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authorJohannes Ranke <jranke@uni-bremen.de>2022-11-18 09:12:49 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2022-11-18 09:12:49 +0100
commit13b3daaaa7c47d178ee59ab116aa71b7bf2f5c9b (patch)
tree5241148230437590a835b4400f817a3d07f37b6f /custom_lsoda_call_edited.patch
parent72c4bb7b4bb3b9f1f6cceba484f1de7adcc104a3 (diff)
Remove candidate patches that were accidentally committed
Diffstat (limited to 'custom_lsoda_call_edited.patch')
-rw-r--r--custom_lsoda_call_edited.patch116
1 files changed, 0 insertions, 116 deletions
diff --git a/custom_lsoda_call_edited.patch b/custom_lsoda_call_edited.patch
deleted file mode 100644
index a79cbbcd..00000000
--- a/custom_lsoda_call_edited.patch
+++ /dev/null
@@ -1,116 +0,0 @@
---- 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) {
-

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