Complete update of online docs for v1.2.0

1 files changed, 116 insertions, 0 deletions

diff --git a/custom_lsoda_call_edited.patch b/custom_lsoda_call_edited.patch
new file mode 100644
index 00000000..a79cbbcd
--- /dev/null
+++ b/custom_lsoda_call_edited.patch
@@ -0,0 +1,116 @@
+--- a/R/mkinfit.R
++++ b/R/mkinfit.R
+ 
++  # Get native symbol before iterations info for speed
++  call_lsoda <- getNativeSymbolInfo("call_lsoda", PACKAGE = "deSolve")
++  if (solution_type == "deSolve" & use_compiled[1] != FALSE) {
++    mkinmod$diffs_address <- getNativeSymbolInfo("diffs",
++      PACKAGE = mkinmod$dll_info[["name"]])$address
++    mkinmod$initpar_address <- getNativeSymbolInfo("initpar",
++      PACKAGE = mkinmod$dll_info[["name"]])$address
++  }
++
+
+@@ -610,7 +619,8 @@ mkinfit <- function(mkinmod, observed,
+                          solution_type = solution_type,
+                          use_compiled = use_compiled,
+                          method.ode = method.ode,
+-                         atol = atol, rtol = rtol, ...)
++                         atol = atol, rtol = rtol,
++                         call_lsoda = call_lsoda, ...)
+ 
+--- a/R/mkinpredict.R
++++ b/R/mkinpredict.R
+
+@@ -116,9 +114,10 @@ mkinpredict.mkinmod <- function(x,
+   outtimes = seq(0, 120, by = 0.1),
+   solution_type = "deSolve",
+   use_compiled = "auto",
+-  method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000,
++  method.ode = "lsoda", atol = 1e-8, rtol = 1e-10, maxsteps = 20000L,
+   map_output = TRUE,
+   na_stop = TRUE,
++  call_lsoda = NULL,
+   ...)
+ {
+ 
+@@ -173,20 +172,80 @@ mkinpredict.mkinmod <- function(x,
+   if (solution_type == "deSolve") {
+     if (!is.null(x$cf) & use_compiled[1] != FALSE) {
+ 
+-      out <- deSolve::ode(
+-        y = odeini,
+-        times = outtimes,
+-        func = "diffs",
+-        initfunc = "initpar",
+-        dllname = if (is.null(x$dll_info)) inline::getDynLib(x$cf)[["name"]]
+-          else x$dll_info[["name"]],
+-        parms = odeparms[x$parms], # Order matters when using compiled models
+-        method = method.ode,
+-        atol = atol,
+-        rtol = rtol,
+-        maxsteps = maxsteps,
+-        ...
++      # Prepare call to "call_lsoda"
++      # Simplified code from deSolve::lsoda() adapted to our use case
++      if (is.null(call_lsoda)) {
++        call_lsoda <- getNativeSymbolInfo("call_lsoda", PACKAGE = "deSolve")
++      }
++      if (is.null(x$diffs_address)) {
++        x$diffs_address <- getNativeSymbolInfo("diffs",
++          PACKAGE = x$dll_info[["name"]])$address
++        x$initpar_address <- getNativeSymbolInfo("initpar",
++          PACKAGE = x$dll_info[["name"]])$address
++      }
++      rwork <- vector("double", 20)
++      rwork[] <- 0.
++      rwork[6] <- max(abs(diff(outtimes)))
++
++      iwork <- vector("integer", 20)
++      iwork[] <- 0
++      iwork[6] <- maxsteps
++
++      n <- length(odeini)
++      lmat <- n^2 + 2     # from deSolve::lsoda(), for Jacobian type full, internal (2)
++      # hard-coded default values of lsoda():
++      maxordn <- 12L
++      maxords <- 5L
++      lrn <- 20 + n * (maxordn + 1) + 3 * n  # length in case non-stiff method
++      lrs <- 20 + n * (maxords + 1) + 3 * n + lmat        # length in case stiff method
++      lrw <- max(lrn, lrs)                       # actual length: max of both
++      liw <- 20 + n
++
++      on.exit(.C("unlock_solver", PACKAGE = "deSolve"))
++
++      out_raw <- .Call(call_lsoda,
++        as.double(odeini),   # y
++        as.double(outtimes), # times
++        x$diffs_address,     # derivfunc
++        as.double(odeparms[x$parms]), # parms
++        rtol, atol,
++        NULL, NULL, # rho, tcrit
++        NULL, # jacfunc
++        x$initpar_address, # initfunc
++        NULL, # eventfunc
++        0L,   # verbose
++        1L,   # iTask
++        as.double(rwork), # rWork
++        as.integer(iwork), # iWork
++        2L,     # jT full Jacobian calculated internally
++        0L,    # nOut
++        as.integer(lrw), # lRw
++        as.integer(liw), # lIw
++        1L, # Solver
++        NULL, # rootfunc
++        0L, as.double(0), 0L, # nRoot, Rpar, Ipar
++        0L, # Type
++        list(fmat = 0L, tmat = 0L, imat = 0L, ModelForc = NULL), # flist
++        list(), # elist
++        list(islag = 0L) # elag
+       )
++
++      out <- t(out_raw)
++      colnames(out) <- c("time", mod_vars)
+     } else {
+       mkindiff <- function(t, state, parms) {
+