``year'' to account for changes over time.

\hypertarget{first-striped-bass}{%
\subsubsection{First, striped bass}\label{first-striped-bass}}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{SB }\OtherTok{=} \FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"logSB"}\NormalTok{)}
\NormalTok{FD1 }\OtherTok{=} \FunctionTok{lm}\NormalTok{(Value }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear }\SpecialCharTok{+}\NormalTok{ Year, }\AttributeTok{data =}\NormalTok{ SB)}
\FunctionTok{summary}\NormalTok{(FD1)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## 
## Call:
## lm(formula = Value ~ DroughtYear + Year, data = SB)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -1.45583 -0.53370  0.06044  0.51148  1.50960 
## 
## Coefficients:
##                 Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   187.693029  14.387779  13.045  < 2e-16 ***
## DroughtYear1   -0.554860   0.263277  -2.108  0.04055 *  
## DroughtYear2   -1.126090   0.343270  -3.280  0.00198 ** 
## DroughtYear3+  -0.655741   0.292645  -2.241  0.02991 *  
## Year           -0.090656   0.007222 -12.554  < 2e-16 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.7344 on 46 degrees of freedom
##   (2 observations deleted due to missingness)
## Multiple R-squared:  0.8263, Adjusted R-squared:  0.8112 
## F-statistic: 54.72 on 4 and 46 DF,  p-value: < 2.2e-16
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{plot}\NormalTok{(FD1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-2-1.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-2-2.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-2-3.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-2-4.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{emmeans}\NormalTok{(FD1, pairwise }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## $emmeans
##  DroughtYear emmean    SE df lower.CL upper.CL
##  0             6.67 0.157 46     6.36     6.99
##  1             6.12 0.212 46     5.69     6.55
##  2             5.55 0.302 46     4.94     6.16
##  3+            6.02 0.239 46     5.54     6.50
## 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast estimate    SE df t.ratio p.value
##  0 - 1       0.555 0.263 46   2.108  0.1660
##  0 - 2       1.126 0.343 46   3.280  0.0103
##  0 - (3+)    0.656 0.293 46   2.241  0.1275
##  1 - 2       0.571 0.369 46   1.548  0.4180
##  1 - (3+)    0.101 0.320 46   0.315  0.9890
##  2 - (3+)   -0.470 0.380 46  -1.238  0.6064
## 
## P value adjustment: tukey method for comparing a family of 4 estimates
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{visreg}\NormalTok{(FD1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-2-5.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-2-6.pdf}
So, droughts are bad, but long droughts aren't much worse than short
ones after accounting for long-term population trajectory

\hypertarget{now-longfin-smelt}{%
\subsubsection{Now longfin smelt}\label{now-longfin-smelt}}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{LFS }\OtherTok{=} \FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"logLFS"}\NormalTok{)}
\NormalTok{LFS1 }\OtherTok{=} \FunctionTok{lm}\NormalTok{(Value }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear }\SpecialCharTok{+}\NormalTok{ Year, }\AttributeTok{data =}\NormalTok{ LFS)}
\FunctionTok{summary}\NormalTok{(LFS1)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## 
## Call:
## lm(formula = Value ~ DroughtYear + Year, data = LFS)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -2.26460 -0.79994  0.05845  0.79698  3.05904 
## 
## Coefficients:
##                Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   163.27414   23.36338   6.988 9.48e-09 ***
## DroughtYear1   -2.01296    0.42752  -4.708 2.32e-05 ***
## DroughtYear2   -1.43022    0.55741  -2.566   0.0136 *  
## DroughtYear3+  -2.59382    0.47521  -5.458 1.86e-06 ***
## Year           -0.07801    0.01173  -6.652 3.03e-08 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.193 on 46 degrees of freedom
##   (2 observations deleted due to missingness)
## Multiple R-squared:  0.7207, Adjusted R-squared:  0.6964 
## F-statistic: 29.67 on 4 and 46 DF,  p-value: 3.196e-12
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{plot}\NormalTok{(LFS1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-3-1.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-3-2.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-3-3.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-3-4.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{emmeans}\NormalTok{(LFS1, pairwise }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## $emmeans
##  DroughtYear emmean    SE df lower.CL upper.CL
##  0             7.50 0.254 46     6.99     8.02
##  1             5.49 0.344 46     4.80     6.18
##  2             6.07 0.490 46     5.09     7.06
##  3+            4.91 0.389 46     4.13     5.69
## 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast estimate    SE df t.ratio p.value
##  0 - 1       2.013 0.428 46   4.708  0.0001
##  0 - 2       1.430 0.557 46   2.566  0.0631
##  0 - (3+)    2.594 0.475 46   5.458  <.0001
##  1 - 2      -0.583 0.599 46  -0.972  0.7657
##  1 - (3+)    0.581 0.520 46   1.117  0.6810
##  2 - (3+)    1.164 0.617 46   1.886  0.2482
## 
## P value adjustment: tukey method for comparing a family of 4 estimates
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{visreg}\NormalTok{(LFS1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-3-5.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-3-6.pdf}

