Type:	Package
Title:	Calculate Sample Sizes Required for Critical Thermal Limits Experiments
Version:	0.1.2
Maintainer:	Clarke JM van Steenderen <vsteenderen@gmail.com>
Description:	We present a range of simulations to aid researchers in determining appropriate sample sizes when performing critical thermal limits studies (e.g. CTmin/CTmin experiments). A number of wrapper functions are provided for plotting and summarising outputs from these simulations. This package is presented in van Steenderen, C.J.M., Sutton, G.F., Owen, C.A., Martin, G.D., and Coetzee, J.A. Sample size assessments for thermal physiology studies: An R package and R Shiny application. 2023. Physiological Entomology. <doi:10.1111/phen.12416>. The GUI version of this package is available on the R Shiny online server at: https://clarkevansteenderen.shinyapps.io/ThermalSampleR_Shiny/ , or it is accessible via GitHub at https://github.com/clarkevansteenderen/ThermalSampleR_Shiny/. We would like to thank Grant Duffy (University of Otago, Dundedin, New Zealand) for granting us permission to use the source code for the Test of Total Equivalency function.
License:	GPL-3
Encoding:	UTF-8
LazyData:	true
Depends:	R (≥ 2.10)
Imports:	tidyr, dplyr, purrr, rlang, MASS (≥ 7.3), stats (≥ 3.4.0), graphics (≥ 3.4.0), base (≥ 3.4.0), magrittr, utils, ggplot2, cowplot, EnvStats, sn, janitor, testthat
RoxygenNote:	7.2.3
Suggests:	rmarkdown, knitr
VignetteBuilder:	knitr
NeedsCompilation:	no
Packaged:	2024-02-12 14:45:11 UTC; s1000334
Author:	Guy Frederick Sutton [aut] (Wrote original R functions, and adapted the Duffy et. al. 2021 R function into this package.), Clarke JM van Steenderen [aut, cre] (Compiled the R package, and the associated R Shiny application.), Grant Duffy [cph] (Granted permission to use the source code for the Test of Total Equivalency function.)
Repository:	CRAN
Date/Publication:	2024-02-17 23:30:08 UTC

Bootstrap sampling to calculate summary statistics of CTL values

Description

Calculate mean and CI's of CTL for a single population

Arguments

Value

A data frame of CTL summary statistics from bootstrap resamples

Examples

head(coreid_data)
sims <- boot_one(data = coreid_data,
                    groups_col = col,
                    groups_which = "Catorhintha schaffneri_APM",
                    response = response,
                    n_max = 49,
                    iter = 99)

Bootstrap sampling for difference in means between two groups

Description

Calculate difference in mean CT limits between two groups.

Arguments

Value

A data frame of bootstrap resamples

Examples

head(coreid_data)
sims <- boot_two(data = coreid_data,
                        groups_col = col,
                        response = response,
                        group1 = "Catorhintha schaffneri_APM",
                        group2 = "Catorhintha schaffneri_NPM",
                        n_max = 49,
                        iter = 99)

Example critical thermal limit data for ThermalSampleN package

Description

A dataset containing critical thermal limit (CTmin) data for the sap-sucking bug, Catorintha schaffneri.

Usage

coreid_data

Format

A data frame with 60 rows and 2 variables:

col

insect population tested, string

response

CTmin value for individual insect, in degrees celsius

...

Source

"Unpublished data provided by Philippa Muskett (Centre for Biological Control, Rhodes University, South Africa)

equiv_tost

Description

Perform a Test of Total Equivalence as adapted from Duffy et al. (2021) (<https://doi.org/10.1111/1365-2435.13928>)

Arguments

Value

Two plots; (a) equivalence of means, and (b) equivalence of variances

Examples

head(coreid_data)
res <- equiv_tost(data = coreid_data,
                    groups_col = col,
                    groups_which = "Catorhintha schaffneri_APM",
                    response = response,
                    skews = c(1,10),
                    colrs = c("lightblue", "lightpink"),
                    equiv_margin = 1,
                    pop_n = 5)

Plot output from boot_sample

Description

Plot output from boot_one.

Arguments

Value

Two plots; (a) precision of the CTmin estimate across experimental and extrapolated sample sizes; (b) the sampling distribution (range of plausible CTmin values) across experimental and extrapolated sample sizes.

Examples

sims <- boot_one(coreid_data,
                    groups_col = col,
                    groups_which = "Catorhintha schaffneri_APM",
                    n_max = 30,
                    response = response)
plot_one_group(x = sims,
               n_min = 3,
               n_max = 15,
               colour_exp = "darkblue",
               colour_extrap = "green",
               legend.position = "right")

Plot output from boot_two_groups

Description

Plot output from boot_two.

Arguments

Value

Two plots: (a) the precision of the estimates for the difference in CTmin between the two selected groups across sample sizes; (b) the 95

Examples

sims <- boot_two(data = coreid_data,
                        groups_col = col,
                        response = response,
                        group1 = "Catorhintha schaffneri_APM",
                        group2 = "Catorhintha schaffneri_NPM",
                        n_max = 30,
                        iter = 99)

plots <- plot_two_groups(x = sims,
                         n_min = 3,
                         n_max = 30,
                         colour_exp = "gold",
                         colour_extrap = "darkgreen",
                         legend.position = "right")