Literature Search for Nexus Biodiversity
Felipe Melo
2023-02-24
Sources for this tutorial are:
https://elizagrames.github.io/litsearchr/#tutorials
and
https://luketudge.github.io/litsearchr-tutorial/litsearchr_tutorial.html
Load litsearchr
library(litsearchr)
library(dplyr)
library(ggplot2)
library(ggraph)
library(igraph)
library(readr)Import results from a file donwloaded from any search engine and check their structure
In this case I used a file downloaded with the search terms “rights AND conservation AND biodiversity AND restoration” as a matter of example
test_results <- import_results(file="scopus.ris")## Reading file scopus.ris ... donenrow(test_results) # 314 articles## [1] 314Here we can see how the table looks like
head(test_results) # so far so good!## database document_type
## 1 Scopus Article
## 2 Scopus Article
## 3 Scopus Article
## 4 Scopus Article
## 5 Scopus Article
## 6 Scopus Article
## author year
## 1 Hobbs, R.J. and Hallett, L.M. and Ehrlich, P.R. and Mooney, H.A. 2011
## 2 Pryke, J.S. and Samways, M.J. 2009
## 3 Billionnet, A. 2013
## 4 Fiedler, A.K. and Landis, D.A. and Wratten, S.D. 2008
## 5 Fisher, J.L. and Loneragan, W.A. and Dixon, K. and Veneklaas, E.J. 2009
## 6 Czembor, C.A. and Vesk, P.A. 2009
## title
## 1 Intervention ecology: Applying ecological science in the twenty-first century
## 2 Recovery of invertebrate diversity in a rehabilitated city landscape mosaic in the heart of a biodiversity hotspot
## 3 Mathematical optimization ideas for biodiversity conservation
## 4 Maximizing ecosystem services from conservation biological control: The role of habitat management
## 5 Soil seed bank compositional change constrains biodiversity in an invaded species-rich woodland
## 6 Incorporating between-expert uncertainty into state-and-transition simulation models for forest restoration
## source volume issue start_page end_page
## 1 BioScience 61 6 442 450
## 2 Landscape and Urban Planning 93 1 54 62
## 3 European Journal of Operational Research 231 3 514 534
## 4 Biological Control 45 2 254 271
## 5 Biological Conservation 142 2 256 269
## 6 Forest Ecology and Management 259 2 165 175
## abstract
## 1 Rapid, extensive, and ongoing environmental change increasingly demands that humans intervene in ecosystems to maintain or restore ecosystem services and biodiversity. At the same time, the basic principles and tenets of restoration ecology and conservation biology are being debated and reshaped. Escalating global change is resulting in widespread no-analogue environments and novel ecosystems that render traditional goals unachievable. Policymakers and the general public, however, have embraced restoration without an understanding of its limitations, which has led to perverse policy outcomes. Therefore, a new ecology, free of pre-and misconceptions and directed toward meaningful interventions, is needed. Interventions include altering the biotic and abiotic structures and processes within ecosystems and changing social and policy settings. Interventions can be aimed at leverage points, both within ecosystems and in the broader social system particularly, feedback loops that either maintain a particular state or precipitate a rapid change from one state to another. © 2011 by American Institute of Biological Sciences. All rights reserved.
## 2 We investigate here invertebrate response to alien pine plantations, their removal in comparison with natural vegetation, recovering indigenous forests and a botanical garden around Cape Town, South Africa, within a biodiversity hotspot. Pines had low invertebrate species richness and abundance. The botanical garden had the highest species richness and abundance. Natural fynbos vegetation was more similar to pines than to recovering fynbos, while recovering forest was more similar to pines than to any other site. The botanical garden is a major refugium for invertebrate species. Surprisingly, invertebrate assemblages in natural fynbos were more similar to those in pines than in recovering fynbos after the removal of pines. This suggests that some invertebrate species colonize the fynbos soon after rehabilitation disturbance, a response similar to the influence of fire. However, it takes longer for other natural climax invertebrate species to establish, some of which find refuge in pines and the botanical garden. Invertebrate assemblages of indigenous natural forests are more difficult to restore than those of fynbos, thus the protection of the remaining natural forests is a conservation priority. Invasive alien Argentine ant (Linepithema humile) was far more abundant in recovering fynbos than in natural fynbos or in the botanical garden and pines. It benefits from initial restoration disturbance, although is likely to decline as the natural fynbos mature. This study strongly supports removal of alien pines in an urban context, and also emphasizes that an urban botanical garden of indigenous plants has major invertebrate conservation value. © 2009 Elsevier B.V. All rights reserved.
## 3 Several major environmental issues like biodiversity loss and climate change currently concern the international community. These topics that are related to the development of human societies have become increasingly important since the United Nations Conference on Environment and Development (UNCED) or Earth Summit in Rio de Janeiro in 1992. In this article, we are interested in the first issue. We present here many examples of the help that using mathematical programming can provide to decision-makers in the protection of biodiversity. The examples we have chosen concern the selection of nature reserves, the control of adverse effects caused by landscape fragmentation, including the creation or restoration of biological corridors, the ecological exploitation of forests, the control of invasive species, and the maintenance of genetic diversity. Most of the presented models are - or can be approximated with - linear-, quadratic- or fractional-integer formulations and emphasize spatial aspects of conservation planning. Many of them represent decisions taken in a static context but temporal dimension is also considered. The problems presented are generally difficult combinatorial optimization problems, some are well solved and others less well. Research is still needed to progress in solving them in order to deal with real instances satisfactorily. Moreover, relations between researchers and practitioners have to be strengthened. Furthermore, many recent achievements in the field of robust optimization could probably be successfully used for biodiversity protection, a domain in which many data are uncertain. © 2013 Elsevier B.V. All rights reserved.
## 4 The intentional provision of flowering plants and plant communities in managed landscapes to enhance natural enemies is termed habitat management and is a relatively new but growing aspect of conservation biological control. The focus of most habitat management research has been on understanding the role of these plant-provided resources on natural enemy biology, ecology, and their ability to enhance suppression of pest populations. Far less attention has been paid to additional ecosystem services that habitat management practices could provide in managed landscapes. We first evaluate whether habitat management is well positioned to advance in these areas. Our analysis of past habitat management studies indicates that four plant species have been tested in the majority of field evaluations, while plants native to the test area and perennial plants are particularly underrepresented. We suggest that synergies among biodiversity conservation, ecological restoration, human cultural values, tourism, biological control and other ecosystem services have largely been overlooked in past habitat management research and we illustrate how these potential ecosystem services could be evaluated and enhanced. We then review two case studies in which broader ecosystem services were explicitly addressed in plant selection criteria. One case study demonstrates that native plants useful in restoration of rare ecosystems can increase natural enemy abundance as much as widely recommended non-natives. The second addresses additional ecosystem services provided by habitat management in New Zealand vineyards. We conclude that addressing 'stacked' ecosystem services with multiple ecosystem service goals can decrease agriculture's dependence on 'substitution' methods such as the current reliance on oil-based agro-chemical inputs. © 2007 Elsevier Inc. All rights reserved.
## 5 Relationships between plant invasion and the soil seed bank in highly diverse fire adapted mediterranean woodlands are poorly understood, yet critical for that ecosystem's conservation. Within the biodiversity hotspot of southwest Australia we investigated the composition and diversity of the Banksia woodland soil seed bank in good condition (GC), medium condition (MC) and poor condition invaded by the South African perennial species Ehrharta calycina (PCe) and Pelargonium capitatum (PCp). The investigation assessed three questions: (1) Do soil seed banks of invaded sites have fewer germinants of native species and more germinants of introduced (non-native) species than sites with minimal invasion? (2) Do soil seed banks show shifts in ecological functional types with invasion? (3) Is the soil seed bank of introduced species persistent? Native species germinants, mainly shrubs and perennial herbs, were highest in GC sites and least in poorer condition sites suggesting a reduction in their numbers had occurred over time. Introduced germinants were dominated by perennial and annual grasses, and annual herbs. E. calycina had the greatest seed density (8328 germinants m-2). More introduced than native germinants occurred in the litter. Rapid germination of introduced species (30% in week 1) compared to native species (4% in week 1) provides the capacity for their early dominance. A limited native soil seed bank and dominant persistent introduced soil seed bank represent great challenges for the structural and functional conservation and restoration of woodland ecosystems. This study provides key new knowledge, applicable to a wide range of ecosystems, to help formulate conservation protocols to control dominant introduced species and conserve and restore biodiverse-rich woodlands. © 2008 Elsevier Ltd. All rights reserved.
## 6 Anthropogenic utilization of forests alters vegetation structure and can negatively affect flora and fauna. Ecological simulation models assist in restoring such degraded forests by predicting the effects of alternative management and restoration actions on vegetation structure. However, the lack of empirical ecological data to parameterize models often necessitates the use of expert opinion. Differences in opinion between experts may be large and lead to uncertainty in model predictions, but this is rarely acknowledged in forest simulation models. In this paper, we constructed state-and-transition simulation models (STSMs) based on expert opinion to predict whether management will expedite the development of stands with large, old trees - a habitat resource considered critical to forest-dependent biodiversity - in the Box-Ironbark forests and woodlands of Victoria, Australia. Three candidate management actions are modified timber harvesting regulations, establishing no-cutting National Parks, and a new ecological thinning prescription. We also investigated the importance of uncertainty caused by differences between experts when constructing STSMs. Model results predict that mature woodlands with large trees will likely not develop sooner with either ecological thinning or modified harvesting than natural development alone, and may lead to a loss of desired vegetation. In addition, differences in model predictions caused by between-expert variation are substantial and can be used to identify biological processes requiring better understanding in this ecosystem. © 2009 Elsevier B.V. All rights reserved.
