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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
About me
Posts
Regular expressions for replication
Published:
As part of the publication process for my recent article on how states preempt separatist conflict, I needed to submit replication materials to the journal. I took my graduate quantitative methods sequence with the late Tom Carsey, so I’ve long been a proponent replicability efforts in social science. I also had an hourly job in grad school replicating quantitative results for multiple political science journals, so I’m very familiar with best practices for replication. Unfortunately, in the four years since I wrote the first line of code for this project, somewhere in between defending my dissertation and starting a new job (ok, fine, almost immediately after writing that first line of code), I got a little lazy.
Faceted maps in R
Published:
I recently needed to create a choropleth of a few different countries for a project on targeting of UN peacekeepers by non-state armed actors I’m working on. A choropleth is a type of thematic map where data are aggregated up from smaller areas (or discrete points) to larger ones and then visualized using different colors to represent different numeric values.
Finding Backcountry Campsites with CalTopo, OpenStreetMap, and R
Published:
Like many people, I’ve been spending more time outdoors during this pandemic. While this means daily walks in my neighborhood, it also means getting out into the wilderness and sleeping in a tent when I can. Although outdoor recreation is one of the safer ways to entertain yourself these days, it’s not without its own concerns. The difficulty of safely getting to trailheads means that while I’m backpacking more than usual, it’s still not as often as I’d like.
R Markdown, Jekyll, and Footnotes
Published:
I use jekyll to create my website. Jekyll converts Markdown files into the HTML that your browser renders into the pages you see. As others and I have written before, it’s pretty easy to use R Markdown to generate pages with R code and output all together. One thing has consistently eluded me, however: footnotes.
Working with Large Spatial Data in R
Published:
In my research I frequently work with large datasets. Sometimes that means datasets that cover the entire globe, and other times it means working with lots of micro-level event data. Usually, my computer is powerful enough to load and manipulate all of the data in R without issue. When my computer’s fallen short of the task at hand, my solution has often been to throw it at a high performance computing cluster. However, I finally ran into a situation where the data proved too large even for that approach.
Jekyll and HTML Widgets
Published:
I’m currently compiling a list of university-affiliated programs designed to help prepare students for graduate study in political science and assist them in the process of applying to graduate school (a labyrinthine and opaque process in many regards). Since travel costs can be a deciding factor for some students when deciding whether to apply to these programs, I thought it would be nice to also put them on a map.
Extracting UN Peacekeeping Data from PDF Files
Published:
Some coauthors and I recently published a piece in the Monkey Cage on the recent military coup in Mali and the overthrow of president Ibrahim Boubacar Keïta. We examine what the ouster of Keïta means for the future of MINUSMA, the United Nations peacekeeping mission in Mali. One of my contributions that didn’t make the final cut was this plot of casualties to date among UN peacekeepers in the so-called big 5 peacekeeping missions .
Adding Content to an Academic Website
Published:
One thing I haven’t covered in my previous posts on creating and customizing an academic website is how to actually add content to your site. You know, the stuff that’s the reason why people go to your website in the first place? If you’ve followed those guides, your website should be professional looking and already feeling a little bit different from the stock template. However, adding new pages or tweaking the existing pages can be a little intimidating, and I realized I should probably walk through how to do so. Luckily Jekyll’s use of Markdown makes it really easy to add new content!
Customizing an Academic Website
Published:
This is a followup to my previous post on creating an academic website. If you’ve followed that guide, you should have a website that’s professional-looking and informative, but it’s probably lacking something to really make it feel like your own. There are an infinite number of ways you could customize the academicpages template (many of them far, far beyond my abilities) but I’m going to walk you through the process I used to start tweaking my website. The goal here isn’t to tell you how you should personalize your website, but to give you the tools to learn how to implement whatever changes you want to make.
Building an Academic Website
Published:
If you’re an academic, you need a website. Obviously I agree with this since you’re reading this on my website, but if you don’t have one, you should get one. Most universities these days provide a free option, usually powered by WordPress (both WashU and UNC use WordPress for their respective offerings). While these sites are quick to set up and come with the prestige of a .edu URL, they have several drawbacks that have been extensively written on.
Visualizing Police Militarization
Published:
Much has been written lately about the increasing militarization of US law enforcement. One of the most visible indicators of this shift in recent decades is the increased frequency of tactical gear and equipment worn and carried by police officers. However, this pales in comparison to images of police departments bringing armored vehicles to peaceful protests.
Counting Words in a Snap
Published:
14 pt periods. 1.05” margins. 2.1 spaced lines. Times Newer Roman. I’ve seen them all, and I’m tired of trying to catch them. So, I’ve stopped assigning papers in terms of page length and switched to word counts. Unfortunately, counting words is more time-intensive than counting pages.
