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performance: An R Package for Assessment, Comparison and Testing of Statistical Models
Abstract
A crucial part of statistical analysis is evaluating a model's quality and fit, or performance. During analysis, especially with regression models, investigating the fit of models to data also often involves selecting the best fitting model amongst many competing models. Upon investigation, fit indices should also be reported both visually and numerically to bring readers in on the investigative effort. While functions to build and produce diagnostic plots or to compute fit statistics exist, these are located across many packages, which results in a lack of a unique and consistent approach to assess the performance of many types of models. The result is a difficult-to-navigate, unorganized ecosystem of individual packages with different syntax, making it onerous for researchers to locate and use fit indices relevant for their unique purposes. The performance package in R fills this gap by offering researchers a suite of intuitive functions with consistent syntax for computing, building, and presenting regression model fit statistics and visualizations.
... No significant problems were detected for any of the models reported in the results. We also computed marginal and conditional r-squared values using the performance R package (Lüdecke et al., 2021). Model visualizations and predictions were generated via the ggeffects R package (Lüdecke, 2018), and trend comparisons were made through the emmeans R package (Russell, 2021). ...
The development of tool use in early childhood is a topic of continuing interest in developmental psychology. However, the lack of studies in ecological settings results in many unknowns about how children come to use artifacts according to their cultural function. We report a longitudinal study with 17 sociodemographically diverse children (8 female) attending a nursery school in Madrid (Spain) and their two adult female teachers. Using mixed-effects models and Granger causality analysis, we measured changes in the frequency and duration of children's object uses between 7 and 17 months of age and in the directional influences among pairs of behaviors performed by teachers and children. Results show a clear shift in how children use artifacts. As early as 12 months of age, the frequency of conventional uses outweighs that of all other types of object use. In addition, object uses become shorter in duration with age, irrespective of their type. Moreover, certain teachers' nonlinguistic communicative strategies (e.g., demonstrations of canonical use and placing gestures) significantly influence and promote children's conventional tool use. Findings shed light on how children become increasingly proficient in conventional tool use through interactions with artifacts and others in nursery school.
... In models inspecting age, we included data on 36 males; in models inspecting song, we included 25 males. We checked for overdispersion and zeroinflation in the models using the 'performance' package (Lüdecke et al. 2021) (see results in Table S3). Models were run using the 'lme4' package (Bates et al. 2015). ...
In many avian species, age, body size, and song could signal quality or individual breeding experience and these traits are often correlated with reproductive success. The relationship between sexually selected signals and avian mating systems is a topic of active research, but still remains poorly investigated in species from southern latitudes. Here, we explored the relationships between body size, condition, age, song and social and genetic reproductive success in Sicalis flaveola pelzelni, a Neotropical thraupid. This socially monogamous species has both age-related changes in song and plumage colouration and extra-pair paternity. When measuring male song we found that a lower peak frequency may be associated with patterns of extra-pair paternity gain by males. We also found that male age may not have a marked effect on paternity assurance. In addition, we found that female body condition appears to influence on the proportion of extra-pair nestlings in females’ nests. We contribute novel data to help bridge the geographic and taxonomic gap in this research field.
... All analyses were performed using R version 4.0.5 (R Core Team, 2021) and necessitate lme4 (Bates et al., 2015), glmmADMB (Skaug et al., n.d.;Fournier et al., 2012), performance (Lüdecke et al., 2021), MuMIn (Barton, 2020), DHARMa (Hartig, 2021) and emmeans (Lenth, 2021) r packages. ...
Contemporary climate change affects population dynamics, but its influence varies with landscape structure. It is still unclear whether landscape fragmentation buffers or amplifies the effects of climate on population size and the age and body size of individuals composing these populations.
This study aims to investigate the impacts of warm climates on lizard life‐history traits and population dynamics in habitats that vary in their connectivity.
