size script small edit

RAnalysis/Scripts/.Rhistory

@@ -1,37 +1,3 @@
-# str(df)
-# number of runs
-unique(df$Generation) # 1, 2, and 3
-Rep_Summary_all <- df %>% dplyr::select(c(Generation, Age, Parent_pCO2, Larvae_pCO2)) %>%
-dplyr::group_by_all() %>%
-dplyr::summarise(n=n())
-# print the runs
-# summary:
-Rep_Summary_G1 <- Rep_Summary_all %>%  dplyr::filter(Generation %in% 1) #
-Rep_Summary_G1 %>%  kbl() %>% kable_classic(full_width = F, html_font = "Cambria")
-Rep_Summary_G2 <- Rep_Summary_all %>%  dplyr::filter(Generation %in% 2) #
-Rep_Summary_G2 %>%  kbl() %>% kable_classic(full_width = F, html_font = "Cambria")
-Rep_Summary_G3 <- Rep_Summary_all %>%  dplyr::filter(Generation %in% 3) #
-Rep_Summary_G3 %>%  kbl() %>% kable_classic(full_width = F, html_font = "Cambria")
-df_Exp2 <- df%>%
-filter(Generation=="1") %>% dplyr::mutate(Experiment = 2)
-df_Exp4 <- df%>%
-filter(Generation=="2") %>% dplyr::mutate(Experiment = 4)
-df_Exp6 <- df%>%
-filter(Generation=="3") %>% dplyr::mutate(Experiment = 6)
-# create new columns for live and dead based on the count and proportion (of alive) to back calculate dead - these are integers!
-df_Exp6 <- df_Exp6 %>%
-dplyr::mutate(Count =
-as.numeric(gsub(",","",Count))) %>% # remove the commas from these numbers- id as character if not removed!
-dplyr::rename(Count_alive = Count) %>% # rename to avoid confusion
-dplyr::mutate(proportion = Percent_Survival/100,
-Count_total = case_when(proportion == 0 ~ 0,
-proportion >0 ~
-(1/as.numeric(proportion))*
-as.numeric(Count_alive)),# proportion is that of alive
-Count_dead = Count_total - Count_alive)
-# create new columns for live and dead based on the count and proportion (of alive) to back calculate dead - these are integers!
-df_Exp6 <- df_Exp6 %>%
-dplyr::mutate(Count =
 as.numeric(gsub(",","",Count))) %>% # remove the commas from these numbers- id as character if not removed!
 dplyr::rename(Count_alive = Count) %>% # rename to avoid confusion
 dplyr::mutate(proportion = Percent_Survival/100,
@@ -510,3 +476,37 @@ tbl_regression(exp = TRUE)
 Exp6_coxph_test_table_3
 Exp6_hazardratio_plot_3   <- ggforest(Exp6_coxph_test_3, data = binary_Exp6_larvae)
 Exp6_hazardratio_plot_3
+knitr::opts_chunk$set(echo = TRUE)
+# SET WORKING DIRECTORY
+#knitr::opts_knit$set(root.dir = "C:/Users/samjg/Documents/Github_repositories/EAD-ASEB-Airradians_Larvae_crossgen_OA/RAnalysis") # Sam's
+# knitr::opts_knit$set(root.dir =
+# "C:/Users/samjg/Documents/Github_repositories/EAD-ASEB-Airradians_Larvae_crossgen_OA/RAnalysis/") # Sam's work
+knitr::opts_knit$set(root.dir =
+"C:/Users/samuel.gurr/Documents/Github_repositories/EAD-ASEB-Airradians_Larvae_crossgen_OA/RAnalysis/") # Sam's work
+# install.packages('gcookbook')
+# LOAD PACKAGES :::::::::::::::::::::::::::::::::::::::::::::::::::::::
+library(dplyr)
+library(ggplot2)
+# install.packages('gcookbook')
+# LOAD PACKAGES :::::::::::::::::::::::::::::::::::::::::::::::::::::::
+library(dplyr)
+library(ggplot2)
+library(reshape2)
+# install.packages('gcookbook')
+# LOAD PACKAGES :::::::::::::::::::::::::::::::::::::::::::::::::::::::
+library(dplyr)
+library(ggplot2)
+library(reshape2)
+library(knitr)
+library(car)
+library(gcookbook)
+library(ggpubr)
+# LOAD DATA :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
+# 8.16/2025 shannon assembled a means and SD dataset for the DIC+TA to calculate
+CarbChem_Meseck_means <- read.csv(file="Data/Seawater_chemistry/raw/Seawater_Chemsitry_means_Meseck_20240816.csv",
+header=TRUE) # load the chem data
+# This is all the data, we can back calculate to get to what Shannon assembled or just use the one above..
+# if we come toa conclusion that TA+pH or pH+DIC is desired than we can do that
+CarbChem_all <- read.csv(file="Data/Seawater_chemistry/raw/Seawater_Chemsitry_raw.csv",
+header=TRUE) # load the chem data
+CarbChem_Meseck_means

RAnalysis/Scripts/Size.Rmd

@@ -12,8 +12,8 @@ output: html_document
 knitr::opts_chunk$set(echo = TRUE)
 # SET WORKING DIRECTORY 
 #knitr::opts_knit$set(root.dir = "C:/Users/katherine.mcfarland/Documents/GitHub/EAD-ASEB-Airradians_Larvae_crossgen_OA/RAnalysis") # Katie's
-knitr::opts_knit$set(root.dir = "C:/Users/samjg/Documents/Github_repositories/EAD-ASEB-Airradians_Larvae_crossgen_OA/RAnalysis") # Sam's
-#knitr::opts_knit$set(root.dir = "C:/Users/samuel.gurr/Documents/Github_repositories/EAD-ASEB-Airradians_Larvae_crossgen_OA/RAnalysis") # Sam's work
+#knitr::opts_knit$set(root.dir = "C:/Users/samjg/Documents/Github_repositories/EAD-ASEB-Airradians_Larvae_crossgen_OA/RAnalysis") # Sam's
+knitr::opts_knit$set(root.dir = "C:/Users/samuel.gurr/Documents/Github_repositories/EAD-ASEB-Airradians_Larvae_crossgen_OA/RAnalysis") # Sam's work
 ```
 
 
@@ -34,7 +34,7 @@ library(nlme)
 library(lme4)
 library(multcomp)
 library(Matrix)
-
+?Matrix
 ```
 
 
@@ -805,6 +805,9 @@ lme_Exp4.emmeans.Age.letters <- multcomp::cld(object = lme_Exp4.emmeans.Age$emme
 library(DHARMa)
 # (2) GLMMs 
 
+library(lmerTest) # otherwise lme4 does not report table
+
+hist(Exp2_GLMMs$Length)
 
 # (2.1) All treatment Low, moderate, and high
 Exp2_GLMMs    <-  Exp2 %>%
@@ -818,9 +821,7 @@ str(Exp2_GLMMs)
 # RUN STATISTICAL MODEL  ::::::::::::::::::::::::::::::::::
 library(nlme)
 library(lme4)
-library(lmerTest) # otherwise lme4 does not report table
-
-hist(Exp2_GLMMs$Length)
+library(Matrix)
 
 # adjust a difference in two proportions for confounders: 
 # to do so, you would run a logistic GLM with identity link.