The R Project SVN R-packages

.onLoad <- function(libname, pkgname) .Call("sdf_init_workspace");

.onUnload <- function(libpath) {
    .Call("sdf_finalize_workspace")
    library.dynam.unload("SQLiteDF", libpath)
}

# -------------------------------------------------------------------------
# workspace functions
# -------------------------------------------------------------------------
lsSdf <- function(pattern=NULL) .Call("sdf_list_sdfs", pattern);
getSdf <- function(name) .Call("sdf_get_sdf", name);

readTableSdf <- function(filename, sep=",", quote="\"'", name=NULL, 
                            rownames, colnames)
    .Call("sdf_import_table", filename, name, sep, quote, rownames, colnames);

attachSdf <- function(sdf_filename, sdf_iname=NULL) 
    invisible(.Call("sdf_attach_sdf", sdf_filename, sdf_iname));
detachSdf <- function(iname) .Call("sdf_detach_sdf", iname);

# -------------------------------------------------------------------------
# sqlite.data.frame functions
# -------------------------------------------------------------------------
"sqlite.data.frame" <- function(x, name=NULL) {
    if (inherits(x, "sqlite.data.frame")) x 
    else .Call("sdf_create_sdf", as.data.frame(x), name)
}

dupSdf <- function(sdf) { 
    if (!inherits(sdf, "sqlite.data.frame")) stop("Not a sqlite.data.frame.");
    sdf[1:length(sdf)]
}
renameSdf <- function(sdf, name) { 
    if (!inherits(sdf, "sqlite.data.frame")) stop("Not a sqlite.data.frame.");
    if (!is.character(name)) stop("name argument must be a string.");
    .Call("sdf_rename_sdf", sdf, name);
}
inameSdf <- function(sdf) .Call("sdf_get_iname", sdf)

# -------------------------------------------------------------------------
# sqlite.matrix functions
# -------------------------------------------------------------------------
sqlite.matrix <- function(data, name=NULL) {
    if (inherits(data, "sqlite.matrix")) data
    else if (inherits(data, "sqlite.data.frame")) .Call("sdf_as_matrix", data, name)
    else .Call("smat_create_smat", as.matrix(data), name)
}

# -------------------------------------------------------------------------
# external data functions
# -------------------------------------------------------------------------
sdfImportDBI <- function(con, sql, batch.size=2048, rownames="row_names", iname = NULL) {
    on.exit(DBI:::dbClearResult(rs));
    rs <- DBI:::dbSendQuery(con, sql);
    df <- DBI:::fetch(rs, batch.size);
    if (length(rownames) > 1) stop("more than one column containing row names?")

    if (is.numeric(rownames)) has_rn <- rownames
    else if (is.character(rownames)) has_rn <- (1:length(df))[names(df) == row.names];

    if (length(has_rn) == 0) has_rn <- FALSE;

    if (has_rn) { 
        rn <- df[,has_rn]; df <- df[,-has_rn]; row.names(df) <- rn;
    }
    sdf <- sqlite.data.frame(df, iname);
    rowname <- batch.size
    while (! dbHasCompleted(rs)) {
        df <- DBI:::fetch(rs, batch.size);
        if (has_rn) { 
            rn <- df[,has_rn]; df <- df[,-has_rn]; row.names(df) <- rn;
        }
        rbind.sqlite.data.frame(sdf, df);
    }
    sdf;
}

sdfImportSQLite <- function(dbfilename, tablename, iname = tablename) {
    .Call("sdf_import_sqlite_table", dbfilename, tablename, iname);
}

sdfImportText <- function(file, iname=NULL, sep="", quote="\"'", dec=".", as.is=FALSE, 
        na.strings="NA", colClasses=NA, skip=0, fill=!blank.lines.skip, 
        strip.white=FALSE, blank.lines.skip=FALSE, comment.char="#", allowEscapes=FALSE, 
        flush=FALSE, batch.size=2048) {  
    
    data <- read.table(file=file,sep=sep,quote=quote,dec=dec,as.is=as.is,na.strings=na.strings,
                colClasses=colClasses,skip=skip,fill=fill,strip.white=strip.white,
                blank.lines.skip=blank.lines.skip,comment.char=comment.char,
                allowEscapes=allowEscapes,flush=flush,nrows=batch.size);
    sdf <- sqlite.data.frame(data, iname);
    