We monitored common lizard Zootoca vivipara populations for 3 years in an experimental system in which both climatic conditions and connectivity among habitats were simultaneously manipulated. We considered two climatic treatments (i.e. present‐day climate and warm climate [+1.4°C than present‐day climate]) and two connectivity treatments (i.e. a connected treatment in which individuals could move from one climate to the other and an isolated treatment in which movement between climates was not possible). We monitored survival, reproduction, growth, dispersal, age and body size of each individual in the system as well as population density through time.
We found that the influence of warm climates on life‐history traits and population dynamics depended on connectivity among thermal habitats. Populations in warm climates were (i) composed of younger individuals only when isolated; (ii) larger in population size only in connected habitats and (iii) composed of larger age‐specific individuals independently of the landscape configuration. The connectivity among habitats altered population responses to climate warming likely through asymmetries in the flow and phenotype of dispersers between thermal habitats.
Our results demonstrate that landscape fragmentation can drastically change the dynamics and persistence of populations facing climate change.
... Yield and RFV were also tested as a function of GDD accumulation using linear and quadratic models. Models were compared using maximum likelihood ratio tests and marginal r 2 was calculated using the performance package (Lüdecke et al., 2021). An value of 0.05 was used to assess statistical significance for all statistical tests. ...
Abstract Intermediate wheatgrass [Thinopyrum intermedium (Host) Barkworth & Dewey] (IWG) is a perennial forage grass being domesticated to function as a perennial grain crop. Grain yield of improved, grain‐type IWG cultivars decline by the third year of production and managing aging stands for forage production presents economic opportunities. Limited research is available on the response of second‐ and third‐year grain‐type IWG to different forage harvest schedules. We measured forage yield and nutritive value of grain‐type IWG in the second and third year of production under nine forage harvest schedules varying in the timing of the first harvest (at boot, anthesis, or soft dough stage) and the number of fall harvests (none, one [Sept.], or two [Sept. and Nov.]). As timing of the first harvest was delayed and IWG maturity increased from boot to soft dough, yield increased from 2.4 to 3.7 Mg ha–1 and relative feed value decreased from 113 to 82. Yield at subsequent September and November harvests averaged 30% and 12% of the initial harvest yield, respectively. Total annual forage yield was not affected by the timing of the first harvest but was predictably greater for two or three harvests compared with one harvest; however, additional harvests in September and November decreased net returns. Grain‐type IWG stands harvested in the third year after peak grain production have potential to provide forage similar to common perennial cool season forage grasses. Tradeoffs between forage yield and nutritive value should be considered when selecting the timing of the initial spring forage harvest.
... Models included an offset term to account for the differences in days between sampling periods. Marginal significance of habitat type was determined using likelihood ratio tests (anova function) models with and without the habitat type predictor and evaluated using the r2_nakagawa function in the performance package (Lüdecke et al., 2021). Only the best model is discussed. ...
Abstract Forest management is often practiced to enhance conditions for wildlife, including native bees. Evaluations of the effects of forest management on bees have shown that abundance and diversity are higher in newly created early‐successional conditions. To date, studies have restricted sampling to the forest understory; however, recent research finds that bee abundance is as high or higher in forest canopies than in understories, suggesting that previous observations of substantially greater bee abundance and diversity in recently managed areas could be an artifact of incomplete sampling of the vertical gradient within forests. To examine the potential implications of sampling biases associated with the failure of previous studies to include canopy samples in comparisons of managed and unmanaged forests, we sampled bees within a recently harvested forest as well as the understory and canopy of adjacent unmanaged forest. Bee abundance and diversity were an order of magnitude higher in managed areas compared to the unmanaged forest, even when understory and canopy samples were combined. These results suggest that not sampling the canopy is inconsequential with respect to the broadly reported conclusion that managed areas support more abundant and diverse bee communities than surrounding forest cover.
... [43] using the packages MASS [44] and lme4 [45]. Model assumptions were checked with the package performance [46], and figures were produced using the package ggplot2 [47]. ...