## keywords
## 1 ecosystem services and Intervention and leverage points and offsets and restoration ecology
## 2 Animals and Biodiversity and Conservation and Invertebrates and Pinus and Plantations and Recovery and Sugar and Africa and Cape Town and South Africa and Southern Africa and Sub-Saharan Africa and Western Cape and Invertebrata and Linepithema humile and Biodiversity and Conservation and Forestry and Patient rehabilitation and Restoration and Vegetation and Biodiversity conservation and Botanical gardens and Invertebrates and Pine plantations and Urban conservation and abundance index and biodiversity and colonization and fynbos and invasive species and invertebrate and landscape and plantation and restoration ecology and species richness and Recovery and Biodiversity conservation and Botanical gardens and Invertebrates and Pine plantations and Rehabilitation and Urban conservation
## 3 Biodiversity and Climate change and Combinatorial optimization and Conservation and Decision making and Environmental protection and Genetic programming and Biodiversity protection and Genetic diversity and Landscape fragmentation and Mathematical optimizations and Nature reserves and Integer programming and Biodiversity protection and Genetic diversity and Integer programming and Landscape fragmentation and Mathematical optimization and Nature reserve
## 4 Magnoliophyta and Biodiversity conservation and Biological control and Ecological restoration and Ecosystem services and Native plants
## 5 Banksia and Ehrharta calycina and Pelargonium and Pelargonium capitatum and Poaceae and biodiversity and biological invasion and germination and invasive species and Mediterranean environment and seed bank and woodland and Banksia species and Community transformation and Ehrharta calycina and Fire and Mediterranean and Seed persistence
## 6 Biodiversity and Conservation and Ecology and Forecasts and Forestry and Harvesting and Legislation and Logging and Plants and Restoration and Australasia and Australia and Victoria [Australia] and Biodiversity and Conservation and Ecology and Forecasting and Harvesting and Laws and legislation and Logging (forestry) and Parks and Restoration and Vegetation and Alternative management and Biological process and Degraded forests and Ecological data and Expert opinion and Forest restoration and Forest simulation and Model prediction and Model results and National parks and Old trees and Simulation model and State-and-transition models and Timber harvesting and Vegetation structure and Victoria , Australia and anthropogenic effect and deforestation and dicotyledon and ecological modeling and evergreen tree and forest ecosystem and restoration ecology and stand dynamics and thinning and timber harvesting and vegetation structure and woodland and Simulators and Box-Ironbark and Elicitation and Forest restoration and Multiple experts and State-and-transition models and Uncertainty
## doi
## 1 10.1525/bio.2011.61.6.6
## 2 10.1016/j.landurbplan.2009.06.003
## 3 10.1016/j.ejor.2013.03.025
## 4 10.1016/j.biocontrol.2007.12.009
## 5 10.1016/j.biocon.2008.10.019
## 6 10.1016/j.foreco.2009.10.002
## url
## 1 https://www.scopus.com/inward/record.uri?eid=2-s2.0-79958852871&doi=10.1525%2fbio.2011.61.6.6&partnerID=40&md5=a7ea5d944fd877b1de0a5914bd488c1c
## 2 https://www.scopus.com/inward/record.uri?eid=2-s2.0-69849095960&doi=10.1016%2fj.landurbplan.2009.06.003&partnerID=40&md5=3ae736b8583c20e4094956df36a0b1f2
## 3 https://www.scopus.com/inward/record.uri?eid=2-s2.0-84881261595&doi=10.1016%2fj.ejor.2013.03.025&partnerID=40&md5=37e11da6f012365f40b0116b0c84fb8c
## 4 https://www.scopus.com/inward/record.uri?eid=2-s2.0-41149115506&doi=10.1016%2fj.biocontrol.2007.12.009&partnerID=40&md5=59bfbfa130c46fd1d93913a8f6f1e904
## 5 https://www.scopus.com/inward/record.uri?eid=2-s2.0-58149215818&doi=10.1016%2fj.biocon.2008.10.019&partnerID=40&md5=76be53acaba54e848d5ec6cd4b1a009e
## 6 https://www.scopus.com/inward/record.uri?eid=2-s2.0-70449707093&doi=10.1016%2fj.foreco.2009.10.002&partnerID=40&md5=c3d0509ac4ecd388fe4a6a14662bf42f
## notes ZZ source_type
## 1 Export Date: 24 February 2023; Cited By: 291 TY - JOUR <NA>
## 2 Export Date: 24 February 2023; Cited By: 55 <NA> JOUR
## 3 Export Date: 24 February 2023; Cited By: 57 <NA> JOUR
## 4 Export Date: 24 February 2023; Cited By: 287 <NA> JOUR
## 5 Export Date: 24 February 2023; Cited By: 65 <NA> JOUR
## 6 Export Date: 24 February 2023; Cited By: 32 <NA> JOUR
## article_number supertaxa
## 1 <NA> <NA>
## 2 <NA> <NA>
## 3 <NA> <NA>
## 4 <NA> <NA>
## 5 <NA> <NA>
## 6 <NA> <NA>It is also possible to explore what values the columns refer to as to check whether you search came with the results you wanted
colnames(test_results) # the column names## [1] "database" "document_type" "author" "year"
## [5] "title" "source" "volume" "issue"
## [9] "start_page" "end_page" "abstract" "keywords"
## [13] "doi" "url" "notes" "ZZ"
## [17] "source_type" "article_number" "supertaxa"test_results[1, "title"] # checking the title of the first article## [1] "Intervention ecology: Applying ecological science in the twenty-first century"Filtering the “potential terms” of search
Search terms can be found in either keywords, titles, abstract or text body. We tend to rely on search terms that appear on the first three options but not all paper provide keywords, for example. There is a way to deal with it.
sum(is.na(test_results[, "keywords"])) ## [1] 2727 out of the 314 papers did not provide keywords!! Not too manyt, but….
Extracting the keywords
keywords<-extract_terms(keywords=test_results[, "keywords"], method="tagged", min_n=2) # this last argument say that it can retrieve keywords that is formed by a two word
keywords # 643 terms!!!## [1] "-transition models"
## [2] "100-year-old naturally regenerated forests"
## [3] "20th century"
## [4] "21st century"
## [5] "40-year-old regenerating plantations"
## [6] "abandoned land"
## [7] "aboveground biomass"
## [8] "abundance index"
## [9] "acacia koa"
## [10] "acid mine drainage"
## [11] "adaptive management"
## [12] "aerial photography"
## [13] "agri-environment schemes"
## [14] "agri-environmental policy"
## [15] "agricultural ecosystem"
## [16] "agricultural intensification"
## [17] "agricultural land"
## [18] "agricultural landscapes"
## [19] "agricultural management"
## [20] "agricultural worker"
## [21] "animal hunting"
## [22] "animal rights"
## [23] "anthropogenic activities"
## [24] "anthropogenic effect"
## [25] "aquatic environment"
## [26] "arable land"
## [27] "artificial habitats"
## [28] "artificial reef"
## [29] "assisted migration"
## [30] "atlantic forest"
## [31] "atlantic rainforest"
## [32] "baltic states"
## [33] "banks bodies of water"
## [34] "basalt quarry"
## [35] "bavarian forest national park"
## [36] "benthic foraminifera"
## [37] "benthic macrofauna"
## [38] "betula pendula"
## [39] "biodiversity conservation"
## [40] "biodiversity conservation planning"
## [41] "biodiversity monitoring programme"
## [42] "biodiversity offsets"
## [43] "biodiversity offsetting"
## [44] "biodiversity protection"
## [45] "biodiversity value"
## [46] "biological control"
## [47] "biological diversity"
## [48] "biological invasion"
## [49] "biotic homogenization"
## [50] "bird assemblages"
## [51] "body size"
## [52] "boreal forest"
## [53] "bos taurus"
## [54] "botanical gardens"
## [55] "british columbia"
## [56] "broad-leaved forest"
## [57] "bromus tectorum"
## [58] "buffer zone"
## [59] "calcareous grassland"
## [60] "calluna vulgaris"
## [61] "cape floristic region"
## [62] "carabid beetles"
## [63] "carbon credits"
## [64] "carbon dioxide"
## [65] "carbon markets"
## [66] "carbon sequestration"
## [67] "carex arenaria"
## [68] "cellular organisms"
## [69] "central america"
## [70] "central europe"
## [71] "changing climate"
## [72] "chromolaena odorata"
## [73] "clean development mechanism"
## [74] "clearcut openings"
## [75] "climate change"
## [76] "climate change mitigation"
## [77] "climate modeling"
## [78] "cluster analysis"
## [79] "coarse woody debris"
## [80] "coastal zone management"
## [81] "coastal zones"
## [82] "community composition"
## [83] "community development"
## [84] "community dynamics"
## [85] "community forestry"
## [86] "community participation"
## [87] "community