trashbirdecology/parrot_mgmt

Systematic review of management of non-native and invasive parrots

Using GeoDeepDive (xDD) to Ping the White and Grey Literature for Parrot Management

Last updated: 2020-03-19

About

This project seeks to identify publications within which keywords related to parrot management or parrot culling has been referenced or mentioned. This project uses pre-extracted information available via API from the GeoDeepDive infrastructure.

Note: This readme is difficult, I know, but is not currenlty intended for a broad audience. Note2: Reproduction requires some knowledge or patience with Jupyter and R.

Hit up the GeoDeepDive (xDD) API using a Jupyter Notebook

Open the Jupyter notebook in your web browser by doing the following:
1. Open terminal (Mac) or Command Line (Windows, Linux)
2. Navigate to this directory (cd ~/path/to/parrot_xdd/)
3. Open the .ipynb (type: jupyter notebook). This opens the notebook directory in your web browser.
4. Navigate to (i.e. click) the file parrot_xDD.ipynb: this will open the notebook and a Kernel.
5. Edit the terms (keywords, search phrases). Edit the code chunk containing terms. See section: Set a term or loop through terms, and edit inside brackets at terms = [...]
6. Save the notebook (it typically autosaves but just to be safe). Ctrl+S (MS) or Cmd+S (Mac) or >File>Save and Checkpoint
7. Execute the notebook (Run or >Kernel>Restart and Run All)
8. Navigate to the results (~/xdd_json/)

Import the JSON results to R

# Import the JSON files and munge into a single data frame ----------------
files <- list.files(here::here("xdd_json"), pattern='.txt', full.names=TRUE)
# Identify and delete the empty .txt files. Yes, this is poor practice but oh well!
for(i in seq_along(files)){
  if(i==1) keep <-NULL
if(file.info(files[i])$size > 5){ # retrieve file only if it's >5bytes.
  keep <- c(keep,i)}
}

Import and munge the xdd json into an R df

parrot_xdd <- get_xdd_df(files[keep])
parrot_unique <- parrot_xdd %>% distinct(doi, .keep_all = TRUE) %>% dplyr::select(-searchterm)

Overview of parrot records (N= 50) retrieved from the GeoDeepDive database.

We have used various search terms to identify potential works of relevance to parrot management. Using various searches (see parrot_xdd.ipynb), we identified 50 unique publications.