Better Beamer Presentations the Easy Way
Published:
Everyone knows that Beamer makes frankly terrible presentations without a good deal of help. A well crafted Beamer presentation can be a thing of beauty, especially since you can use knitr or R Markdown to automatically generate tables and figures, but it takes a lot of work.
Checking Progress with Bash
Published:
I’m currently cleaning and wrangling a large (> 2 billion observations) dataset. Due to its size, I’m running code in batch mode on a remote cluster. Not running interactively makes it harder for me to check on my code’s progress.
Fancy Icons and LaTeX Quirks
Published:
I recently updated my CV to add my ORCiD identifier to it up top among the other places to find me online. An ORCiD is an online identifier that persists through any changes to your name, institution, or email address throughout your life.
Combining PDF Documents the Smarter Way
Published:
My previous post on combining multiple PDF files had an important caveat that things would end up in the wrong order if you had files with leading ID numbers that started at 1 and ended at 12, you’d end up with PDFs combined in the order 1, 10, 11, 12, 2, 3, …, 9.
Combining PDF Documents
Published:
How many times have you found that your institution has access to a digital version of a book you need only to discover that it comes in 15 different PDF files?
expeditions
publications
The phylogenetic origins and evolutionary history of holocentric chromosomes
Escudero M, Márquez-Corro JI, Hipp AL. 2016. "The phylogenetic origins and evolutionary history of holocentric chromosomes" Systematic Botany 41(3): 580-585. doi:10.1600/036364416X692442
Novedades para la brioflora de la Sierra de Gredos (Sistema Central, España)
Luceño M, Cerrejón C, Guerra-Cárdenas S, Márquez-Corro JI, Pineda-Labella V, Infante M, Muñoz J. 2016. "Novedades para la brioflora de la Sierra de Gredos (Sistema Central, España)" Boletín de la Sociedad Española de Briología 46-47: 43-68.
Two new species in Carex sect. Schoenoxiphium (Cyperaceae) from Southern Africa
Márquez-Corro JI, Maguilla E, Villaverde T, Martín-Bravo S, Luceño M. 2017. "Two new species in Carex sect. Schoenoxiphium (Cyperaceae) from Southern Africa" Phytotaxa 303(1): 320-329. doi:10.11646/phytotaxa.303.1.2
Long-distance dispersal explains the bipolar disjunction in Carex macloviana
Márquez-Corro JI, Escudero M, Martín-Bravo S, Villaverde T, Luceño M. 2017. "Long-distance dispersal explains the bipolar disjunction in Carex macloviana" American Journal of Botany 104(5): 663-673. doi:10.3732/ajb.1700012
New insights into the systematics of the Schoenoxiphium clade (Carex, Cyperaceae)
Villaverde T, Maguilla E, Escudero M, Márquez-Corro JI, Jiménez-Mejías P, Gehrke B, Martín-Bravo S, Luceño M. 2017. "New insights into the systematics of the Schoenoxiphium clade (Carex, Cyperaceae)" International Journal of Plant Sciences 178(4): 320-329. doi:10.1086/691144
A contribution to the knowledge of bryophytes from Sierra de Gredos (Central Spain) including a reevaluation of their national conservation status
Luceño M, Guerra-Cárdenas S, Márquez-Corro JI, Pineda-Labella V, Martín-Bravo S, Infante M, Muñoz J. 2017. "A contribution to the knowledge of bryophytes from Sierra de Gredos (Central Spain) including a reevaluation of their national conservation status" Cryptogamie, Bryologie 38(3): 281-302. doi:10.7872/cryb/v38.iss3.2017.281
Novedades para la brioflora de la Sierra de Gredos (Sistema Central, España), con especial énfasis en la comunidad de Extremadura
Luceño M, Márquez-Corro JI, Guerra-Cárdenas S, Sánvhez-Villegas R, Jurado-Castillo I, Rodríguez-Velasco E, Rodríguez-Escobar JC, Sánchez-Villegas M, Cerrejón C, Estévez-Rodríguez F, Muñoz J. 2017. "Novedades para la brioflora de la Sierra de Gredos (Sistema Central, España), con especial énfasis en la comunidad de Extremadura" Acta Botanica Malacitana 42(2): 195-202. doi:10.24310/abm.v42i2.3366
Present and future of ecological and evolutionary research in Mediterranean-type ecosystems: Conclusions from the last International Mediterranean Ecosystems Conference
The XIV MEDECOS and XIII AEET Consortium. 2017. "Present and future of ecological and evolutionary research in Mediterranean-type ecosystems: Conclusions from the last International Mediterranean Ecosystems Conference" American Journal of Botany 104(12): 1777-1782. doi:10.3732/ajb.1700367
Do holocentric chromosomes represent an evolutionary advantage?