structure"
## [88] "comparative study"
## [89] "compensatory mortality"
## [90] "computer simulation"
## [91] "computer software"
## [92] "conference paper"
## [93] "conflict-transformation games"
## [94] "coniferous forest"
## [95] "conservation biology"
## [96] "conservation land acquisition"
## [97] "conservation management"
## [98] "conservation of natural resources"
## [99] "conservation planning"
## [100] "conservation policy"
## [101] "conservation priorities"
## [102] "conservation status"
## [103] "conservation value"
## [104] "conservatory management"
## [105] "controlled study"
## [106] "coppice selection system"
## [107] "coral bleaching"
## [108] "coral reef"
## [109] "coral reefs"
## [110] "cost-benefit analysis"
## [111] "costa rica"
## [112] "cultural heritage"
## [113] "czech republic"
## [114] "dam construction"
## [115] "data collection"
## [116] "data set"
## [117] "dead wood"
## [118] "deciduous forest"
## [119] "deciduous tree"
## [120] "decision making"
## [121] "decision support system"
## [122] "degraded forests"
## [123] "density dependence"
## [124] "detrented correspondence analysis"
## [125] "direct seeding"
## [126] "dry forest"
## [127] "early-successional communities"
## [128] "eastern hemisphere"
## [129] "ecological approach"
## [130] "ecological classification"
## [131] "ecological economics"
## [132] "ecological engineering"
## [133] "ecological impact"
## [134] "ecological indicators"
## [135] "ecological integrity"
## [136] "ecological modeling"
## [137] "ecological network"
## [138] "ecological networks"
## [139] "ecological niche modeling"
## [140] "ecological restoration"
## [141] "ecological status"
## [142] "ecological-coenotic groups"
## [143] "economic analysis"
## [144] "economic development"
## [145] "ecosystem approach"
## [146] "ecosystem degradation"
## [147] "ecosystem function"
## [148] "ecosystem functions"
## [149] "ecosystem management"
## [150] "ecosystem modeling"
## [151] "ecosystem regeneration"
## [152] "ecosystem resilience"
## [153] "ecosystem response"
## [154] "ecosystem restoration"
## [155] "ecosystem service"
## [156] "ecosystem services"
## [157] "ecosystem services markets"
## [158] "ecosystem structure"
## [159] "ecosystem-based management"
## [160] "edge habitats"
## [161] "effectiveness monitoring"
## [162] "ehrharta calycina"
## [163] "el nino"
## [164] "emission control"
## [165] "endangered species"
## [166] "endemic species"
## [167] "environmental assessment"
## [168] "environmental change"
## [169] "environmental conditions"
## [170] "environmental degradation"
## [171] "environmental disturbance"
## [172] "environmental economics"
## [173] "environmental education"
## [174] "environmental factor"
## [175] "environmental flow"
## [176] "environmental flows"
## [177] "environmental impact"
## [178] "environmental impact assessment"
## [179] "environmental impacts"
## [180] "environmental issue"
## [181] "environmental justice"
## [182] "environmental legislation"
## [183] "environmental management"
## [184] "environmental monitoring"
## [185] "environmental planning"
## [186] "environmental policy"
## [187] "environmental pollution"
## [188] "environmental protection"
## [189] "environmental quality"
## [190] "environmental regulations"
## [191] "environmental remediation"
## [192] "environmental restoration"
## [193] "environmental values"
## [194] "environmental water"
## [195] "environmental watering"
## [196] "erosion control"
## [197] "estuarine environment"
## [198] "eucalyptus smithii"
## [199] "european union"
## [200] "euterpe edulis"
## [201] "existence value"
## [202] "expert knowledge"
## [203] "fagus sylvatica"
## [204] "falco naumanni"
## [205] "far east"
## [206] "farming system"
## [207] "fertilizer application"
## [208] "field margins"
## [209] "fisheries management"
## [210] "flood control"
## [211] "floodplain forest"
## [212] "floodplain wetlands"
## [213] "fluvial ecosystems"
## [214] "food industry"
## [215] "food web"
## [216] "forest canopy"
## [217] "forest conservation"
## [218] "forest cover"
## [219] "forest dynamics"
## [220] "forest ecosystem"
## [221] "forest fire"
## [222] "forest fragmentation"
## [223] "forest landscape restoration"
## [224] "forest management"
## [225] "forest regeneration"
## [226] "forest remnants"
## [227] "forest resource"
## [228] "forest restoration"
## [229] "forest restoration implementation"
## [230] "forest structure"
## [231] "forest types"
## [232] "forestry production"
## [233] "fresh water"
## [234] "freshwater biodiversity"
## [235] "freshwater ecosystem"
## [236] "freshwater lakes"
## [237] "fulica cristata"
## [238] "gap analysis"
## [239] "gap dynamics"
## [240] "gap felling"
## [241] "genetic differentiation"
## [242] "genetic diversity"
## [243] "genetic resource"
## [244] "genetic variation"
## [245] "geographic distribution"
## [246] "geographic information systems"
## [247] "geologic sediments"
## [248] "giant panda habitat"
## [249] "global change"
## [250] "global warming"
## [251] "gmelina arborea"
## [252] "governance approach"
## [253] "graph theory"
## [254] "graphical method"
## [255] "grassland management"
## [256] "grazing management"
## [257] "greenhouse effect"
## [258] "greenhouse gas"
## [259] "ground water"
## [260] "groundwater pollution"
## [261] "growth rate"
## [262] "habitat availability"
## [263] "habitat banking"
## [264] "habitat conservation"
## [265] "habitat corridor"
## [266] "habitat creation"
## [267] "habitat fragmentation"
## [268] "habitat loss"
## [269] "habitat management"
## [270] "habitat modelling"
## [271] "habitat quality"
## [272] "habitat re-creation"
## [273] "habitat restoration"
## [274] "habitat selection"
## [275] "habitat structure"
## [276] "habitat type"
## [277] "habitats directive"
## [278] "herbivorous fish"
## [279] "hevea brasiliensis"
## [280] "hipparchia semele"
## [281] "historic preservation"
## [282] "historical ecology"
## [283] "human activities"
## [284] "human activity"
## [285] "human disturbance"
## [286] "human disturbances"
## [287] "human rights"
## [288] "humber estuary"
## [289] "hydrogen-ion concentration"
## [290] "hydrological response"
## [291] "hydrophytic vegetation"
## [292] "hypothesis testing"
## [293] "implementation process"
## [294] "income distribution"
## [295] "index of biotic integrity"
## [296] "indian ocean"
## [297] "indian ocean islands"
## [298] "indicator species"
## [299] "indicator species analysis"
## [300] "indigenous peoples"
## [301] "indigenous population"
## [302] "information processing"
## [303] "institutional framework"
## [304] "integer programming"
## [305] "intertidal flat"
## [306] "invasive species"
## [307] "issoria lathonia"
## [308] "jinan city"
## [309] "kyoto protocol"
## [310] "lake ecosystem"
## [311] "lake urmia"
## [312] "land cover"
## [313] "land management"
## [314] "land reclamation"
## [315] "land reform"
## [316] "land sharing"
## [317] "land sparing"
## [318] "land use"
## [319] "land use change"
## [320] "land use conversion"
## [321] "land use planning"
## [322] "land-cover simulation"
## [323] "land-use change"
## [324] "landscape change"
## [325] "landscape dynamics"
## [326] "landscape ecology"
## [327] "landscape elements"
## [328] "landscape fragmentation"
## [329] "landscape patterns"
## [330] "landscape planning"
## [331] "landscape protection"
## [332] "landscape restoration"
## [333] "landscape structure"
## [334] "local community"
## [335] "local extinction"
## [336] "local participation"
## [337] "logging forestry"
## [338] "logging timber"
## [339] "longleaf pine"
## [340] "macrofaunal colonisation"
## [341] "managed lands"
## [342] "managed realignment"
## [343] "marine ecosystem"
## [344] "marine engineering"
## [345] "marine environment"
## [346] "marine protected areas"
## [347] "marine species"
## [348] "mass bleaching"
## [349] "mass extinctions"
## [350] "mathematical models"
## [351] "mediterranean forest restoration"
## [352] "mediterranean region"
## [353] "microbial community"
## [354] "microbial diversity"
## [355] "middle aged"
## [356] "middle east"
## [357] "mine tailings"
## [358] "moisture content"
## [359] "mudflat development"
## [360] "multicriteria analysis"
## [361] "multiple regression"
## [362] "national forest inventory"
## [363] "national park"