title	coveryear	pubname	doi	URL
Monk Parakeets An Expanding Problem on Power Lines and Other Electrical Utility Structures	2008	Environment Concerns in Rights-of-Way Management 8th International Symposium 12–16 September 2004 Saratoga Springs, New York, USA	10.1016/B978-044453223-7.50043-5	http://www.sciencedirect.com/science/article/pii/B9780444532237500435
Contaminant-induced feminization and demasculinization of nonmammalian vertebrate males in aquatic environments	2006	Environmental Research	10.1016/j.envres.2005.04.002	http://www.sciencedirect.com/science/article/pii/S0013935105000551
Avian quarantine	1997	Australian Veterinary Journal	10.1111/j.1751-0813.1997.tb15361.x	http://doi.wiley.com/10.1111/j.1751-0813.1997.tb15361.x
The evolution of plumage colouration in parrots: a review	2010	Emu - Austral Ornithology	10.1071/MU09076	https://www.tandfonline.com/doi/full/10.1071/MU09076
Plant invasions in the rivers of the Iberian Peninsula, south-western Europe: A review	2013	Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology	10.1080/11263504.2013.861539	http://www.tandfonline.com/doi/abs/10.1080/11263504.2013.861539
Using Myriophyllum aquaticum (Vell.) Verdc. to remove heavy metals from contaminated water: Better dead or alive?	2018	Journal of Environmental Management	10.1016/j.jenvman.2018.02.074	https://www.sciencedirect.com/science/article/pii/S0301479718301816
Projections of the oval nucleus of the hyperstriatum ventrale in the budgerigar: Relationships with the auditory system	2001	The Journal of Comparative Neurology	10.1002/cne.1115	http://doi.wiley.com/10.1002/cne.1115
Harvesting, local trade, and conservation of parrots in the Northeastern Peruvian Amazon	2003	Biological Conservation	10.1016/S0006-3207(03)00071-5	https://www.sciencedirect.com/science/article/pii/S0006320703000715
KERATOCONJUNCTIVITIS AND CHLAMYDIOSIS IN CAGE BIRDS	1974	Australian Veterinary Journal	10.1111/j.1751-0813.1974.tb14106.x	http://doi.wiley.com/10.1111/j.1751-0813.1974.tb14106.x
Assessment of UAV Operator Workload in A Reconfigurable Multi-Touch Ground Control Station Environment	2016	Journal of Unmanned Vehicle Systems	10.1139/juvs-2015-0039	http://www.nrcresearchpress.com/doi/10.1139/juvs-2015-0039
Drone services: issues in drones for location-based services from human-drone interaction to information processing	NA	Journal of Location Based Services	10.1080/17489725.2018.1564845	https://www.tandfonline.com/doi/full/10.1080/17489725.2018.1564845
Certified organic agriculture in China and Brazil: Market accessibility and outcomes following adoption	2010	Ecological Economics	10.1016/j.ecolecon.2010.04.016	http://www.sciencedirect.com/science/article/pii/S092180091000159X
ANATOMY OF A BOTTLENECK: DIAGNOSING FACTORS LIMITING POPULATION GROWTH IN THE PUERTO RICAN PARROT	2008	Ecological Monographs	10.1890/07-0018.1	http://doi.wiley.com/10.1890/07-0018.1
Strategic collection planning: Theory and practice	1995	Zoo Biology	10.1002/zoo.1430140103	http://doi.wiley.com/10.1002/zoo.1430140103
The effect of a closed area and beach seine exclusion on coral reef fish catches	2001	Fisheries Management and Ecology	10.1046/j.1365-2400.2001.00239.x	http://doi.wiley.com/10.1046/j.1365-2400.2001.00239.x
A novel herpesvirus associated with respiratory disease in Bourke’s parrots ( Neopsephotus bourkii )	2012	Avian Pathology	10.1080/03079457.2012.732692	http://www.tandfonline.com/doi/abs/10.1080/03079457.2012.732692
Avian research in the Caribbean: past contributions and current priorities	2012	Journal of Field Ornithology	10.1111/j.1557-9263.2012.00361.x	http://doi.wiley.com/10.1111/j.1557-9263.2012.00361.x
A review and an empirical analysis of privacy policy and notices for consumer Internet of things	NA	Security and Privacy	10.1002/spy2.15	http://doi.wiley.com/10.1002/spy2.15
Nest tree selection in a crowded introduced population of Monk Parakeet ( Myiopsitta monachus ) in Rome (central Italy): evidence for selectivity	2017	Zoology and Ecology	10.1080/21658005.2017.1366293	https://www.tandfonline.com/doi/full/10.1080/21658005.2017.1366293
Trade and conservation implications of new beak and feather disease virus detection in native and introduced parrots	2018	Conservation Biology	10.1111/cobi.13214	http://doi.wiley.com/10.1111/cobi.13214
Potential distribution of alien parakeets in Tuscany (Central Italy): a bioclimatic model approach	2014	Ethology Ecology & Evolution	10.1080/03949370.2014.895424	http://www.tandfonline.com/doi/abs/10.1080/03949370.2014.895424
Detailed monitoring of a small but recovering population reveals sublethal effects of disease and unexpected interactions with supplemental feeding	2015	Journal of Animal Ecology	10.1111/1365-2656.12348	http://doi.wiley.com/10.1111/1365-2656.12348
The parakeet protectors: Understanding opposition to introduced species management	2019	Journal of Environmental Management	10.1016/j.jenvman.2017.11.036	https://www.sciencedirect.com/science/article/pii/S0301479717311118
Deterring hooded crows from re-nesting on power poles	2012	Wildlife Society Bulletin	10.1002/wsb.211	http://doi.wiley.com/10.1002/wsb.211
Long-term, fine-scale temporal patterns of genetic diversity in the restored Mauritius parakeet reveal genetic impacts of management and associated demographic effects on reintroduction programmes	2013	Biological Conservation	10.1016/j.biocon.2013.02.013	http://www.sciencedirect.com/science/article/pii/S000632071300061X