Again, droughts are bad, but long droughts aren't much worse than short
ones after accounting for long-term population trajectory

\hypertarget{delta-smelt}{%
\subsubsection{Delta Smelt}\label{delta-smelt}}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{DS }\OtherTok{=} \FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"logDS"}\NormalTok{)}
\NormalTok{DS1 }\OtherTok{=} \FunctionTok{lm}\NormalTok{(Value }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear }\SpecialCharTok{+}\NormalTok{ Year, }\AttributeTok{data =}\NormalTok{ DS)}
\FunctionTok{summary}\NormalTok{(DS1)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## 
## Call:
## lm(formula = Value ~ DroughtYear + Year, data = DS)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -2.4207 -0.7723 -0.1449  0.6740  2.6136 
## 
## Coefficients:
##                Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   234.02469   23.66651   9.888 5.81e-13 ***
## DroughtYear1   -0.69550    0.43307  -1.606    0.115    
## DroughtYear2   -0.69398    0.56465  -1.229    0.225    
## DroughtYear3+  -0.42266    0.48137  -0.878    0.384    
## Year           -0.11471    0.01188  -9.657 1.22e-12 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.208 on 46 degrees of freedom
##   (2 observations deleted due to missingness)
## Multiple R-squared:  0.716,  Adjusted R-squared:  0.6913 
## F-statistic:    29 on 4 and 46 DF,  p-value: 4.648e-12
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{plot}\NormalTok{(DS1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-4-1.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-4-2.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-4-3.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-4-4.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{visreg}\NormalTok{(DS1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-4-5.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-4-6.pdf}
Delta Smelt just don't want to behave.

\hypertarget{american-shad}{%
\subsubsection{American Shad}\label{american-shad}}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{shad }\OtherTok{=} \FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"logShad"}\NormalTok{)}
\NormalTok{shad1 }\OtherTok{=} \FunctionTok{lm}\NormalTok{(Value }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear }\SpecialCharTok{+}\NormalTok{ Year, }\AttributeTok{data =}\NormalTok{ shad)}
\FunctionTok{summary}\NormalTok{(shad1)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## 
## Call:
## lm(formula = Value ~ DroughtYear + Year, data = shad)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -2.18734 -0.62640  0.02317  0.58049  1.53875 
## 
## Coefficients:
##                Estimate Std. Error t value Pr(>|t|)   
## (Intercept)   29.282382  16.281836   1.798  0.07867 . 
## DroughtYear1  -0.999479   0.297936  -3.355  0.00160 **
## DroughtYear2  -1.240137   0.388459  -3.192  0.00254 **
## DroughtYear3+ -0.906320   0.331169  -2.737  0.00879 **
## Year          -0.010822   0.008172  -1.324  0.19196   
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.8311 on 46 degrees of freedom
##   (2 observations deleted due to missingness)
## Multiple R-squared:  0.3501, Adjusted R-squared:  0.2935 
## F-statistic: 6.194 on 4 and 46 DF,  p-value: 0.0004496
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{emmeans}\NormalTok{(shad1, pairwise }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## $emmeans
##  DroughtYear emmean    SE df lower.CL upper.CL
##  0             7.67 0.177 46     7.32     8.03
##  1             6.67 0.240 46     6.19     7.16
##  2             6.43 0.341 46     5.75     7.12
##  3+            6.77 0.271 46     6.22     7.31
## 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast estimate    SE df t.ratio p.value
##  0 - 1      0.9995 0.298 46   3.355  0.0084
##  0 - 2      1.2401 0.388 46   3.192  0.0131
##  0 - (3+)   0.9063 0.331 46   2.737  0.0422
##  1 - 2      0.2407 0.418 46   0.576  0.9387
##  1 - (3+)  -0.0932 0.362 46  -0.257  0.9940
##  2 - (3+)  -0.3338 0.430 46  -0.776  0.8648
## 
## P value adjustment: tukey method for comparing a family of 4 estimates
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{plot}\NormalTok{(shad1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-5-1.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-5-2.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-5-3.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-5-4.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{visreg}\NormalTok{(shad1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-5-5.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-5-6.pdf}
It's all about dry versus wet, not multi-year droughts

\hypertarget{now-salmon-crr}{%
\subsubsection{Now Salmon CRR}\label{now-salmon-crr}}

I calculated a mean CRR for all the runs combined. I''m not sure that's
appropriate, but I went for it. I could break them out if you don't like
it.

I wasn't quite sure if I needed Year as a predictor here, so I did a
quick plot

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{CRRs }\OtherTok{=} \FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"Salmon CRR"}\NormalTok{)}
\FunctionTok{ggplot}\NormalTok{(CRRs, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x=}\NormalTok{Year, }\AttributeTok{y =}\NormalTok{ Value))}\SpecialCharTok{+} \FunctionTok{geom\_point}\NormalTok{()}\SpecialCharTok{+} \FunctionTok{geom\_smooth}\NormalTok{()}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## `geom_smooth()` using method = 'loess' and formula = 'y ~ x'
\end{verbatim}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-6-1.pdf}

No real trend over time, so I'll skip that.

