Insects data

Description

This dataset provides reference information on two groups of insects to illustrate the usage of functions within this package.

Usage

Insects

Format

A data frame with 404 rows and 6 columns:

Group

Name of the group ("Group1", "Group2"). It is a variable of class "character".

Female

The number of the female to which each row belongs. It is a variable of class "integer".

Age

It is the age corresponding to the female. Stage in which it is found. It is a variable of class "integer".

Eggs

Eggs laid by each female at each age. It is a variable of class "integer".

Sexrate

Sexrate at each age. It is a variable of class "numeric".

Survival

Survival at each age. It is a variable of class "numeric".

Source

This dataset serves as an example for running the provided code snippets or as a reference for analyzing the functionality of this package.

Plot for the Pseudo-Values of Parameters

Description

Construction of Plots for the pseudo-values of associated Life Table parameters.

Usage

PlotPseudoVals(object)

Arguments

Value

Returns an object of class c("gg", "ggplot").

Examples

## The main object will be created using the Insects database:
lft <- lifertable(ColumnFemale = Female,
                  ColumnAge = Age,
                  ColumnEggs = Eggs,
                  SexRate = Sexrate,
                  ColumnGroups = Group,
                  data = Insects,
                  CI = TRUE)

PlotPseudoVals(lft)

Coerce CI to a Data Frame

Description

Function to coerce the object displaying the Confidence Interval into a data frame.

Usage

## S3 method for class 'lifertableCI'
as.data.frame(x, row.names = NULL, ...)

Arguments

Value

as.data.frame.lifertableCI returns a data frame.

Examples

## Make the main object:
lft <- lifertable(ColumnFemale = Female,
                  ColumnAge = Age,
                  ColumnEggs = Eggs,
                  SexRate = Sexrate,
                  ColumnGroups = Group,
                  data = Insects,
                  CI = TRUE)


as.data.frame(lft$CI)

Coerce Life Table to a Data Frame

Description

Function to coerce the object displaying Life Table into a data frame.

Usage

## S3 method for class 'lifertableLFT'
as.data.frame(x, row.names = NULL, ...)

Arguments

Value

as.data.frame.lifertableLFT returns a data frame.

Examples

## Make the main object:
lft <- lifertable(ColumnFemale = Female,
                  ColumnAge = Age,
                  ColumnEggs = Eggs,
                  SexRate = Sexrate,
                  ColumnGroups = Group,
                  data = Insects)


as.data.frame(lft$LIFERTABLE)

Coerce Parameters to a Data Frame

Description

Function to coerce the object displaying Parameters into a data frame.

Usage

## S3 method for class 'lifertableParmEst'
as.data.frame(x, row.names = NULL, ...)

Arguments

Value

as.data.frame.lifertableParmEst returns a data frame.

Examples

## Make the main object:
lft <- lifertable(ColumnFemale = Female,
                  ColumnAge = Age,
                  ColumnEggs = Eggs,
                  SexRate = Sexrate,
                  ColumnGroups = Group,
                  data = Insects)


as.data.frame(lft$PARAMETERS)

Coerce Total Eggs to a Data Frame

Description

Function to coerce the object displaying Total Eggs into a data frame.

Usage

## S3 method for class 'lifertableTotEggs'
as.data.frame(x, row.names = NULL, ...)

Arguments

Value

as.data.frame.lifertableTotEggs returns a data frame.

Examples

## Make the main object:
lft <- lifertable(ColumnFemale = Female,
                  ColumnAge = Age,
                  ColumnEggs = Eggs,
                  SexRate = Sexrate,
                  ColumnGroups = Group,
                  data = Insects,
                  TotalEggs = TRUE)


as.data.frame(lft$TOTAL.EGGS)

Life and Fertility Table

Description

This function enables users to obtain Life and Fertility Tables, offering various configuration options for optimal usage. See "Details" section.

Usage

lifertable(
  ColumnFemale,
  ColumnAge,
  ColumnEggs,
  SexRate,
  Survival = 1,
  ColumnGroups,
  data,
  InitiationOfAdultStage = 0,
  CI = FALSE,
  TotalEggs = FALSE
)

## S3 method for class 'lifertable'
print(x, ...)

## S3 method for class 'lifertableCI'
print(x, title = TRUE, ...)

## S3 method for class 'lifertableLFT'
print(x, ...)

## S3 method for class 'lifertableParmEst'
print(x, ...)

## S3 method for class 'lifertableTest'
print(x, ...)

## S3 method for class 'lifertableTotEggs'
print(x, ...)

Arguments

Details

ColumnFemale and ColumnGroups can be either a numeric vector or a character vector. This means they may contain either numerical values or labels corresponding to the female and to their respective group assignments.

The standard approach for storing the Sex Rate and Survival rate during the experiment is to input this information into the corresponding columns for each variable. If this information remains consistent within a group, you can input that value without repeating it each time. If your database encompasses a single experimental group, simply enter the corresponding value in the SexRate and Survival arguments. In the case of having more than one group, you can input the values of SexRate and Survival correspondingly into a vector containing as many elements as there are groups (one sex ratio and one survival rate for each group).

A similar situation applies to InitiationOfAdultStage: you can enter either a single value or a vector of values corresponding to the involved groups.

Estimated Parameters:

Net Reproductive Rate (Ro)

Mean net contribution per female to the next generation.

Intrinsic Rate of Increase (Rm)

Rate of natural increase in a closed population that has been subject to a constant age-specific schedule of fertility and mortality for a long period, and has converged to be a stable population.

Mean Generation Time (GT)

Mean time span between the birth of individuals of a generation and that of the next generation.

Doubling Time (DT)

Time span necessary for doubling the initial population.

