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get_tm_s.R
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## get_tm_s
# Obtains scaled mean age at death fro short growth periods
##
# function [tm, Sb, Sp, info] =
#' Obtains scaled mean age at death fro short growth periods
#'
#' Obtains scaled mean age at death assuming a short growth period relative to the life span
#' Divide the result by the somatic maintenance rate coefficient to arrive at the mean age at death.
#' The variant get_tm_foetus does the same in case of foetal development.
#' If the input parameter vector has only 4 elements (for [g, lT, ha/ kM2, sG]),
#' it skips the calulation of the survival probability at birth and puberty.
#'
#' @param p 4 or 7-vector with parameters: [g lT ha sG] or [g k lT vHb vHp ha SG]
#' @param f optional scalar with scaled reserve density at birth (default eb = 1)
#' @param lb optional scalar with scaled length at birth (default: lb is obtained from get_lb)
#' @param lp optional scalar with scaled length at puberty
#'
#' @return [tm, Sb, Sp, info]
#' * tm: scalar with scaled mean life span
#' * Sb: scalar with survival probability at birth (if length p = 7)
#' * Sp: scalar with survival prabability at puberty (if length p = 7)
#' * info: indicator equals 1 if successful, 0 otherwise
#'
#' @export
#'
#' @importFrom pracma quad expint erfc
#'
get_tm_s = function(p, f, lb, lp) {
# created 2009/02/21 by Bas Kooijman, modified 2014/03/17, 2015/01/18
## Syntax
# [tm, Sb, Sp, info] = <../get_tm_s.m *get_tm_s*>(p, f, lb, lp)
## Description
# Obtains scaled mean age at death assuming a short growth period relative to the life span
# Divide the result by the somatic maintenance rate coefficient to arrive at the mean age at death.
# The variant get_tm_foetus does the same in case of foetal development.
# If the input parameter vector has only 4 elements (for [g, lT, ha/ kM2, sG]),
# it skips the calulation of the survival probability at birth and puberty.
#
# Input
#
# * p:
# * f:
# * lb:
# * lp:
#
# Output
#
# * tm: scalar with scaled mean life span
# * Sb: scalar with survival probability at birth (if length p = 7)
# * Sp: scalar with survival prabability at puberty (if length p = 7)
# * info: indicator equals 1 if successful, 0 otherwise
## Remarks
# Theory is given in comments on DEB3 Section 6.1.1.
# See <get_tm.html *get_tm*> for the general case of long growth period relative to life span
## Example of use
# get_tm_s([.5, .1, .1, .01, .2, .1, .01])
if (!exists('f')) {
f = 1
} else if (is.na(f)) {
f = 1;
}
if (length(p) >= 7){
# unpack pars
g = p[1] # energy investment ratio
#k = p[2] # k_J/ k_M, ratio of maturity and somatic maintenance rate coeff
lT = p[3] # scaled heating length {p_T}/[p_M]Lm
#vHb = p[4] # v_H^b = U_H^b g^2 kM^3/ (1 - kap) v^2; U_B^b = M_H^b/ {J_EAm}
#vHp = p[5] # v_H^p = U_H^p g^2 kM^3/ (1 - kap) v^2; U_B^p = M_H^p/ {J_EAm}
ha = p[6] # h_a/ k_M^2, scaled Weibull aging acceleration
sG = p[7] # Gompertz stress coefficient
} else if (length(p) == 4){
# unpack pars
g = p[1] # energy investment ratio
lT = p[2] # scaled heating length {p_T}/[p_M]Lm
ha = p[3] # h_a/ k_M^2, scaled Weibull aging acceleration
sG = p[4] # Gompertz stress coefficient
}
if (abs(sG) < 1e-10) {
sG = 1e-10
}
li = f - lT
hW3 = ha * f * g/ 6/ li
hW = hW3^(1/3) # scaled Weibull aging rate
hG = sG * f * g * li^2
hG3 = hG^3 # scaled Gompertz aging rate
tG = hG/ hW
tG3 = hG3/ hW3 # scaled Gompertz aging rate
info_lp = 1
if (length(p) >= 7) {
if (!exists('lp') & !exists('lb')) {
lplbinfo = get_lp(p, f)
lp=lplbinfo[1]
lb=lplbinfo[2]
info_lp=lplbinfo[3]
} else if (!exists('lp') || is.na('lp')){
lplbinfo = get_lp(p, f, lb)
lp=lplbinfo[1]
lb=lplbinfo[2]
info_lp=lplbinfo[3]
}
# get scaled age at birth, puberty: tb, tp
tblbinfo_tb = get_tb(p, f, lb)
tb=tblbinfo_tb[1]
lb=tblbinfo_tb[2]
info_tb=tblbinfo_tb[3]
irB = 3 * (1 + f/ g)
tp = tb + irB * log((li - lb)/ (li - lp))
hGtb = hG * tb
Sb = exp((1 - exp(hGtb) + hGtb + hGtb^2/ 2) * 6/ tG3)
hGtp = hG * tp
Sp = exp((1 - exp(hGtp) + hGtp + hGtp^2/ 2) * 6/ tG3)
if (info_lp == 1 && info_tb == 1){
info = 1
} else{
info = 0
}
} else { # length(p) == 4
Sb = NaN
Sp = NaN
info = 1
}
if (abs(sG) < 1e-10) {
tm = gamma(4/3)/ hW
tm_tail = 0
} else if (hG > 0) {
tm = 10/ hG # upper boundary for main integration of S(t)
#library(pracma)
tm_tail = pracma::expint(exp(tm * hG) * 6/ tG3)/ hG
tm = pracma::quad(fnget_tm_s, 0, tm * hW, tol = 1.0e-12, trace = FALSE,tG)/ hW + tm_tail
} else {# hG < 0
tm = -1e4/ hG # upper boundary for main integration of S(t)
hw = hW * sqrt( - 3/ tG) # scaled hW
tm_tail = sqrt(pi)* pracma::erfc(tm * hw)/ 2/ hw
tm = pracma::quad(fnget_tm_s, 0, tm * hW, tol = 1.0e-12, trace = FALSE, tG)/ hW + tm_tail
}
}
# subfunction
#function S =
fnget_tm_s=function(t, tG){
# modified 2010/02/25
# called by get_tm_s for life span at short growth periods
# integrate ageing surv prob over scaled age
# t: age * hW
# S: ageing survival prob
hGt = tG * t # age * hG
if (tG > 0) {
a= matrix(hGt) %*% t(matrix((1/(4:500))))
S = exp(-(1 + apply((t(apply(a, 1, cumprod))),1, sum)) * t^3) #apply((t(apply(a, 1, cumprod))),2, sum)?
} else {# tG < 0
S = exp((1 + hGt + hGt^2/ 2 - exp(hGt)) * 6/ tG^3)
}
return(S)
}