## [364] "national parks"
## [365] "native plants"
## [366] "native species"
## [367] "natural capital"
## [368] "natural enemy"
## [369] "natural protected areas"
## [370] "natural regeneration"
## [371] "natural resource"
## [372] "natural resources management"
## [373] "nature conservation"
## [374] "nature reserve"
## [375] "nature reserves"
## [376] "nature restoration"
## [377] "nature-based solutions"
## [378] "nature-society relations"
## [379] "neotropical region"
## [380] "net present value"
## [381] "new south wales"
## [382] "new zealand"
## [383] "niche space"
## [384] "non-timber forest products"
## [385] "north africa"
## [386] "north america"
## [387] "northern europe"
## [388] "northern region"
## [389] "nurse plant"
## [390] "nutrient availability"
## [391] "ocean acidification"
## [392] "ocean habitats"
## [393] "oceanic regions"
## [394] "oedipoda caerulescens"
## [395] "old-growth forest"
## [396] "olympic national park"
## [397] "organic carbon"
## [398] "organic farming"
## [399] "ovis aries"
## [400] "pacific ocean"
## [401] "panama canal watershed"
## [402] "participatory approach"
## [403] "patch size"
## [404] "patient rehabilitation"
## [405] "pest control"
## [406] "ph effects"
## [407] "picea abies"
## [408] "pilot study"
## [409] "pine plantations"
## [410] "pine shoot beetle"
## [411] "pinus palustris"
## [412] "pinus ponderosa"
## [413] "pinus radiata"
## [414] "pinus sylvestris"
## [415] "pitfall trap"
## [416] "plant communities"
## [417] "plant community"
## [418] "plant development"
## [419] "plant functional types"
## [420] "plant protection"
## [421] "plantation forest"
## [422] "plantation forestry"
## [423] "planting palette"
## [424] "plants botany"
## [425] "policy implementation"
## [426] "policy making"
## [427] "policy strategy"
## [428] "political economy"
## [429] "pollution effect"
## [430] "pollution monitoring"
## [431] "ponderosa pine"
## [432] "population abundance"
## [433] "population decline"
## [434] "population density"
## [435] "population distribution"
## [436] "population dynamics"
## [437] "population genetics"
## [438] "population growth"
## [439] "population modelling"
## [440] "population statistics"
## [441] "populus nigra"
## [442] "potential distribution"
## [443] "poverty alleviation"
## [444] "predator-prey dynamics"
## [445] "predator-prey interaction"
## [446] "predatory behavior"
## [447] "prescribed burning"
## [448] "primary succession"
## [449] "primula sieboldii"
## [450] "principal component analysis"
## [451] "priority areas"
## [452] "priority journal"
## [453] "private land"
## [454] "private lands"
## [455] "project management"
## [456] "property rights"
## [457] "protected area"
## [458] "protected areas"
## [459] "public policy"
## [460] "qilian mountains"
## [461] "qinghai-tibet plateau"
## [462] "qinling mountains"
## [463] "quality control"
## [464] "quarry rehabilitation"
## [465] "quarrying restoration"
## [466] "rare species"
## [467] "rare taxa"
## [468] "red list"
## [469] "red sea"
## [470] "reference conditions"
## [471] "reforestation policy"
## [472] "regression analysis"
## [473] "relative abundance"
## [474] "relative density"
## [475] "remote sensing"
## [476] "renewable energy"
## [477] "reserve design"
## [478] "reserve selection"
## [479] "reservoirs water"
## [480] "resnet place prioritization algorithm"
## [481] "resource management"
## [482] "restoration ecology"
## [483] "restoration index"
## [484] "restoration management"
## [485] "restoration project"
## [486] "riparian ecosystem"
## [487] "riparian vegetation"
## [488] "riparian zone"
## [489] "risk assessment"
## [490] "river basin"
## [491] "river dynamics"
## [492] "river ecosystem"
## [493] "river management"
## [494] "river restoration"
## [495] "river system"
## [496] "rural areas"
## [497] "rural development"
## [498] "sap flow"
## [499] "satellite communications"
## [500] "satellite data"
## [501] "sciurus niger shermani"
## [502] "sea pollution"
## [503] "secondary forest"
## [504] "secondary forests"
## [505] "seed bank"
## [506] "seed dispersal"
## [507] "selection criteria"
## [508] "semi-natural woodlands"
## [509] "sensitivity analysis"
## [510] "seral community"
## [511] "sherman's fox squirrel"
## [512] "silicon dioxide"
## [513] "site-specific management"
## [514] "ski piste"
## [515] "slope protection"
## [516] "smallmouth bass"
## [517] "sobol' sensitivity index"
## [518] "social capital"
## [519] "social effects"
## [520] "social impact"
## [521] "social-ecological systems"
## [522] "soil conditions"
## [523] "soil conservation"
## [524] "soil cover"
## [525] "soil degradation"
## [526] "soil erosion"
## [527] "soil fertility"
## [528] "soil management"
## [529] "soil microbiology"
## [530] "soil productivity"
## [531] "soil type"
## [532] "south africa"
## [533] "south america"
## [534] "south australia"
## [535] "south island"
## [536] "southeast asia"
## [537] "southern africa"
## [538] "southern europe"
## [539] "spatial analysis"
## [540] "spatial distribution"
## [541] "spatial heterogeneity"
## [542] "spatial orientation"
## [543] "spatial variation"
## [544] "spatially-explicit models"
## [545] "spatiotemporal analysis"
## [546] "species composition"
## [547] "species conservation"
## [548] "species decline"
## [549] "species difference"
## [550] "species distribution"
## [551] "species diversity"
## [552] "species endemicity"
## [553] "species extinction"
## [554] "species habitat"
## [555] "species identification"
## [556] "species pool"
## [557] "species reintroduction"
## [558] "species richness"
## [559] "species selection"
## [560] "species specificity"
## [561] "spontaneous succession"
## [562] "stand dynamics"
## [563] "stand structure"
## [564] "state role"
## [565] "statistical analysis"
## [566] "statistical methods"
## [567] "strategic approach"
## [568] "structural complexity"
## [569] "stylophora pistillata"
## [570] "sub-saharan africa"
## [571] "surface structure"
## [572] "surface water"
## [573] "sustainability simulation models"
## [574] "sustainable development"
## [575] "sustainable forest management"
## [576] "sustainable forestry"
## [577] "sustainable use"
## [578] "swietenia macrophylla"
## [579] "systematic conservation planning"
## [580] "temporary pools"
## [581] "textile industry"
## [582] "theoretical model"
## [583] "threatened species"
## [584] "timber harvesting"
## [585] "time factors"
## [586] "time series analysis"
## [587] "topographic effect"
## [588] "tradable development rights"
## [589] "traditional knowledge"
## [590] "traditional management"
## [591] "treatment restoration"
## [592] "tree attributes"
## [593] "tree cavities"
## [594] "tridacna gigas"
## [595] "triticum aestivum"
## [596] "tropical environment"
## [597] "tropical forest"
## [598] "twenty first century"
## [599] "ulva lactuca"
## [600] "un decade on ecosystem restoration"
## [601] "understorey vegetation"
## [602] "understory community"
## [603] "united kingdom"
## [604] "united states"
## [605] "uranium mining"
## [606] "urban area"
## [607] "urban biodiversity"
## [608] "urban conservation"
## [609] "urban planning"
## [610] "vascular plant"
## [611] "vegetation cover"
## [612] "vegetation dynamics"
## [613] "vegetation structure"
## [614] "vegetation type"
## [615] "water conservation"
## [616] "water content"
## [617] "water flow"
## [618] "water framework directive"
## [619] "water framework directives"
## [620] "water management"
## [621] "water movements"
## [622] "water planning"
## [623] "water pollutants"
## [624] "water pollution"
## [625] "water quality"
## [626] "water resources"
## [627] "water supply"
## [628] "water temperature"
## [629] "water use"
## [630] "watershed services"
## [631] "west africa"
## [632] "western australia"
## [633] "western europe"
## [634] "western hemisphere"
## [635] "wetland restoration"
## [636] "wildlife management"
## [637] "wood products"
## [638] "world bank"
## [639] "world wide web"
## [640] "xerophilous grasslands"
## [641] "xysticus sabulosus"
## [642] "yield gaps"
## [643] "zoige marsh"Extracting from titles
Pretty much the same process as above but now we have to deal with stopwords that may confound our search. Fortunetely, litsearchr hgas a funstion that uses a comprehensive list of stopwords that helps to filter terms.