    if (length(colClasses) < length(data) || colClasses == NA) 
        colClasses <- sapply(data, function(x) class(x)[1]);

    sskip <- skip;
    while (nrow(data) == batch.size) {
        sskip <- sskip + batch.size;
        data <- read.table(file=file,sep=sep,quote=quote,dec=dec,as.is=as.is,
                    na.strings=na.strings, colClasses=colClasses,skip=skip,fill=fill,
                    strip.white=strip.white, blank.lines.skip=blank.lines.skip,
                    comment.char=comment.char, allowEscapes=allowEscapes,flush=flush,
                    nrows=batch.size);
        rbind(sdf, data);
    }
    sdf;
}


# -------------------------------------------------------------------------
# overriden primitives
# -------------------------------------------------------------------------
# the default rbind's dispatch is "not normal," won't dispatch to rbind.sdf
# even if all args are sdf's
rbind <- function(..., deparse.level) UseMethod("rbind")
rbind.default <- function(..., deparse.level) .Internal(rbind(deparse.level, ...));

sort.default <- base::sort; sort <- function(x, ...) UseMethod("sort");
formals(sort.default) <- c(formals(sort.default), alist(...=))
environment(quantile.default) <- .GlobalEnv

median <- function(x, na.rm=FALSE) quantile(x, 0.5, na.rm=na.rm)

eval <- function(expr, envir=parent.frame(), enclos=if (is.list(envir) || is.pairlist(envir)) parent.frame() else baseenv()) {
    if (inherits(envir, "sqlite.data.frame")) envir <- as.list(envir);
    .Internal(eval(expr, envir, enclos));
}

# -------------------------------------------------------------------------
# biglm stuffs
# -------------------------------------------------------------------------
sdflm <- function(formula, sdf, batch.size=1024) {
    n <- 1:batch.size;
    sdf.nrows <- nrow(sdf);
    res <- biglm:::biglm(formula, sdf[n,]);
    n <- n + batch.size;
    while (n[1] < sdf.nrows) {
        if (n[batch.size] > sdf.nrows) n <- n[1]:sdf.nrows;
        res <- update(res, sdf[n,]);
        n <- n + batch.size;
    }
    res;
}

# -------------------------------------------------------------------------
# S3 methods for sqlite.data.frame
# -------------------------------------------------------------------------
names.sqlite.data.frame <- function(x) .Call("sdf_get_names", x);
length.sqlite.data.frame <- function(x) .Call("sdf_get_length", x);
nrow.sqlite.data.frame <- function(x) .Call("sdf_get_row_count", x);
dim.sqlite.data.frame <- function(x)
    c(nrow.sqlite.data.frame(x), length.sqlite.data.frame(x));
dimnames.sqlite.data.frame <- function(x) list(row.names(x), names(x))
"$.sqlite.data.frame" <- function(x, name) .Call("sdf_get_variable", x, name);
"[[.sqlite.data.frame" <- function(x, idx) {
    if (length(idx) != 1) stop("index must be a 1-element vector.");
    if (is.character(idx)) .Call("sdf_get_variable", x, idx)
    else if (is.numeric(idx)) {
        if (idx > length(x)) stop("subscript out of bounds")
        else .Call("sdf_get_variable", x, names(x)[idx])
    } else stop("don't know how to handle index.");
}
"[.sqlite.data.frame" <- function(x, row=NULL, col=NULL) {
#    if (row == NULL || col == NULL) { data.frame(NULL) }
#    if (missing(row)) row = NULL;
#    if (missing(col)) col = NULL; 
    .Call("sdf_get_index", x, row, col); 
}
as.list.sqlite.data.frame <- function(x, ...) {
    ret <- list();
    for (i in names(x)) ret[[i]] <- x[[i]];
    ret;
}
is.list.sqlite.data.frame <- function(x) FALSE;
rbind.sqlite.data.frame <- function(..., deparse.level=1) {
    args <- list(...);
    .Call("sdf_rbind", args[[1]], args[[2]]);
}
with.sqlite.data.frame <- function(data, expr, ...)  
    eval(substitute(expr), as.list(data), enclos=parent.frame())
as.data.frame.sqlite.data.frame <- function(x, ...) x
as.matrix.sqlite.data.frame <- function(x, ...) {
    args <- as.list(...);
    if ("name" %in% as.list) name <- args$name else name <- NULL;
    sqlite.matrix(x, name)
}