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{CRRs1 }\OtherTok{=} \FunctionTok{lm}\NormalTok{(Value }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear, }\AttributeTok{data =}\NormalTok{ CRRs)}
\FunctionTok{summary}\NormalTok{(CRRs1)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## 
## Call:
## lm(formula = Value ~ DroughtYear, data = CRRs)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -1.5045 -0.5492 -0.1386  0.2978  1.8332 
## 
## Coefficients:
##               Estimate Std. Error t value Pr(>|t|)    
## (Intercept)    1.45259    0.17898   8.116 2.75e-10 ***
## DroughtYear1  -0.02169    0.29681  -0.073    0.942    
## DroughtYear2   0.42873    0.37967   1.129    0.265    
## DroughtYear3+ -0.86769    0.32677  -2.655    0.011 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.8202 on 44 degrees of freedom
## Multiple R-squared:  0.1969, Adjusted R-squared:  0.1421 
## F-statistic: 3.595 on 3 and 44 DF,  p-value: 0.02079
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{plot}\NormalTok{(CRRs1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-7-1.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-7-2.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-7-3.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-7-4.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{emmeans}\NormalTok{(CRRs1, pairwise }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## $emmeans
##  DroughtYear emmean    SE df lower.CL upper.CL
##  0            1.453 0.179 44   1.0919     1.81
##  1            1.431 0.237 44   0.9537     1.91
##  2            1.881 0.335 44   1.2065     2.56
##  3+           0.585 0.273 44   0.0339     1.14
## 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast estimate    SE df t.ratio p.value
##  0 - 1      0.0217 0.297 44   0.073  0.9999
##  0 - 2     -0.4287 0.380 44  -1.129  0.6737
##  0 - (3+)   0.8677 0.327 44   2.655  0.0518
##  1 - 2     -0.4504 0.410 44  -1.098  0.6924
##  1 - (3+)   0.8460 0.362 44   2.339  0.1046
##  2 - (3+)   1.2964 0.432 44   2.999  0.0222
## 
## P value adjustment: tukey method for comparing a family of 4 estimates
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{visreg}\NormalTok{(CRRs1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-7-5.pdf}

THree or more years of drought is REALLY bad for salmon.

\hypertarget{threadfin}{%
\subsubsection{Threadfin}\label{threadfin}}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{TFshad }\OtherTok{=} \FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"logTFS"}\NormalTok{)}
\NormalTok{TFshad1 }\OtherTok{=} \FunctionTok{lm}\NormalTok{(Value }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear }\SpecialCharTok{+}\NormalTok{ Year, }\AttributeTok{data =}\NormalTok{ TFshad)}
\FunctionTok{summary}\NormalTok{(TFshad1)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## 
## Call:
## lm(formula = Value ~ DroughtYear + Year, data = TFshad)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -2.8064 -0.6783  0.2244  0.6866  2.4686 
## 
## Coefficients:
##                Estimate Std. Error t value Pr(>|t|)    
## (Intercept)   114.01026   23.58090   4.835 1.53e-05 ***
## DroughtYear1   -0.23063    0.43150  -0.534    0.596    
## DroughtYear2   -0.39681    0.56260  -0.705    0.484    
## DroughtYear3+  -0.48075    0.47963  -1.002    0.321    
## Year           -0.05331    0.01184  -4.504 4.54e-05 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 1.204 on 46 degrees of freedom
##   (2 observations deleted due to missingness)
## Multiple R-squared:  0.3759, Adjusted R-squared:  0.3216 
## F-statistic: 6.925 on 4 and 46 DF,  p-value: 0.0001887
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{emmeans}\NormalTok{(TFshad1, pairwise }\SpecialCharTok{\textasciitilde{}}\NormalTok{ DroughtYear)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## $emmeans
##  DroughtYear emmean    SE df lower.CL upper.CL
##  0             7.56 0.257 46     7.05     8.08
##  1             7.33 0.347 46     6.63     8.03
##  2             7.17 0.495 46     6.17     8.16
##  3+            7.08 0.392 46     6.29     7.87
## 
## Confidence level used: 0.95 
## 
## $contrasts
##  contrast estimate    SE df t.ratio p.value
##  0 - 1      0.2306 0.431 46   0.534  0.9502
##  0 - 2      0.3968 0.563 46   0.705  0.8945
##  0 - (3+)   0.4807 0.480 46   1.002  0.7488
##  1 - 2      0.1662 0.605 46   0.275  0.9927
##  1 - (3+)   0.2501 0.525 46   0.477  0.9639
##  2 - (3+)   0.0839 0.623 46   0.135  0.9991
## 
## P value adjustment: tukey method for comparing a family of 4 estimates
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{plot}\NormalTok{(TFshad1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-8-1.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-8-2.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-8-3.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-8-4.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{visreg}\NormalTok{(TFshad1)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-8-5.pdf}
\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-8-6.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{\#final plot for paper}

