more tidying of namespaces and imported functions

DESCRIPTION

@@ -5,9 +5,10 @@ Version: 0.1.0
 Author: DEBtool maintainers
 Maintainer: Philipp Boersch-Supan <[email protected]>
 Description: Functions copied from the DEBtool_R git repository and repackaged in a CRAN compliant manner to simplify parameter estimation for DEB models. This package is not intended to replace the DEBtool_R translation effort, but rather a quick fix to make functions for initial value calculation accessible in R.
-License: What license is it under?
+License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.0.1
 Suggests: testthat
-Imports: pracma
+Imports: pracma,
+    deSolve

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2018
+COPYRIGHT HOLDER: Your name goes here

NAMESPACE

@@ -3,6 +3,13 @@
 export(beta0)
 export(dget_tb)
 export(get_lb)
+export(get_lj)
 export(get_tb)
+export(get_tm_s)
 export(get_ue0)
+importFrom(deSolve,ode)
+importFrom(pracma,erfc)
+importFrom(pracma,expint)
+importFrom(pracma,ones)
 importFrom(pracma,quad)
+importFrom(pracma,zeros)

R/get_lb2.R

@@ -9,18 +9,18 @@ get_lb2= function(p, eb, lb0=NA){
 # [lb info] = <../get_lb2.m *get_lb2*> (p, eb, lb0)
 
 ## Description
-# Obtains scaled length at birth, given the scaled reserve density at birth. 
+# Obtains scaled length at birth, given the scaled reserve density at birth.
 # Like get_lb, but using the shooting method, rather than Newton Raphson
 #
 # Input
 #
 # * p: 3-vector with parameters: g, k, v_H^b (see below)
 # * eb: optional scalar with scaled reserve density at birth (default eb = 1)
 # * lb0: optional scalar with initial estimate for scaled length at birth (default lb0: lb for k = 1)
-#  
+#
 # Output
 #
-# * lb: scalar with scaled length at birth 
+# * lb: scalar with scaled length at birth
 # * info: indicator equals 1 if successful, 0 otherwise
 
 ## Remarks
@@ -30,12 +30,12 @@ get_lb2= function(p, eb, lb0=NA){
   g = p[1]   # g = [E_G] * v/ kap * {p_Am}, energy investment ratio
   k = p[2]   # k = k_J/ k_M, ratio of maturity and somatic maintenance rate coeff
   vHb = p[3] # v_H^b = U_H^b g^2 kM^3/ (1 - kap) v^2; U_H^b = M_H^b/ {J_EAm}
-  
+
   info = 1
-  
-  
+
+
   if (is.na(lb0)) {
-    lb = as.complex(vHb)^(1/ 3) # exact solution for k = 1     
+    lb = as.complex(vHb)^(1/ 3) # exact solution for k = 1
   } else {
     lb = lb0
   }
@@ -44,22 +44,22 @@ get_lb2= function(p, eb, lb0=NA){
   } else if (is.na(eb)){
     eb = 1
   }
-  
-  
+
+
   xb = g/ (eb + g)
   xb3 = xb^(1/3)
-  
+
   xbxb3gvHbk=c(xb, xb3, g, vHb, k)
   lb=Re(lb)
-  
-  lbflaginfo = fzero(fnget_lb2, lb, maxiter = 100, tol = 10e-8, xbxb3gvHbk)
+
+  lbflaginfo = pracma::fzero(fnget_lb2, lb, maxiter = 100, tol = 10e-8, xbxb3gvHbk)
   #lbflaginfo = uniroot(fnget_lb2, c(-10, 10), xbxb3gvHbk)
   lb=lbflaginfo$x
   info=1
-  
+
   if (lb < 0 || lb > 1){
     info = 0
   }
   return(c(lb, info))
 }
-  
+

R/get_lj.R

@@ -2,23 +2,42 @@
 # Gets scaled length at metamorphosis
 
 ##
-  #function [lj, lp, lb, info] = 
+  #function [lj, lp, lb, info] =
 
+#' Gets scaled length at metamorphosis
+#'
+#' Type M-acceleration: Isomorph, but V1-morph between vHb and vHj
+#' This routine obtaines scaled length at metamorphosis lj given scaled muturity at metamorphosis vHj.
+#' The theory behind get_lj, is discussed in the comments to DEB3.
+#' If scaled length at birth (third input) is not specified, it is computed (using automatic initial estimate);
+#'  if it is specified. however, is it just copied to the (third) output.
+#' The code assumes vHb < vHj < vHp (see first input).
+#'
+#' @param p 6-vector with parameters: g, k, l_T, v_H^b, v_H^j, v_H^p; if p is a 5-vector, output lp is empty
+#' @param f optional scalar with scaled functional responses (default 1)
+#' @param lb0 optional scalar with scaled length at birth
+#'
+#' @return [lj, lp, lb, info]  lj: scalar with scaled length at metamorphosis; * lp: scalar with scaled length at puberty; lb: scalar with scaled length at birth;  info: indicator equals 1 if successful
+#'
+#' @export
+#'
+#' @importFrom deSolve ode
+#'
 get_lj=function(p, f, lb0) {
 
