version 0.7.2

Author: Kyun-Seop Bae

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: wnl
-Version: 0.7.1
+Version: 0.7.2
 Title: Minimization Tool for Pharmacokinetic-Pharmacodynamic Data
         Analysis
 Description: This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model. 
-Depends: R (>= 3.0.0), numDeriv
+Depends: R (>= 3.5.0), numDeriv
 Author: Kyun-Seop Bae [aut]
 Maintainer: Kyun-Seop Bae <[email protected]>
 Copyright: 2017-, Kyun-Seop Bae
@@ -12,5 +12,5 @@ NeedsCompilation: no
 LazyLoad: yes
 Repository: CRAN
 URL: https://cran.r-project.org/package=wnl
-Packaged: 2022-11-29 23:50:28 UTC; Kyun-SeopBae
-Date/Publication: 2022-11-30 00:10:02 UTC
+Packaged: 2023-03-26 08:42:19 UTC; Kyun-SeopBae
+Date/Publication: 2023-03-26 09:00:02 UTC

MD5

@@ -1,7 +1,8 @@
-8ff22a4a870171d4b3a47ffc0b0e9b48 *DESCRIPTION
-ee3bb2eb18e141b2c4e9490e06578bc7 *NAMESPACE
-272b0f9cff1702c382130e84e0b02fd3 *R/BasicUtil.R
+c9516afbbbaa87491b313b106c506057 *DESCRIPTION
+390de0872c5e034f3bb65922b8b78051 *NAMESPACE
+83d6bb93ca7f2ebe336d3d1c70e6d5de *R/BasicUtil.R
 ba1255e411249f4db6f2caa66ee30cfe *R/Comp1.R
+6ee187dd007ec9a4d1193101fb331c53 *R/EnvObj.R
 cf5ef0c31a8433b8f966716f203471b9 *R/ExpandDH.R
 82c430639b2aec87a2d8257e1ed87b19 *R/Objs.R
 f7a61f78602501325418063cc00df4d4 *R/Secondary.R
@@ -11,17 +12,18 @@ b801ef09ac2e1d9c931f1d08fe4a6b90 *R/cmpChi.R
 752433b1b66c620b33c3def811efdc8f *R/dx.R
 9bf4095904c0bf59982cb603c2b69e5c *R/hSkew.R
 ca032758dcb79150beac3ef4564b7cb8 *R/nComp.R
-704803c86f0249b33ac74f5854471253 *R/nlr.R
+93e6378dd2b8a641a72a71c2a3177071 *R/nlr.R
 969cb4bf5cab158d9f4b9fbd260ae4e1 *R/pComp.R
-93992a72ede869c9d1980d0c4f2151ac *R/sysdata.rda
-4d4407fdd2c2a05691dcff5a9e26d18f *R/wnl5.R
-b5a08d37bc6fe85f346b6d2f6a9e59de *inst/NEWS.Rd
+d937f14557cd2f6a8416f6e1bd5c2ca5 *R/pProf.R
+3a85a468ae0dc2bbb899524ea01feccf *R/sysdata.rda
+1c9e1b28728c0f1fc96017efc560b0d6 *R/wnl5.R
+bfc553c5d4e48153218304487a993cc1 *inst/NEWS.Rd
 75463c4d3bd42432719b597f93dd859d *inst/doc/Compartment-vignette.pdf
-846bed422184b36f2aaf96a2894bf9f6 *inst/doc/NCA.pdf
-ee2fd12b6324d60dc40613252ef9078c *inst/doc/wnl-manual.pdf
-40e13ff56df7c96e607461bcb32b4b86 *man/BasicUtil.Rd
+bcc928b45c5b3565a7eb37ffb9ec41dc *inst/doc/wnl-manual.pdf
+57010db082832f52da4856e4b3521524 *man/BasicUtil.Rd
 f9ab397c3e89d4acba0f7c5f06e91923 *man/Comp1.Rd
 6c87b1f721849279be48c7474dee83b5 *man/DAT.Rd
+e13ddd41e50eb0c2aa0a6fe811650f58 *man/EnvObj.Rd
 1d89dcf882509be8a127789a9d87c4c3 *man/ExpandDH.Rd
 4c8010f47e5cd1f1c27e78b5b0337e06 *man/Objs.Rd
 473916c208b3d722e54944b5f2a4a18f *man/Secondary.Rd
@@ -32,7 +34,8 @@ e1e7543809d439770aa7d1cb6e897193 *man/dx.Rd
 ee0ea2d2db69f309039e2d70a791ac0a *man/e.Rd
 d60a1682e9d37ff616877f1ce4738665 *man/hSkew.Rd
 62aedc1f108c168426e5402b454b82e1 *man/nComp.Rd
-adc2a17ef835341750000347246dfbe2 *man/nlr.Rd
+ce1ed05a960198b528a52d5009c50d24 *man/nlr.Rd
 3a1b70982f3cf42a7bd0a912b81ca182 *man/pComp.Rd
+5fb26ef5fe3aa387797a8b26d2785da0 *man/pProf.Rd
 8640ba18696633870f706cd63f6d440c *man/wnl-package.Rd
 902adeb3c4af0439299bbd830aa6ed04 *man/wnl5.Rd

