Repbio

The Repbio package: Reproductive biology analysis is a methodological package developed to carry out the analyzes of the article: Salas-Singh et al. (2022) to describe updated information on the basic reproductive biology of a bullseye puffer Sphoeroides annulatus females and potential use of the gonadosomatic index as input data to assess length at 50% maturity and identify the breeding season. Also to verify the maturity patterns of the analysed data assessed by single and double sigmoid models, including the selection of the most suitable model. For this purpose, some functions and a vignette were created to explain the process step by step. The tables and figures were personalized.

The length at 50 maturity is estimated by fitting the accumulated data of mature females from two models: simple sigmoid (MSS) and double sigmoid (MDS), using two data sources: histological (MATURE) and gonadosomatic index (GSI).

The package consists of sixteen functions that facilitate the implementation of the methodology used in this analysis:

ANOVA_1: Performs 1-way ANOVA using the function aov() from the R Stats Package, it returns the list av1 and save the ANOVA results as txt file.

BCA: Nonparametric confidence intervals. This function takes a data frame (df), requires the significance value (pval) and calculates the nonparametric confidence intervals (CI): Symmetric (IC), Bias-corrected (BC) and BC accelerated (BCA).

bs: The function ‘bs’ generates a matrix that resamples length with replacement. The original data set is stored in the first row, while the resamples are stored in the ith row Bi+1, where B is the total number of resamples.

fn_Barplot: A very simple barplot is generated with no labels or marks for the X-axis, which serves as the basis for those that will be generated through the analysis, whether they are simple or compound figures.

fn_Boxplot: A very simple multiple boxplots (more than one level of factor) is generated with no labels or marks for the X-axis. It serves as the basis for the figures that will be generated through the analysis, whether they are simple or complex.

fn_coincide: The coincidence between microscopy classification and GSI is analyzed. The count is based on the number of pairs that coincide (C) and the number of pairs that are misqualified: mature by immature (MI) and immature by mature (IM).

fn_freq: The interval and class mark are defined and the absolute, cumulative and relative cumulative frequency is calculated in a table.

fn_hsd: The factor column resulting from the TukeyHSD test is sorted by its row name, these are renamed with the name of the phases and finally, they are sorted, in decreasing way, by the average response values (column 1).

fn_Idioma The figure labels are defined as either English (1) or Spanish (2).

fn_LTGSI: The scattering plot is generated without any labels or marks for the X-axis, which is very simple. A horizontal line is included with the threshold value, which serves as the basis for the figures that will be generated through the analysis, whether they are simple or compound figures.

fn_porcentaje: Calculates the percentage of each category (rows) per column (month), and also includes the total number of data per column (N).

IC_plot: Cumulative percentage of mature females against length. Fitting model for the estimation of the L50 values and its confidence interval.

Label_Phases: Returns the maturity phase label that will be used in tables or figures. It returns a ‘Phases_legend’ vector in roman numeral or name in English or Spanish.

modelo: Fit the model using the nlsLM function. For more details see the function documentation: nlsLM() from minpack.lm (version 1.2-4).

strb: This function helps in the visual search of the starting input parameters for nlsLM, to fit the specified model (mod), using a graph for visual adjustment of model parameters (Trial and Error Strategy).

Tukey_HSD: This function performs multiple comparisons of treatments by means of Tukey only if the p value of the ANOVA_1 test is equal to or less than pval defined by the user. HSD.test() came from the agricolae package.

References

Salas‐Singh, C., Morales‐Bojórquez, E., & Aguirre‐Villaseñor, H. (2022). Reproductive biology of the bullseye puffer Sphoeroides annulatus: Gonadosomatic index and its suitability for estimating length at maturity. Journal of Fish Biology, 101(5), 1119-1133.https://doi.org/10.1111/jfb.15174

Repbio: Reproductive biology analysis

Repbio

References