Márquez-Corro JI, Escudero M, Luceño M. 2018. "Do holocentric chromosomes represent an evolutionary advantage? A study of paired analyses of diversification rates of lineages with holocentric chromosomes and their monocentric closest relatives" Chromosome Research 26(3): 139-152. doi:10.1007/s10577-017-9566-8
Cyperaceae chromosome numbers reports in IAPT/IOPB chromosome data 28.
Márquez-Corro JI*, Luceño M*, Jiménez-Mejías P, Escudero M, Martín-Bravo S, Hipp AL, Chung K-S, Muasya AM, Rothrock PE, Weber JE, Naczi R. 2018. "Cyperaceae" in Marhold K & Kucera J (eds.), IAPT/IOPB chromosome data 28. Taxon 67(6): 1240-1242.
Plantas silvestres y ornamentales del campus de la Universidad Pablo de Olavide [Book]
Luceño M, Martín-Bravo S, Sánchez-Villegas R, Escudero M, Sánchez-Villegas M, Márquez-Corro JI, Pulgar Sañudo I. 2019. "Plantas silvestres y ornamentales del campus de la Universidad Pablo de Olavide" Fundación Universidad Pablo de Olavide pp. 448, Sevilla. ISBN 978-84-949948-0-7
Inferring hypothesis-based transitions in clade-specific models of chromosome number evolution in sedges (Cyperaceae)
Márquez-Corro JI, Martín-Bravo S, Spalink D, Luceño M, Escudero M. 2019. "Inferring hypothesis-based transitions in clade-specific models of chromosome number evolution in sedges (Cyperaceae)" Molecular Phylogenetics and Evolution 135(4): 203-209. doi:10.1016/j.ympev.2019.03.006
Karyotype evolution in holocentric organisms [Review]
Márquez-Corro JI, Martín-Bravo S, Pedrosa-Harand A, Hipp AL, Luceño M, Escudero M. 2019. "Karyotype evolution in holocentric organisms" eLS pp. 1-7. doi:10.1002/9780470015902.a0028758
A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification
Martín-Bravo S, Jiménez-Mejías P, Villaverde T, Escudero M, Hahn M, Spalink D, Roalson EH, Hipp AL, Benítez-Benítez B, Bruederle LP, Fitzek E, Ford BA, Ford KA, Garner M, Gebauer S, Hoffmann MA, Xiao-Feng J, Larridon I, Léveillé-Bourret É, Lu Y-F, Luceño M, Maguilla E, Márquez-Corro JI, Míguez M, Naczi R, Reznicek AA, Starr JR. 2019. "A tale of worldwide success: Behind the scenes of Carex (Cyperaceae) biogeography and diversification" Journal of Systematics and Evolution 57(6): 695-718. doi:10.1111/jse.12549
The systematic position of the enigmatic rare South African endemic Carex acocksii: Its relevance on the biogeography and evolution of Carex sect. Schoenoxiphium (Cyperaceae)
Márquez-Corro JI, Jiménez-Mejías P, Helme NA, Luceño M, Martín-Bravo S. 2020. "The systematic position of the enigmatic rare South African endemic Carex acocksii: Its relevance on the biogeography and evolution of Carex sect. Schoenoxiphium (Cyperaceae)" South African Journal of Botany 131: 475-483. doi:10.1016/j.sajb.2020.03.027
Novedades corológicas para la flora vascular de la sierra de Gredos (Sistema Central, España)
Sánchez-Villegas R, Sánchez-Villegas M, Robles Fernández JL, Sánchez Benz C, Sánchez Benz L, Martín-García B, Román Hernández R, Valduciel García MÁ, Márquez-Corro JI, Rico Jiménez JC, Estévez Rodríguez LF, Sánchez-Amador E, De Sande Velicia FJ; Marín Martín P; Rico E, Luceño M. 2020. "Novedades corológicas para la flora vascular de la sierra de Gredos (Sistema Central, España)" Flora Montiberica 75: 101-110.
