Added carbon table demo

AquaticEcoDynamics · Aug 19, 2021 · 33bf344 · 33bf344
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diff --git a/docs/Carbon-1.html b/docs/Carbon-1.html
diff --git a/docs/DO-1.html b/docs/DO-1.html
diff --git a/docs/abbreviations.html b/docs/abbreviations.html
diff --git a/docs/acid-sulfate-soils.html b/docs/acid-sulfate-soils.html
diff --git a/docs/aqueous-geochemistry.html b/docs/aqueous-geochemistry.html
diff --git a/docs/benthic-habitat-quality.html b/docs/benthic-habitat-quality.html
diff --git a/docs/bioactive-particles.html b/docs/bioactive-particles.html
diff --git a/docs/bivalves.html b/docs/bivalves.html
diff --git a/docs/coupling-to-host-models.html b/docs/coupling-to-host-models.html
diff --git a/docs/foreward.html b/docs/foreward.html
diff --git a/docs/generic-utilities-functions.html b/docs/generic-utilities-functions.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/introduction.html b/docs/introduction.html
diff --git a/docs/macroalgae.html b/docs/macroalgae.html
diff --git a/docs/nitrogen.html b/docs/nitrogen.html
diff --git a/docs/nomenclature.html b/docs/nomenclature.html
diff --git a/docs/organic-matter.html b/docs/organic-matter.html
diff --git a/docs/organisation-of-the-library-module-structure.html b/docs/organisation-of-the-library-module-structure.html
diff --git a/docs/pathogens-microbial-indicator-organisms.html b/docs/pathogens-microbial-indicator-organisms.html
diff --git a/docs/phosphorous.html b/docs/phosphorous.html
diff --git a/docs/phytoplankton.html b/docs/phytoplankton.html
diff --git a/docs/preface.html b/docs/preface.html
diff --git a/docs/publications-25.html b/docs/publications-25.html
diff --git a/docs/reference-keys.txt b/docs/reference-keys.txt
@@ -2,6 +2,7 @@ fig:aed-sites
 tab:vardatatypes
 tab:modules
 tab:modules2
+tab:11-summary
 eq:nitrogen1
 eq:nitrogen2
 fig:nitrogen-1
@@ -173,6 +174,7 @@ setup-configuration-2
 case-studies-examples-2
 case-study-2
 publications-2
+Carbon_1
 contributors-3
 overview-3
 model-description-3

diff --git a/docs/references.html b/docs/references.html
diff --git a/docs/riparian-habitat-quality.html b/docs/riparian-habitat-quality.html
diff --git a/docs/riparian-vegetation.html b/docs/riparian-vegetation.html
diff --git a/docs/search_index.json b/docs/search_index.json
diff --git a/docs/sediment-biogeochemistry.html b/docs/sediment-biogeochemistry.html
diff --git a/docs/silica.html b/docs/silica.html
diff --git a/docs/soil-biogeochemistry.html b/docs/soil-biogeochemistry.html
diff --git a/docs/soil-hydrology.html b/docs/soil-hydrology.html
diff --git a/docs/stable-isotopes.html b/docs/stable-isotopes.html
diff --git a/docs/submerged-macrophytes.html b/docs/submerged-macrophytes.html
diff --git a/docs/suspended-sediment.html b/docs/suspended-sediment.html
diff --git a/docs/totals.html b/docs/totals.html
diff --git a/docs/tracers-water-age.html b/docs/tracers-water-age.html
diff --git a/docs/zooplankton.html b/docs/zooplankton.html
diff --git a/rmd/11-carbon.Rmd b/rmd/11-carbon.Rmd
@@ -1,10 +1,47 @@
-# Carbon {#Carbon_1 -}
+# Carbon {#Carbon_1 }
 