Winter represents a challenging period for insects inhabiting temperate regions. A plethora of studies have investigated how environmental conditions such as temperature affect insect overwintering success. However, only a few studies have focused on biotic factors and the mechanisms affecting the overwintering performance of insects. Here, we investigated the effects of the parasitic fungus Hesperomyces virescens on the overwintering performance and immune system functioning of the invasive ladybird Harmonia axyridis. Winter survival was significantly lower for infected than for uninfected ladybirds. Body mass loss during overwintering tends to be higher for infected individuals compared to uninfected ones and for larger ladybirds. In addition, parasitic infection reduced post-winter longevity without food in male but not female ladybirds. Total haemocyte and protein concentration as well as antimicrobial activity against Escherichia coli significantly decreased during ladybird overwintering. However, haemolymph parameters were only poorly affected by Hesperomyces infection, with the exception of antimicrobial activity against E. coli that tended to be higher in infected ladybirds. Interestingly, none of the pre-winter haemolymph parameters were good predictors of ladybird winter survival. Overall, our results indicate that energy exhaustion unrelated to immune system challenge is the most probable explanation for increased overwintering mortality in infected ladybirds.
... was used for statistical analyses and scientific graphics [33]. The following R packages were included: "agricolae" (non-parametric Kruskal-Wallis test) [34], "lme4" and "lmerTest" (mixed models) [26,35], "ggplot2" (graphs) [36], and "performance" (r-squared values) [37]. ...
Intercropping results in high overall system productivity on a given piece of land due to the efficient use of available plant growth resources. Weed control in intercropping systems is, however, still a challenge. This study focuses on the effect of the type of weed control (chemical/mechanical) and the timing of chemical herbicide application (pre-emergence/post-emergence) on weed control and crop productivity in a maize bean mixture. For this purpose, the results of a three-year field experiment (2017 to 2019) in northeast Germany will be presented. The experimental setup included a control, three chemical methods, and one mechanical method of weed control. Except for the mechanical treatment, a completely randomized block design was established. Weeds were assessed at BBCH 12 of the maize, immediately before the first weed control treatments to estimate the initial weed infestation, and twice in the six to eight leaf stage of the maize. The weed coverage (%) was estimated. The maize bean mixture was harvested and yields (t ha−1) were measured. The results confirm that the type of weed control, as well as the timing of herbicide application, significantly affects the weed coverage of the maize bean mixture. The most successful weed control strategy was the double chemical herbicide application, in which chemical herbicides are in used pre-emergence beans (BBCH 12 maize) and post-emergence beans (BBCH 12 bean). Weed coverage was reduced by up to 75% using this most effective herbicide strategy and by up to 61% through mechanical weed control, compared to the control. The additional effects of post-emergence treatment on the pre-emergence herbicide control resulted in a 16.5% weed coverage decline. The yield surplus of double chemical herbicide application (pre/post-emergence) was up to 53%, and for the mechanical weed control up to 23%. Additionally, post-emergence herbicide use in intercropped maize and bean resulted in a 16% yield surplus, compared to the single pre-emergence chemical weed control. Optimal timing of weed control during the most sensitive phenology stages of the maize bean mixture is crucial for productivity. The results of this study provide an additional option for suitable weed control of intercropped maize and bean.
Terrestrial leaf litter is a large contributor to the metabolism and secondary production of freshwaters. Decomposition rates of leaf litter in freshwaters are often used as a proxy for ecosystem function; however, there are many sources of variation in decomposition rates within and between freshwater ecosystems that still have not been tested. In particular, the variation in decomposition rates between different freshwater ecosystems has rarely been addressed. Here, we compared decomposition rates of red alder (Alnus rubra) leaf litter in streams, ponds, and lakes within a single forest, while controlling for water temperatures. Using coarse-mesh and fine-mesh bags we found that when accounting for degree days, decomposition rates were higher in streams than ponds, and twice as high in streams than lakes, for either mesh size. The overall densities of invertebrates per leaf pack or per gram of leaf litter were very similar between the three ecosystems. However, detritivores were six-fold or more abundant in leaf packs from streams than those from lakes or ponds. There were fewer specialized macroinvertebrate consumers of leaf litter in the lentic environments. Specialized shredders such as Plecoptera were absent from lentic sites, and their absence in terms of decomposition rates was not compensated for by litter decomposition by generalist taxa. While we did not test the specific mechanisms responsible, differences may be associated with the relative temporal and spatial variation in the abundance of this resource and lack of specialist consumers in lakes and ponds.
