Author: David Bridgwood dbridg15@gmail.com
Description: Project to determine if the timing of moth flights (first flight day and last flight day) are being affected by changing climate (specifically temperature).
The following R packages are required
- ggplot2-----------------------plotting
- RColorBrewer--------------setting colour gradient of seaons on combined plots
- gridExtra---------------------combining plots
- lme4---------------------------models
- reshape2---------------------reshaping dataframes
Set working directory to moths_project/Code/ and Rscript/source the file 0_run_moths_project.R The default has sensitivity Analysis turned off and take aprox 5 mins to run. With sensitivity analysis on (see below). Run time is >30mins.
In R
source 0_run_moths_project.R
In terminal
Rscript 0_run_moths_project.R
To turn on sensitivity analysis amend 0_run_moths_project.R file line 24.
with_sensitivity <- TRUE # set to TRUE to run with sensitivity analysis
By default sensitvity analysis runs though these values - which can be ammended.
# values for sesitivity analysis *MUST INCLUDE X=3 and N=20 TO RUN*
X.vals <- c(1, 3, 5, 10, 15, 25) # sightings for mean ffd day
N.vals <- c(3, 5, 10, 15, 20, 25) # minimum years to include
- Current choice of colour gradient for combined plot does not have enough colours for all seasons when more leniant values are used in sensitivity analysis
moths_project/
│
├── Code/
│ │
│ ├── 0_run_moths_project.R-------------source/Rscript this file to run the project
│ │
│ ├── functions.R-----------------------code for functions used in project
│ │
│ ├── 1_read_sort_data.R----------------reads in moth and climate data and produces summaries
│ │
│ ├── 2_analyse_climate.R---------------analysis of climate data
│ │
│ ├── 3_select_&_adjust_abundance.R-----select species for analysis & adjust FFD/LFD by sampling to least abundant year
│ │
│ ├── 4_effects_on_moths.R--------------are moths flying earlier/later/longer
│ │
│ ├── 5_the_model.R---------------------produces general lines model from the data and plots for each species
│ │
│ ├── 6_sorting_results.R---------------reads in and amalgamates results and saves to csv file
│ │
│ ├── 7_example_plots.R-----------------plots FFD and LFD response for example species (Silver-ground carpet)
│ │
│ └── extract_mean_temp.py--------------python script to extract data from required grid squares
│
├── Data/
│ │
│ ├── Climate/-------------------------contains all climate data
│ │ │
│ │ ├── MeanTemp_1.csv-------------⎤
│ │ ├── MeanTemp_2.csv-------------⎥
│ │ ├── MeanTemp_3.csv-------------⎥
│ │ ├── MeanTemp_4.csv-------------⎥
│ │ ├── MeanTemp_5.csv-------------⎬ mean daily temp at each grid square
│ │ ├── MeanTemp_6.csv-------------⎥
│ │ ├── MeanTemp_7.csv-------------⎥
│ │ ├── MeanTemp_8.csv-------------⎥
│ │ └── MeanTemp_9.csv-------------⎦
│ │
│ ├── Climate_Source/------------------RAW climate data (in .gitignore)
│ │
│ └── Moths/---------------------------contains all moth filght data
│ │
│ ├── Days.csv---------------------days where no moths were recorded
│ │
│ ├── Moths1990.csv--------------⎤
│ ├── Moths1991.csv--------------⎥
│ ├── Moths1992.csv--------------⎥
│ ├── Moths1993.csv--------------⎥
│ ├── Moths1994.csv--------------⎥
│ ├── Moths1995.csv--------------⎥
│ ├── Moths1996.csv--------------⎥
│ ├── Moths1997.csv--------------⎥
│ ├── Moths1998.csv--------------⎥
│ ├── Moths1999.csv--------------⎥
│ ├── Moths2000.csv--------------⎥
│ ├── Moths2001.csv--------------⎥
│ ├── Moths2002.csv--------------⎬ moth flight data for given year
│ ├── Moths2003.csv--------------⎥
│ ├── Moths2004.csv--------------⎥
│ ├── Moths2005.csv--------------⎥
│ ├── Moths2006.csv--------------⎥
│ ├── Moths2007.csv--------------⎥
│ ├── Moths2008.csv--------------⎥
│ ├── Moths2009.csv--------------⎥
│ ├── Moths2010.csv--------------⎥
│ ├── Moths2011.csv--------------⎥
│ ├── Moths2012.csv--------------⎥
│ ├── Moths2013.csv--------------⎥
│ ├── Moths2014.csv--------------⎦
│ │
│ └── Speciesindexlist.csv--------species index list id, B&F, common name
│
└── Results/----------------------------files in this directory are produced when the project is run
│
├── ChiSqr_Results.csv--------------csv with results from Chi-Squared tests or each sensitivity analysis
│
├── Models_summary.txt--------------summary of every model for for each run of the sensitivity analysis
│
├── plots/--------------------------pdfs of plots
│
└── r_data/-------------------------.rda files from each run of sensitivity analysis