Reshaping Data with the<b>reshape</b>Package

Wickham, Hadley

doi:10.18637/jss.v021.i12

Cited by 2,520 publications

(1,759 citation statements)

References 2 publications

Supporting

Mentioning

1,601

Contrasting

Unclassified

Order By: Relevance

“…Other statistical analyses were performed using R version 3.2.3 [26] and additional R packages [27][28][29][30][31]. Surveys were analysed independently, except when stated otherwise.…”

Section: Methodsmentioning

confidence: 99%

BritishEscherichia coliO157 in Cattle Study (BECS): to determine the prevalence ofE. coliO157 in herds with cattle destined for the food chain

et al. 2017

View full text Add to dashboard Cite

SUMMARYEscherichia coli O157 are zoonotic bacteria for which cattle are an important reservoir. Prevalence estimates for E. coli O157 in British cattle for human consumption are over 10 years old. A new baseline is needed to inform current human health risk. The British E. coli O157 in Cattle Study (BECS) ran between September 2014 and November 2015 on 270 farms across Scotland and England & Wales. This is the first study to be conducted contemporaneously across Great Britain, thus enabling comparison between Scotland and England & Wales. Herd-level prevalence estimates for E. coli O157 did not differ significantly for Scotland (0·236, 95% CI 0·166-0·325) and England & Wales (0·213, 95% CI 0·156-0·283) (P = 0·65). The majority of isolates were verocytotoxin positive. A higher proportion of samples from Scotland were in the super-shedder category, though there was no difference between the surveys in the likelihood of a positive farm having at least one super-shedder sample. E. coli O157 continues to be common in British beef cattle, reaffirming public health policy that contact with cattle and their environments is a potential infection source.

show abstract

“…Other statistical analyses were performed using R version 3.2.3 [26] and additional R packages [27][28][29][30][31]. Surveys were analysed independently, except when stated otherwise.…”

Section: Methodsmentioning

confidence: 99%

BritishEscherichia coliO157 in Cattle Study (BECS): to determine the prevalence ofE. coliO157 in herds with cattle destined for the food chain

et al. 2017

View full text Add to dashboard Cite

show abstract

“…ArcGIS 10.3 was used to generate validation datasets, and Python was used for image processing (ESRI, 2014). Modelling and statistical analysis were conducted in R using the following packages: ggplot2 (Wickham, 2009), dplyr (Wickham and Francois, 2015), rasterVis (Perpinan and Hijmans, 2016), randomForest (Liaw and Wiener, 2002), reshape2 (Wickham, 2007), ROCR (Sing et al, 2005), SDMTools (VanDerWal et al, 2014), and spatial.tools (Greenberg, 2014).…”

Section: Analysis Toolsmentioning

confidence: 99%

Three decades of Landsat-derived spring surface water dynamics in an agricultural wetland mosaic; Implications for migratory shorebirds

Schaffer‐Smith

Swenson

Barbaree

et al. 2017

Remote Sensing of Environment

View full text Add to dashboard Cite

Satellite measurements of surface water offer promise for understanding wetland habitat availability at broad spatial and temporal scales; reliable habitat is crucial for the persistence of migratory shorebirds that depend on wetland networks. We analyzed water extent dynamics within wetland habitats at a globally important shorebird stopover site for a 1983-2015 Landsat time series, and evaluated the effect of climate on water extent. A range of methods can detect open water from imagery, including supervised classification approaches and thresholds for spectral bands and indices. Thresholds provide a time advantage; however, there is no universally superior index, nor single best threshold for all instances. We used random forest to model the presence or absence of water from >6200 reference pixels, and derived an optimal water probability threshold for our study area using receiver operating characteristic curves. An optimized mid-infrared (1.5-1.7 μm) threshold identified open water in the Sacramento Valley of California at 30-m resolution with an average of 90% producer's accuracy, comparable to approaches that require more intensive user input. SLC-off Landsat 7 imagery was integrated by applying a customized interpolation that mapped water in missing data gaps with 99% user's accuracy. On average we detected open water on ~26000 ha (~3% of the study area) in early April at the peak of shorebird migration, while water extent increased five-fold after the migration rush. Over the last three decades, late March water extent declined by ~1300 ha per year, primarily due to changes in the extent and timing of agricultural flood-irrigation. Water within shorebird habitats was significantly associated with an index of water availability at the peak of migration. Our approach can be used to optimize thresholds for time series analysis and near-real-time mapping in other regions, and requires only marginally more time than generating a confusion matrix.

show abstract

“…We used R version 3.3.0 (Core Team 2016) with the following packages: data.table (Dowle and Srinivasan 2016), plyr (Wickham 2011), reshape2 (Wickham 2007), Rmisc (Hope 2013) to run the model and statistical analyses. The R packages ggplot2 (Wickham 2009), scales (Wickham 2016), and cowplot (Wilke 2016) were used to create the figures.…”

Section: Statistical Analyses and Figuresmentioning

confidence: 99%

Third-party mutualists have contrasting effects on host invasion under the enemy-release and biotic-resistance hypotheses

et al. 2017

View full text Add to dashboard Cite

Plants engage in complex multipartite interactions with mutualists and antagonists, but these interactions are rarely included in studies that explore plant invasiveness. When considered in isolation, we know that beneficial microbes can enhance an exotic plant's invasive ability and that herbivorous insects often decrease an exotic plant's likeliness of success. However, the effect of these partners on plant fitness has not been well characterized when all three species coevolve. We use computational evolutionary modeling of a trait-based system to test how microbes and herbivores simultaneously coevolving with an invading plant affect the invaders' probability of becoming established. Specifically, we designed a model that explores how a beneficial microbe would influence the outcome of an interaction between a plant and herbivore. To model novel interactions, we included a phenotypic trait shared by each species. Making this trait continuous and selectable allows us to explore how trait similarities between coevolving plants, herbivores and microbes affect fitness. Using this model, we answer the following questions: (1) Can a beneficial plant-microbe interaction influence the evolutionary outcome of antagonistic interactions between plants and herbivores? (2) How does the initial trait similarity between interacting organisms affect the likelihood of plant survival in novel locations? (3) Does the effect of tripartite interactions on the invasion success of a plant depend on whether organisms interact through trait similarity [ -017-9912-5 plants to invade under the ERH but that beneficial microbes increase the probability of plant survival in a novel range under both hypotheses. To our knowledge, this model is the first to use tripartite interactions to explore novel species introductions. It represents a step towards gaining a better understanding of the factors influencing establishment of exotic species to prevent future invasions.

show abstract

Reshaping Data with thereshapePackage

Cited by 2,520 publications

References 2 publications

BritishEscherichia coliO157 in Cattle Study (BECS): to determine the prevalence ofE. coliO157 in herds with cattle destined for the food chain

BritishEscherichia coliO157 in Cattle Study (BECS): to determine the prevalence ofE. coliO157 in herds with cattle destined for the food chain

Three decades of Landsat-derived spring surface water dynamics in an agricultural wetland mosaic; Implications for migratory shorebirds

Third-party mutualists have contrasting effects on host invasion under the enemy-release and biotic-resistance hypotheses

Contact Info

Product

Resources

About