One of the frequent questions by users of the mixed model function lmer of the lme4 package has been: How can I get p values for the F and t tests for objects returned by lmer? The lmerTest package extends the 'lmerMod' class of the lme4 package, by overloading the anova and summary functions by providing p values for tests for fixed effects. We have implemented the Satterthwaite's method for approximating degrees of freedom for the t and F tests. We have also implemented the construction of Type I - III ANOVA tables. Furthermore, one may also obtain the summary as well as the anova table using the Kenward-Roger approximation for denominator degrees of freedom (based on the KRmodcomp function from the pbkrtest package). Some other convenient mixed model analysis tools such as a step method, that performs backward elimination of nonsignificant effects - both random and fixed, calculation of population means and multiple comparison tests together with plot facilities are provided by the package as well.

/pdf/lmertest-package-tests-in-linear-mixed-effects-models-1x6b86x8v9.pdf

lmerTest Package: Tests in Linear Mixed Effects Models

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Modern Applied Statistics With S

In 1974 an article appeared in Science magazine with the dry-sounding title “Judgment Under Uncertainty: Heuristics and Biases” by a pair of psychologists who were not well known outside their discipline of decision theory. In it Amos Tversky and Daniel Kahneman introduced the world to Prospect Theory, which mapped out how humans actually behave when faced with decisions about gains and losses, in contrast to how economists assumed that people behave. Prospect Theory turned Economics on its head by demonstrating through a series of ingenious experiments that people are much more concerned with losses than they are with gains, and that framing a choice from one perspective or the other will result in decisions that are exactly the opposite of each other, even if the outcomes are monetarily the same. Prospect Theory led cognitive psychology in a new direction that began to uncover other human biases in thinking that are probably not learned but are part of our brain’s wiring.

Thinking fast and slow.

Extended-connectivity fingerprints (ECFPs) are a novel class of topological fingerprints for molecular characterization. Historically, topological fingerprints were developed for substructure and similarity searching. ECFPs were developed specifically for structure−activity modeling. ECFPs are circular fingerprints with a number of useful qualities: they can be very rapidly calculated; they are not predefined and can represent an essentially infinite number of different molecular features (including stereochemical information); their features represent the presence of particular substructures, allowing easier interpretation of analysis results; and the ECFP algorithm can be tailored to generate different types of circular fingerprints, optimized for different uses. While the use of ECFPs has been widely adopted and validated, a description of their implementation has not previously been presented in the literature.

Extended-Connectivity Fingerprints

The measurement of meaning

PURPOSE. Prolonged multifocal electroretinogram (mfERG) implicit times have been observed in diabetes, although the acute response to hyperglycemia is an acceleration of the ERG. The hypothesis for the current investigation was that this discrepancy is caused by a protracted adaptational response of the retina to hyperglycemia. METHODS. Fourteen patients with type 1 diabetes without retinopathy were blood glucose clamped at 5 mM for 75 minutes before the recording of the mfERG. The results were compared with those found in 14 age-matched healthy subjects. RESULTS. During acute normoglycemia, patients with type 1 diabetes without retinopathy demonstrated an overall 1.36-ms delay of the P1 first-order implicit times (P = 0.0013) and a 0.72-ms delay of the second-order P1 (P = 0.0049) compared with healthy subjects at 4.9 ± 0.28 mM blood glucose. During acute hyperglycemia, the P1 first-order delay was only 0.81 ms (P = 0.02), and the P1 second-order implicit time was comparable to that of healthy subjects (P > 0.05). The magnitude of the diabetes-associated implicit time delay, at both levels of glycemia, was proportional to the level of chronic hyperglycemia at study entry, as expressed by the patients' HbA1c. CONCLUSIONS. During acute normoglycemia, patients with type 1 diabetes without retinopathy demonstrated a delayed mfERG response compared with the healthy subjects. The delay was more pronounced during euglycemia than during hyperglycemia, and at both levels of glycemia, the delay was proportional to the patients' habitual hyperglycemia. The results show that chronic hyperglycemia induces an adaptational response that tends to normalize retinal implicit times at a higher level of habitual glycemia.

The multifocal ERG in diabetic patients without retinopathy during euglycemic clamping.