Mediterranean versus Atlantic monk parakeets Myiopsitta monachus : Towards differentiated management at the European scale	NA	Pest Management Science	10.1002/ps.5320	http://doi.wiley.com/10.1002/ps.5320
Unrelenting spread of the alien monk parakeet Myiopsitta monachus in Israel. Is it time to sound the alarm?	2016	Pest Management Science	10.1002/ps.4349	http://doi.wiley.com/10.1002/ps.4349
Concerns regarding the scientific evidence informing impact risk assessment and management recommendations for invasive birds	2011	Biological Conservation	10.1016/j.biocon.2011.05.001	http://www.sciencedirect.com/science/article/pii/S0006320711001881
Social–ecological mismatches create conservation challenges in introduced species management	2019	Frontiers in Ecology and the Environment	10.1002/fee.2000	https://onlinelibrary.wiley.com/doi/abs/10.1002/fee.2000
Monk parakeet nest-site selection of electric utility structures in Texas	2014	Landscape and Urban Planning	10.1016/j.landurbplan.2014.04.016	http://www.sciencedirect.com/science/article/pii/S0169204614001005
Worldwide impact of alien parrots (Aves Psittaciformes) on native biodiversity and environment: a review	2014	Ethology Ecology & Evolution	10.1080/03949370.2014.905981	http://www.tandfonline.com/doi/abs/10.1080/03949370.2014.905981
Interspecific interactions in nesting and feeding urban sites among introduced Monk Parakeet ( Myiopsitta monachus ) and syntopic bird species	2016	Ethology Ecology & Evolution	10.1080/03949370.2015.1119761	https://www.tandfonline.com/doi/full/10.1080/03949370.2015.1119761
Preliminary evidence suggests extra-pair mating in the endangered echo parakeet, Psittacula eques	2015	African Zoology	10.1080/15627020.2009.11407440	https://www.tandfonline.com/doi/full/10.1080/15627020.2009.11407440
AFFECTIVE ETHOLOGIES	2015	Angelaki	10.1080/0969725X.2015.1065118	https://www.tandfonline.com/doi/full/10.1080/0969725X.2015.1065118
Characterization of Mauritius parakeet ( Psittacula eques ) microsatellite loci and their cross-utility in other parrots (Psittacidae, Aves)	2009	Molecular Ecology Resources	10.1111/j.1755-0998.2009.02621.x	http://doi.wiley.com/10.1111/j.1755-0998.2009.02621.x
Establishment success of invasive ring-necked and monk parakeets in Europe	2009	Journal of Biogeography	10.1111/j.1365-2699.2009.02177.x	http://doi.wiley.com/10.1111/j.1365-2699.2009.02177.x
Diazacon Inhibits Reproduction in Invasive Monk Parakeet Populations	2008	Journal of Wildlife Management	10.2193/2007-391	http://www.bioone.org/doi/abs/10.2193/2007-391
Preferences of Orange-winged Amazon parrots (Amazona amazonica) for cage enrichment devices	2009	Applied Animal Behaviour Science	10.1016/j.applanim.2009.06.006	http://www.sciencedirect.com/science/article/pii/S0168159109001932
Ecological rhythms and the management of humid tropical forests Examples from the Caribbean National Forest, Puerto Rico	2001	Forest Ecology and Management	10.1016/S0378-1127(01)00515-1	http://www.sciencedirect.com/science/article/pii/S0378112701005151
An economic assessment of the potential for predator management to benefit Puerto Rican parrots	2003	Ecological Economics	10.1016/S0921-8009(03)00143-5	http://www.sciencedirect.com/science/article/pii/S0921800903001435
Ground Parrots and fire in east Gippsland, Victoria: habitat occupancy modelling from automated sound recordings	2016	Emu - Austral Ornithology	10.1071/MU16014	https://www.tandfonline.com/doi/full/10.1071/MU16014
Spatial and seasonal variation in abundance within an insular grey parrot population	2017	African Journal of Ecology	10.1111/aje.12367	http://doi.wiley.com/10.1111/aje.12367
Situation-dependant management of large parrots by manipulation of the social environment	2000	International Zoo Yearbook	10.1111/j.1748-1090.2000.tb00729.x	http://doi.wiley.com/10.1111/j.1748-1090.2000.tb00729.x
Management of the Double-eyed or Red-browed fig parrot Cyclopsitta diophthalma macleayana at Currumbin Sanctuary, Queensland	2000	International Zoo Yearbook	10.1111/j.1748-1090.2000.tb00716.x	http://doi.wiley.com/10.1111/j.1748-1090.2000.tb00716.x
The Large-Scale Removal of Mammalian Invasive Alien Species in Northern Europe	2015	Pest Management Science	10.1002/ps.4224	http://doi.wiley.com/10.1002/ps.4224
Factors Related to Farmers’ Preferences to Decrease Monk Parakeet Damage to Crops	2013	Human Dimensions of Wildlife	10.1080/10871209.2013.745102	http://www.tandfonline.com/doi/abs/10.1080/10871209.2013.745102
Threats from introduced birds to native birds	2014	Emu - Austral Ornithology	10.1071/MU12122	https://www.tandfonline.com/doi/full/10.1071/MU12122
General management principles and a checklist of strategies to guide forest biodiversity conservation	2006	Biological Conservation	10.1016/j.biocon.2006.02.019	http://www.sciencedirect.com/science/article/pii/S0006320706000814
Reed warblers discriminate cuckoos from sparrowhawks with graded alarm signals that attract mates and neighbours	2008	Animal Behaviour	10.1016/j.anbehav.2008.03.020	https://www.sciencedirect.com/science/article/pii/S0003347208002170
Foraging ‘enrichment’ as treatment for pterotillomania	2008	Applied Animal Behaviour Science	10.1016/j.applanim.2007.05.015	https://www.sciencedirect.com/science/article/pii/S0168159107001669