\CommentTok{\#data frame of pairwise comparison results}
\CommentTok{\# FishDrought = droplevels(FishDrought)}
\CommentTok{\# pairs = data.frame(MetricL = rep(levels(FishDrought$MetricL), each = 4), }
\CommentTok{\#                    DroughtYear = rep(c("0", "1", "2", "3+"), 5),}
\CommentTok{\#                    Group = c("A", "B", "B", "B", "A", "A", "A", "A", "A", }
\CommentTok{\#                              "B", "B", "B", "A", "B", "B", "B",}
\CommentTok{\#                              "A", "A", "A", "B"),}
\CommentTok{\#                    Y = c(rep(10, 4), rep(8, 4), rep(12, 4), rep(10, 4), rep(4, 4)))}

\FunctionTok{ggplot}\NormalTok{(FishDrought, }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =} \FunctionTok{as.factor}\NormalTok{(DroughtYear), }\AttributeTok{y =}\NormalTok{ Value, }\AttributeTok{fill =} \FunctionTok{as.factor}\NormalTok{(DroughtYear))) }\SpecialCharTok{+} 
  \FunctionTok{geom\_boxplot}\NormalTok{() }\SpecialCharTok{+}
  \FunctionTok{geom\_quasirandom}\NormalTok{()}\SpecialCharTok{+}
 \CommentTok{\# geom\_signif(comparisons = list(c("0", "1"), c("0", "2"), c("0", "3+"), c("1", "2"), }
\CommentTok{\#                                  c("1", "3+"), c("2, 3+")), position = c())+}
   \FunctionTok{theme\_bw}\NormalTok{()}\SpecialCharTok{+}
 \CommentTok{\# geom\_text(data = pairs, aes(y = Y, label = Group))+}
  \FunctionTok{xlab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+}
  \FunctionTok{scale\_fill\_brewer}\NormalTok{(}\AttributeTok{palette =} \StringTok{"Dark2"}\NormalTok{, }\AttributeTok{name =} \ConstantTok{NULL}\NormalTok{, }\AttributeTok{labels =} \FunctionTok{c}\NormalTok{(}\StringTok{"Wet years"}\NormalTok{, }\StringTok{"First/only dry year"}\NormalTok{,}
                                                                            \StringTok{"Second dry year"}\NormalTok{, }\StringTok{"Thrid or more dry year"}\NormalTok{))}\SpecialCharTok{+}