The evolutionary history of sedges (Cyperaceae) in Madagascar
Larridon I, Spalink D, Jiménez-Mejías P, Márquez-Corro JI, Martín-Bravo S, Muasya AM, Escudero M. 2021. "The evolutionary history of sedges (Cyperaceae) in Madagascar" Journal of Biogeography 48(4): 917-932. doi:10.1111/jbi.14048
A new classification of Cyperaceae (Poales) supported by phylogenomic data
Larridon I, Zuntini A, Léveillé-Bourret É, Barrett RL, Starr JR, Muasya MA, Villaverde T, Bauters K, Brewer G, Bruhl J, Costa S, Elliott T, Epitawalage N, Escudero M, Fairlie I, Goetghebeur P, Hipp AL, Jiménez-Mejías P, Kikuchi IS, Luceño M, Márquez-Corro JI, Martín-Bravo S, Maurin O, Pokorny L, Roalson EH, Semmouri I, Simpson D, Spalink D,Thomas W, Wilson KL, Xanthos M, Forest F, Baker W. 2021. "A new classification of Cyperaceae (Poales) supported by phylogenomic data" Journal of Systematic and Evolution 59(4): 852-895. doi:10.1111/jse.12757
Macroevolutionary insights in sedges (Carex: Cyperaceae): The effects of rapid chromosome number evolution on lineage diversification
Márquez-Corro JI, Martín-Bravo S, Jiménez-Mejías P, Hipp AL, Spalink D, Naczi RFC, Roalson EH, Luceño M, Escudero M. 2021. "Macroevolutionary insights in sedges (Carex: Cyperaceae): The effects of rapid chromosome number evolution on lineage diversification" Journal of Systematic and Evolution 59(4): 776-790. doi:10.1111/jse.12730
A framework infrageneric classification of Carex (Cyperaceae) and its organizing principles
Roalson EH, Jiménez-Mejías P, Hipp AL, Benítez-Benítez C, Bruederle LP, Chung K-S, Escudero M, Ford BA, Ford K, Gebauer S, Gehrke B, Hahn M, Hayat MQ, Hoffmann MH, Jin X-F, Kim S, Larridon I, Léveillé-Bourret É, Lu Y-F, Luceño M, Maguilla E, Márquez-Corro JI, Martín-Bravo S, Masaki T, Míguez M, Naczi RFC, Reznicek AA, Spalink D, Starr JR, Uzma, Villaverde T, Waterway MJ, Wilson KL, Zhang S. 2021. " A framework infrageneric classification of Carex (Cyperaceae) and its organizing principles" Journal of Systematics and Evolution 59(4): 726-762. doi:10.1111/jse.12722
A synopsis of the androgynous species of Carex subgenus Vignea (Cyperaceae) in South America
Jiménez-Mejías P, Martín-Bravo S, Márquez-Corro JI, Donadío S, Roalson EH, Naczi R. 2021. "A synopsis of the androgynous species of Carex subgenus Vignea (Cyperaceae) in South America" Botanical Journal of the Linnean Society 196(2): 188-220. doi:10.1093/botlinnean/boaa100
An integrative monograph of Carex section Schoenoxiphium (Cyperaceae)
Luceño M, Villaverde T, Márquez-Corro JI, Sánchez-Villegas R, Maguilla M, Escudero M, Jiménez-Mejías P, Sánchez-Villegas M, Míguez M, Benítez-Benítez C, Muasya AM, Martín-Bravo S. 2021. "An integrative monograph of Carex section Schoenoxiphium (Cyperaceae)" PeerJ 9: e11336. doi:10.7717/peerj.11336
I Biomaratón de Flora Española: ciencia ciudadana para visibilizar la biodiversidad vegetal
Márquez-Corro JI, Jiménez-Mejías P, Fernández-Mazuecos M, Ramos-Gutiérrez I, Martín-Hernanz S, Martín-Bravo S, Alfaro-Saiz E, Blanco-Salas J, Borras J, Capó M, Carrera-Bonet D, De La Fuente Brun P, Fernandez-Lesaga A, Garnatje T, Gorriz-Huarte L, Molino S, Nualart N, Mairal M. 2021. "I Biomaratón de Flora Española: ciencia ciudadana para visibilizar la biodiversidad vegetal" Conservación Vegetal 25: 33-37
Chromosome size matters: genome evolution in the cyperid clade
Elliott TL, Zedek F, Barrett RL, Bruhl JJ, Escudero M, Hroundová Z, Joly S, Larridon I, Luceño M, Márquez-Corro JI, Martín-Bravo S, Muasya AM, Šmarda P, Thomas WW, Wilson KL, Bureš P. 2022. "Chromosome size matters: genome evolution in the cyperid clade" Annals of Botany 130: 999-1013. doi:10.1093/aob/mcac136
Cyperaceae, sedges [Book chapter]
