| Title: | Relative Growth Rate |
|---|---|
| Description: | Calculates the relative growth rate (RGR) of a series of individuals by building a life table and solving the Lotka-Birch equation. (See Birch, L. C. 1948. The intrinsic rate of natural increase of an insect population. - Journal of Animal Ecology 17: 15-26) <doi:10.2307/1605>. |
| Authors: | Jean-Sebastien Pierre <[email protected]> |
| Maintainer: | Jean-Sebastien Pierre <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.0 |
| Built: | 2025-02-28 04:00:35 UTC |
| Source: | https://github.com/cran/petitr |
a life table with 100 individuals to test the time required by jackknife estimation
data(grosdata)data(grosdata)
A data frame with 100 observations on the following 22 variables.
V1fecundity of day 1
V2fecundity of day 2
V3fecundity of day 3
V4fecundity of day 4
V5fecundity of day 5
V6fecundity of day 6
V7fecundity of day 7
V8fecundity of day 8
V9fecundity of day 9
V10fecundity of day 10
V11fecundity of day 11
V12fecundity of day 12
V13fecundity of day 13
V14fecundity of day 14
V15fecundity of day 15
V16fecundity of day 16
V17fecundity of day 17
V18fecundity of day 18
V19fecundity of day 19
V20fecundity of day 20
V21fecundity of day 21
V22fecundity of day 22
fictitious data designed to check the time needed and the effect of the m parameter of the jackknife estimation
J.S. Pierre, fictitious
data(grosdata) petitr(grosdata)data(grosdata) petitr(grosdata)
Daily fecundity of ten individuals (fictitious data)
data(life)data(life)
A data frame with 10 observations on the following 11 variables.
X1numeric vector, age
X2numeric vector, first individual
X3numeric vector, second individual
X4numeric vector, ...
X5numeric vector, ...
X6numeric vector, ...
X7numeric vector, ...
X8numeric vector, ...
X9numeric vector, ...
X10numeric vector, ...
X11numeric vector, tenth individual
the first columns stands for the age of the individual. must be sorted in ascending order and represent equal age classes.
data(life) petitr(life)data(life) petitr(life)
Daily fecundity of ten individuals (fictitious data)
data(life1)data(life1)
A data frame with 10 observations on the following 11 variables.
X1numeric vector, age
X2numeric vector, first individual
X3numeric vector, second individual
X4numeric vector, ...
X5numeric vector, ...
X6numeric vector, ...
X7numeric vector, ...
X8numeric vector, ...
X9numeric vector, ...
X10numeric vector, ...
X11numeric vector, tenth individual
the first columns stands for the age of the individual. must be sorted in ascending order and represent equal age classes.
data(life1,life2,life3) ranova(list(life1,life2,life3))data(life1,life2,life3) ranova(list(life1,life2,life3))
Daily fecundity of ten individuals (fictitious data)
data(life2)data(life2)
A data frame with 10 observations on the following 11 variables.
X1numeric vector, age
X2numeric vector, first individual
X3numeric vector, second individual
X4numeric vector, ...
X5numeric vector, ...
X6numeric vector, ...
X7numeric vector, ...
X8numeric vector, ...
X9numeric vector, ...
X10numeric vector, ...
X11numeric vector, tenth individual
the first columns stands for the age of the individual. must be sorted in ascending order and represent equal age classes.
data(life1,life2,life3) ranova(list(life1,life2,life3))data(life1,life2,life3) ranova(list(life1,life2,life3))
Daily fecundity of ten individuals (fictitious data)
data(life3)data(life3)
A data frame with 10 observations on the following 11 variables.
X1numeric vector, age
X2numeric vector, first individual
X3numeric vector, second individual
X4numeric vector, ...
X5numeric vector, ...
X6numeric vector, ...
X7numeric vector, ...
X8numeric vector, ...
X9numeric vector, ...
X10numeric vector, ...