Finite Rate of Increase (Lambda)

It is a multiplication factor of the original population at each time period.

Rm it was determined by analytical approximation using Lotka’s (1907, 1913) equation:

\sum_{x=0}^{\infty}{\exp^{-R_{m}x}l_x m_x} = 1

Value

lifertable returns an object of class "lifertable".

An object of class "lifertable" is a list containing the following components:

Methods (by generic)

• print(lifertable): Print a lifertable object

Functions

• print(lifertableCI): Print a lifertableCI object, this is the object showing the Confidence Interval

• print(lifertableLFT): Print a lifertableLFT object, this is the object showing the Life and Fertility Table

• print(lifertableParmEst): Print a lifertableParmEst object, this is the object showing the Estimated Parameters

• print(lifertableTest): Print a lifertableTest object, this is the object showing the Student t - test

• print(lifertableTotEggs): Print a lifertableTotEggs object, this is the object showing the Eggs laid per Female

References

Maia, A. H., Luis, A. J., & Campanhola, C. (2000). "Statistical Inference on Associated Fertility Life Table Parameters Using Jackknife Technique: Computational Aspects". Journal of Economic Entomology, 93(2), 511-518. doi:10.1603/0022-0493-93.2.511

Portilla, M., Morales-Ramos, J. A., Guadalupe Rojas, M., & Blanco, C. A. (2014). "Chapter 8 - Life Tables as Tools of Evaluation and Quality Control for Arthropod Mass Production". Mass Production of Beneficial Organisms (241-275). doi:10.1016/B978-0-12-391453-8.00008-X

Examples

## The Insects database will be utilized:

lifertable(ColumnFemale = Female,
           ColumnAge = Age,
           ColumnEggs = Eggs,
           SexRate = Sexrate,
           Survival = Survival,
           ColumnGroups = Group,
           data = Insects,
           CI = TRUE,
           TotalEggs = TRUE)

## The following expressions will yield the same result as above:

## lifertable(ColumnFemale = Insects$Female,
##            ColumnAge = Insects$Age,
##            ColumnEggs = Insects$Eggs,
##            SexRate = Insects$Sexrate,
##            Survival = Insects$Survival,
##            ColumnGroups = Insects$Group,
##            CI = TRUE, TotalEggs = TRUE)

## lifertable(ColumnFemale = Insects$Female,
##            ColumnAge = Insects$Age,
##            ColumnEggs = Insects$Eggs,
##            SexRate = 0.7, Survival = 0.9,
##            ColumnGroups = Insects$Group,
##            CI = TRUE, TotalEggs = TRUE)

## lifertable(ColumnFemale = Insects$Female,
##            ColumnAge = Insects$Age,
##            ColumnEggs = Insects$Eggs,
##            SexRate = c(0.7, 0.7),
##            Survival = c(0.9, 0.9),
##            ColumnGroups = Insects$Group,
##            CI = TRUE, TotalEggs = TRUE)

Plot for Distribution of Age at Oviposition

Description

This function generates a plot illustrating the Distribution of Oviposition (y-axis) versus Age (x-axis), with separate representations for each group if multiple groups exist. The data is sourced from the original database.

Usage

plotDistrOvipos(
  ColumnFemale,
  ColumnAge,
  ColumnEggs,
  ColumnGroups,
  data,
  InitiationOfAdultStage = 0
)

Arguments

Value

Returns an object of class c("gg", "ggplot").

Examples

## The Insects database will be used to generate the plot.

plotDistrOvipos(ColumnFemale = Female,
                ColumnAge = Age,
                ColumnEggs = Eggs,
                ColumnGroups = Group,
                data = Insects)

## The following expression will yield the same result as described above:

plotDistrOvipos(ColumnFemale = Insects$Female,
                ColumnAge = Insects$Age,
                ColumnEggs = Insects$Eggs,
                ColumnGroups = Insects$Group)

Plot for the Number of Eggs Laid per Female

Description

This function generates a Plot representing the number of Eggs Laid by each Female throughout the entire experiment.

Usage

plotEggs(object)

Arguments

Value

Returns an object of class c("gg", "ggplot").

Examples

## The main object will be created using the Insects database:
lft <- lifertable(ColumnFemale = Female,
                  ColumnAge = Age,
                  ColumnEggs = Eggs,
                  SexRate = Sexrate,
                  ColumnGroups = Group,
                  data = Insects,
                  TotalEggs = TRUE)

## Possible usage scenarios

## 1. Direct Usage of the "lft" Object:
plotEggs(lft)

## 2. Assigning the component "TOTAL.EGGS" to an object:
TEggs <- lft$TOTAL.EGGS
plotEggs(TEggs)

## 3. Direct usage of the component:
plotEggs(lft$TOTAL.EGGS)

Survival curve for the Life and Fertility Table

Description

This function generates the graphical representation of the Life Table. Survival (y-axis) versus Age (x-axis)

Usage

plotSurvivalCurve(object)

Arguments

Value

Returns an object of class c("gg", "ggplot").

Examples

## The main object will be created using the Insects database:
lft <- lifertable(ColumnFemale = Female,
                  ColumnAge = Age,
                  ColumnEggs = Eggs,
                  SexRate = Sexrate,
                  ColumnGroups = Group,
                  data = Insects)

## Possible usage scenarios

## 1. Direct Usage of the "lft" Object:
plotSurvivalCurve(lft)

## 2. Assigning the component "LIFERTABLE" to an object:
lifeTable <- lft$LIFERTABLE
plotSurvivalCurve(lifeTable)

## 3. Direct usage of the component:
plotSurvivalCurve(lft$LIFERTABLE)