title<- extract_terms(text=test_results[, "title"], method="fakerake", min_freq=2, min_n=2) # setting min_freq = 2 we only grab words taht appear at least two times among titles and setting min_n=2 we tend to exclude stopwords
title # 90 termns## [1] "abandoned agricultural"
## [2] "abandoned quarries"
## [3] "agricultural landscapes"
## [4] "arable farmland"
## [5] "artificial reefs"
## [6] "atlantic forest"
## [7] "biodiversity conservation"
## [8] "biodiversity existence"
## [9] "biodiversity hotspot"
## [10] "biodiversity protection"
## [11] "biological diversity"
## [12] "biosphere reserve"
## [13] "boreal forest"
## [14] "brazilian atlantic"
## [15] "brazilian atlantic forest"
## [16] "calcareous grasslands"
## [17] "carbon sequestration"
## [18] "central mexico"
## [19] "changing world"
## [20] "climate change"
## [21] "conservation areas"
## [22] "conservation financing"
## [23] "conservation planning"
## [24] "conservation policy"
## [25] "coral reefs"
## [26] "current status"
## [27] "ecological niche"
## [28] "ecological niche modeling"
## [29] "ecological restoration"
## [30] "ecosystem management"
## [31] "ecosystem service"
## [32] "ecosystem services"
## [33] "endangered species"
## [34] "environmental education"
## [35] "floristic region"
## [36] "focal species"
## [37] "forest biodiversity"
## [38] "forest conservation"
## [39] "forest ecosystem"
## [40] "forest fragments"
## [41] "forest landscape"
## [42] "forest management"
## [43] "forest remnants"
## [44] "forest restoration"
## [45] "forest stands"
## [46] "future prospects"
## [47] "genetic diversity"
## [48] "genetic resources"
## [49] "green spaces"
## [50] "habitat management"
## [51] "habitat quality"
## [52] "improving markets"
## [53] "invasive alien"
## [54] "landscape approach"
## [55] "landscape restoration"
## [56] "local communities"
## [57] "longicaudis annectens"
## [58] "lontra longicaudis"
## [59] "lontra longicaudis annectens"
## [60] "marine scientists"
## [61] "native species"
## [62] "natural resource"
## [63] "nature conservation"
## [64] "niche modeling"
## [65] "northwestern china"
## [66] "otter lontra"
## [67] "otter lontra longicaudis"
## [68] "otter lontra longicaudis annectens"
## [69] "panamanian market"
## [70] "plant communities"
## [71] "plant diversity"
## [72] "plant species"
## [73] "plant species richness"
## [74] "priority areas"
## [75] "river otter"
## [76] "river otter lontra"
## [77] "river otter lontra longicaudis"
## [78] "river otter lontra longicaudis annectens"
## [79] "river restoration"
## [80] "semi-natural grasslands"
## [81] "software package"
## [82] "south africa"
## [83] "south wales"
## [84] "species diversity"
## [85] "species ecological"
## [86] "species ecological niche"
## [87] "species ecological niche modeling"
## [88] "species richness"
## [89] "timber plantations"
## [90] "urban green"Obtaining the terms from kewords and titles
terms <- unique(c(keywords, title))
terms## [1] "-transition models"
## [2] "100-year-old naturally regenerated forests"
## [3] "20th century"
## [4] "21st century"
## [5] "40-year-old regenerating plantations"
## [6] "abandoned land"
## [7] "aboveground biomass"
## [8] "abundance index"
## [9] "acacia koa"
## [10] "acid mine drainage"
## [11] "adaptive management"
## [12] "aerial photography"
## [13] "agri-environment schemes"
## [14] "agri-environmental policy"
## [15] "agricultural ecosystem"
## [16] "agricultural intensification"
## [17] "agricultural land"
## [18] "agricultural landscapes"
## [19] "agricultural management"
## [20] "agricultural worker"
## [21] "animal hunting"
## [22] "animal rights"
## [23] "anthropogenic activities"
## [24] "anthropogenic effect"
## [25] "aquatic environment"
## [26] "arable land"
## [27] "artificial habitats"
## [28] "artificial reef"
## [29] "assisted migration"
## [30] "atlantic forest"
## [31] "atlantic rainforest"
## [32] "baltic states"
## [33] "banks bodies of water"
## [34] "basalt quarry"
## [35] "bavarian forest national park"
## [36] "benthic foraminifera"
## [37] "benthic macrofauna"
## [38] "betula pendula"
## [39] "biodiversity conservation"
## [40] "biodiversity conservation planning"
## [41] "biodiversity monitoring programme"
## [42] "biodiversity offsets"
## [43] "biodiversity offsetting"
## [44] "biodiversity protection"
## [45] "biodiversity value"
## [46] "biological control"
## [47] "biological diversity"
## [48] "biological invasion"
## [49] "biotic homogenization"
## [50] "bird assemblages"
## [51] "body size"
## [52] "boreal forest"
## [53] "bos taurus"
## [54] "botanical gardens"
## [55] "british columbia"
## [56] "broad-leaved forest"
## [57] "bromus tectorum"
## [58] "buffer zone"
## [59] "calcareous grassland"
## [60] "calluna vulgaris"
## [61] "cape floristic region"
## [62] "carabid beetles"
## [63] "carbon credits"
## [64] "carbon dioxide"
## [65] "carbon markets"
## [66] "carbon sequestration"
## [67] "carex arenaria"
## [68] "cellular organisms"
## [69] "central america"
## [70] "central europe"
## [71] "changing climate"
## [72] "chromolaena odorata"
## [73] "clean development mechanism"
## [74] "clearcut openings"
## [75] "climate change"
## [76] "climate change mitigation"
## [77] "climate modeling"
## [78] "cluster analysis"
## [79] "coarse woody debris"
## [80] "coastal zone management"
## [81] "coastal zones"
## [82] "community composition"
## [83] "community development"
## [84] "community dynamics"
## [85] "community forestry"
## [86] "community participation"
## [87] "community structure"
## [88] "comparative study"
## [89] "compensatory mortality"
## [90] "computer simulation"
## [91] "computer software"
## [92] "conference paper"
## [93] "conflict-transformation games"
## [94] "coniferous forest"
## [95] "conservation biology"
## [96] "conservation land acquisition"
## [97] "conservation management"
## [98] "conservation of natural resources"
## [99] "conservation planning"
## [100] "conservation policy"
## [101] "conservation priorities"
## [102] "conservation status"
## [103] "conservation value"
## [104] "conservatory management"
## [105] "controlled study"
## [106] "coppice selection system"
## [107] "coral bleaching"
## [108] "coral reef"
## [109] "coral reefs"
## [110] "cost-benefit analysis"
## [111] "costa rica"
## [112] "cultural heritage"
## [113] "czech republic"
## [114] "dam construction"
## [115] "data collection"
## [116] "data set"
## [117] "dead wood"
## [118] "deciduous forest"
## [119] "deciduous tree"
## [120] "decision making"
## [121] "decision support system"
## [122] "degraded forests"
## [123] "density dependence"
## [124] "detrented correspondence analysis"
## [125] "direct seeding"
## [126] "dry forest"
## [127] "early-successional communities"
## [128] "eastern hemisphere"
## [129] "ecological approach"
## [130] "ecological classification"
## [131] "ecological economics"
## [132] "ecological engineering"
## [133] "ecological impact"
## [134] "ecological indicators"
## [135] "ecological integrity"
## [136] "ecological modeling"
## [137] "ecological network"
## [138] "ecological networks"
## [139] "ecological niche modeling"
## [140] "ecological restoration"
## [141] "ecological status"
## [142] "ecological-coenotic groups"
## [143] "economic analysis"
## [144] "economic development"
## [145] "ecosystem approach"
## [146] "ecosystem degradation"
## [147] "ecosystem function"
## [148] "ecosystem functions"
## [149] "ecosystem management"
## [150] "ecosystem modeling"
## [151] "ecosystem regeneration"
## [152] "ecosystem resilience"
## [153] "ecosystem response"
## [154] "ecosystem restoration"
## [155] "ecosystem service"
## [156] "ecosystem services"
## [157] "ecosystem services markets"
## [158] "ecosystem structure"
## [159] "ecosystem-based management"
## [160] "edge habitats"
## [161] "effectiveness monitoring"
## [162] "ehrharta calycina"
## [163] "el nino"
## [164] "emission control"
## [165] "endangered species"
## [166] "endemic species"
## [167] "environmental assessment"
## [168] "environmental change"
## [169] "environmental conditions"
## [170] "environmental degradation"
## [171] "environmental disturbance"
## [172] "environmental economics"
## [173] "environmental education"
## [174] "environmental factor"
## [175] "environmental flow"
## [176] "environmental flows"
## [177] "environmental impact"
## [178] "environmental impact assessment"
## [179] "environmental impacts"
## [180] "environmental issue"
## [181] "environmental justice"
## [182] "environmental legislation"
## [183] "environmental management"
## [184] "environmental monitoring"
## [185] "environmental planning"
## [186] "environmental policy"
## [187] "environmental pollution"
## [188] "environmental protection"
## [189] "environmental quality"
## [190] "environmental regulations"
## [191] "environmental remediation"
## [192] "environmental restoration"
## [193] "environmental values"
## [194] "environmental water"
## [195] "environmental watering"
## [196] "erosion control"
## [197] "estuarine environment"
## [198] "eucalyptus smithii"
## [199] "european union"
## [200] "euterpe edulis"
## [201] "existence value"
## [202] "expert knowledge"
## [203] "fagus sylvatica"
## [204] "falco naumanni"
## [205] "far east"
## [206] "farming system"
## [207] "fertilizer application"
## [208] "field margins"
## [209] "fisheries management"
## [210] "flood control"
## [211] "floodplain forest"
## [212] "floodplain wetlands"
## [213] "fluvial ecosystems"
## [214] "food industry"
## [215] "food web"
## [216] "forest