State space model (SSM) code as a suplementary material: Determining consumptive and nonconsumptive predator effects on prey population growth and density via state space models

We present our code and data in the folder:

CODES:

1_Bosmina_in_SSM.R : this file presents the R code for the predator-prey system (Eq.1 in Manuscript) for Bosmina Combined Sites

2_Model_fit.R : We make parameter estimates of our State Space Model (SSM) in this file 

3_Profile_alpha.R : To capture Confident intervals and profile of a parameter we use this file and visualize  plots and CIs in the “Profile_Analysis.R” file

All the explanations about codes in these three files are given in the R markdown file named as: “R_codes_in_SSM_June14_2024”

DATA: Areal density data for Daphnia, Bosmina, and Bythotrephes for 45m and 100m: 

zoop45m_plus_110m.csv:  This csv data file includes areal density data of two prey (Daphnia and Bosmina) and their predator Bythotrephes 

Temperature data for 45m site:

Surface_Tempdata_for_45m.csv : This CSV file is for Surface temperature data for 45m site and arranged for the years we used in 45m site 

Temp_at40m_Depth_98-18_for45m.csv:  This file is for Temperature at 40m depth for 45m site

Temperature data for 110m site:

Tempdata_final_94-18.csv : This CSV file is for Surface temperature data for 110m site and arranged for the years we used in 110m site 

Temp_at40m_94-18.csv:  This file is for Temperature at 40m depth for 110m site