DOI: 10.5061/dryad.08kprr5cb
title: Arthropod density observations and measures of crop production in California citrus

description: Early studies and theory suggested that complex landscapes harboring
 remnants of natural land should support natural enemy populations and
 reduce pest buildup in adjacent crops, whereas landscapes interspersed
 with urban land often provide alternate host plants of crop pests,
 facilitating pest spillover and amplifying pest pressure. However, recent
 meta-analyses have demonstrated that both pest and beneficial agricultural
 arthropods respond inconsistently to surrounding landscapes. These
 meta-analyses relied on studies of one to two pests per crop across many
 different crop and landscape contexts, which limits inferences about how
 growers might design landscapes for effective control of a full suite of
 pests attacking a given crop. Here, we harnessed an ecoinformatics dataset
 from California Citrus to examine the effects of surrounding natural and
 urban land on the densities of a complete suite of seven major pest
 species (7,625 observations) and one beneficial predator (335
 observations). We also explored landscape effects on pesticide use and
 fruit production. Despite restricting this analysis to data collected in
 the same region and cropping system, we found that arthropods still
 exhibited mixed responses to surrounding landscapes. Among the eight
 Citrus-associated arthropods surveyed, greater amounts of nearby natural
 land resulted in two outcomes beneficial for farmers (lower pest densities
 or fewer pesticide applications targeting that pest), three adverse
 outcomes, and three neutral outcomes. Similarly, greater amounts of urban
 land resulted in one beneficial outcome, three adverse outcomes, and four
 neutral outcomes for growers. Our economic analysis demonstrated no
 significant effects of either natural or urban land on total pesticide use
 or fruit quality, but reduced total fruit yield in Citrus groves with more
 nearby natural land. Taken altogether, our results do not demonstrate
 clear support for the retention of natural habitat or minimization of
 urban land near cropland solely for the purpose of enhancing conservation
 biocontrol. Nonetheless, the value of natural land extends far beyond its
 utility for conservation biocontrol, and agricultural landscapes must
 still be managed to strike a balance between crop production and the
 preservation of biodiversity and ecosystem function.
description: These data were aggregated from several independent sources.
 These include Citrus growers, pest control advisors, packing houses, the
 USGS National Land Cover Database. and the USDA CropScape data
 layer. Natural, urban, and crop land use data were
 extracted from the USGS National Land Cover Database by creating circular
 buffers around focal Citrus fields at four spatial scales (500m, 1km, 2km,
 and 4km). These data were grouped into three main categories including
 urban land, natural land, cropland, and other noncropland. The
 "other" category comprised mostly water and barren land.
   For citrus cover, we used the USDA CropScape Data
 Layer (CDL). We subtracted citrus cover from the NLCD cropland area to
 create the two land use categories of citrus and other cropland.
 Arthropod observations and pesticide applications were reported
 by independent pest control advisors hired by Citrus growers. Each species
 was sampled differently, and the methods are described in detail in the
 associated manuscript.  Fruit quality and yield were
 reported by packing houses hired by Citrus growers. 
 Abundance observations of arthropods were averaged across samples
 taken within focal Citrus fields because fields were sampled more than
 once per year. The unique identifier for each field is
 "field_code", and the unique identifier of the field per year is
 "field_year".