X11numeric vector, tenth individual
the first columns stands for the age of the individual. must be sorted in ascending order and represent equal age classes.
data(life1,life2,life3) ranova(list(life1,life2,life3))data(life1,life2,life3) ranova(list(life1,life2,life3))
calculates the per capita growth rate of a series of individuals through the set of individual life tables
petitr(tabvie, niter = 100, eps = 1e-07, m = 1, alpha = 0.05, s = 1)petitr(tabvie, niter = 100, eps = 1e-07, m = 1, alpha = 0.05, s = 1)
tabvie |
A data.frame with a first column recording the endpoint of age classes, and as many columns as individuals. For each individual, each row represents the number of offspring produced by the individual vetween age x-1 and age x. After death or after the end of reproductive life, each column must be filled by zeros . The last row represents therefore the maximum reproductive age observed in the data set. The number of columns is n+1, where n is the number of individuals. |
niter |
the maximum number of iterations for the Newton's method. Default is 100 |
eps |
Precision required for the Newton's method. Default is 1e-07. |
m |
Size of the subsamples to drop one after one in the Jackknife method. Default is m=1. Any other value must divide exactly n,the number of individuals. |
alpha |
First kind error risk. Default is alpha=0.05. |
s |
ex ratio expressed as the proportion of females in the total population. Default is 1, meaning a parthenogenetic population (ex. aphids). For a sexual population one would often set s=0.5. |
Calls r, and xlxmx, called by ranova.
a vector with the pseudovalues of r calculated by the jackknife method
Jean-Sebastien Pierre [email protected]
Birch, L. C. 1948. The intrinsic rate of natural increase of an insect population. - Journal of Animal Ecology 17: 15-26. Lotka, A. (1924). Elements of mathematical biology. Reprinted 1956 by Dover Publications Inc., New York, USA.
r, and xlxmx, called by ranova
data(life) petitr(life)data(life) petitr(life)
Calculates the intrinsic rate of increase by solving the Birch equation. Uses the Newton method.
r(tab, eps = eps, maxiter = 100)r(tab, eps = eps, maxiter = 100)
tab |
a data.frame with three columns : x, the age, lx, the proportion of survivors at age x, mx, the offspring number per individual in the age class x |
eps |
Precision for the convergence of Newton method. Default is object eps transmitted by the calling function r. must be defined for a standalone use |
maxiter |
maximum number of iterations for the Newton's method. default = 100 |
a single numeric value : r
Jean-Sebastien PIERRE
Lotka 1924, Birch 1948.
petitr,xlxmx,ranova
data (tblif) r(tblif,eps=0.0000001)data (tblif) r(tblif,eps=0.0000001)
Accepts as input a series (list) of individual life tables (see r,petitr,life1), calculates the Jackknife estimator of r (per capita growth rate) on each table, and achieves a one way analysis of variance on the set of pseudovalues corresponding to each table.
ranova(listab, levels = NULL)ranova(listab, levels = NULL)
listab |
list of life tables. must be of class list, and each table of class data.frame |
levels |
a character vector giving level names for each life table. If NULL, the levels are named l1,l2, etc.. |
a data frame with two columns: the set of pseudovalues, and a factor named pop. Can be retrieved and used for more sophisticated factor organisation
Jean-Sebastien Pierre
Lotka 1924, Birch 1948, Wratten 1982
r, and xlxmx, called by petitr~
data(life1,life2,life3) ranova(list(life1,life2,life3))data(life1,life2,life3) ranova(list(life1,life2,life3))
a population life table with three columns, x, lx, mx (See below)
data(tblif)data(tblif)
A data frame with 10 observations on the following 3 variables.
xa numeric vector, age
lxa numeric vector, Proportion of survivors at age x
mxa numeric vector, mean number of offspring produced in the age class x
x must represent equal age classes in ascending order
Application of the function xlxmx on the data set life
data(tblif) r(tblif, eps=10e-08)data(tblif) r(tblif, eps=10e-08)
Calculates a life table with three columns, x, lx mx from the age specific birth data of a set of individuals. Called by petitr, but may be used as standalone function.
xlxmx(X, s)xlxmx(X, s)
X |
a data.frame. See petitr |
s |
Sex ratio expressed as the proportion of females in the population |
a data.frame with three columns, x (age), lx (survival at age x), mx (birth rate at age x)
Jean-Sebastien Pierre [email protected]
Lotka 1924, Birch 1948
r, and petitr, called by ranova
data(life) tablif=xlxmx(life,s=1)data(life) tablif=xlxmx(life,s=1)