-  #  created at 2010/02/10 by Bas Kooijman, 
+  #  created at 2010/02/10 by Bas Kooijman,
   #  modified 2014/03/03 Starrlight Augustine, 2015/01/18 Bas Kooijman
-  
+
   ## Syntax
   # [lj, lp, lb, info] = <../get_lj.m *get_lj*>(p, f, lb0)
-  
+
   ## Description
   # Type M-acceleration: Isomorph, but V1-morph between vHb and vHj
-  # This routine obtaines scaled length at metamorphosis lj given scaled muturity at metamorphosis vHj. 
-  # The theory behind get_lj, is discussed in the comments to DEB3. 
-  # If scaled length at birth (third input) is not specified, it is computed (using automatic initial estimate); 
-  #  if it is specified. however, is it just copied to the (third) output. 
-  # The code assumes vHb < vHj < vHp (see first input). 
+  # This routine obtaines scaled length at metamorphosis lj given scaled muturity at metamorphosis vHj.
+  # The theory behind get_lj, is discussed in the comments to DEB3.
+  # If scaled length at birth (third input) is not specified, it is computed (using automatic initial estimate);
+  #  if it is specified. however, is it just copied to the (third) output.
+  # The code assumes vHb < vHj < vHp (see first input).
   #
   # Input
   #
@@ -35,22 +54,22 @@ get_lj=function(p, f, lb0) {
   # * lp: scalar with scaled length at puberty
   # * lb: scalar with scaled length at birth
   # * info: indicator equals 1 if successful
-  
+
   ## Remarks
   # Similar to <get_lj1.html get_lj1>, which uses root finding, rather than integration
-  # Scaled length l = L/ L_m with L_m = kap {p_Am}/ [p_M] where {p_Am} is of embryo, 
+  # Scaled length l = L/ L_m with L_m = kap {p_Am}/ [p_M] where {p_Am} is of embryo,
   #  because the amount of acceleration is food-dependent so the value after metamorphosis is not a parameter.
   # {p_Am} and v increase between maturities v_H^b and v_H^j till
   #    {p_Am} l_j/ l_b  and v l_j/ l_b at metamorphosis.
   # After metamorphosis l increases from l_j till l_i = f l_j/ l_b - l_T.
   # Scaled length l can thus be larger than 1.
-  # See <get_lj_foetus.html *get_lj_foetus*> for foetal development. 
-  
+  # See <get_lj_foetus.html *get_lj_foetus*> for foetal development.
+
   ## Example of use
   # get_lj([.5, .1, .1, .01, .2, .3])
-  
+
   n_p = length(p)
-  
+
   # unpack pars
   g   = p[1] # energy investment ratio
   k   = p[2] # k_J/ k_M, ratio of maturity and somatic maintenance rate coeff
@@ -60,13 +79,13 @@ get_lj=function(p, f, lb0) {
   if (n_p > 5){
     vHp = p[6] # v_H^p = U_H^j g^2 kM^3/ (1 - kap) v^2; U_B^j = M_H^j/ {J_EAm}
   }
-  
+
   if (!exists('f')) {
     f = 1
   } else if  (is.na(f)){
     f = 1
   }
-  
+
   # get lb
   if (!exists('lb0')){
     lb0 = NA
@@ -79,37 +98,37 @@ get_lj=function(p, f, lb0) {
     info = 1
     lb = lb0
   }
-  
+
   if (lT > f - lb) { # no growth is possible at birth
     lj = NA
     lp = NA
     info = 0
   }
-  
+
   # no acceleration
   if (vHb == vHj){
     if (n_p == 5){ # no puberty specified
       lbinfo = get_lb(p[c(1, 2, 4)], f, lb0)
       lb=lbinfo[1]
       info=lbinfo[2]
       lj = lb
-      lp = NA 
+      lp = NA
     } # else {        # puberty specified
 #       [lp, lb, info] = get_tp(p([1 2 3 4 6]), f, lb0);
-#       lj = lb; 
+#       lj = lb;
 #     }
   }
 
-  
+
   # get lj
-  library(deSolve)
+  #library(deSolve)
   tspan=seq(vHb, vHj, length=100)
   lini=c(l=lb)
-  out = ode(lini, tspan, dget_l_V1, parms=c(k, lT, g, f, lb), method="ode45") 
+  out = deSolve::ode(lini, tspan, dget_l_V1, parms=c(k, lT, g, f, lb), method="ode45")
   vH=out[,1]
   lj=out[length(out[,2]),2]
   sM = lj/ lb
-  
+
   # get lp
   if (n_p > 5){
     tspan=seq(vHj, vHp, length=100)
@@ -122,4 +141,4 @@ get_lj=function(p, f, lb0) {
 
 return(c(lj, lp, lb, info))
 
-}
+}