Larridon I, Spalink D, Jiménez-Mejías P, Márquez-Corro JI, Martín-Bravo S, Muasya AM, Escudero M. 2022. "Cyperaceae, sedges" The New Natural History of Madagascar edited by Goodman SM, Princeton University Press, pp. 580-585. doi:10.2307/j.ctv2ks6tbb.70
Addressing inconsistencies in Cyperaceae and Juncaceae taxonomy: Comment on Brožová et al. (2022)
Elliott TL, Larridon I, Barrett RL, Bruhl JJ, Costa SM, Escudero M, Hipp AL, Jiménez-Mejías P, Kirschner J, Luceño M, Márquez-Corro JI, Martín-Bravo S, Roalson EH, Semmouri I, Spalink D, Thomas WW, Villaverde T, Wilson, KL, Muasya AM. 2023. "Addressing inconsistencies in Cyperaceae and Juncaceae taxonomy: Comment on Brožová et al. (2022)" Molecular Phylogenetics and Evolution 179: 107665. doi:10.1016/j.ympev.2022.107665
Guía de campo de las ciperáceas de España y Portugal [Book]
Luceño M, Sánchez-Villegas R, Quirós de la Peña B, Sánchez-Villegas M, Martín-Bravo S, Maguilla E, Escudero M, Benítez-Benítez C, Villaverde T, Jiménez-Mejías P, Márquez-Corro JI, Sanz-Arnal M, Míguez M. 2023. "Guía de campo de las ciperáceas de España y Portugal" Jolube Consultoría Ambiental pp. 598, Jaca. ISBN 978-84-126656-0-4
Using ChromEvol to determine the mode of chromosomal evolution [Book chapter]
Escudero M, Maguilla E, Márquez-Corro JI, Martín-Bravo S, Mayrose I, Shafir A, Tribble C, Zenil-Ferguson R. 2023. "Using ChromEvol to determine the mode of chromosomal evolution" Plant Cytogenetics and Cytogenomics. Methods in Molecular Biology, vol 2672 edited by Heitkam T and García S, New York, pp. 529–547. doi:10.1007/978-1-0716-3226-0_32
The holocentric chromosome microevolution: from phylogeographic patterns to genomic associations with environmental gradients
Márquez-Corro JI, Martín-Bravo S, Blanco-Pastor JL, Luceño M, Escudero M. 2023. "The holocentric chromosome microevolution: from phylogeographic patterns to genomic associations with environmental gradients" Molecular Ecology 00: 1-13. doi:10.1111/mec.17156
SEBOTA: un encuentro para conocer de cerca la diversidad de nuestra flora
Ramos-Gutiérrez I, Márquez-Corro JI, Martín-Hernanz S. 2023. "SEBOTA: un encuentro para conocer de cerca la diversidad de nuestra flora" Conservación Vegetal 27: 50-51
Genome size of Chilean plants in IAPT/IOPB chromosome data 40.
Márquez-Corro JI, Muñoz-Schüler P, Penneckamp DN, García-Moro P, Sanz-Arnal M, Martín-Bravo S, Alarcón D, Mian S, Leitch IJ, Jiménez-Mejías P, Pellicer J. 2023. "IAPT chromosome data 40/7" in Marhold K & Kucera J (eds.), IAPT/IOPB chromosome data 40. Taxon 72(6): 1388-1389.
The genus Carex (Cyperaceae) in Chile: a general update of its knowledge, with an identification key
Muñoz-Schüler P, García-Moro P, Márquez-Corro JI, Penneckamp D, Sanz-Arnal M, Martín-Bravo S, Jiménez-Mejías P. 2023. "The genus Carex (Cyperaceae) in Chile: a general update of its knowledge, with an identification key" Gayana Botanica 80: 103-132. doi:10.4067/S0717-66432023000200103
Global analysis of Poales diversification – parallel evolution in space and time into open and closed habitats
Elliott TL, Spalink D, Larridon I, Zuntini AR, Escudero M, Hackel J, Barrett RL, Martín-Bravo S, Márquez-Corro JI, Granados-Mendoza C, Mashau AC, Romero-Soler KJ, Zhigila DA, Gehrke B, Andrino CO, Crayn DM, Vorontsova MS, Forest F, Baker WJ, Wilson KL, Simpson DA, Muasya AM. 2024. "Global analysis of Poales diversification – parallel evolution in space and time into open and closed habitats" New Phytologist 242: 727-743. doi:10.1111/nph.19421
A new remarkable species of Scleria (Cyperaceae) from northern Madagascar
Larridon I, Bauters K, Rasaminirina F, Galán-Díaz J, Márquez-Corro JI, Gautier L. 2024. "A new remarkable species of Scleria (Cyperaceae) from northern Madagascar" Candollea 79: 107-116. doi:10.15553/c2024v791a6
