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About this repository

This repository contains all code used to generate SSP5-RCP8.5 estimates for the manuscript, "Predicting changes in agricultural yields from climate change scenarios and their implications for global food security" (April 27, 2023). All analysis was performed in the R.4.2.2. environment.

Scripts

This repository uses the targets framework for reproducible workflow developed by William Landau. The script _targets.R describes the targets pipeline as a modular list of smaller, nested target pipelines that are stored inside all scripts with targets_ prefixes in the scripts/ folder. The target pipeline as a whole describes the dependencies between targets (i.e. cached objects). We recommend that users become familiar with the targets pipeline and associated targets commands in the link provided, but users only need to use tar_make() to run the pipeline and build targets, or tar_make_future() to build targets using parallelisation. As the targets pipeline takes care of dependencies, users can create the entire targets pipeline with tar_make() or create individual targets x with tar_make(x).

Users should first run scripts/init.R to install packages and set the relative file path dependencies to the root project folder.

Data

The validated CGIAR dataset is saved in processed/agimpacts_final.csv. Certain data inputs, such as observational and projected temperature, precipitation and CO2 data, spatial crop production, calendar information and food security data exceed Github's repository size limits. Please refer to the list below and additional details in the manuscript to download data directly from cited sources and deposit these in the directory structure that has been set up and outlined in the targets pipeline or contact me for assistance.

Historical data

Spatial production data c. 2000, 0.5 degrees/30 minutes spatial resolution

Files not provided: X_Production.tiff where X is crop Maize, Rice, Soybean, Wheat

Monfreda, C., Ramankutty, N. & Foley, J. A. Farming the planet: 2. Geographic distribution of crop areas, yields, physiological types, and net primary production in the year 2000. Global Biogeochemical Cycles 22 (2008).

Spatial yields and hectares harvested data c. 2015, 5 minutes spatial resolution

Files not provided: GAEZAct2015HarvArea_X_Total.tiff and GAEZAct2015Yield_X_Mean.tiff where X is crop Maize, Rice, Soybean, Wheat

Grogan, D., Frolking, S., Wisser, D., Prusevich, A. & Glidden, S. Global gridded crop harvested area, production, yield, and monthly physical area data circa 2015. Scientific Data 9. Number: 1 Publisher: Nature Publishing Group, 15 (2022).

Spatial crop calendar data c. 2000, 0.5 degrees/30 minutes spatial resolution

Files not provided: X.crop.calendar.fill.nc where X is crop Maize, Maize.2, Rice, Rice.2, Soybeans, Wheat, Wheat.Winter

Sacks, W. J., Deryng, D., Foley, J. A. & Ramankutty, N. Crop planting dates: an analysis of global patterns. Global Ecology and Biogeography 19, 607--620 (2010).

File provided at data/MIRCA data/CELL_SPECIFIC_CROPPING_CALENDARS_30MN.txt

Portmann, F. T., Siebert, S. & Döll, P. MIRCA2000---Global monthly irrigated and rainfed crop areas around the year 2000: A new high-resolution data set for agricultural and hydrological modeling. Global Biogeochemical Cycles 24 (2010).

Monthly spatial temperature and precipitation observations 1901--2020, 0.5 degrees/30 minutes spatial resolution

Files not provided: CRU TS 4.05.1901.2020.tmp.dat.nc, CRU TS 4.05.1901.2020.tmp.dat, CRU TS 4.05.1901.2020.tmp.stn, CRU TS 4.05.1901.2020.pre.dat.nc, CRU TS 4.05.1901.2020.pre.dat, CRU TS 4.05.1901.2020.pre.stn

Harris, I., Osborn, T. J., Jones, P. & Lister, D. Version 4 of the CRU TS monthly high-resolution gridded multivariate climate dataset. Scientific Data 7, 109 (2020).

Annual global CO2 observations 1959--2021

File provided at data/co2_annmean_mlo.csv

Accessed from \url{gml.noaa.gov/ccgg/trends/}.

FAOSTAT Food Balance Sheets data 2014--2016, country level

Files accessed from FAOSTAT Food Balance Sheets https://www.fao.org/faostat/en/#data/FBS (2023):

• Production Quantity, Import Quantity, Export Quantity and crop allocation data for staple products, files provided in data/Food security data/FAOSTAT_FBS_staple_201416/ folder

• Production Quantity for staple products, file provided in data/Food security data/ folder

• Food Supply (kcal) for all products, file provided in data/Food security data/ folder

• Annual Dietary Energy Requirements, file provided in data/Food security data/ folder

FAOSTAT Population 2014--2016 data, country level

File provided in data/Food security data/ folder

FAOSTAT. Food Balance Sheets https://www.fao.org/faostat/en/#data/FBS (2023).

FAOSTAT Detailed Trade Matrix 2014--2016 data, country level

Files provided in data/Food security data/FAOSTAT_trade_data_201416 folder

FAOSTAT. Detailed Trade Matrix https://www.fao.org/faostat/en/#data/TM (2023).

Future data

CMIP6 individual GCM data, 10 minutes

Files not provided

WorldClim. Future climate, 10 minutes spatial resolution --- WorldClim 1 documentation https://www.worldclim.org/data/cmip6/cmip6_clim10m.html (2023).

CMIP5 multi-model mean data, 0.5 degrees/30 minutes spatial resolution

Files not provided: iRCP3PD_CO2_1860_2100.nc, iRCP45_CO2_1860_2100.nc, iRCP85_CO2_1860_2100.nc

KNMI, C. E. Monthly CMIP5 scenario runs https://climexp.knmi.nl/start.cgi (2023).

Population projections, country level

File provided at data/Food security data/iamc_db.xslx and accessed from the International Institute of Applied Systems Analysis (IIASA).

KC, S. & Lutz, W. The human core of the shared socioeconomic pathways: Population scenarios by age, sex and level of education for all countries to 2100. Global Environmental Change 42, 181--192 (2017).