canopy"
## [217] "forest conservation"
## [218] "forest cover"
## [219] "forest dynamics"
## [220] "forest ecosystem"
## [221] "forest fire"
## [222] "forest fragmentation"
## [223] "forest landscape restoration"
## [224] "forest management"
## [225] "forest regeneration"
## [226] "forest remnants"
## [227] "forest resource"
## [228] "forest restoration"
## [229] "forest restoration implementation"
## [230] "forest structure"
## [231] "forest types"
## [232] "forestry production"
## [233] "fresh water"
## [234] "freshwater biodiversity"
## [235] "freshwater ecosystem"
## [236] "freshwater lakes"
## [237] "fulica cristata"
## [238] "gap analysis"
## [239] "gap dynamics"
## [240] "gap felling"
## [241] "genetic differentiation"
## [242] "genetic diversity"
## [243] "genetic resource"
## [244] "genetic variation"
## [245] "geographic distribution"
## [246] "geographic information systems"
## [247] "geologic sediments"
## [248] "giant panda habitat"
## [249] "global change"
## [250] "global warming"
## [251] "gmelina arborea"
## [252] "governance approach"
## [253] "graph theory"
## [254] "graphical method"
## [255] "grassland management"
## [256] "grazing management"
## [257] "greenhouse effect"
## [258] "greenhouse gas"
## [259] "ground water"
## [260] "groundwater pollution"
## [261] "growth rate"
## [262] "habitat availability"
## [263] "habitat banking"
## [264] "habitat conservation"
## [265] "habitat corridor"
## [266] "habitat creation"
## [267] "habitat fragmentation"
## [268] "habitat loss"
## [269] "habitat management"
## [270] "habitat modelling"
## [271] "habitat quality"
## [272] "habitat re-creation"
## [273] "habitat restoration"
## [274] "habitat selection"
## [275] "habitat structure"
## [276] "habitat type"
## [277] "habitats directive"
## [278] "herbivorous fish"
## [279] "hevea brasiliensis"
## [280] "hipparchia semele"
## [281] "historic preservation"
## [282] "historical ecology"
## [283] "human activities"
## [284] "human activity"
## [285] "human disturbance"
## [286] "human disturbances"
## [287] "human rights"
## [288] "humber estuary"
## [289] "hydrogen-ion concentration"
## [290] "hydrological response"
## [291] "hydrophytic vegetation"
## [292] "hypothesis testing"
## [293] "implementation process"
## [294] "income distribution"
## [295] "index of biotic integrity"
## [296] "indian ocean"
## [297] "indian ocean islands"
## [298] "indicator species"
## [299] "indicator species analysis"
## [300] "indigenous peoples"
## [301] "indigenous population"
## [302] "information processing"
## [303] "institutional framework"
## [304] "integer programming"
## [305] "intertidal flat"
## [306] "invasive species"
## [307] "issoria lathonia"
## [308] "jinan city"
## [309] "kyoto protocol"
## [310] "lake ecosystem"
## [311] "lake urmia"
## [312] "land cover"
## [313] "land management"
## [314] "land reclamation"
## [315] "land reform"
## [316] "land sharing"
## [317] "land sparing"
## [318] "land use"
## [319] "land use change"
## [320] "land use conversion"
## [321] "land use planning"
## [322] "land-cover simulation"
## [323] "land-use change"
## [324] "landscape change"
## [325] "landscape dynamics"
## [326] "landscape ecology"
## [327] "landscape elements"
## [328] "landscape fragmentation"
## [329] "landscape patterns"
## [330] "landscape planning"
## [331] "landscape protection"
## [332] "landscape restoration"
## [333] "landscape structure"
## [334] "local community"
## [335] "local extinction"
## [336] "local participation"
## [337] "logging forestry"
## [338] "logging timber"
## [339] "longleaf pine"
## [340] "macrofaunal colonisation"
## [341] "managed lands"
## [342] "managed realignment"
## [343] "marine ecosystem"
## [344] "marine engineering"
## [345] "marine environment"
## [346] "marine protected areas"
## [347] "marine species"
## [348] "mass bleaching"
## [349] "mass extinctions"
## [350] "mathematical models"
## [351] "mediterranean forest restoration"
## [352] "mediterranean region"
## [353] "microbial community"
## [354] "microbial diversity"
## [355] "middle aged"
## [356] "middle east"
## [357] "mine tailings"
## [358] "moisture content"
## [359] "mudflat development"
## [360] "multicriteria analysis"
## [361] "multiple regression"
## [362] "national forest inventory"
## [363] "national park"
## [364] "national parks"
## [365] "native plants"
## [366] "native species"
## [367] "natural capital"
## [368] "natural enemy"
## [369] "natural protected areas"
## [370] "natural regeneration"
## [371] "natural resource"
## [372] "natural resources management"
## [373] "nature conservation"
## [374] "nature reserve"
## [375] "nature reserves"
## [376] "nature restoration"
## [377] "nature-based solutions"
## [378] "nature-society relations"
## [379] "neotropical region"
## [380] "net present value"
## [381] "new south wales"
## [382] "new zealand"
## [383] "niche space"
## [384] "non-timber forest products"
## [385] "north africa"
## [386] "north america"
## [387] "northern europe"
## [388] "northern region"
## [389] "nurse plant"
## [390] "nutrient availability"
## [391] "ocean acidification"
## [392] "ocean habitats"
## [393] "oceanic regions"
## [394] "oedipoda caerulescens"
## [395] "old-growth forest"
## [396] "olympic national park"
## [397] "organic carbon"
## [398] "organic farming"
## [399] "ovis aries"
## [400] "pacific ocean"
## [401] "panama canal watershed"
## [402] "participatory approach"
## [403] "patch size"
## [404] "patient rehabilitation"
## [405] "pest control"
## [406] "ph effects"
## [407] "picea abies"
## [408] "pilot study"
## [409] "pine plantations"
## [410] "pine shoot beetle"
## [411] "pinus palustris"
## [412] "pinus ponderosa"
## [413] "pinus radiata"
## [414] "pinus sylvestris"
## [415] "pitfall trap"
## [416] "plant communities"
## [417] "plant community"
## [418] "plant development"
## [419] "plant functional types"
## [420] "plant protection"
## [421] "plantation forest"
## [422] "plantation forestry"
## [423] "planting palette"
## [424] "plants botany"
## [425] "policy implementation"
## [426] "policy making"
## [427] "policy strategy"
## [428] "political economy"
## [429] "pollution effect"
## [430] "pollution monitoring"
## [431] "ponderosa pine"
## [432] "population abundance"
## [433] "population decline"
## [434] "population density"
## [435] "population distribution"
## [436] "population dynamics"
## [437] "population genetics"
## [438] "population growth"
## [439] "population modelling"
## [440] "population statistics"
## [441] "populus nigra"
## [442] "potential distribution"
## [443] "poverty alleviation"
## [444] "predator-prey dynamics"
## [445] "predator-prey interaction"
## [446] "predatory behavior"
## [447] "prescribed burning"
## [448] "primary succession"
## [449] "primula sieboldii"
## [450] "principal component analysis"
## [451] "priority areas"
## [452] "priority journal"
## [453] "private land"
## [454] "private lands"
## [455] "project management"
## [456] "property rights"
## [457] "protected area"
## [458] "protected areas"
## [459] "public policy"
## [460] "qilian mountains"
## [461] "qinghai-tibet plateau"
## [462] "qinling mountains"
## [463] "quality control"
## [464] "quarry rehabilitation"
## [465] "quarrying restoration"
## [466] "rare species"
## [467] "rare taxa"
## [468] "red list"
## [469] "red sea"
## [470] "reference conditions"
## [471] "reforestation policy"
## [472] "regression analysis"
## [473] "relative abundance"
## [474] "relative density"
## [475] "remote sensing"
## [476] "renewable energy"
## [477] "reserve design"
## [478] "reserve selection"
## [479] "reservoirs water"
## [480] "resnet place prioritization algorithm"
## [481] "resource management"
## [482] "restoration ecology"
## [483] "restoration index"
## [484] "restoration management"
## [485] "restoration project"
## [486] "riparian ecosystem"
## [487] "riparian vegetation"
## [488] "riparian zone"
## [489] "risk assessment"
## [490] "river basin"
## [491] "river dynamics"
## [492] "river ecosystem"
## [493] "river management"
## [494] "river restoration"
## [495] "river system"
## [496] "rural areas"
## [497] "rural development"
## [498] "sap flow"
## [499] "satellite communications"
## [500] "satellite data"
## [501] "sciurus niger shermani"
## [502] "sea pollution"
## [503] "secondary forest"
## [504] "secondary forests"
## [505] "seed bank"
## [506] "seed dispersal"
## [507] "selection criteria"
## [508] "semi-natural woodlands"
## [509] "sensitivity analysis"
## [510] "seral community"
## [511] "sherman's fox squirrel"
## [512] "silicon dioxide"
## [513] "site-specific management"
## [514] "ski piste"
## [515] "slope protection"
## [516] "smallmouth bass"
## [517] "sobol' sensitivity index"
## [518] "social capital"
## [519] "social effects"
## [520] "social impact"
## [521] "social-ecological systems"
## [522] "soil conditions"
## [523] "soil conservation"
## [524] "soil cover"
## [525] "soil degradation"
## [526] "soil erosion"
## [527] "soil fertility"
## [528] "soil management"
## [529] "soil microbiology"
## [530] "soil productivity"
## [531] "soil type"
## [532] "south africa"
## [533] "south america"
## [534] "south australia"
## [535] "south island"
## [536] "southeast asia"
## [537] "southern africa"
## [538] "southern europe"
## [539] "spatial analysis"
## [540] "spatial distribution"
## [541] "spatial heterogeneity"
## [542] "spatial orientation"
## [543] "spatial variation"
## [544] "spatially-explicit models"
## [545] "spatiotemporal analysis"
## [546] "species