Japanese Night Heron Gorsachius goisagi has recently been down-listed in status from Endangered to Vulnerable by BirdLife International due to the presence of a likely larger population than previously considered. However, there is still relatively little known about the ecology and current population status of this rare, elusive, and solitary species. In this study, we used infrared cameras to study its behaviour. We installed cameras at 120 locations on the forest floor of Awaji Island, Hyogo Prefecture, Japan, over approximately one year. Japanese Night Heron was recorded at 15 locations (132 video files of 25 independent events). All records except one were obtained during the daytime, and all involved herons walking on the forest floor where they were searching for potential prey items (most likely earthworms). Both adult and recently fledged juvenile herons were recorded, providing direct evidence that the species breeds on Awaji Island. Additionally, a zero-inflated Poisson GLMM analysis showed that Japanese Night Heron may not prefer evergreen coniferous plantations. Our results not only indicate that the species forages diurnally, contrary to its common name, but also sheds light on the importance of maintaining forests and foraging ground environments for the conservation of this species.
We studied the impacts of site, stand and tree variables on the diameter growth of beech trees (Fagussylvatica L.) on carbonate bedrock and examined to what extent the regional diameter growth model can be used at the forest type level. Based on 12,193 permanent sampling plots (500 m² each) with 94,770 beech trees, we first developed a linear mixed-effect model of the periodic diameter increment at the regional level (Dinaric region, Slovenia, 1.7 thousand km²). Subsequently, we parametrized the model for five forest types within the region (submontane, thermophilous, montane, upper montane and subalpine) and used a homogeneity-of-slopes model to test whether the covariates have different effects in the five forest types. The regional model suggested the positive impact of tree diameter (nonlinear), tree diameter diversity, mean diurnal temperature range and mean annual temperature and the negative impact of basal area, proportion of beech, inclination, rockiness and annual amount of precipitation. Stand basal area and the proportion of beech contributed > 50% of the total explained diameter increment variability, followed by tree diameter (44%), topographic (3%) and climatic variables (< 2%). The regional model was well transferable to forest types; the only variable with a significantly different effect in forest types was tree diameter. However, models at the forest type level differed with respect to the slopes and significance of several predictors, wherein coefficients for some predictors were even of opposite sign. Not all predictors from the regional model were included in the forest type models if predictor selection and model parameterization were performed independently for each forest type. Our study suggests that some growth characteristics of beech can be detected at the regional level only, while analyses at the forest type level can reveal significant differences in beech growth response to tree, stand and environmental variables.
Tree crowns and growth rings are physiologically and functionally connected through supporting and resource sharing. Management interventions may strongly influence tree growth by altering this linkage. However, conventional approaches have limited ability to characterize crown shape precisely, thus hindering our understanding of the relationship between crown shape and tree ring patterns. We, thus, aimed to test three hypotheses: (HI) Crown shape (regularity vs. irregularity) and ring patterns (regularity or irregularity) are significantly correlated and (HII) vary across density gradients; if so, (HIII) internal ring patterns could be predicted from external crown shape metrics. We, therefore, employed terrestrial laser scan-based crown shape and coring-based TRP metrics for Norway spruce (Picea abies (L.) H. Karst.) trees covering a range of density gradients to assess temporal changes of crown shape and tree ring patterns. We found a significant and positive influence of crown shape quantifying metrics on ring patterns, indicating crown regularity or irregularity strongly reflects tree ring regularity or irregularity (p
Micronutrients, particularly amino acids, are thought to play an important role in sleep regulation and maintenance. While tryptophan is a known predictor of sleep, less is known about branched-chain amino acids (BCAAs), which compete with tryptophan for transport across the blood-brain barrier. The aim of this study was to determine the association between BCAAs and actigraphy-derived sleep duration, timing and efficiency, and self-reported trouble sleeping. This study examined data on children and adults collected as part of the Child Health CheckPoint study. Linear mixed models, adjusted for geographic clustering, were used to determine the association between BCAAs and sleep characteristics. Complete-case analysis was conducted for 741 children aged 11-12 years old (51% females) and 941parents (87% mothers). While BCAAs were significantly associated with children's sleep duration, timing and self-reported trouble sleeping, no associations were observed in adults, in fully adjusted models. In children, higher levels of BCAAs are associated with shorter sleep duration, delayed sleep timing, and more frequent reports of trouble sleeping.