The sensory intensity measured as theabsolute threshold value of spice andrecognition of spice was evaluated for summer savory and rosemary in meat balls. The values forabsolute threshold value of spice were found to be significantly lower for rosemary than for summer savory. The antioxidative activity of the spices was analysed in two accelerated model systems and in a storage experiment. In one of the model systems, oxidation was accelerated by heat and by an elevated pressure of oxygen. Both spices significantly improved the oxidative stability of the meat balls in this model system. In the second model system metal catalyst oxidation in a meat slurry was used and a reduction in the oxidative processes in samples containing the spices was again shown. In both model systems a slightly higher antioxidative activity was seen for rosemary compared to summer savory. In the storage experiment, the spices were added at a sensorially acceptable level and the heat-treated meat balls were stored at 5°C. A significant reduction in the development of warmed-over flavour (WOF) caused by the addition of spices was measured by a reduction in 2-thiobarbituricacid-reactivesubstances (TBARS) and in hexanal. A reduction in TBARS of approximately 30% in meat balls containing added spices was seen independently of packaging in 1% oxygen or in atmospheric air and the reduction (30%) was constant throughout the storage period.

Antioxidative activity of summer savory (Satureja hortensis L.) and rosemary (Rosmarinus officinalis L.) in minced, cooked pork meat

The contents of fat, astaxanthin, and tocopherols and the fatty acid composition of a homogeneous group of 145 farmed Atlantic salmon (Salmo salar) were determined. The analytical variation of the data was stastistically separated from the biological variation. The fat content in the muscle near the head was 15.0% with a biological standard deviation of 3.0%. The astaxanthin concentration was 5.5 mg/kg of muscle with a biological standard deviation of 1.1 mg/kg of muscle, and the canthaxanthin concentration was 200 μg/kg of muscle with a standard deviation of 47 μg/kg of muscle. The concentrations of α-, γ-, and δ- tocopherols were approximately 32, 2.9, and 0.4 mg/kg of muscle, respectively, and the biological standard deviations were 4.5, 0.4, and 0.07 mg/kg (14, 14, and 20%), respectively. In another group of five salmon the distributions throughout the fillet were determined, longitudinally as well as transversally. The distribution of fat, astaxanthin, and tocopherols varied throughout the salmon. Th...

Biological variation of lipid constituents and distribution of tocopherols and astaxanthin in farmed Atlantic salmon (Salmo salar)

Thurstonian models for sensory discrimination tests as generalized linear models

The objective of the present investigation was to elucidate sensory attributes that influence consumer perception of apple freshness. A total of 4,758 consumers rated the freshness of six apple cultivars stored at different conditions. The apples were further characterized by consumer and panel sensory analyses as well as by physico-chemical analyses. The contribution of these characteristics to freshness was tested with principal component regression. Texture properties were shown to be of main importance for freshness, and flavor attributes of less importance. It is hypothesized that the evaluation of freshness might be a measurement of apple aging through the evaluation of its texture. Consumers of different age and levels of apple consumption did not vary in their perception of freshness. However, differences by gender were observed. Attributes shown to influence freshness were in agreement when measured by consumer, panel and physico-chemical analyses.



PRACTICAL APPLICATIONS

Freshness is an important characteristic of fruits and vegetables. A better understanding of what freshness means to consumers helps in the provision of high-quality products perceived as fresh. A key finding of this study, which concentrates basically on the sensory aspects of freshness, is that freshness in case of apples is mainly related to high textural quality. Providing consumers with apples that meet their expectations of a fresh product might increase consumption.

http://www.ds.uzh.ch/semantik-der-sinne/files/Peneauetal_JSensorystud_22_313_2007.pdf

Per B. Brockhoff

Papers

The multifocal ERG in diabetic patients without retinopathy during euglycemic clamping.

Antioxidative activity of summer savory (Satureja hortensis L.) and rosemary (Rosmarinus officinalis L.) in minced, cooked pork meat

Biological variation of lipid constituents and distribution of tocopherols and astaxanthin in farmed Atlantic salmon (Salmo salar)

Thurstonian models for sensory discrimination tests as generalized linear models

Relating consumer evaluation of apple freshness to sensory and physico-chemical measurements