  \FunctionTok{theme}\NormalTok{(}\AttributeTok{legend.position =} \StringTok{"bottom"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-9-1.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{LF }\OtherTok{=} \FunctionTok{ggplot}\NormalTok{(}\FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"logLFS"}\NormalTok{),  }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =} \FunctionTok{as.factor}\NormalTok{(DroughtYear), }\AttributeTok{y =}\NormalTok{ Value, }\AttributeTok{fill =} \FunctionTok{as.factor}\NormalTok{(DroughtYear))) }\SpecialCharTok{+} 
  \FunctionTok{geom\_boxplot}\NormalTok{() }\SpecialCharTok{+}
  \FunctionTok{geom\_quasirandom}\NormalTok{()}\SpecialCharTok{+}
  \FunctionTok{geom\_signif}\NormalTok{(}\AttributeTok{comparisons =} \FunctionTok{list}\NormalTok{(}\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"1"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"2"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"3+"}\NormalTok{), }
                                 \FunctionTok{c}\NormalTok{(}\StringTok{"1"}\NormalTok{, }\StringTok{"2"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"1"}\NormalTok{, }\StringTok{"3+"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"2"}\NormalTok{, }\StringTok{"3+"}\NormalTok{)), }
              \AttributeTok{y\_position =} \FunctionTok{c}\NormalTok{(}\DecValTok{10}\NormalTok{,}\DecValTok{11}\NormalTok{,}\DecValTok{12}\NormalTok{,}\DecValTok{8}\NormalTok{, }\DecValTok{9}\NormalTok{), }\AttributeTok{test =}\NormalTok{ t.test, }
              \AttributeTok{map\_signif\_level=}\NormalTok{T)}\SpecialCharTok{+}
  \FunctionTok{facet\_wrap}\NormalTok{(MetricL}\SpecialCharTok{\textasciitilde{}}\NormalTok{., }\AttributeTok{scales =} \StringTok{"free\_y"}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{theme\_bw}\NormalTok{()}\SpecialCharTok{+}
 \CommentTok{\# geom\_text(data = pairs, aes(y = Y, label = Group))+}
  \FunctionTok{xlab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylim}\NormalTok{(}\DecValTok{0}\NormalTok{, }\DecValTok{13}\NormalTok{)}\SpecialCharTok{+}
  \FunctionTok{scale\_fill\_brewer}\NormalTok{(}\AttributeTok{palette =} \StringTok{"Dark2"}\NormalTok{, }\AttributeTok{name =} \ConstantTok{NULL}\NormalTok{, }\AttributeTok{guide =} \ConstantTok{NULL}\NormalTok{)}
\NormalTok{LF}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-9-2.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{sh }\OtherTok{=} \FunctionTok{ggplot}\NormalTok{(}\FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"logShad"}\NormalTok{),  }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =} \FunctionTok{as.factor}\NormalTok{(DroughtYear), }\AttributeTok{y =}\NormalTok{ Value, }\AttributeTok{fill =} \FunctionTok{as.factor}\NormalTok{(DroughtYear))) }\SpecialCharTok{+} 
  \FunctionTok{geom\_boxplot}\NormalTok{() }\SpecialCharTok{+}
  \FunctionTok{geom\_quasirandom}\NormalTok{()}\SpecialCharTok{+}
  \FunctionTok{geom\_signif}\NormalTok{(}\AttributeTok{comparisons =} \FunctionTok{list}\NormalTok{(}\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"1"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"2"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"3+"}\NormalTok{), }
                                 \FunctionTok{c}\NormalTok{(}\StringTok{"1"}\NormalTok{, }\StringTok{"2"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"1"}\NormalTok{, }\StringTok{"3+"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"2"}\NormalTok{, }\StringTok{"3+"}\NormalTok{)), }
              \AttributeTok{y\_position =} \FunctionTok{c}\NormalTok{(}\DecValTok{9}\NormalTok{,}\FloatTok{9.5}\NormalTok{,}\DecValTok{10}\NormalTok{,}\DecValTok{8}\NormalTok{, }\FloatTok{8.5}\NormalTok{), }\AttributeTok{test =}\NormalTok{ t.test, }
              \AttributeTok{map\_signif\_level=}\NormalTok{T)}\SpecialCharTok{+}
  \FunctionTok{facet\_wrap}\NormalTok{(MetricL}\SpecialCharTok{\textasciitilde{}}\NormalTok{., }\AttributeTok{scales =} \StringTok{"free\_y"}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{theme\_bw}\NormalTok{()}\SpecialCharTok{+}
 \CommentTok{\# geom\_text(data = pairs, aes(y = Y, label = Group))+}
  \FunctionTok{xlab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylim}\NormalTok{(}\DecValTok{3}\NormalTok{,}\DecValTok{11}\NormalTok{)}\SpecialCharTok{+}
  \FunctionTok{scale\_fill\_brewer}\NormalTok{(}\AttributeTok{palette =} \StringTok{"Dark2"}\NormalTok{, }\AttributeTok{name =} \ConstantTok{NULL}\NormalTok{, }\AttributeTok{guide =} \ConstantTok{NULL}\NormalTok{)}
\NormalTok{sh  }
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-9-3.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{crr }\OtherTok{=} \FunctionTok{ggplot}\NormalTok{(}\FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"Salmon CRR"}\NormalTok{),  }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =} \FunctionTok{as.factor}\NormalTok{(DroughtYear), }\AttributeTok{y =}\NormalTok{ Value, }\AttributeTok{fill =} \FunctionTok{as.factor}\NormalTok{(DroughtYear))) }\SpecialCharTok{+} 
  \FunctionTok{geom\_boxplot}\NormalTok{() }\SpecialCharTok{+}
  \FunctionTok{geom\_quasirandom}\NormalTok{()}\SpecialCharTok{+}
  \FunctionTok{geom\_signif}\NormalTok{(}\AttributeTok{comparisons =} \FunctionTok{list}\NormalTok{(}\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"1"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"2"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"3+"}\NormalTok{), }
                                 \FunctionTok{c}\NormalTok{(}\StringTok{"1"}\NormalTok{, }\StringTok{"2"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"1"}\NormalTok{, }\StringTok{"3+"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"2"}\NormalTok{, }\StringTok{"3+"}\NormalTok{)), }
              \AttributeTok{y\_position =} \FunctionTok{c}\NormalTok{(}\DecValTok{4}\NormalTok{,}\FloatTok{4.5}\NormalTok{,}\DecValTok{5}\NormalTok{,}\FloatTok{4.2}\NormalTok{, }\FloatTok{3.7}\NormalTok{), }\AttributeTok{test =}\NormalTok{ t.test, }
              \AttributeTok{map\_signif\_level=}\NormalTok{T)}\SpecialCharTok{+}
  \FunctionTok{facet\_wrap}\NormalTok{(MetricL}\SpecialCharTok{\textasciitilde{}}\NormalTok{., }\AttributeTok{scales =} \StringTok{"free\_y"}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{theme\_bw}\NormalTok{()}\SpecialCharTok{+}
 \CommentTok{\# geom\_text(data = pairs, aes(y = Y, label = Group))+}
  \FunctionTok{xlab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylim}\NormalTok{(}\DecValTok{0}\NormalTok{,}\FloatTok{5.5}\NormalTok{)}\SpecialCharTok{+}
  \FunctionTok{scale\_fill\_brewer}\NormalTok{(}\AttributeTok{palette =} \StringTok{"Dark2"}\NormalTok{, }\AttributeTok{name =} \ConstantTok{NULL}\NormalTok{, }\AttributeTok{guide =} \ConstantTok{NULL}\NormalTok{)}