The ongoing COVID-19 pandemic is among the worst in recent history, resulting in excess of 520,000,000 cases and 6,200,000 deaths worldwide. The United States (U.S.) has recently surpassed 1,000,000 deaths. Individuals who are elderly and/or immunocompromised are the most susceptible to serious sequelae. Rising sentiment often implicates younger, less-vulnerable populations as primary introducers of COVID-19 to communities, particularly around colleges and universities. Adjusting for more than 32 key socio-demographic, economic, and epidemiologic variables, we (1) implemented regressions to determine the overall community-level, age-adjusted COVID-19 case and mortality rate within each American county, and (2) performed a subgroup analysis among a sample of U.S. colleges and universities to identify any significant preliminary mitigation measures implemented during the fall 2020 semester. From January 1, 2020 through March 31, 2021, a total of 22,385,335 cases and 374,130 deaths were reported to the CDC. Overall, counties with increasing numbers of university enrollment showed significantly lower case rates and marginal decreases in mortality rates. County-level population demographics, and not university level mitigation measures, were the most significant predictor of adjusted COVID-19 case rates. Contrary to common sentiment, our findings demonstrate that counties with high university enrollments may be more adherent to public safety measures and vaccinations, likely contributing to safer communities.
Extensively managed grasslands are globally recognized for their high biodiversity value. Over the past century, a continuous loss and degradation of grassland habitats has been observed across Europe that is mainly attributable to agricultural intensification and land abandonment. Particularly insects have suffered from the loss of grassland habitats due to land-use change and the decrease in habitat quality, either due to an increase in livestock density, higher mowing frequency, and an increase in nitrogen fertilization, or by abandonment. However, only a few studies have used nationwide datasets to analyse the effects of land cover and land-use intensity on insects. It further remains largely unexplored how these effects are modulated by species traits, i.e. habitat specialisation and mobility. Using nationwide butterfly data originating from the German Butterfly Monitoring Scheme, we investigated the effect of three indicators related to land cover and agricultural land-use intensity on species richness as well as trait composition of butterfly communities. Based on agricultural census data at the municipality scale, we calculated the share of permanent grasslands (measure of habitat availability), the total livestock density (proxy for organic fertilization) and the livestock density of domestic herbivores (proxy for management intensity in grasslands) within a 2 km buffer surrounding each butterfly transect. To analyse the relationships between butterflies and indicators of land cover and land-use intensity, we applied generalised linear mixed effect models. We found a negative relationship between butterfly species richness and the livestock density of domestic herbivores. Further, the ratio of butterfly generalist to specialist species shifted towards generalists and the size of butterflies increased with higher herbivore livestock density, indicating a shift in communities towards mobile habitat generalists. Our results are in accordance with previous studies carried out across smaller geographic extents, highlighting the importance of low herbivore livestock densities to halt the loss of pollinating insects and safeguard biodiversity and associated ecosystem services in agricultural landscapes. We here demonstrate that indicators based on livestock distribution data at the municipality scale can provide insights into processes and spatial diversity patterns of butterflies at the national level. Further, we highlight potentials and limitations of using agricultural census data to quantify and assess effects of land cover and land-use intensity on butterflies, and make recommendations for further research needs.
