506 create.cms <- function(Rank = 1, M, MSratio = 1, which, p1 = 1) {  argument
513   names(Hlist.) <- if (p1 == 1) c("(Intercept)", names(which)) else stop()
542   queue <- qbig <- Rank  # 20051019; number of smooths per species
606   which <- p1 + (1:Rank)  # These columns are smoothed  functionVar
607   nwhich <- names(which) <- mynames5
611                        which = which, p1 = p1)  # For 1 species only
615                         which = which,
655     c(n = nrow(nu1mat), p. = ncol(nu1mat), q = length(which),
694       which = as.integer(which),
755       qrank <- npetc[7]  # Assume all species have the same qrank value
876   which <- p1 + (1:Rank)  # The first 1 is the intercept term  functionVar
877   nwhich <- names(which) <- mynames5
881                which = which, p1 = p1)  # For 1 species
888                           smomat = NULL, which = which,
915     queue <- qbig <- Rank  # 20051019; number of smooths per species
956       c(n = n, p = 1+Rank, length(which), se.fit = control$se.fit, 0,
964                q = length(which),
997     as.integer(which),
1051     qrank <- npetc[7]  # Assume all species have the same qrank value
1173     which.species <- 1:NOS  # Do it for all species
1184     for (sppno in seq_along(which.species)) {
1190       thisSpecies <- which.species[sppno]
1191       indexSpecies <- if (is.character(which.species))
1192           match(which.species[sppno], ynames) else which.species[sppno]
1195         stop("mismatch found in 'which.species'")
1391           which.species = NULL,  argument
1406     if (!length(which.species))
1407       which.species <- 1:NOS
1429                     object@y[, which.species, drop = FALSE] else
1430                     r.curves[, which.species, drop = FALSE],
1433         matplot(c(Coeflist@Optimum[1, which.species], latvarmat[, 1]),
1434                 c(Coeflist@Optimum[2, which.species], latvarmat[, 2]),
1440     pch     <- rep_len(pch,     length(which.species))
1441     pcol    <- rep_len(pcol,    length(which.species))
1442     pcex    <- rep_len(pcex,    length(which.species))
1443     llty    <- rep_len(llty,    length(which.species))
1444     lcol    <- rep_len(lcol,    length(which.species))
1445     llwd    <- rep_len(llwd,    length(which.species))
1446     adj.arg <- rep_len(adj.arg, length(which.species))
1451       for (sppno in seq_along(which.species)) {
1452         thisSpecies <- which.species[sppno]
1453         indexSpecies <- if (is.character(which.species))
1454            match(which.species[sppno], sppnames) else which.species[sppno]
1456           stop("mismatch found in 'which.species'")
1479       for (sppno in seq_along(which.species)) {
1480           thisSpecies <- which.species[sppno]
1481           indexSpecies <- if (is.character(which.species))
1482                match(which.species[sppno], sppnames) else
1483                which.species[sppno]
1485             stop("mismatch found in 'which.species'")
1491         for (sppno in seq_along(which.species)) {
1492           thisSpecies <- which.species[sppno]
1493           indexSpecies <- if (is.character(which.species))
1494              match(which.species[sppno], sppnames) else
1495                    which.species[sppno]
1593     which.species <- 1:NOS  # Do it all for all species
1594     for (sppno in seq_along(which.species)) {
1595       thisSpecies <- which.species[sppno]
1596       indexSpecies <- if (is.character(which.species))
1597         match(which.species[sppno], sppnames) else which.species[sppno]
1599         stop("mismatch found in 'which.species'")
1726            which.species = NULL,  # a numeric or character vector  argument
1751   if (!length(which.species)) which.species <- 1:NOS
1753     ylab <- rep_len(ylab, length(which.species))  # Too long if overlay
1755     main <- rep_len(main, length(which.species))  # Too long if overlay
1763   for (sppno in seq_along(which.species)) {
1764     thisSpecies <- which.species[sppno]
1765     indexSpecies <- if (is.character(which.species))
1766         match(which.species[sppno], sppnames) else which.species[sppno]
1768       stop("mismatch found in 'which.species'")
1822            which.species = NULL,  argument
1840   NOS <- ncol(fvmat)    # Number of species
1866   if (!length(which.species)) {
1867     which.species <- sppNames[1:NOS]
1868     which.species.numer <- 1:NOS
1870   if (is.numeric(which.species)) {
1871     which.species.numer <- which.species
1872     which.species <- sppNames[which.species.numer]  # Convert to character
1874     which.species.numer <- match(which.species, sppNames)
1892         ylim <- c(0, max(fitvals[,which.species.numer]) * stretch)
1893       col <- rep_len(col, length(which.species.numer))
1894       lty <- rep_len(lty, length(which.species.numer))
1895       lwd <- rep_len(lwd, length(which.species.numer))
1899       for (sppno in seq_along(which.species.numer)) {
1900         ptr2 <- which.species.numer[sppno]  # points to species column
1914     max.fitted <- matrix(fitvals[,which.species[1]],
1916     if (length(which.species) > 1)
1917       for (sppno in which.species[-1]) {
2022   cat("\nNumber of species: ", x@NOS, "\n")