 ## Contributors
 ## Overview
 ## Model Description
 ###	Process Descriptions
 ###	Variable Summary
+
+```{r 11-summary, echo=FALSE, message=FALSE, warning=FALSE}
+library(knitr)
+library(kableExtra)
+library(readxl)
+library(rmarkdown)
+carbon <- read_excel('tables/carbonTable.xlsx', sheet = 3)
+carbonGroups <- unique(carbon$Group)
+carbon$`AED name` <- paste0("`",carbon$`AED name`,"`")
+
+for(i in seq_along(carbon$Symbol)){
+  if(!is.na(carbon$Symbol[i])==TRUE){
+    carbon$Symbol[i] <- paste0("$$",carbon$Symbol[i],"$$")
+  } else {
+    carbon$Symbol[i] <- NA
+  }
+}
+
+kbl(carbon[,2:8], caption = "Carbon table", align = "l",) %>%
+  pack_rows(carbonGroups[1], 
+            min(which(carbon$Group == carbonGroups[1])), 
+            max(which(carbon$Group == carbonGroups[1])),
+            background = '#ebebeb') %>% 
+  pack_rows(carbonGroups[2], 
+            min(which(carbon$Group == carbonGroups[2])), 
+            max(which(carbon$Group == carbonGroups[2])),
+            background = '#ebebeb') %>% 
+  pack_rows(carbonGroups[3], 
+            min(which(carbon$Group == carbonGroups[3])), 
+            max(which(carbon$Group == carbonGroups[3])),
+            background = '#ebebeb') %>% 
+  row_spec(0, background = "#14759e", bold = TRUE, color = "white") %>% 
+  kable_styling(full_width = F,font_size = 12) %>% 
+  scroll_box(width = "770px", height = "500px",
+             fixed_thead = FALSE) 
+```
+
 ###	Parameter Summary
 ###	Optional Module Links
 ###	Feedbacks to the Host Model

diff --git a/scripts/animatedPlotly/animatedPlotly.R b/scripts/animatedPlotly/animatedPlotly.R
@@ -1,23 +1,12 @@
-# They require PAR as a vector (x-axis) and then each equation has a parameter (I_K or I_S)
-# 
-# Could we try to do 2 or 3 of these (Case 1 and Case 3)?
-#   
-#   We would range PAR (par_c) on the x-axis from 0 to 2000.
-# y-axis (fI) would be 0 – 1
-# I_K would be on a slider from 10 - 500.
 library(plotly)
 library(dplyr)
 
 #case 1
-# x = par_c/I_K
-# fI = (par_c/I_K) / (1 + (par_c/I_K))
-
 case1 <- data.frame(
   par_c = double(),
   I_K = double(),
   fI = double()
 )
-
 for(i in seq(10, 500, by = 10)){
   case1_temp <- data.frame(
     par_c = seq(0, 2000, by = 10),
@@ -27,6 +16,20 @@ for(i in seq(10, 500, by = 10)){
   case1 <- bind_rows(case1,case1_temp)
 }
 
+#case 4
+case4 <- data.frame(
+  par_c = double(),
+  I_K = double(),
+  fI = double()
+)
+for(i in seq(10, 500, by = 10)){
+  case4_temp <- data.frame(
+    par_c = seq(0, 2000, by = 10),
+    I_K = i
+  )
+  case4_temp$fI <- tanh(case4_temp$par_c/case4_temp$I_K)
+  case4 <- bind_rows(case4,case4_temp)
+}
 
 
 #case 3
@@ -35,7 +38,6 @@ case3 <- data.frame(
   I_K = double(),
   fI = double()
 )
-
 for(i in seq(10, 500, by = 10)){
   case3_temp <- data.frame(
     par_c = seq(0, 2000, by = 10),
@@ -47,26 +49,51 @@ for(i in seq(10, 500, by = 10)){
 
