Adding the param spreadsheet to data and updating the code

Parameters/GetParams2.R

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+###Generate oxygen distribution parameters from literature review
+###Cayelan Carey
+###originally created 19 January 2023
+
+#Install the required googlesheets4 package
+install.packages('googlesheets4')
+#Load the library 
+library(googlesheets4)
+library(tidyverse)
+library(fitdistrplus)
+sites <- read.csv("data/MichaelisMentenOxygenParameters.csv")
+str(sites)
+
+sites$Fsed_oxy_value <- as.numeric(unlist(sites$Fsed_oxy_value)) #remove list from googlesheets
+sites$Fsed_oxy_units <- as.character(unlist(sites$Fsed_oxy_units)) 
+
+#focus on fsed_oxy values right now, assuming ksed values stay constant
+sites_trim <- sites %>% 
+  dplyr::select(LakeName, LakeTrophicState, Fsed_oxy_value, Fsed_oxy_units) %>% 
+  drop_na()
+
+#identify all units being used for Fsed_oxy values
+unique(sites_trim$Fsed_oxy_units)
+
+#convert all the different units to g/m2/day
+for(i in 1:length(sites_trim$LakeName)){
+  if(sites_trim$Fsed_oxy_units[i]=="mmol/m2/d"){
+    sites_trim[i,5] = sites_trim$Fsed_oxy_value[i]*0.032 
+  } #mmol/m2/day * (32 mg O2/1 mmol O2)* (1 g O2/1000 mg O2)
+  if(sites_trim$Fsed_oxy_units[i]=="mg/L/d"){
+    sites_trim[i,5] = sites_trim$Fsed_oxy_value[i]
+  } #mg/L/day * (1 g O2/1000 mg O2)*(1000L/m3)*(1 m3/1 m2) assuming cubic m box of water on sediments
+  if(sites_trim$Fsed_oxy_units[i]=="mol/L/s"){
+    sites_trim[i,5] = sites_trim$Fsed_oxy_value[i]*2764800000
+  } #mol/L/sec * (86400 sec/day)*(32 g/1 mol)*(1000L/1 m3)*(1 m3/1 m2)
+  if(sites_trim$Fsed_oxy_units[i]=="NA"){
+    sites_trim[i,5] = NA
+  }
+  if(sites_trim$Fsed_oxy_units[i]=="g/m2/d"){
+    sites_trim[i,5] = sites_trim$Fsed_oxy_value[i]
+  } #no need to convert, these are in correct units
+  if(sites_trim$Fsed_oxy_units[i]=="mg/m2/d"){
+    sites_trim[i,5] = sites_trim$Fsed_oxy_value[i]/1000
+  } #mg/m2/d * (1 g/1000 mg)
+}
+
+#rename our new column
+names(sites_trim)[(which(names(sites_trim)=='V5'))]<-'F_sed_oxy_gm2d'
+
+sites_trim<-sites_trim %>% 
+  drop_na()
+
+#calculate oligotrophic normal distributions
+Oligo <- fitdist(data = sites_trim$F_sed_oxy_gm2d[sites_trim$LakeTrophicState=="Oligotrophic"], 
+                  distr = "norm", method = "mle")
+
+#Oligo Parameters:
+#estimate Std. Error
+#mean 0.2731324 0.03099747
+#sd   0.1669265 0.02191498
+
+#calculate eutrophic normal distributions
+Eutro <- fitdist(data = sites_trim$F_sed_oxy_gm2d[sites_trim$LakeTrophicState=="Eutrophic"], 
+                 distr = "norm", method = "mle")
+
+#Eutro Parameters:
+#  estimate Std. Error
+#mean -170.1525   154.3945
+#sd    873.4926   109.1734
+