composition"
## [547] "species conservation"
## [548] "species decline"
## [549] "species difference"
## [550] "species distribution"
## [551] "species diversity"
## [552] "species endemicity"
## [553] "species extinction"
## [554] "species habitat"
## [555] "species identification"
## [556] "species pool"
## [557] "species reintroduction"
## [558] "species richness"
## [559] "species selection"
## [560] "species specificity"
## [561] "spontaneous succession"
## [562] "stand dynamics"
## [563] "stand structure"
## [564] "state role"
## [565] "statistical analysis"
## [566] "statistical methods"
## [567] "strategic approach"
## [568] "structural complexity"
## [569] "stylophora pistillata"
## [570] "sub-saharan africa"
## [571] "surface structure"
## [572] "surface water"
## [573] "sustainability simulation models"
## [574] "sustainable development"
## [575] "sustainable forest management"
## [576] "sustainable forestry"
## [577] "sustainable use"
## [578] "swietenia macrophylla"
## [579] "systematic conservation planning"
## [580] "temporary pools"
## [581] "textile industry"
## [582] "theoretical model"
## [583] "threatened species"
## [584] "timber harvesting"
## [585] "time factors"
## [586] "time series analysis"
## [587] "topographic effect"
## [588] "tradable development rights"
## [589] "traditional knowledge"
## [590] "traditional management"
## [591] "treatment restoration"
## [592] "tree attributes"
## [593] "tree cavities"
## [594] "tridacna gigas"
## [595] "triticum aestivum"
## [596] "tropical environment"
## [597] "tropical forest"
## [598] "twenty first century"
## [599] "ulva lactuca"
## [600] "un decade on ecosystem restoration"
## [601] "understorey vegetation"
## [602] "understory community"
## [603] "united kingdom"
## [604] "united states"
## [605] "uranium mining"
## [606] "urban area"
## [607] "urban biodiversity"
## [608] "urban conservation"
## [609] "urban planning"
## [610] "vascular plant"
## [611] "vegetation cover"
## [612] "vegetation dynamics"
## [613] "vegetation structure"
## [614] "vegetation type"
## [615] "water conservation"
## [616] "water content"
## [617] "water flow"
## [618] "water framework directive"
## [619] "water framework directives"
## [620] "water management"
## [621] "water movements"
## [622] "water planning"
## [623] "water pollutants"
## [624] "water pollution"
## [625] "water quality"
## [626] "water resources"
## [627] "water supply"
## [628] "water temperature"
## [629] "water use"
## [630] "watershed services"
## [631] "west africa"
## [632] "western australia"
## [633] "western europe"
## [634] "western hemisphere"
## [635] "wetland restoration"
## [636] "wildlife management"
## [637] "wood products"
## [638] "world bank"
## [639] "world wide web"
## [640] "xerophilous grasslands"
## [641] "xysticus sabulosus"
## [642] "yield gaps"
## [643] "zoige marsh"
## [644] "abandoned agricultural"
## [645] "abandoned quarries"
## [646] "arable farmland"
## [647] "artificial reefs"
## [648] "biodiversity existence"
## [649] "biodiversity hotspot"
## [650] "biosphere reserve"
## [651] "brazilian atlantic"
## [652] "brazilian atlantic forest"
## [653] "calcareous grasslands"
## [654] "central mexico"
## [655] "changing world"
## [656] "conservation areas"
## [657] "conservation financing"
## [658] "current status"
## [659] "ecological niche"
## [660] "floristic region"
## [661] "focal species"
## [662] "forest biodiversity"
## [663] "forest fragments"
## [664] "forest landscape"
## [665] "forest stands"
## [666] "future prospects"
## [667] "genetic resources"
## [668] "green spaces"
## [669] "improving markets"
## [670] "invasive alien"
## [671] "landscape approach"
## [672] "local communities"
## [673] "longicaudis annectens"
## [674] "lontra longicaudis"
## [675] "lontra longicaudis annectens"
## [676] "marine scientists"
## [677] "niche modeling"
## [678] "northwestern china"
## [679] "otter lontra"
## [680] "otter lontra longicaudis"
## [681] "otter lontra longicaudis annectens"
## [682] "panamanian market"
## [683] "plant diversity"
## [684] "plant species"
## [685] "plant species richness"
## [686] "river otter"
## [687] "river otter lontra"
## [688] "river otter lontra longicaudis"
## [689] "river otter lontra longicaudis annectens"
## [690] "semi-natural grasslands"
## [691] "software package"
## [692] "south wales"
## [693] "species ecological"
## [694] "species ecological niche"
## [695] "species ecological niche modeling"
## [696] "timber plantations"
## [697] "urban green"Network Analysis
The text bellow is literally from the source of this tutorial
“Our list of new search terms is looking fairly good. But there are probably still some in there that are unrelated to the others and to our topic of interest. These perhaps only occur in a small number of articles that do not mention many of the other search terms. We would like some systematic way of identifying these ‘isolated’ search terms.
One way to do this is to analyze the search terms as a network. The idea behind this is that terms are linked to each other by virtue of appearing in the same articles. If we can find out which terms tend to occur together in the same article, we can pick out groups of terms that are probably all referring to the same topic (because they occur in the same subset of articles), and we can filter out terms that do not often occur together with any of the main groups of terms.
We don’t have the full texts of the articles, and in any case checking for search terms in a large number of full texts would be a big task for my puny computer. So we will take the title and abstract of each article as the ‘content’ of that article, and count a term as having occurred in that article if it is to be found in either the title or abstract. For this, we need to join the title of each article to its abstract.”
docs <- paste(test_results[, "title"], test_results[, "abstract"])
docs[1] # Now we have a structured file to perform a network analysis## [1] "Intervention ecology: Applying ecological science in the twenty-first century Rapid, extensive, and ongoing environmental change increasingly demands that humans intervene in ecosystems to maintain or restore ecosystem services and biodiversity. At the same time, the basic principles and tenets of restoration ecology and conservation biology are being debated and reshaped. Escalating global change is resulting in widespread no-analogue environments and novel ecosystems that render traditional goals unachievable. Policymakers and the general public, however, have embraced restoration without an understanding of its limitations, which has led to perverse policy outcomes. Therefore, a new ecology, free of pre-and misconceptions and directed toward meaningful interventions, is needed. Interventions include altering the biotic and abiotic structures and processes within ecosystems and changing social and policy settings. Interventions can be aimed at leverage points, both within ecosystems and in the broader social system particularly, feedback loops that either maintain a particular state or precipitate a rapid change from one state to another. © 2011 by American Institute of Biological Sciences. All rights reserved."Lets create a matrix of the terms
dfm <- create_dfm(elements=docs, features=terms)creating the network
g <- create_network(dfm, min_studies=3) # the argument min_studies excludes terms that occur in fewer than a given number of articles.Plotting results
ggraph(g, layout="stress") +
coord_fixed() +
expand_limits(x=c(-3, 3)) +
geom_edge_link(aes(alpha=weight)) +
geom_node_point(shape="circle filled", fill="white") +
geom_node_text(aes(label=name), hjust="outward", check_overlap=TRUE) +
guides(edge_alpha=FALSE)
Pruning
Lets get the strenght of each word
strengths <- strength(g)
data.frame(term=names(strengths), strength=strengths, row.names=NULL) %>%
mutate(rank=rank(strength, ties.method="min")) %>%
arrange(strength) ->
term_strengths
term_strengths## term strength rank
## 1 spatial heterogeneity 9 1
## 2 focal species 9 1
## 3 soil conditions 10 3
## 4 south america 10 3
## 5 genetic resource 11 5
## 6 rural development 11 5
## 7 genetic resources 11 5
## 8 artificial reef 12 8
## 9 czech republic 12 8
## 10 freshwater ecosystem 12 8
## 11 longleaf pine 12 8
## 12 artificial reefs 12 8
## 13 21st century 13 13
## 14 coral reefs 13 13
## 15 ecological status 13 13
## 16 marine environment 13 13
## 17 priority areas 13 13
## 18 relative abundance 13 13
## 19 green spaces 13 13
## 20 urban green 13 13
## 21 growth rate 14 21
## 22 landscape planning 14 21
## 23 local extinction 14 21
## 24 riparian ecosystem 14 21
## 25 current status 14 21
## 26 environmental restoration 15 26
## 27 field margins 15 26
## 28 nature restoration 15 26
## 29 population growth 15 26
## 30 remote sensing 15 26
## 31 river restoration 15 26
## 32 biological control 16 32
## 33 lake ecosystem 16 32
## 34 landscape ecology 16 32
## 35 national parks 16 32
## 36 north africa 16 32
## 37 spatial analysis 16 32
## 38 coarse woody debris 17 38
## 39 economic development 17 38
## 40 environmental flow 17 38
## 41 environmental flows 17 38
## 42 forest fire 17 38
## 43 rural areas 17 38
## 44 western australia 17 38
## 45 timber plantations 17 38
## 46 arable land 18 46
## 47 broad-leaved forest 18 46
## 48 freshwater biodiversity 18 46
## 49 private lands 18 46
## 50 future prospects 18 46
## 51 cultural heritage 19 51
## 52 dead wood 19 51
## 53 degraded forests 19 51
## 54 food web 19 51
## 55 forest