Merge branch 'master' of https://github.com/InteragencyEcologicalProg…

…ram/ND-FASTR
InteragencyEcologicalProgram · Nov 22, 2023 · c4bf325 · c4bf325
2 parents 11ebc43 + f387ffb
commit c4bf325
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Showing 53 changed files with 37,422 additions and 14,690 deletions.
diff --git a/NEWzooptables.xlsx b/NEWzooptables.xlsx
diff --git a/Zoop_code/FASTR_exploration_JA.R → ...esse-zoop-analyses/FASTR_exploration_JA.R b/Zoop_code/FASTR_exploration_JA.R → ...esse-zoop-analyses/FASTR_exploration_JA.R
diff --git a/FASTR_zoop_multivariate.R → ...e-zoop-analyses/FASTR_zoop_multivariate.R b/FASTR_zoop_multivariate.R → ...e-zoop-analyses/FASTR_zoop_multivariate.R
@@ -9,8 +9,8 @@ library(lme4)
 library(car)
 library(emmeans)
 library(gratia)
-library(here)
 library(forcats)
+library(here)
 # Source functions
 source(here("global_ndfa_funcs.R"))
 source(here("Water_Quality/global_wq_funcs.R"))
@@ -295,22 +295,27 @@ plot(m_cpue_gam, pages=1, residuals=TRUE)
 # Plot Upstream and Downstream Total BV by ActionPhase for each year
 fig1 <- ggplot(data=zoopNDFA7, aes(y= log10(cpue), 
                                    x = factor(Regions2,levels = c("Upstream","Downstream")),
-                                   color = SamplePeriod)) +
-  geom_boxplot() 
+                                   fill = SamplePeriod)) +
+  geom_boxplot(size=.2,outlier.size = .5)
 
 fig1 +
   labs(title = "Total Zooplankton Abundance by Year",
        y = bquote(Log[10]~'Zooplankton Abundance'~(indiv.~L^-1)), 
        x = "Sampling Region",
-       color = "Pulse Period") +
+       fill = "Pulse Period") + 
+  theme_bw()+
+  scale_fill_manual(values = c("#4DAF4A",
+                               "#984EA3",
+                               "#A3D0D4"),
+                    labels=c("Before", "During", "After"))+
   facet_wrap(Year ~ ., ncol = 2)  
 
-ggsave(path = output,
+ggsave(path = "Plots",
        filename = "fig1_log_zoop_cpue_by_year_and_AP.png", 
-       device = "png",
+       device = "tiff",
        scale=1.0, 
        units="in",
        height=4,
        width=6, 
-       dpi="print")
+       dpi= "print")
 
diff --git a/Zoop_code/Jesse-zoop-analyses/NEWzooptables.xlsx b/Zoop_code/Jesse-zoop-analyses/NEWzooptables.xlsx
diff --git a/Zoop_code/Jesse-zoop-analyses/P_forbesi_regfpp.png b/Zoop_code/Jesse-zoop-analyses/P_forbesi_regfpp.png
diff --git a/Zoop_code/Jesse-zoop-analyses/P_forbesi_regfpp_zeroes.png b/Zoop_code/Jesse-zoop-analyses/P_forbesi_regfpp_zeroes.png
diff --git a/Zoop_code/Jesse-zoop-analyses/P_forbesi_regfpp_zeroes_facet_yr.png b/Zoop_code/Jesse-zoop-analyses/P_forbesi_regfpp_zeroes_facet_yr.png
diff --git a/adon.results.csv → ...code/Jesse-zoop-analyses/adon.results.csv b/adon.results.csv → ...code/Jesse-zoop-analyses/adon.results.csv
diff --git a/Zoop_code/Jesse-zoop-analyses/fig1_log_zoop_cpue_by_year_and_AP.png b/Zoop_code/Jesse-zoop-analyses/fig1_log_zoop_cpue_by_year_and_AP.png