\NormalTok{  crr}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-9-4.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{ds }\OtherTok{=} \FunctionTok{ggplot}\NormalTok{(}\FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"logDS"}\NormalTok{),  }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =} \FunctionTok{as.factor}\NormalTok{(DroughtYear), }\AttributeTok{y =}\NormalTok{ Value, }\AttributeTok{fill =} \FunctionTok{as.factor}\NormalTok{(DroughtYear))) }\SpecialCharTok{+} 
  \FunctionTok{geom\_boxplot}\NormalTok{() }\SpecialCharTok{+}
  \FunctionTok{geom\_quasirandom}\NormalTok{()}\SpecialCharTok{+}
  \FunctionTok{geom\_signif}\NormalTok{(}\AttributeTok{comparisons =} \FunctionTok{list}\NormalTok{(}\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"3+"}\NormalTok{)), }\AttributeTok{annotations =} \StringTok{"All comparisons NS"}\NormalTok{)}\SpecialCharTok{+}
  \FunctionTok{facet\_wrap}\NormalTok{(MetricL}\SpecialCharTok{\textasciitilde{}}\NormalTok{., }\AttributeTok{scales =} \StringTok{"free\_y"}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{theme\_bw}\NormalTok{()}\SpecialCharTok{+}
 \CommentTok{\# geom\_text(data = pairs, aes(y = Y, label = Group))+}
  \FunctionTok{xlab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylim}\NormalTok{(}\DecValTok{0}\NormalTok{,}\DecValTok{9}\NormalTok{)}\SpecialCharTok{+}
  \FunctionTok{scale\_fill\_brewer}\NormalTok{(}\AttributeTok{palette =} \StringTok{"Dark2"}\NormalTok{, }\AttributeTok{name =} \ConstantTok{NULL}\NormalTok{, }\AttributeTok{guide =} \ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+}

  \FunctionTok{theme}\NormalTok{(}\AttributeTok{legend.position =} \ConstantTok{NULL}\NormalTok{)}

\NormalTok{  ds}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-9-5.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{  sb }\OtherTok{=} \FunctionTok{ggplot}\NormalTok{(}\FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"logSB"}\NormalTok{, }\SpecialCharTok{!}\FunctionTok{is.na}\NormalTok{(Value)),  }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =} \FunctionTok{as.factor}\NormalTok{(DroughtYear), }\AttributeTok{y =}\NormalTok{ Value, }\AttributeTok{fill =} \FunctionTok{as.factor}\NormalTok{(DroughtYear))) }\SpecialCharTok{+} 
  \FunctionTok{geom\_boxplot}\NormalTok{() }\SpecialCharTok{+}
  \FunctionTok{geom\_quasirandom}\NormalTok{()}\SpecialCharTok{+}
  \FunctionTok{geom\_signif}\NormalTok{(}\AttributeTok{comparisons =} \FunctionTok{list}\NormalTok{(}\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"1"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"2"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"3+"}\NormalTok{), }
                                 \FunctionTok{c}\NormalTok{(}\StringTok{"1"}\NormalTok{, }\StringTok{"2"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"1"}\NormalTok{, }\StringTok{"3+"}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\StringTok{"2"}\NormalTok{, }\StringTok{"3+"}\NormalTok{)), }
              \AttributeTok{y\_position =} \FunctionTok{c}\NormalTok{(}\DecValTok{10}\NormalTok{,}\DecValTok{11}\NormalTok{,}\DecValTok{12}\NormalTok{,}\FloatTok{8.5}\NormalTok{, }\FloatTok{9.5}\NormalTok{), }\AttributeTok{test =}\NormalTok{ t.test, }
              \AttributeTok{map\_signif\_level=}\NormalTok{T)}\SpecialCharTok{+}
  \FunctionTok{facet\_wrap}\NormalTok{(MetricL}\SpecialCharTok{\textasciitilde{}}\NormalTok{., }\AttributeTok{scales =} \StringTok{"free\_y"}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{theme\_bw}\NormalTok{()}\SpecialCharTok{+}
 \CommentTok{\# geom\_text(data = pairs, aes(y = Y, label = Group))+}
  \FunctionTok{xlab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylim}\NormalTok{(}\DecValTok{0}\NormalTok{,}\FloatTok{12.5}\NormalTok{)}\SpecialCharTok{+}
  \FunctionTok{scale\_fill\_brewer}\NormalTok{(}\AttributeTok{palette =} \StringTok{"Dark2"}\NormalTok{, }\AttributeTok{name =} \ConstantTok{NULL}\NormalTok{, }\AttributeTok{labels =} \FunctionTok{c}\NormalTok{(}\StringTok{"0, Wet years"}\NormalTok{, }\StringTok{"1, First/only dry year"}\NormalTok{,}
                                                                            \StringTok{"2, Second dry year"}\NormalTok{, }\StringTok{"3+ Third or more dry year"}\NormalTok{))}\SpecialCharTok{+}
    \FunctionTok{theme}\NormalTok{(}\AttributeTok{legend.position =} \StringTok{"bottom"}\NormalTok{)}

