switched to roxygen2 docs, more work on get_lb and get_ue0

DEButilities.Rproj

@@ -18,3 +18,4 @@ StripTrailingWhitespace: Yes
 BuildType: Package
 PackageUseDevtools: Yes
 PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace

DESCRIPTION

@@ -8,3 +8,5 @@ Description: Functions copied from the DEBtool_R git repository and repackaged i
 License: What license is it under?
 Encoding: UTF-8
 LazyData: true
+RoxygenNote: 6.0.1
+Suggests: testthat

NAMESPACE

@@ -1 +1,5 @@
-exportPattern("^[[:alpha:]]+")
+# Generated by roxygen2: do not edit by hand
+
+export(dget_tb)
+export(get_tb)
+export(get_ue0)

R/get_tb.R

@@ -1,8 +1,21 @@
-## get_tb
-#
 
-##
-get_tb= function(p, eb = 1, lb=NA){
+#' get_tb
+#'
+#' Obtains scaled age at birth, given the scaled reserve density at birth.
+#' Divide the result by the somatic maintenance rate coefficient to arrive at age at birth.
+#'
+#' @param p 1 or 3-vector with parameters g, k_J/ k_M, v_H^b; Last 2 values are optional in invoke call to get_lb
+#' @param eb 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)
+#'
+#' @author Bas Kooijman
+#'
+#' @return 3-element vector containing tb: scaled age at birth tau_b = a_b k_M; lb: scalar with scaled length at birth: L_b/ L_m; info: indicator equals 1 if successful, 0 otherwise
+#' @export
+#'
+#' @examples
+#' get_tb(p = c(.1,.5,.03))
+get_tb <- function(p, eb = 1, lb=NA){
 #  created at 2007/07/27 by Bas Kooijman; modified 2014/03/17, 2015/01/18
 
 ## Syntax
@@ -42,7 +55,7 @@ get_tb= function(p, eb = 1, lb=NA){
 
   info = 1
 
-  if (!exists('lb')) {
+  if (is.na(lb)) {
     if (length(p) < 3){
       print('not enough input parameters, see get_lb \n')
       tb = NA
@@ -70,7 +83,17 @@ get_tb= function(p, eb = 1, lb=NA){
 
   # subfunction
 
-dget_tb= function(x, abxb){
+#' dget_tb
+#'
+#' Subroutine called by get_tb
+#'
+#' @param x x
+#' @param abxb abxb
+#'
+#' @return f
+#' @export
+#'
+dget_tb <- function(x, abxb){
   # called by get_tb
   ab=abxb[1]
   xb=abxb[2]

R/get_ue0.R

@@ -1,47 +1,58 @@
-## get_ue0
-# gets initial scaled reserve
-
-##
-#  function [uE0, lb, info] = 
-get_ue0=function(p, eb, lb0){
+#' get_ue0
+#'
+#' gets initial scaled reserve.
+#' Obtains the initial scaled reserve for eggs given the scaled reserve density at birth.
+#' Specification of length at birth as third input by-passes its computation, so if you want to specify an initial value for this quantity, you should use get_lb directly.
+#'
+#' @param p 1 or 3 -vector with parameters g, k_J/ k_M, v_H^b, see get_lb
+#' @param eb optional scalar with scaled reserbe density at birth (default: eb = 1)
+#' @param lb0 optional scalar with scaled length at birth (default: lb is optained from get_lb)
+#'
+#' @return [uE0, lb, info] scaled with scaled reserve at t=0: $U_E^0 g^2 k_M^3/ v^2$ with $U_E^0 = M_E^0/ \{J_{EAm}\}$; lb: scalar with scaled length at birth; info: indicator equals 1 if successful, 0 otherwise
+#' @export
+#'
+#' @examples
+#' g = 6; k = 6; kap = .8; uHb = .001; vHb = uHb/ (1 - kap);
+#' par = c(g, k, vHb);
+get_ue0=function(p, eb = 1, lb0 = NA){
   # created at 2007/07/27 by Bas Kooijman; modified 2010/05/02
-  
+
   ## Syntax
   # [uE0, lb, info] = <../get_ue0.m *get_ue0*>(p, eb, lb0)
-  
+
   ## Description
-  # Obtains the initial scaled reserve given the scaled reserve density at birth. 
-  # Function get_ue0 does so for eggs, get_ue0_foetus for foetuses. 
-  # Specification of length at birth as third input by-passes its computation, 
-  #   so if you want to specify an initial value for this quantity, you should use get_lb directly. 
+  # Obtains the initial scaled reserve given the scaled reserve density at birth.
+  # Function get_ue0 does so for eggs, get_ue0_foetus for foetuses.
+  # Specification of length at birth as third input by-passes its computation,
+  #   so if you want to specify an initial value for this quantity, you should use get_lb directly.
   #
   # Input
   #
   # * p: 1 or 3 -vector with parameters g, k_J/ k_M, v_H^b, see get_lb
-  # * eb: optional scalar with scaled reserbe density at birth 
+  # * eb: optional scalar with scaled reserbe density at birth
   #   (default: eb = 1)
-  # * lb0: optional scalar with scaled length at birth 
+  # * lb0: optional scalar with scaled length at birth
   #   (default: lb is optained from get_lb)
   #
   # Output
   #
-  # * uE0: scaled with scaled reserve at t=0: $U_E^0 g^2 k_M^3/ v^2$ 
+  # * uE0: scaled with scaled reserve at t=0: $U_E^0 g^2 k_M^3/ v^2$
     #   with $U_E^0 = M_E^0/ \{J_{EAm}\}$
     # * lb: scalar with scaled length at birth
   # * info: indicator equals 1 if successful, 0 otherwise
-  
+
   ## Remarks
   # See <get_ue0_foetus.html *get_ue0_foetus*> for foetal development.
   # See <initial_scaled_reserve.html *initial_scaled_reserve*>, for a non-dimensionless scaling.
-  
+
   ## Example of use
   # see <../mydata_ue0.m *mydata_ue0*>
-    
-  if (!exists('eb')) {
-    eb = 1 # maximum value as juvenile
-  }
-  
-  if (!exists('lb0')){
+
+  # if (!exists('eb')) {
+  #   eb = 1 # maximum value as juvenile
+  # }
+
+  if (is.na(lb0)){
     if (length(p) < 3) {
       print('not enough input parameters, see get_lb \n');
       uE0 = NA
@@ -56,12 +67,14 @@ get_ue0=function(p, eb, lb0){
     info = 1
   }
 
-  
+
   # unpack p
   g = p[1]  # energy investment ratio
-  
+
   xb = g/ (eb + g)
   uE0 = (3 * g/ (3 * g * xb^(1/ 3)/ lb - beta0(0, xb)))^3
 
+  print(paste("uE0", uE0))
+
   return(c(uE0, lb, info))
 }