The pine processionary moth (PPM), Thaumetopoea pityocampa (Denis and Schiffermüller), is one of the most economically important forest defoliators in southern Europe. This pest is a univoltine oligophagous insect species, and the genus Pinus represents its main host. Investigations were carried out in the five-year period 2016–2020 in NW Italy. PPM males were monitored using commercial funnel traps baited with sex pheromone. The infestation index was recorded by counting the number of nests per tree. Temperature and rainfall were automatically recorded by 94 georeferenced meteorological stations. Adult presence was evaluated as the maximum number of captured individuals in a day, total captures during the season, the Julian day at max captures, or at first or last captures. Environmental variables (altitude, cumulative rain, and cumulative degree-days) and biological parameters were summarized using principal component analysis. Our study showed that the analyzed variables contribute to driving and affecting the PPM population dynamics, which also exhibited a year-to-year decrease. Due to the environmental and sanitary importance, all the data collected about the PPM will be useful to develop predictive risk models, as to deploy countermeasures in a timely and cost-effective manner.
Background
Homeothermic marine animals in Polar Regions face an energetic bottleneck in winter. The challenges of short days and cold temperatures are exacerbated for flying seabirds with small body size and limited fat stores. We use biologging approaches to examine how habitat, weather, and moon illumination influence behaviour and energetics of a marine bird species, thick-billed murres (Uria lomvia).
Methods
We used temperature-depth-light recorders to examine strategies murres use to survive winter in the Northwest Atlantic, where contrasting currents create two distinct marine habitats: cold (−0.1 ± 1.2 °C), shallower water along the Labrador Shelf and warmer (3.1 ± 0.3 °C), deep water in the Labrador Basin.
Results
In the cold shelf water, murres used a high-energy strategy, with more flying and less diving each day, resulting in high daily energy expenditure and also high apparent energy intake; this strategy was most evident in early winter when day lengths were shortest. By contrast, murres in warmer basin water employed a low-energy strategy, with less time flying and more time diving under low light conditions (nautical twilight and night). In warmer basin water, murres increased diving at night when the moon was more illuminated, likely taking advantage of diel vertically migrating prey. In warmer basin water, murres dove more at night and foraging efficiency increased under negative North Atlantic Oscillation (calmer ocean conditions).
Conclusions
The proximity of two distinct marine habitats in this region allows individuals from a single species to use dual (low-energy/high-energy) strategies to overcome winter energy bottlenecks.
Unlabelled:
Mating patterns in animal populations can respond to environmental conditions and consequently vary across time. To examine this variation in nature, studies must include temporal replicates from the same population. Here, we report temporal variation in genetic parentage in the socially monogamous cichlid Variabilichromis moorii from Lake Tanganyika, using samples of broods and their brood-tending parents that were collected across five field trips from the same study population. The sampled broods were either spawned during the dry season (three field trips) or during the rainy season (two trips). In all seasons, we detected substantial rates of extra-pair paternity, which were ascribed to cuckoldry by bachelor males. Paternity shares of brood-tending males were consistently higher, and the numbers of sires per brood were consistently lower, in broods that were spawned in the dry seasons compared to broods from the rainy seasons. In contrast, the strength of size-assortative pairing in our V. moorii population did not vary temporally. Seasonal fluctuations in environmental conditions, such as water turbidity, are proposed as a mechanism behind variable cuckolder pressure. Our data demonstrate the utility of long-term monitoring to improve our understanding of animal mating patterns.
Supplementary information:
The online version contains supplementary material available at 10.1007/s10750-022-05042-0.
Scientists’ research interests are often skewed toward charismatic organisms, but quantifying research biases is challenging. By combining bibliometric data with trait-based approaches and using a well-studied alpine flora as a case study, we demonstrate that morphological and colour traits, as well as range size, have significantly more impact on species choice for wild flowering plants than traits related to ecology and rarity. These biases should be taken into account to inform more objective plant conservation efforts.
