nls() error: Object not found
Yang, Richard wrote:
Dear R-helpers;
Using nls() to fit a function,Rdum, defined below I stumbled on an
error: "Error in eval(expr, envir, enclos): Object "s0" not found."
The function Rdum is defined as
Rdum <- deriv(~ h1 * (s0 + sl0*sl + sm0*sm + sp01*sp1 + sp02*sp2 +
sp03*sp3+sp04*sp4) *
((1 - exp(-(s1 + sl1*sl + sm1*sm + sp11*sp1 + sp12*sp2 +
sp14*sp4)*t2)) /
(1 - exp(-(s1 + sl1*sl + sm1*sm + sp11*sp1 + sp12*sp2 +
sp14*sp4)*t1)))^
(s2 + sl2*sl+sm2*sm+ sp21*sp1+sp22*sp2+sp23*sp3+sp24*sp4),
c("s0", "s10","sm0", "sp01","sp02","sp03","sp04",
"s1", "sl1","sm1", "sp11", "sp12","sp14",
"s2","sl2","sm2", "sp21","sp22","sp23","sp24"),
function(s0,sl0,sm0,sp01,sp02,sp03,sp04, s1, sl1, sm1, sp11,sp12, sp14,
s2, sl2, sm2, sp21,sp22, sp23, sp24, h1, t1,t2, sl, sm,sp1, sp2, sp3,
sp4){})
and variables t1, t2, h1, h2, sl, sm, sp1, sp2, sp3, and sp4 in the gbht10D
data frame are fitted to the function by
Dum.nls <- nls(h2 ~ Rdum(s0, sl0, sm0, sp01, sp02, sp03, sp04, sl,
sl1,sm1,sp11,sp12, sp14,
s2, sl2, sm2, sp21, sp22, sp23, sp24,h1, t1, t2, sl, sm, sp1, sp2, sp3,
sp4), data=gbht10D,
start=c(0.8413,-0.1602,-0.0156,0.0527,0.0513,0.00314,0.0378,
-0.00598,-0.0125,0.00328,0.00989,0.0113,0.00583,
1.9255,0.9427,0.2408,-0.0643,0.0047,0.0016,-0.00519))
The complained object "s0" is one of the 20 parameters in the function
to be estimated from the dataset gbht10D.
The nls() script is relatively short. Stepping into the source code, I
located the offending line:
Browse[1]> start
[1] 0.84130 -0.16020 -0.01560 0.05270 0.05130 0.00314 0.03780 -0.00598
-0.01250
[10] 0.00328 0.00989 0.01130 0.00583 1.92550 0.94270 0.24080 -0.06430
0.00470
[19] 0.00160 -0.00519
Browse[1]> n
debug: pnames <- names(start)
Browse[1]> n
debug: varNames <- varNames[is.na(match(varNames, pnames, nomatch = NA))]
Browse[1]> n
debug: varIndex <- sapply(varNames, function(varName, data, respLength) {
length(eval(as.name(varName), data))%%respLength == 0
}, data, length(eval(formula[[2]], data)))
Browse[1]> varNames
[1] "h2" "s0" "sl0" "sm0" "sp01" "sp02" "sp03" "sp04" "sl" "sl1"
"sm1" "sp11"
[13] "sp12" "sp14" "s2" "sl2" "sm2" "sp21" "sp22" "sp23" "sp24" "h1"
"t1" "t2"
[25] "sm" "sp1" "sp2" "sp3" "sp4"
Browse[1]> n
Error in eval(expr, envir, enclos) : Object "s0" not found.
The "s0" is shown in varNames. Is the error message misleading? Or did I
miss something?
The part of the manual page that states that start must be a named
vector?
start: a named list or named numeric vector of starting estimates
The piece of code you are examining matches the starting values against
the parameter names. Because you did not name the starting values it
cannot find a match for "s0".