description: # Arthropod density observations and measures of crop production in
 California citrus **GENERAL INFORMATION** Title of Dataset: Arthropod
 density observations and measures of crop production in California Citrus
 Author/Principal Investigator Information Name: Mia Lippey
 ORCID:0000-0002-8292-3444 Institution: University of California, Davis
 Address: 1 Shields Ave, Davis, CA 95616 Email:
 [mklippey@ucdavis.edu](mailto:mklippey@ucdavis.edu) Date of data
 collection: 2006 - 2019 Geographic location of data collection: San
 Joaquin Valley, California Information about funding sources that
 supported the collection of the data: USDA-FACT **SHARING/ACCESS
 INFORMATION** Licenses/restrictions placed on the data: none; data were
 previously restricted, but all sensitive information has been redacted Was
 data derived from another source? If yes, list source(s): Citrusformatics
 database (privately hosted) Recommended citation for this dataset: pending
 DATA & FILE OVERVIEW Are there multiple versions of the dataset? Yes
 If yes, name of file(s) that was updated: Data_Dump_9_20_23 Why was the
 file updated? It was raw data that needed to be wrangled for analysis When
 was the file updated? 09-27-2023 **METHODOLOGICAL INFORMATION**
 Description of methods used for collection/generation of data: This data
 is an ecoinformatics dataset, so all arthropod observations and measures
 of crop production were reported by independent Citrus growers and
 associated pest control advisors in the San Joaquin Valley. Arthropod
 density observations were recorded by field scouts employed by growers,
 and each species was sampled a different way. Methods include
 presence/absence sampling and count data (more details described in
 associated publication). Measures of crop production were recorded by
 packing houses employed by growers, and they include metrics such as crop
 yield and crop quality. Pesticide use data were reported by pest control
 advisors employed by growers. Methods for processing the data: The
 submitted data were processed from the raw data for various purposes. The
 first process was cleaning typos in the dataset. The second process
 included data interpolation for missing time steps or sites. Both were
 conducted by Bodil Cass, and specifics of the data wrangling process have
 been published. Instrument- or software-specific information needed to
 interpret the data: The version of R used for this analysis is R version
 4.3.2 (2023-10-31 ucrt). The packages need to run the script include
 tidyverse, dplyr, car, ape, mgcv, ggplot2, mdthemes, glmmTMB, DHARMa, and
 ggeffects. Standards and calibration information, if appropriate: N/A
 Environmental/experimental conditions: California has a Mediterranean
 climate. Summers are hot and dry, winters are mild and wet. Annual
 precipitation falls almost entirely in the winter months. Describe any
 quality-assurance procedures performed on the data: Each step of data
 cleaning was checked by hand to ensure that mutations and various
 calculations were correct. People involved with sample collection,
 processing, analysis and/or submission: Bodil Cass, Jay Rosenheim, and Mia
 Lippey. DATA-SPECIFIC INFORMATION FOR: Arthropod density observations and
 measures of crop production in California Citrus Number of variables: 43
 Number of cases/rows: 3998 Variable List: * field_code: a number for each
 unique field site - crop_year -the year that the data were collected *
 field_year is a variable that pastes field_code with crop_year to create a
 unique identifier for each field site for each year - field_size_ha -size
 of focal citrus field in ha * observer -the anonymized name of pest
 control agents who collected the data. We aggregated individual PCAs into
 "PCA_group_1" and "PCA_group_2", putting together PCAs
 with comparable sampling methods.  - region_16 is a variable used to
 control for spatial autocorrelation which divides the entire San Joaquin
 Valley site into 16 equally sized squares (a proxy for lat/long, which is
 sensitive information and has been redacted) * tree_age -age of each
 citrus focal field - urban_proportions -the absolute proportional area of
 urban land within each circular buffer around each focal field at radii
 scales of 500m, 1km, 2km, and 4km * natural_proportions -the absolute
 proportional area of natural land within each circular buffer around each
 focal field at radii scales of 500m, 1km, 2km, and 4km -
 citrus_proportions -the absolute proportional area of citrus crops within
 each circular buffer around each focal field at radii scales of 500m, 1km,
 2km, and 4km * other_cropland_proportions -the absolute proportional area
 of non-citrus cropland within each circular buffer around each focal field
 at radii scales of 500m, 1km, 2km, and 4km - other_noncropland_proportions
 -the absolute proportional area of other land uses (water, barren land,
 etc.) within each circular buffer around each focal field at radii scales
 of 500m, 1km, 2km, and 4km * katydid_area_percent_infested -an average of
 density observations for katydids per field per year - katydid_sprays
 -number of pesticide sprays targeting katydids per field per year *
 citricola_area_percent_infested -an average of density observations for
 citricola per field per year - citricola_sprays -number of pesticide
 sprays targeting citricola per field per year *
 fruit_dam_per_bin_red_scale -an average of density observations for red
 scale per field per year - red_scale_sprays -number of pesticide sprays
 targeting red scale per field per year * thrips_area_percent_infested -an
 average of density observations for thrips per field per year -
 thrips_sprays -number of pesticide sprays targeting thrips per field per
 year * red_mite_area_percent_infested -an average of density observations
 for red mite per field per year - red_mite_sprays -number of pesticide
 sprays targeting red mite per field per year *
 cottony_area_percent_infested -an average of density observations for
 cottony cushion scale per field per year - fruit_dam_per_bin_peelminer -an
 average of density observations for peelminer per field per year *
 Euseius_area_insect_count -an average of density observations for Euseius
 per field per year - total_num_sprays -total number of pesticide sprays
 across all pests per field per year * fruit_quality_metric -fruit quality
 of citrus blocks per year, on a continuous scale from 0-2 -
 harvest_total_kg_per_ha -total fruit harvested per block per year in kg/ha
 Missing data codes: N/A          Specialized formats or other
 abbreviations used: N/A