The recent growth of data science is partly fueled by the ever-growing amount of data and the joint important developments in statistical modeling, with new and powerful models and frameworks becoming accessible to users. Although there exist some generic functions to obtain model summaries and parameters, many package-specific modeling functions do not provide such methods to allow users to access such valuable information. Aims of the Package parameters is an R-package (R Core Team, 2020) that fills this important gap. Its primary goal is to provide utilities for processing the parameters of various statistical models. Beyond computing p-values, standard errors, confidence intervals (CI), Bayesian indices and other measures for a wide variety of models, this package implements features like parameters bootstrapping and engineering (such as variables reduction and/or selection), as well as tools for data reduction like functions to perform cluster, factor or principal component analysis. Another important goal of the parameters package is to facilitate and streamline the process of reporting results of statistical models, which includes the easy and intuitive calculation of standardized estimates in addition to robust standard errors and p-values. parameters therefor offers a simple and unified syntax to process a large variety of (model) objects from many different packages. parameters is part of the easystats ecosystem, a collaborative project created to facilitate the usage of R for statistical analyses.
Correlations tests are arguably one of the most commonly used statistical procedures, and are used as a basis in many applications such as exploratory data analysis, structural modelling, data engineering etc. In this context, we present correlation, a toolbox for the R language (R Core Team, 2019) and part of the easystats collection, focused on correlation analysis. Its goal is to be lightweight, easy to use, and allows for the computation of many different kinds of correlations.
The Bayesian framework for statistics is quickly gaining in popularity among scientists, for reasons such as reliability and accuracy (particularly in noisy data and small samples), the possibility of incorporating prior knowledge into the analysis, and the intuitive interpretation of results (Andrews & Baguley, 2013; Etz & Vandekerckhove, 2016; Kruschke, 2010; Kruschke, Aguinis, & Joo, 2012; Wagenmakers et al., 2017). Adopting the Bayesian framework is more of a shift in the paradigm than a change in the methodology; all the common statistical procedures (t-tests, correlations, ANOVAs, regressions, etc.) can also be achieved within the Bayesian framework. One of the core difference is that in the frequentist view, the effects are fixed (but unknown) and data are random. On the other hand, instead of having single estimates of the “true effect”, the Bayesian inference process computes the probability of different effects given the observed data, resulting in a distribution of possible values for the parameters, called the posterior distribution. The bayestestR package provides tools to describe these posterior distributions.
Using the Kullback-Leibler information criterion to measure the closeness of a model to the truth, the author proposes new likelihood-ratio-based statistics for testing the null hypothesis that the competing models are as close to the true data generating process against the alternative hypothesis that one model is closer. The tests are directional and are derived for the cases where the competing models are non-nested, overlapping, or nested and whether both, one, or neither is misspecified. As a prerequisite, the author fully characterizes the asymptotic distribution of the likelihood ratio statistic under the most general conditions. Copyright 1989 by The Econometric Society.
Tools for performing model selection and model averaging. Automated model selection through subsetting the maximum model, with optional constraints for model inclusion. Model parameter and prediction averaging based on model weights derived from information criteria (AICc and alike) or custom model weighting schemes.
[Please do not request the full text - it is an R package. The up-to-date manual is available from CRAN].
effectsize: Compute and interpret indices of effect size
- K Barton
- M S Ben-Shachar
- D Makowski
- D Lüdecke
Barton, K. (2020). MuMIn: Multi-model inference. https://CRAN.R-project.org/package=
MuMIn
Ben-Shachar, M. S., Makowski, D., & Lüdecke, D. (2020). effectsize: Compute and interpret
indices of effect size. CRAN. https://doi.org/10.5281/zenodo.3952214
2020). see: Visualisation toolbox for 'easystats' and extra geoms, themes and color palettes for 'ggplot2
- D Lüdecke
- M S Ben-Shachar
- I Patil
- P Waggoner
- D Makowski
Lüdecke, D., Ben-Shachar, M. S., Patil, I., Waggoner, P., & Makowski, D. (2020). see: Visualisation toolbox for 'easystats' and extra geoms, themes and color palettes for 'ggplot2'.
CRAN. https://doi.org/10.5281/zenodo.3952153