# R/nlmrt.R In nlmrt: Functions for Nonlinear Least Squares Solutions (Deprecated!)

#### Documented in coef.nlmrtprint.nlmrtsummary.nlmrt

```# nlmrt.R -- print and summary methods
#   result <- list(resid = resbest, jacobian = Jac, feval = feval,
#        jeval = jeval, coefficients = pnum, ssquares = ssbest)
#    class(result) <- "nlmrt"

summary.nlmrt <- function(object, ...) {
sumnlmrt<-list() # set up the stub
smalltol <- .Machine\$double.eps * 1000
options(digits = 5) # 7 is default
resname <- deparse(substitute(object))
JJ <- object\$jacobian
res <- object\$resid
coeff <- object\$coefficients
pname<-names(coeff)
npar <- length(coeff)
lo <- object\$lower
if (is.null(lo)) lo <- rep( -Inf, npar)
up <- object\$upper
if (is.null(up)) up <- rep( Inf, npar)
mt[mi] <- "M" # Put in the masks
bdmsk <- rep(1, npar) # bounds and masks indicator ?? should it be 1L
for (i in seq_along(coeff)){
if (lo[[i]] - coeff[[i]] > 0) {
ct[[i]] <- "-" # lower bound violation
if (bdmsk[[i]] == 1) bdmsk[[i]] <- -3
} else {
if (coeff[[i]] - lo[[i]] < smalltol*(abs(coeff[[i]])+smalltol) ) {
ct[[i]] <- "L" # "at" lower bound
if (bdmsk[[i]] != 0) bdmsk[[i]] <- -3 # leave mask indication intact
}
}
if (coeff[[i]] - up[[i]] > 0) {
ct[[i]] <- "+" # upper bound violation
if (bdmsk[[i]] == 1) bdmsk[[i]] <- -1
} else {
if (up[[i]] - coeff[[i]] < smalltol*(abs(coeff[[i]])+smalltol) ) {
ct[[i]] <- "U" # "at" upper bound
if (bdmsk[[i]] != 0) bdmsk[[i]] <- -1 # leave mask indication intact
}
}
}
ss <- object\$ssquares
nobs <- length(res)
ndof <- nobs - npar
if (ndof <= 0) {
if (ndof < 0) { stop(paste("Inadmissible degrees of freedom =",ndof,sep='')) }
else { sighat2 <- Inf }
} else {
sighat2 <- as.numeric(ss)/(ndof) # 160302 NOT an array
}
dec <- svd(JJ)
U <- dec\$u
V <- dec\$v
Sd <- dec\$d
if (min(Sd) <= smalltol * max(Sd)) { # singular
SEs <- rep(NA, npar) # ?? Inf or NA
} else {
Sinv <- 1/Sd
Sinv[which(bdmsk != 1)] <- 0
if (npar > 1) {
VS <- crossprod(t(V), diag(Sinv))
} else {
VS <- V*Sinv
}
Jinv <- crossprod(t(VS))
var <- Jinv * sighat2
SEs <- sqrt(diag(var))
}
gr <- crossprod(JJ, res)
if (any(is.na(SEs))) {
tstat<-rep(NA, npar)
} else {
if (any(SEs == 0)){
tstat <- rep(0, npar)
} else {
tstat <- coeff/SEs
}
}
pval<-2*(1-pt(abs(tstat), df=ndof)) # This will carry through NAs
object<-list(resname=resname, ssquares=ss, nobs=nobs, coeff=coeff, ct=ct, mt=mt,
SEs=SEs, tstat=tstat, pval=pval, Sd=Sd, gr=gr, jeval=object\$jeval,
feval=object\$feval)
##? LEAVE OUT: JJ  res
##? Sd
##? gr
invisible(object)
}

# ?? coef() function
coef.nlmrt <- function(object, ...) {
out <- object\$coefficients
# print(object\$coefficients)
attr(out,"pkgname")<-"nlmrt"
invisible(out)
}

print.nlmrt <- function(x, ...) {
xx<-summary(x)
with(xx, {
cat("nlmrt class object:",resname,"\n")
pname<-names(coeff)
npar <- length(coeff)
cat("residual sumsquares = ",ssquares," on ",nobs,"observations\n")
cat("    after ",jeval,"   Jacobian and ",feval,"function evaluations\n")
cat("  name     ","      coeff    ","     SE   ","   tstat  ",
"   pval  ","   gradient  "," JSingval  ","\n")
for (i in seq_along(coeff)){
cat(format(pname[i], width=10)," ")
cat(format(coeff[[i]], digits=6, width=12))
cat(ct[[i]],mt[[i]]," ")
cat(format(SEs[[i]], digits=4, width=9)," ")
cat(format(tstat[[i]], digits=4, width=9)," ")
cat(format(pval[[i]], digits=4, width=9)," ")
cat(format(gr[[i]], digits=4, width=10)," ")
cat(format(Sd[[i]], digits=4, width=10)," ")
cat("\n")
}
}) # remember to close with()
invisible(x)
}
```

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nlmrt documentation built on Sept. 19, 2017, 3 a.m.