 #create plot
 fig <- plot_ly()
+fig <- fig %>% add_trace(
+  case1,
+  name="Case 1",
+  x = case1$par_c, 
+  y = case1$fI, 
+  #frame = case1$I_K, 
+  hovertemplate = 'fI: %{y:.2f}<extra></extra>',
+  type = 'scatter',
+  mode = 'lines')
 fig <- fig %>% add_trace(
   case3,
-  name="case3",
+  name="Case 3",
   x = case3$par_c, 
   y = case3$fI, 
-  frame = case3$I_K, 
+  #frame = case3$I_K, 
+  hovertemplate = 'fI: %{y:.2f}<extra></extra>',
   type = 'scatter',
   mode = 'lines')
 fig <- fig %>% add_trace(
-  case1,
-  name="case1",
-  x = case1$par_c, 
-  y = case1$fI, 
-  frame = case1$I_K, 
+  case4,
+  name="Case 4",
+  x = case4$par_c, 
+  y = case4$fI, 
+  #frame = case4$I_K, 
+  hovertemplate = 'fI: %{y:.2f}<extra></extra>',
   type = 'scatter',
   mode = 'lines')
+
 fig <- fig %>%
-  animation_opts(
-    250, easing = "linear", redraw = FALSE
-  ) %>% 
-  config(displayModeBar = FALSE,
-         displaylogo = FALSE)
+  layout(
+    hovermode = "x unified",
+    xaxis = list(title='PAR C',hoverformat = "PAR C"), 
+    yaxis = list(title='Light limitation (fI)'),
+    sliders = list(active = 2, 
+                   currentvalue = list(prefix = "Test: "), 
+                   pad = list(t = 10), 
+
+                   steps = list(1:10)))
+  #   ) %>% 
+  # animation_opts(
+  #   250, easing = "linear", redraw = FALSE
+  # ) %>% 
+  # animation_slider(
+  #   currentvalue = list(prefix = "I_K: ")
+  # ) %>% 
+  # config(displayModeBar = FALSE,
+  #        displaylogo = FALSE)
 fig    
diff --git a/scripts/summaryTables.R b/scripts/summaryTables.R
@@ -0,0 +1,64 @@
+library(readxl)
+library(kableExtra)
+library(rmarkdown)
+carbon <- read_excel('tables/carbonTable.xlsx', sheet = 3)
+carbonGroups <- unique(carbon$Group)
+carbon$`AED name` <- paste0("`",carbon$`AED name`,"`")
+
+for(i in seq_along(carbon$Symbol)){
+  if(!is.na(carbon$Symbol[i])==TRUE){
+    carbon$Symbol[i] <- paste0("$$",carbon$Symbol[i],"$$")
+  } else {
+    carbon$Symbol[i] <- NA
+  }
+}
+
+kbl(carbon[,2:8], caption = "Carbon table") %>%
+  kable_paper("striped", full_width = F) %>%
+  pack_rows(carbonGroups[1], 
+            min(which(carbon$Group == carbonGroups[1])), 
+            max(which(carbon$Group == carbonGroups[1]))) %>% 
+  pack_rows(carbonGroups[2], 
+            min(which(carbon$Group == carbonGroups[2])), 
+            max(which(carbon$Group == carbonGroups[2]))) %>% 
+  pack_rows(carbonGroups[3], 
+            min(which(carbon$Group == carbonGroups[3])), 
+            max(which(carbon$Group == carbonGroups[3]))) %>% 
+  row_spec(0, background = "#14759e", bold = TRUE, color = "white") %>% 
+  kable_styling(full_width = F)
+
+
+
+library(knitr)
+library(kableExtra)
+library(readxl)
+library(rmarkdown)
+carbon <- read_excel('tables/carbonTable.xlsx', sheet = 3)
+carbonGroups <- unique(carbon$Group)
+carbon$`AED name` <- paste0("`",carbon$`AED name`,"`")
+
+for(i in seq_along(carbon$Symbol)){
+  if(!is.na(carbon$Symbol[i])==TRUE){
+    carbon$Symbol[i] <- paste0("$$",carbon$Symbol[i],"$$")
+  } else {
+    carbon$Symbol[i] <- NA
+  }
+}
+
+kbl(carbon[,2:8], caption = "Carbon table", align = "l",) %>%
+  pack_rows(carbonGroups[1], 
+            min(which(carbon$Group == carbonGroups[1])), 
+            max(which(carbon$Group == carbonGroups[1])),
+            background = '#ebebeb') %>% 
+  pack_rows(carbonGroups[2], 
+            min(which(carbon$Group == carbonGroups[2])), 
+            max(which(carbon$Group == carbonGroups[2])),
+            background = '#ebebeb') %>% 
+  pack_rows(carbonGroups[3], 
+            min(which(carbon$Group == carbonGroups[3])), 
+            max(which(carbon$Group == carbonGroups[3])),
+            background = '#ebebeb') %>% 
+  row_spec(0, background = "#14759e", bold = TRUE, color = "white") %>% 
+  kable_styling(full_width = F,font_size = 12) %>% 
+  scroll_box(width = "770px", height = "500px",
+             fixed_thead = FALSE) 
diff --git a/tables/carbonTable.xlsx b/tables/carbonTable.xlsx
diff --git a/tables/carbonTableOG.xlsx b/tables/carbonTableOG.xlsx
diff --git a/tables/~$carbonTable.xlsx b/tables/~$carbonTable.xlsx