NAMESPACE

@@ -1,5 +1,5 @@
 exportPattern("^[[:alpha:]]+")
-importFrom("stats", "cov2cor", "optim", "deriv", "pchisq", "coef", "formula", "resid", "sigma", "qnorm", "qt", "uniroot", "terms")
+importFrom("stats", "cov2cor", "optim", "deriv", "pchisq", "coef", "formula", "resid", "sigma", "qnorm", "qt", "qf", "uniroot", "terms")
 importFrom("numDeriv", "hessian")
 importFrom("graphics", "par", "plot", "abline", "arrows", "polygon", "text", "title")
 importFrom("grDevices", "dev.new", "dev.cur")

R/BasicUtil.R

@@ -2,8 +2,6 @@
 
 #Note = function() file.show(system.file("NOTE.txt", package="NonCompart"))
 
-UT  = function(x) toupper(gsub("^\\s+|\\s+$", "", x))
-
 s2o = function(vPara) # scaled to original parameters
 {
   b0 = exp(vPara - e$alpha)
@@ -166,43 +164,43 @@ nHessian = function(fx, x)
   return(H)
 }
 
+g2inv = function(A, Augmented=FALSE, eps=1e-8)
+{
+  idx = abs(diag(A)) > eps
+  p = sum(idx, na.rm=T)
+  p0 = ifelse(Augmented, p - 1, p)
+  if (p == 0 | p0 < 1) { A[, ] = 0 ; attr(A, "rank") = 0 ; return(A) }
+  B = A[idx, idx, drop=F]
+
+  r = 0
+  for (k in 1:p0) {
+    d = B[k, k]
+    if (abs(d) < eps) { B[k, ] = 0 ; B[, k] = 0 ; next }
+    B[k, ] = B[k, ]/d
+    r = r + 1
+    for (i in 1:p) {
+      if (i != k) {
+        c0 = B[i, k]
+        B[i, ] = B[i, ] - c0*B[k, ]
+        B[i, k] = -c0/d
+      }
+    }
+    B[k, k] = 1/d
+  }
+
+  A[!idx, !idx] = 0
+  A[idx, idx] = B
+  attr(A, "rank") = r
+  return(A)
+}
+
 Hougaard = function(J, H, ssq)
 {# J : graident, H: hessian, ssq: sigma square  
   z = NCOL(J)
   m = NROW(J)
   if (z*m == 0) stop("No graident information!")
 
-  G2SWEEP = function(A, Augmented=FALSE, eps=1e-8)
-  {
-    idx = abs(diag(A)) > eps
-    p = sum(idx, na.rm=T)
-    p0 = ifelse(Augmented, p - 1, p)
-    if (p == 0 | p0 < 1) { A[, ] = 0 ; attr(A, "rank") = 0 ; return(A) }
-    B = A[idx, idx, drop=F]
-
-    r = 0
-    for (k in 1:p0) {
-      d = B[k, k]
-      if (abs(d) < eps) { B[k, ] = 0 ; B[, k] = 0 ; next }
-      B[k, ] = B[k, ]/d
-      r = r + 1
-      for (i in 1:p) {
-        if (i != k) {
-          c0 = B[i, k]
-          B[i, ] = B[i, ] - c0*B[k, ]
-          B[i, k] = -c0/d
-        }
-      }
-      B[k, k] = 1/d
-    }
-
-    A[!idx, !idx] = 0
-    A[idx, idx] = B
-    attr(A, "rank") = r
-    return(A)
-  }
-
-  L = G2SWEEP(crossprod(J))
+  L = g2inv(crossprod(J))
   if (attr(L, "rank") < ncol(L)) warning("Crossproduct of gradient is singular!")
 
   W = rep(0, z^3)
@@ -233,51 +231,3 @@ Hougaard = function(J, H, ssq)
   names(SK) = colnames(J)
   return(SK)
 }
-
-pProf = function(Title = "", ...)
-{
-  mfRow = ceiling(sqrt(e$nPara))
-  mfCol = ceiling(e$nPara/mfRow)
-  oPar = par(mfrow=c(mfRow, mfCol))
-  Args = list(...)
-  if (is.null(Args$ylab)) Args$ylab = "-2LL"
-  if (is.null(Args$type)) Args$type = "l"
-
-  for (j in 1:e$nPara) {
-    x = e$mPar[, j]
-    y = e$mOFV[, j]
-    if (is.finite(min(x)) & is.finite(max(x)) & is.finite(min(y, na.rm=T)) & is.finite(max(y, na.rm=T))) {
-      Args$x = x
-      Args$y = y
-      RdUdL = format((e$LI[2, j] - e$PE[j])/(e$PE[j] - e$LI[1, j]), digits=3)
-      Args$xlab = paste0(e$pNames[j], " = ", format(e$PE[j], digits=2), ", dU/dL = ", RdUdL)
-      do.call(plot, Args)
-      abline(h = e$'-2LL' + e$fCut, lty=2)
-      abline(v = e$PE[j], lty=3)
-      text(e$LI[, j], e$'-2LL', labels = format(e$LI[, j], digits=2))
-    }
-  }
-  if (trimws(Title) != "") title(Title, outer=TRUE)
-  par(oPar)
-}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-

R/EnvObj.R

@@ -0,0 +1,9 @@
+EnvObj = function(envir = e)
+{
+  Name0 = ls(envir)
+  nObj = length(Name0)
+  Result = list()
+  for (i in 1:nObj) Result[[i]] = get(Name0[i], envir=envir)
+  names(Result) = Name0
+  return(Result)
+}