Statistical analysis of sperm motility data from Atelopus sp. specimens, evaluating the effect of two cryoprotectant formulations (CPA1 and CPA2) across four post-activation time points. Part of an ongoing amphibian cryopreservation research programme at Fundación Jambatu, Ecuador.
Data note: The dataset used here is a simulated representation of pilot experimental findings, produced to protect confidential project information while preserving the statistical characteristics of the original data. Data collection was conducted personally by the author with explicit permission from supervisor Andrea Terán.
The full analysis — figures, formatted tables, and interpretations — is available as a self-contained HTML document:
.
├── analysis.Rmd # Source document — prose, code, and output in one file
├── analysis.html # Rendered report (knitted from analysis.Rmd)
├── prd.xlsx # Simulated motility dataset
└── Stat_Tests.Rproj # RStudio project file
R 4.x and RStudio. Install required packages before knitting:
install.packages(c("tidyverse", "readxl", "pwr", "ggdist",
"knitr", "kableExtra", "broom"))| Package | Purpose |
|---|---|
tidyverse |
Data wrangling (dplyr, tidyr) and plotting (ggplot2) |
readxl |
Import .xlsx dataset |
pwr |
Power analysis for sample size determination |
ggdist |
stat_halfeye() for raincloud plot half-violins |
knitr / kableExtra |
Formatted, captioned tables in the HTML output |
broom |
Converts ANOVA and Tukey objects to tidy data frames |
- Clone the repository.
- Open
Stat_Tests.Rprojin RStudio — this sets the working directory correctly soprd.xlsxis found automatically. - Open
analysis.Rmdand click Knit, or run from the terminal:
rmarkdown::render("analysis.Rmd")The rendered analysis.html will be written to the project folder.
All code chunks are collapsed by default in the HTML output (code_folding: hide)
— click any Code button to inspect the underlying R.
39 observations across two treatments and four time lapses. Each row is one motility measurement (% motile sperm) for a given treatment and time point.
| Column | Description |
|---|---|
Treatment |
Cryoprotectant formulation — CPA1 or CPA2 |
Time_Lapse |
Minutes post-activation — 5, 10, 15, or 20 |
Motility |
Percentage of motile sperm |
Raincloud plots combine a half-violin (distribution shape), box plot (median and IQR), and raw jittered points. This format is recommended for small samples where bar plots would hide individual variation and distribution shape (Allen et al., 2019; Weissgerber et al., 2015). CPA1 and CPA2 are displayed on a shared axis for direct comparison.
A two-way ANOVA was fitted with Treatment, Time_Lapse, and their interaction as fixed factors. One-way ANOVAs were then fitted per treatment to isolate time effects within each formulation. Tukey's HSD post-hoc test was applied to CPA2, which showed a significant time effect.
- Treatment effect: No significant difference in overall mean motility between CPA1 and CPA2 at the current sample size.
- Time effect: Time_Lapse is a significant predictor of motility for both formulations — motility declines over time regardless of cryoprotectant.
- CPA2 post-hoc: Significant motility decline between Time 5 and Time 15, and between Time 5 and Time 20 (Tukey HSD, p adj < 0.05). All other pairwise comparisons were non-significant.
- CPA1 post-hoc: No significant differences between any time lapse pair.
- Sample size: A power analysis (Cohen's f = 0.25, α = 0.05, power = 0.80) indicates approximately 45 observations per group are needed for a confirmatory study. The current pilot falls below this threshold.
Allen M, Poggiali D, Whitaker K, Marshall TR, Kievit RA (2019). Raincloud plots: a multi-platform tool for robust data visualization. Wellcome Open Research, 4:63. https://doi.org/10.12688/wellcomeopenres.15191.1
Weissgerber TL, Milic NM, Winham SJ, Garovic VD (2015). Beyond bar and line graphs: time for a new data presentation paradigm. PLOS Biology, 13(4):e1002128. https://doi.org/10.1371/journal.pbio.1002128
A. Benjamin Garcés Cifuentes · Fundación Jambatu, Ecuador · R 4.x · Ubuntu 24.04 LTS