\NormalTok{  sb}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-9-6.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{  sb2 }\OtherTok{=}\NormalTok{ sb }\SpecialCharTok{+}  \FunctionTok{scale\_fill\_brewer}\NormalTok{(}\AttributeTok{palette =} \StringTok{"Dark2"}\NormalTok{, }\AttributeTok{guide =} \ConstantTok{NULL}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## Scale for fill is already present.
## Adding another scale for fill, which will replace the existing scale.
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{TFS }\OtherTok{=}  \FunctionTok{ggplot}\NormalTok{(}\FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{==} \StringTok{"logTFS"}\NormalTok{),  }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =} \FunctionTok{as.factor}\NormalTok{(DroughtYear), }\AttributeTok{y =}\NormalTok{ Value, }\AttributeTok{fill =} \FunctionTok{as.factor}\NormalTok{(DroughtYear))) }\SpecialCharTok{+} 
  \FunctionTok{geom\_boxplot}\NormalTok{() }\SpecialCharTok{+}
  \FunctionTok{geom\_quasirandom}\NormalTok{()}\SpecialCharTok{+}
  \FunctionTok{geom\_signif}\NormalTok{(}\AttributeTok{comparisons =} \FunctionTok{list}\NormalTok{(}\FunctionTok{c}\NormalTok{(}\StringTok{"0"}\NormalTok{, }\StringTok{"3+"}\NormalTok{)), }\AttributeTok{annotations =} \StringTok{"All comparisons NS"}\NormalTok{)}\SpecialCharTok{+}
  \FunctionTok{facet\_wrap}\NormalTok{(MetricL}\SpecialCharTok{\textasciitilde{}}\NormalTok{., }\AttributeTok{scales =} \StringTok{"free\_y"}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{theme\_bw}\NormalTok{()}\SpecialCharTok{+}
 \CommentTok{\# geom\_text(data = pairs, aes(y = Y, label = Group))+}
  \FunctionTok{xlab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{ylim}\NormalTok{(}\DecValTok{0}\NormalTok{,}\DecValTok{12}\NormalTok{)}\SpecialCharTok{+}
  \FunctionTok{scale\_fill\_brewer}\NormalTok{(}\AttributeTok{palette =} \StringTok{"Dark2"}\NormalTok{, }\AttributeTok{name =} \ConstantTok{NULL}\NormalTok{, }\AttributeTok{guide =} \ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+}

  \FunctionTok{theme}\NormalTok{(}\AttributeTok{legend.position =} \ConstantTok{NULL}\NormalTok{)}

\NormalTok{  TFS}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-9-7.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\CommentTok{\#print just the legend}
\NormalTok{legend }\OtherTok{\textless{}{-}}\NormalTok{ cowplot}\SpecialCharTok{::}\FunctionTok{get\_legend}\NormalTok{(sb)}
 \FunctionTok{library}\NormalTok{(gridExtra)}
\end{Highlighting}
\end{Shaded}

\begin{verbatim}
## 
## Attaching package: 'gridExtra'
## 
## The following object is masked from 'package:dplyr':
## 
##     combine
\end{verbatim}

\begin{Shaded}
\begin{Highlighting}[]
\NormalTok{plots }\OtherTok{=} \FunctionTok{grid.arrange}\NormalTok{(ds, LF, sh,TFS, sb2, crr, legend,  }\AttributeTok{layout\_matrix =} \FunctionTok{rbind}\NormalTok{(}\FunctionTok{c}\NormalTok{(}\DecValTok{1}\NormalTok{, }\DecValTok{2}\NormalTok{, }\DecValTok{3}\NormalTok{),}
                        \FunctionTok{c}\NormalTok{(}\DecValTok{4}\NormalTok{,}\DecValTok{5}\NormalTok{,}\DecValTok{6}\NormalTok{), }\FunctionTok{c}\NormalTok{(}\ConstantTok{NA}\NormalTok{, }\DecValTok{7}\NormalTok{, }\ConstantTok{NA}\NormalTok{)))}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-9-8.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{ggsave}\NormalTok{(}\AttributeTok{plot =}\NormalTok{ plots,}\StringTok{"FishDrought.tiff"}\NormalTok{, }\AttributeTok{device =} \StringTok{"tiff"}\NormalTok{, }\AttributeTok{width =} \DecValTok{10}\NormalTok{, }\AttributeTok{height =} \DecValTok{10}\NormalTok{, }\AttributeTok{units =} \StringTok{"in"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

Now i need a table with all the statistical results

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{library}\NormalTok{(broom)}

\NormalTok{FD1t }\OtherTok{=} \FunctionTok{tidy}\NormalTok{(FD1) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{mutate}\NormalTok{(}\AttributeTok{Species =} \StringTok{"Striped Bass"}\NormalTok{)}

\NormalTok{LFS1t }\OtherTok{=} \FunctionTok{tidy}\NormalTok{(LFS1) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{mutate}\NormalTok{(}\AttributeTok{Species =} \StringTok{"Longfin Smelt"}\NormalTok{)}

\NormalTok{shad1t }\OtherTok{=} \FunctionTok{tidy}\NormalTok{(shad1) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{mutate}\NormalTok{(}\AttributeTok{Species =} \StringTok{"American Shad"}\NormalTok{)}