      

# -------------------------------------------------------------------------
# S3 methods for sqlite.vector
# -------------------------------------------------------------------------
"[.sqlite.vector" <- function(x, idx) {
    # temporary, better to be in C because assumption is length(x) is large
    if (is.numeric(idx) && all(idx <= 0)) idx <- (1:length(x))[idx];
    .Call("sdf_get_variable_index", x, idx);
}
length.sqlite.vector <- function(x) .Call("sdf_get_variable_length", x);
# methods to "coerce" to ordinary vectors
as.double.sqlite.vector <- function(x, ...) as.double(x[1:length(x)])
as.character.sqlite.vector <- function(x, ...) as.character(x[1:length(x)])
as.logical.sqlite.vector <- function(x, ...) as.logical(x[1:length(x)])
as.integer.sqlite.vector <- function(x, ...) as.integer(x[1:length(x)])
Math.sqlite.vector <- function(x, ...) {
    if (any(inherits(x, "factor"), inherits(x, "ordered"))) 
        stop(paste(.Generic, "not meaningful for factors"));
    if (!any(inherits(x, "numeric"), inherits(x, "integer")))
        stop("Non-numeric argument to mathematical function");
    #.Generic
    extra.args <- list(...);
    nargs <- 1 + length(extra.args);
    nformals <- length(formals(get(.Generic, mode="function")))
    if (nformals == 0) nformals <- 1;
    if (nargs > nformals)
        stop("error in number of arguments\n");
    ret <- .Call("sdf_do_variable_math", .Generic, x, extra.args, nargs);
    if (is.character(ret)) { file.remove(ret); ret <- NULL; }
    ret;
}
Summary.sqlite.vector <- function(x, na.rm=F) {
    if (!any(inherits(x, "numeric"), inherits(x, "integer"), inherits(x, "logical")))
        stop("Non-numeric argument");
    ret <- .Call("sdf_do_variable_summary", .Generic, x, as.logical(na.rm))
    if (is.character(ret)) { file.remove(ret); ret <- NULL; }
    ret;
}
Ops.sqlite.vector <- function(e1, e2) {
    if (inherits(e1, "factor") | inherits(e2, "factor"))
        stop("not meaningful for factors");
    if (!inherits(e1, "sqlite.vector")) { tmp <- e1; e1 <- e2; e2 <- tmp; }
    .Call("sdf_do_variable_op", .Generic, e1, e2);
}
sort.sqlite.vector <- function(x, decreasing=FALSE, ...) {
    .Call("sdf_sort_variable", x, as.logical(decreasing))
}
quantilexx.sqlite.vector <- function(x, probs=seq(0, 1, 0.25), names=FALSE, 
        na.rm=FALSE, type=7, ...) {
    # I just copied these, mostly.
    if (!any(inherits(x,"numeric"), inherits(x,"integer")))
        stop("only for numeric vectors");
    if (any((p.ok <- !is.na(probs)) & (probs < 0 | probs > 1)))
        stop("'probs' outside [0,1]")
    n <- length(x); np <- length(probs);
    xs <- sort(x);
}

quantile.sqlite.vector <- function(x, probs=seq(0,1,0.25), names=FALSE,
        na.rm=FALSE, type=7, ...) NextMethod();
is.numeric.sqlite.vector <- function(x) inherits(x, "numeric") || inherits(x, "integer")
is.character.sqlite.vector <- function(x) inherits(x, "character")
is.integer.sqlite.vector <- function(x) inherits(x, "integer")
summary.sqlite.vector <- function(object, maxsum=100, digits=max(3, getOption("digits")-3), ...) {
    if (inherits(object, "factor") || inherits(object, "logical")) 
        .Call("sdf_variable_summary", object, as.integer(maxsum))
    else NextMethod();
}

# -------------------------------------------------------------------------
# S3 methods for sqlite.matrix
# -------------------------------------------------------------------------
length.sqlite.matrix <- function(x) .Call("sdf_get_variable_length", x);
dim.sqlite.matrix <- function(x) attr(x, "dim");