Data

📚 Data

This project uses data from the Norwood Farm project — Pocock et al. (2012), doi.org/10.5061/dryad.3s36r118. The data describes species and their interactions across the farm's different habitats.

Jump to: 🌱 Raw data  |  📋 All data files at a glance

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🌱 Raw data

A closer look at each of the four raw input files, with a preview of what they contain.

The raw data consists of four files, stored in Data/Raw_data/:

PLANT_HABITAT3.csv

Plant abundances recorded in each habitat.

📄 Preview file format

lower	C	CSF	GM	LP	LU	MH	NH	NL	PP	RG	ST	W
01PLANT.Ash	0	0	0	28	0	28	28	0	0	28	28	28
01PLANT.Autumn Hawkbit	0	0	54	0	0	0	54	0	162	54	0	0
01PLANT.Bindweed sp	0	0	18	18	0	18	18	0	18	54	0	18
01PLANT.Black Bindweed	22	22	0	0	11	0	11	0	0	0	0	0
01PLANT.Blackthorn	110	0	110	110	0	220	110	0	0	110	0	110
01PLANT.Bluebell	0	0	0	0	0	8	0	0	0	0	0	16

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nore2.csv

Interactions between species, plus abundances of the upper trophic group in each habitat and month (scaled up to the area of the transect).

📄 Preview file format

lower	upper	fortotals	habitat	round
01PLANT.Charlock	02FV.Tetramesa sp	747.57433	C	13
01PLANT.Charlock	02FV.Andrena dorsata	747.57433	C	13
01PLANT.Sow-thistle sp	02FV.Sphaerophoria scripta	747.57433	C	16
01PLANT.Sow-thistle sp	02FV.Helophilus pendulus	747.57433	C	16

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service_edgelist.csv

Which species provide which potential NCP or disservice.

📄 Preview file format

lower	upper	weight
02FV.Agriotes pallidulus	Pollination	1
02FV.Alysiinae sp	Pollination	1
02FV.Anapausis soluta	Pollination	1
02FV.Anaspis maculata	Pollination	1
02FV.Anaspis pulicaria	Pollination	1
02FV.Andrena dorsata	Pollination	1
02FV.Andrena minutula	Pollination	1

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habitatarea.csv

Area of each habitat, in the 2007 and 2008 survey years.

📄 Preview file format

HabitatCode	HabitatDescription	Area_2007	Area_2008
C	Cereal – spring-sown barley, lucerne	33	59.8
SF	Spring fallow	5.7	0
GM	Grass margin around arable field	5.5	0.2
LP	Ley pasture (established)	48.2	14.3

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📋 All data files at a glance

A quick-reference table for every file used or produced across the whole pipeline — raw and processed.

🌱 Raw data (Data/Raw_data/)

File	Contains
PLANT_HABITAT3.csv	Plant abundances recorded in each habitat.
nore2.csv	Interactions between species, plus abundances of the upper trophic group in each habitat and month (scaled to transect area).
service_edgelist.csv	Which species provide which potential NCP or disservice.
habitatarea.csv	Area of each habitat (2007 and 2008 survey years).

🧬 Repositories (Data/Repositories/)

File	Contains
BirdFuncDat.txt	Bird body mass data (Wilman et al. 2016), used to assign biomass to seed-feeding birds.
MamFuncDat.txt	Mammal body mass data (Wilman et al. 2016), used to assign biomass to seed-feeding rodents.
bodysizes_2008.txt	Body mass data (Brose et al. 2005), used to assign biomass to aphids, aphid parasitoids, leaf-miner parasitoids, insect seed-feeder parasitoids, and seed-feeding insects.
Orford_et_al_2015.csv	Pollen-transport records, used to identify which flower visitors act as pollinators.
DoPI.csv	Hymenoptera pollen-transport records (DoPI database), used for the same purpose.
coleoptera.xlsx	Body mass data for beetles and other flower-visiting species.