\NormalTok{Deltas }\OtherTok{=} \FunctionTok{tidy}\NormalTok{(DS1) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{mutate}\NormalTok{(}\AttributeTok{Species =} \StringTok{"Delta Smelt"}\NormalTok{)}

\NormalTok{Salmon }\OtherTok{=} \FunctionTok{tidy}\NormalTok{(CRRs1) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{mutate}\NormalTok{(}\AttributeTok{Species =} \StringTok{"Salmon CRR"}\NormalTok{)}

\NormalTok{Threadfin }\OtherTok{=} \FunctionTok{tidy}\NormalTok{(TFshad1) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{mutate}\NormalTok{(}\AttributeTok{Species =} \StringTok{"Threadfin Shad"}\NormalTok{)}

\NormalTok{models }\OtherTok{=} \FunctionTok{bind\_rows}\NormalTok{(FD1t, LFS1t, shad1t, Deltas, Threadfin, Salmon)}
\FunctionTok{write.csv}\NormalTok{(models, }\StringTok{"FishMultiYear.csv"}\NormalTok{, }\AttributeTok{row.names =}\NormalTok{ F)}
\end{Highlighting}
\end{Shaded}

Plots for white papers

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{library}\NormalTok{(ggbeeswarm)}
\NormalTok{FishDrought2 }\OtherTok{=} \FunctionTok{filter}\NormalTok{(FishDrought, Metric }\SpecialCharTok{!=} \StringTok{"Salmon CRR"}\NormalTok{) }\SpecialCharTok{\%\textgreater{}\%}
  \FunctionTok{mutate}\NormalTok{(}\AttributeTok{Whitepaper =} \FunctionTok{factor}\NormalTok{(Whitepaper, }\AttributeTok{levels =} \FunctionTok{c}\NormalTok{(}\StringTok{"Critical"}\NormalTok{, }\StringTok{"Dry"}\NormalTok{, }\StringTok{"Below Normal"}\NormalTok{, }\StringTok{"Above Normal"}\NormalTok{, }\StringTok{"Wet"}\NormalTok{, }\StringTok{"2020"}\NormalTok{, }\StringTok{"2021"}\NormalTok{, }\StringTok{"2022"}\NormalTok{),}
                             \AttributeTok{labels =} \FunctionTok{c}\NormalTok{(}\StringTok{"Critical"}\NormalTok{, }\StringTok{"Dry"}\NormalTok{, }\StringTok{"Below}\SpecialCharTok{\textbackslash{}n}\StringTok{Normal"}\NormalTok{, }\StringTok{"Above}\SpecialCharTok{\textbackslash{}n}\StringTok{Normal"}\NormalTok{, }\StringTok{"Wet"}\NormalTok{, }\StringTok{"2020"}\NormalTok{, }\StringTok{"2021"}\NormalTok{, }\StringTok{"2022"}\NormalTok{)))}
  

\FunctionTok{ggplot}\NormalTok{(FishDrought2,  }\FunctionTok{aes}\NormalTok{(}\AttributeTok{x =}\NormalTok{ Whitepaper, }\AttributeTok{y =}\NormalTok{ Value, }\AttributeTok{fill =}\NormalTok{ Yr\_type)) }\SpecialCharTok{+} 
  \FunctionTok{geom\_boxplot}\NormalTok{() }\SpecialCharTok{+}
  \FunctionTok{drt\_color\_pal\_yrtype}\NormalTok{()}\SpecialCharTok{+}
  \FunctionTok{geom\_quasirandom}\NormalTok{()}\SpecialCharTok{+}
  \FunctionTok{facet\_wrap}\NormalTok{(MetricL}\SpecialCharTok{\textasciitilde{}}\NormalTok{., }\AttributeTok{scales =} \StringTok{"free\_y"}\NormalTok{, }\AttributeTok{nrow =} \DecValTok{5}\NormalTok{)}\SpecialCharTok{+} \FunctionTok{theme\_bw}\NormalTok{()}\SpecialCharTok{+}
   \FunctionTok{ylab}\NormalTok{(}\StringTok{"log FMWT Index"}\NormalTok{)}\SpecialCharTok{+}\FunctionTok{xlab}\NormalTok{(}\ConstantTok{NULL}\NormalTok{)}\SpecialCharTok{+}
  \FunctionTok{theme}\NormalTok{(}\AttributeTok{legend.position =} \StringTok{"none"}\NormalTok{)}
\end{Highlighting}
\end{Shaded}

\includegraphics{fishdrought_files/figure-latex/unnamed-chunk-11-1.pdf}

\begin{Shaded}
\begin{Highlighting}[]
\FunctionTok{ggsave}\NormalTok{(}\StringTok{"plots/whitepaper/fish.tiff"}\NormalTok{, }\AttributeTok{device =} \StringTok{"tiff"}\NormalTok{, }\AttributeTok{height =} \DecValTok{8}\NormalTok{, }\AttributeTok{width =} \DecValTok{5}\NormalTok{)}
\end{Highlighting}
\end{Shaded}


\end{document}