landscape restoration 19 51
## 56 land-use change 19 51
## 57 landscape elements 19 51
## 58 nutrient availability 19 51
## 59 pinus sylvestris 19 51
## 60 rare species 19 51
## 61 river system 19 51
## 62 soil type 19 51
## 63 forest stands 19 51
## 64 climate change mitigation 20 64
## 65 conservation priorities 20 64
## 66 environmental conditions 20 64
## 67 forest dynamics 20 64
## 68 habitat conservation 20 64
## 69 resource management 20 64
## 70 river management 20 64
## 71 seed bank 20 64
## 72 soil fertility 20 64
## 73 water flow 20 64
## 74 biosphere reserve 20 64
## 75 software package 20 64
## 76 coral reef 21 76
## 77 land management 21 76
## 78 water framework directive 21 76
## 79 data collection 22 79
## 80 habitats directive 22 79
## 81 local community 22 79
## 82 marine ecosystem 22 79
## 83 vegetation cover 22 79
## 84 semi-natural grasslands 22 79
## 85 carbon markets 23 85
## 86 changing climate 23 85
## 87 environmental factor 23 85
## 88 forest resource 23 85
## 89 human disturbance 23 85
## 90 managed lands 23 85
## 91 old-growth forest 23 85
## 92 species selection 23 85
## 93 water pollution 23 85
## 94 abandoned agricultural 23 85
## 95 bird assemblages 24 95
## 96 national park 24 95
## 97 patch size 24 95
## 98 sustainable development 24 95
## 99 water use 24 95
## 100 community development 25 100
## 101 land use change 25 100
## 102 native plants 25 100
## 103 vascular plant 25 100
## 104 central europe 26 104
## 105 community composition 26 104
## 106 ecosystem approach 26 104
## 107 environmental education 26 104
## 108 erosion control 26 104
## 109 natural capital 26 104
## 110 seed dispersal 26 104
## 111 south africa 27 111
## 112 brazilian atlantic 27 111
## 113 brazilian atlantic forest 27 111
## 114 global change 28 114
## 115 picea abies 28 114
## 116 plantation forestry 28 114
## 117 property rights 28 114
## 118 urban area 28 114
## 119 water resources 28 114
## 120 20th century 29 120
## 121 ecological indicators 29 120
## 122 ecosystem restoration 29 120
## 123 forest conservation 29 120
## 124 indigenous peoples 29 120
## 125 spatial distribution 29 120
## 126 species distribution 29 120
## 127 boreal forest 30 127
## 128 forest types 30 127
## 129 indicator species 30 127
## 130 river basin 30 127
## 131 invasive alien 30 127
## 132 forest structure 31 132
## 133 ecosystem management 32 133
## 134 genetic diversity 32 133
## 135 greenhouse gas 32 133
## 136 adaptive management 33 136
## 137 conservation policy 33 136
## 138 costa rica 33 136
## 139 land cover 33 136
## 140 forest fragments 33 136
## 141 conservation status 34 141
## 142 habitat quality 34 141
## 143 plant species richness 34 141
## 144 buffer zone 35 144
## 145 united states 35 144
## 146 forest biodiversity 35 144
## 147 landscape structure 36 147
## 148 plantation forest 36 147
## 149 restoration ecology 36 147
## 150 plant diversity 36 147
## 151 community structure 37 151
## 152 ecosystem degradation 37 151
## 153 ecosystem functions 37 151
## 154 potential distribution 37 151
## 155 biodiversity value 38 155
## 156 forest ecosystem 38 155
## 157 natural regeneration 38 155
## 158 conservation biology 39 158
## 159 ecological niche modeling 39 158
## 160 habitat loss 39 158
## 161 ecological niche 39 158
## 162 longicaudis annectens 39 158
## 163 lontra longicaudis 39 158
## 164 lontra longicaudis annectens 39 158
## 165 niche modeling 39 158
## 166 river otter 39 158
## 167 human activities 41 167
## 168 nature reserves 41 167
## 169 private land 42 169
## 170 vegetation type 42 169
## 171 habitat type 43 171
## 172 threatened species 43 171
## 173 north america 44 173
## 174 plant community 44 173
## 175 secondary forests 44 173
## 176 biodiversity hotspot 44 173
## 177 central mexico 44 173
## 178 environmental change 45 178
## 179 natural resource 45 178
## 180 new zealand 45 178
## 181 soil erosion 45 178
## 182 atlantic forest 46 182
## 183 environmental impacts 46 182
## 184 habitat management 46 182
## 185 conservation management 47 185
## 186 forest remnants 47 185
## 187 sustainable use 48 187
## 188 invasive species 51 188
## 189 secondary forest 51 188
## 190 agricultural landscapes 52 190
## 191 forest landscape 53 191
## 192 biodiversity protection 55 192
## 193 endangered species 55 192
## 194 habitat restoration 55 192
## 195 species diversity 56 195
## 196 tropical forest 56 195
## 197 biological diversity 59 197
## 198 environmental impact 59 197
## 199 conservation planning 61 199
## 200 forest cover 63 200
## 201 nature reserve 63 200
## 202 conservation areas 64 202
## 203 local communities 68 203
## 204 carbon sequestration 69 204
## 205 landscape restoration 70 205
## 206 water quality 70 205
## 207 restoration project 73 207
## 208 species composition 75 208
## 209 conservation value 78 209
## 210 nature conservation 79 210
## 211 forest management 80 211
## 212 ecosystem function 85 212
## 213 native species 92 213
## 214 plant communities 95 214
## 215 forest restoration 107 215
## 216 protected areas 110 216
## 217 protected area 118 217
## 218 climate change 127 218
## 219 agricultural land 128 219
## 220 plant species 151 220
## 221 species richness 155 221
## 222 land use 169 222
## 223 ecosystem service 183 223
## 224 ecosystem services 183 223
## 225 ecological restoration 227 225
## 226 biodiversity conservation 378 226This is an ascending order and on the top are the terms less linked to each other. THerefore let’s use some fucntion to order them and choose a cutoff
cutoff_fig <- ggplot(term_strengths, aes(x=rank, y=strength, label=term)) +
geom_line() +
geom_point() +
geom_text(data=filter(term_strengths, rank>5), hjust="right", nudge_y=20, check_overlap=TRUE)
cutoff_fig
Tehre is an automated function to find a cutoff. Here we are using a method that accumulates the importance of each term to sum 30%
cutoff_cum <- find_cutoff(g, method="cumulative", percent=0.3)
cutoff_cum # the limit is with the term with strength 75## [1] 75The new figure
cutoff_fig +
geom_hline(yintercept=cutoff_cum, linetype="dashed")
Lets get to know what are these terms
selected_terms<-get_keywords(reduce_graph(g, cutoff_cum)) # there are 19 terms nowGrouping
“Now that we have got a revised list of search terms from the results of our naive search, we want to turn them into a new search query that we can use to get more articles relevant to the same topic. For this new, hopefully more rigorous, search we will need a combination of OR and AND operators. The OR operator should combine search terms that are all about the same subtopic, so that we get articles that contain any one of them. The AND operator should combine these groups of search terms so that we get only articles that mention at least one term from each of the subtopics that we are interested in.
In our starting example we had three subtopics, medication, cognitive-behavioral therapy, and phobias. So the first step is to take the terms that we have found and group them into clusters related to each of these topics. (Or it may be the case that our work with litsearchr has led us to rethink our subtopics or to add new ones.)
There are methods for automatically grouping networks into clusters, but these are not always so reliable; computers don’t understand what words mean. Currently the litsearchr documentation recommends doing this step manually. We look at our search terms, and put them into a list of separate vectors, one for each subtopic.”
This is not an automated task. We should create groups and place words within groups
grouped_terms <-list(
land_use=selected_terms[c(1,11,15,16)],
management=selected_terms[c(5,9,10)],
conservation=selected_terms[c(2,3,4,6,7,8,13)],
biological=selected_terms[c(14,17,18,19)]
)
grouped_terms## $land_use
## [1] "agricultural land" "land use" "protected area"
## [4] "protected areas"
##
## $management
## [1] "ecological restoration" "forest management" "forest restoration"
##
## $conservation
## [1] "biodiversity conservation" "climate change"
## [3] "conservation value" "ecosystem function"
## [5] "ecosystem service" "ecosystem services"
## [7] "nature conservation"
##
## $biological
## [1] "plant communities" "species composition" "species richness"
## [4] "plant species"Now we can write a new search for the engine
write_search(
grouped_terms,
languages="English",
exactphrase=TRUE,
stemming=FALSE,
closure="left",
writesearch=TRUE
)Reading the file
cat(read_file("search-inEnglish.txt"))## \(\("agricultural land" OR "land use" OR "protected area"\) AND \("ecological restoration" OR "forest management" OR "forest restoration"\) AND \("biodiversity conservation" OR "climate change" OR "conservation value" OR "ecosystem function" OR "ecosystem service" OR "nature conservation"\) AND \("plant communities" OR "species composition" OR "species richness" OR "plant species"\)\)“agricultural land” OR “land use” OR “protected area” AND “ecological restoration” OR “forest management” OR “forest restoration” AND “biodiversity conservation” OR “climate change” OR “conservation value” OR “ecosystem function” OR “ecosystem service” OR “nature conservation” AND “plant communities” OR “species composition” OR “species richness” OR “plant species”
The above is the “clean” terms that if used again in Scopus Engine, will com out with 18,639 documents found
Of course this is pretty difficult to analyze bu please note this refers to terms widely used and therefore we need to be a lot more specific when searching for the papers we want to search for.