Package 'practicalbayes'

Yeast fermentation kinetics

Description

Simulated data that explore the kinetics of 12 different yeast strains (Saccharomyces cerevisiae) when inoculated into Charonnay must.

Usage

fermentation

Format

A tibble with 528 rows and 5 columnes:

souche

Yeast strain.

replicat

Replication code.

jour

Day since inoculation.

sucre_gL

Sugar concentration in g/L.

log10_pop

Number of yeast cells par ml.

Details

The data was simulated to mimic real observations collected at the experimental facility and results from **Fanny Bordet**, **Chloé Roullier-Gall** et **Raphaëlle Tourdot-Maréchal** (UMR PAM, Institut universitaire de la vigne et du vin Jules Guyot, Dijon).

Source

Bordet F., Roullier-Gall C., Ballester J., Vichi S., Quintanilla-Casas B., Gougeon R. D., Julien-Ortiz A., Schmitt-Kopplin P., Alexandre H. (2021). Different wines from different yeasts? Saccharomyces cerevisiae intraspecies differentiation by metabolomic signature and sensory patterns in wine. Microorganisms, 9(11), 2327. https://doi.org/10.3390/microorganisms9112327

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Egg counts in nesting sites

Description

Egg counts in nesting sites of the leatherback turtle (Dermochelys coriacea) on a specific beach, Ya:lima:po Beach (formerly Les Hattes Beach), in French Guiana, which has been monitored since 1979, although there have been a few interruptions in the monitoring programme.

Usage

nestings

Format

A tibble with 1763 rows and 2 columnes:

date

Date of observation.

nombre

Number of eggs.

Source

Girondot, M. (2010). Estimating density of animals during migratory waves: application to marine turtles at nesting site. Endangered Species Research, 12, 85-105. https://doi.org/10.3354/esr00292

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practicalbayes colours

Description

practicalbayes colours

Usage

pb_cols(x)

Arguments

x	color name or object name (e.g. prior, likelihood, posterior)

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Confidence Interval for the residual standard deviation of a linear model

Description

Compute a Confidence Interval

Usage

sigma_ci(x, alpha)

Arguments

x	An object of class lm.
alpha	Significance level.

Value

A data.frame with 1 line and variables parameter, point_est, ll and hh.

References

See, for instance,

Examples

sigma_ci(lm(y ~ 1, data.frame(y = rnorm(1e3, sd = 2))), alpha = 0.05)

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ggplot themes with practicalbayes settings

Description

This ggplot theme uses specific colours and settings for the trining. The 'large' version uses a base size of 24.

Usage

theme_pb(base_size = 20, base_family = "sans")

theme_pb_large()

Arguments

base_size	base size
base_family	base font family

Value

a ggplot theme

Examples

library(ggplot2)
ggplot(data.frame(x = 1, y = 1)) +
  geom_point(aes(x, y)) +
  labs(title = "Main title") +
  theme_pb()

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Temperature-dependent sex determination

Description

Experimental data on the influence of temperature in sexual determination of reptiles. Specifically, the olive ridley sea turtle (Lepidochelys olivacea).

Usage

tsd

Format

A tibble with 20 rows and 4 columns:

males, females

Number of hatchings of each sex.

temp

Nominal incubation temperature.

amplitude

How much the temperature could fluctuate around nominal incubation temperature.

Details

This is a subset of the much larger [embryogrowth::DatabaseTSD] dataset, with selected variables and observations for educational purposes.

Each row contains the number of male and female hatchings for a given nominal incubation temperature and its fluctuation amplitude, in a experimental study.

Source

Girondot M (2026). _embryogrowth: Tools to Analyze the Thermal Reaction Norm of Embryo Growth_. doi:10.32614/CRAN.package.embryogrowth <https://doi.org/10.32614/CRAN.package.embryogrowth>. R package version 2026.8.24, <https://CRAN.R-project.org/package=embryogrowth>.

Abreu-Grobois, F. A., Morales-Mérida, B. A., Hart, C. E., Guillon, J.-M., Godfrey, M. H., Navarro, E., & Girondot, M. (2020). Recent advances on the estimation of the thermal reaction norm for sex ratios. PeerJ, 8, e8451. https://doi.org/10.7717/peerj.8451

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Experimental vine stock data

Description

The educational dataset is derived from an experimental study of several wine-growing seasons.

Usage

vinestock

Format

A tibble with 240 rows and 8 columns:

area, subplot

Experimental block (16 blocks across 3 areas)

vine_stock

Vine identifier (80 individuals)

year

Year of observation (2010-2012)

treatment

Experimental treatment (5 levels)

yield

Vine yield (g)

previous_pw

Pruning weight (g) in the previous year

previous_pw_c

Centred pruning weight (g)

Details

The study is based at an experimental vineyard that has been monitored over several years. Each row in the dataset corresponds to a **vine observed in a given year**.

Source

Guilpart, Nicolas. ‘Relations Entre Services Écosystémiques Dans Un Agroécosystème à Base de Plantes Pérennes : Compromis Entre Rendement de La Vigne et Régulation de l’oïdium’. These de doctorat, Montpellier, SupAgro, 2014. <https://theses.fr/2014NSAM0007>.

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