Distribution across publications:

Results Files

Overviews of the results can be found in the results folder in this repository.

Total records per publication

pubname	count
African Journal of Ecology	2
African Zoology	2
Angelaki	2
Animal Behaviour	1
Applied Animal Behaviour Science	3
Australian Veterinary Journal	2
Avian Pathology	1
Biological Conservation	6
Conservation Biology	2
Ecological Economics	3
Ecological Monographs	1
Emu - Austral Ornithology	4
Environment Concerns in Rights-of-Way Management 8th International Symposium 12–16 September 2004 Saratoga Springs, New York, USA	1
Environmental Research	1
Ethology Ecology & Evolution	6
Fisheries Management and Ecology	1
Forest Ecology and Management	2
Frontiers in Ecology and the Environment	2
Human Dimensions of Wildlife	1
International Zoo Yearbook	4
Journal of Animal Ecology	2
Journal of Biogeography	2
Journal of Environmental Management	5
Journal of Field Ornithology	1
Journal of Location Based Services	1
Journal of Unmanned Vehicle Systems	1
Journal of Wildlife Management	2
Landscape and Urban Planning	2
Molecular Ecology Resources	2
Pest Management Science	7
Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology	1
Security and Privacy	1
The Journal of Comparative Neurology	1
Wildlife Society Bulletin	2
Zoo Biology	1
Zoology and Ecology	2

More Information

This project relies on the UW Deepdive Infrastructure

See the UW deepdive infrastructure for more details. Check out the wiki for more information on getting started.

Disclaimer

This software is preliminary or provisional and is subject to revision. It is being provided to meet the need for timely best science. The software has not received final approval by the U.S. Geological Survey (USGS). No warranty, expressed or implied, is made by the USGS or the U.S. Government as to the functionality of the software and related material nor shall the fact of release constitute any such warranty. The software is provided on the condition that neither the USGS nor the U.S. Government shall be held liable for any damages resulting from the authorized or unauthorized use of the software.

parrot_mgmt's Issues

Compile search terms

terms =
['"parrot+management"',
'parrot+management',
#'"psittacid+management"', # no results...
#'psittacid+management', # no results...
'"management+of+parrot"',
#'"management+of+psittacid"', # no results...
'"managing+parrot"' , # one medical result (parrot bites :D)...
'"managing+psittacid"', # no results...
'culling+parrot', # no results...
'parrot+cull', # no results...
'parrot+control',
'"control+for+parrot"',
'parrot*cull',# no results...
'"cull+of+parrot"', # no results...
# spanish/portugeuse terms

need to update boolean to include other languages. See this issue for a

response re: non-English terms

     #'conflicto*loros',   
     #'manejo+de+loros',  
     #'manejo+de+parabas', 
     #’gestion+de+loros', 
     #’gestion+de+parabas', 
     #'cultivos*loros',  
     #'loros*plaga' 
              ]

Placeholder for notes

Harvesting papers from grey and white literature using XDD (exploratory)
JLB is toying around with using geodeepdive/xdd to identify some otherwise hidden literature.
xDD uses a text mining algorithm to ping an increasingly large (but not yet comprehensive) database.
Here’s a link to the repository containing ^ and the code and notebook, including a very quick and extremely crappy readme.
Here’s a link to the JSON files containing all the grey and white search hits I retrieved using xdd (GeoDeepDive). Note: some of these are empty. These are the raw files grabbed from the REST API, and there are numerous duplicates.
Here’s file containing the unique publications retrieved.

ACTION ITEM: Please let me know what common search terms /phrases would be best for pinging the literature for management-relevant parrot papers. Here’s what I’ve got so far:

terms =
['"parrot+management"',
'parrot+management',
#'"psittacid+management"', # no results...
#'psittacid+management', # no results...
'"management+of+parrot"',
#'"management+of+psittacid"', # no results...
'"managing+parrot"' , # one medical result (parrot bites :D)...
'"managing+psittacid"', # no results...
'culling+parrot', # no results...
'parrot+cull', # no results...
'parrot+control',
'"control+for+parrot"',
'parrot*cull',# no results...
'"cull+of+parrot"', # no results...
# spanish/portugeuse terms

need to update boolean to include other languages. See this issue for a

response re: non-English terms

     #'conflicto*loros',   
     #'manejo+de+loros',  
     #'manejo+de+parabas', 
     #’gestion+de+loros', 
     #’gestion+de+parabas', 
     #'cultivos*loros',  
     #'loros*plaga' 
              ]