⚙️ Processed data (Data/)

File	Contains
species_abundances.csv	Species abundance per habitat.
elist_nore.csv	List of species interactions in each habitat.
nodes.csv	List of species in the farm.
pollinators_sp.csv	List of flower-visiting species confirmed to transport pollen, used to distinguish pollinators from non-pollinators.
Norwood_farm.RData	The multilayer network object: species list (nodes), habitat list (layers), interaction lists (extended, extended_ids), and species-per-habitat list (state_nodes).
biomass.csv	Species list with assigned biomass (body mass, g).
Land_use_state_nodes_M1_M2.csv	Species abundance and taxon, for every land management scenario.
Land_use_edgelist_M1_M2.csv	Species interactions, for every land management scenario.
Land_use_dir_ES_M1_M2.csv	Direct NCP provision per species, for every land management scenario.
Land_use_ind_1hop_M1_M2.csv	First-order (1-hop) indirect effects on NCP. (Intermediate)
Land_use_ind_2hop_M1_M2.csv	Second-order (2-hop) indirect effects on NCP. (Intermediate)
Land_use_ind_ES_M1_M2.csv	Combined 1st + 2nd order indirect effects on NCP, for every land management scenario.
z_score_dir_ES_CP_M1_M2_A2.csv	Z-scores for the proportion of direct NCP retained, vs. the null model.
z_score_amount_ES_CP_M1_M2_A2.csv	Z-scores for the relative change in the amount of NCP provided, vs. the null model.
z_score_ind_ES_CP_M1_M2_A2.csv	Z-scores for the proportion of indirect effects on NCP retained, vs. the null model.
Land_use_shortpath_M1_M2.csv	Each species' shortest path to NCP-provider species, per scenario.
SE_sim_CP_M1_M2_A2.csv	500 randomized edge lists, SE scenario (null model).
SE_sim_state_node_CP_M1_M2_A2.csv	500 randomized state-node lists, SE scenario (null model).
M_sim_CP_M1_M2_A2.csv	500 randomized edge lists, M scenario (null model).
M_sim_state_node_CP_M1_M2_A2.csv	500 randomized state-node lists, M scenario (null model).
SI_sim_CP_M1_M2_A2.csv	500 randomized edge lists, SI scenario (null model).
SI_sim_state_node_CP_M1_M2_A2.csv	500 randomized state-node lists, SI scenario (null model).
I_sim_CP_M1_M2_A2.csv	500 randomized edge lists, I scenario (null model).
I_sim_state_node_CP_M1_M2_A2.csv	500 randomized state-node lists, I scenario (null model).
IM_sim_CP_M1_M2_A2.csv	500 randomized edge lists, IN scenario, after the weed-filtering rule (null model).
IM_sim_state_node_CP_M1_M2_A2.csv	500 randomized state-node lists, IN scenario (null model).
sps_removed_SE_CP_M1_M2_A2.csv	Species randomly removed per iteration, SE scenario, with degree (null model).
sps_removed_M_CP_M1_M2_A2.csv	Species randomly removed per iteration, M scenario (null model).
sps_removed_SI_CP_M1_M2_A2.csv	Species randomly removed per iteration, SI scenario (null model).
sps_removed_I_CP_M1_M2_A2.csv	Species randomly removed per iteration, I scenario (null model).
sps_removed_IM_CP_M1_M2_A2.csv	Species removed by the deterministic weed-filtering rule, IN scenario (null model).
sps_removed_sim_CP_M1_M2_A2.csv	All species-removed files above, combined into one.
shuff_hab_WD_RG_CP_M1_M2_A2.csv	500 randomized WD/RG habitats, SE scenario (null model). (too heavy to upload)
shuff_hab_M_CP_M1_M2_A2.csv	500 randomized habitats, SE + M scenarios combined (null model). (too heavy to upload)
shuff_hab_SI_CP_M1_M2_A2.csv	500 randomized habitats, SE + M + SI scenarios combined (null model). (too heavy to upload)
shuff_hab_I_CP_M1_M2_A2.csv	500 randomized habitats, SE + M + SI + I scenarios combined (null model). (too heavy to upload)
edge_list_sim_CP_M1_M2_A2.csv	All scenarios' randomized edge lists combined, plus the empirical network (null model).
state_node_sim_CP_M1_M2_A2.csv	All scenarios' randomized state-node lists combined, plus the empirical network (null model).
direct_ES_sim_CP_M1_M2_A2.csv	Direct NCP provision per species, for every randomized network (null model).
ind_1hop_sim_CP_M1_M2_A2.csv	First-order (1-hop) indirect effects on NCP, for every randomized network (null model). (too heavy to upload)
ind_2hop_sim_CP_M1_M2_A2_SE.csv / _M / _SI / _I / _IN	Second-order (2-hop) indirect effects on NCP, one file per scenario (null model). (too heavy to upload)
Indirect_ES_sim_CP_M1_M2_A2.csv	Combined 1st + 2nd order indirect effects on NCP, across all 500 randomized networks and all scenarios (null model). (too heavy to upload)