Merge branch 'master' into 780

samples/R/R-qgis-extension.rsx

@@ -0,0 +1,5 @@
+##polyg=vector
+##numpoints=number 10
+##output=output vector
+##[Example scripts]=group
+pts=spsample(polyg,numpoints,type="regular")

samples/R/df.residual.r

@@ -0,0 +1,29 @@
+
+df.residual.mira <- function(object, ...) {
+    fit <- object$analyses[[1]]
+    return(df.residual(fit))
+}
+
+df.residual.lme <- function(object, ...) {
+    return(object$fixDF[["X"]][1])
+}
+
+df.residual.mer <- function(object, ...) {
+    return(sum(object@dims[2:4] * c(1, -1, -1)) + 1)
+}
+
+df.residual.default <- function(object, q = 1.3, ...) {
+    df <- object$df.residual
+    if (!is.null(df)) 
+        return(df)
+    
+    mk <- try(c <- coef(object), silent = TRUE)
+    mn <- try(f <- fitted(object), silent = TRUE)
+    if (inherits(mk, "try-error") | inherits(mn, "try-error")) 
+        return(NULL)
+    n <- ifelse(is.data.frame(f) | is.matrix(f), nrow(f), length(f))
+    k <- length(c)
+    if (k == 0 | n == 0) 
+        return(NULL)
+    return(max(1, n - q * k))
+}

samples/R/import.r

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+#' Import a module into the current scope
+#'
+#' \code{module = import('module')} imports a specified module and makes its
+#' code available via the environment-like object it returns.
+#'
+#' @param module an identifier specifying the full module path
+#' @param attach if \code{TRUE}, attach the newly loaded module to the object
+#'      search path (see \code{Details})
+#' @param attach_operators if \code{TRUE}, attach operators of module to the
+#'      object search path, even if \code{attach} is \code{FALSE}
+#' @return the loaded module environment (invisible)
+#'
+#' @details Modules are loaded in an isolated environment which is returned, and
+#' optionally attached to the object search path of the current scope (if
+#' argument \code{attach} is \code{TRUE}).
+#' \code{attach} defaults to \code{FALSE}. However, in interactive code it is
+#' often helpful to attach packages by default. Therefore, in interactive code
+#' invoked directly from the terminal only (i.e. not within modules),
+#' \code{attach} defaults to the value of \code{options('import.attach')}, which
+#' can be set to \code{TRUE} or \code{FALSE} depending on the user’s preference.
+#'
+#' \code{attach_operators} causes \emph{operators} to be attached by default,
+#' because operators can only be invoked in R if they re found in the search
+#' path. Not attaching them therefore drastically limits a module’s usefulness.
+#'
+#' Modules are searched in the module search path \code{options('import.path')}.
+#' This is a vector of paths to consider, from the highest to the lowest
+#' priority. The current directory is \emph{always} considered first. That is,
+#' if a file \code{a.r} exists both in the current directory and in a module
+#' search path, the local file \code{./a.r} will be loaded.
+#'
+#' Module names can be fully qualified to refer to nested paths. See
+#' \code{Examples}.
+#'
+#' @note Unlike for packages, attaching happens \emph{locally}: if
+#' \code{import} is executed in the global environment, the effect is the same.
+#' Otherwise, the imported module is inserted as the parent of the current
+#' \code{environment()}. When used (globally) \emph{inside} a module, the newly
+#' imported module is only available inside the module’s search path, not
+#' outside it (nor in other modules which might be loaded).
+#'
+#' @examples
+#' # `a.r` is a file in the local directory containing a function `f`.
+#' a = import('a')
+#' a$f()
+#'
+#' # b/c.r is a file in path `b`, containing a function `g`.
+#' import('b/c', attach = TRUE)
+#' g() # No module name qualification necessary
+#'
+#' @seealso \code{unload}
+#' @seealso \code{reload}
+#' @seealso \code{module_name}
+#' @export
+import = function (module, attach, attach_operators = TRUE) {
+    module = substitute(module)
+    stopifnot(inherits(module, 'name'))
+
+    if (missing(attach)) {
+        attach = if (interactive() && is.null(module_name()))
+            getOption('import.attach', FALSE)
+        else
+            FALSE
+    }
+
+    stopifnot(class(attach) == 'logical' && length(attach) == 1)
+
+    module_path = try(find_module(module), silent = TRUE)
+
+    if (inherits(module_path, 'try-error'))
+        stop(attr(module_path, 'condition')$message)
+
+    containing_modules = module_init_files(module, module_path)
+    mapply(do_import, names(containing_modules), containing_modules)
+
+    mod_ns = do_import(as.character(module), module_path)
+    module_parent = parent.frame()
+    mod_env = exhibit_namespace(mod_ns, as.character(module), module_parent)
+
+    if (attach) {
+        if (identical(module_parent, .GlobalEnv))
+            attach(mod_env, name = environmentName(mod_env))
+        else
+            parent.env(module_parent) = mod_env
+    }
+    else if (attach_operators)
+        export_operators(mod_ns, module_parent)
+
+    invisible(mod_env)
+}
+
+do_import = function (module_name, module_path) {
+    if (is_module_loaded(module_path))
+        return(get_loaded_module(module_path))
+
+    # The namespace contains a module’s content. This schema is very much like
+    # R package organisation.
+    # A good resource for this is:
+    # <http://obeautifulcode.com/R/How-R-Searches-And-Finds-Stuff/>
+    namespace = structure(new.env(parent = .BaseNamespaceEnv),
+                          name = paste('namespace', module_name, sep = ':'),
+                          path = module_path,
+                          class = c('namespace', 'environment'))
+    local(source(attr(environment(), 'path'), chdir = TRUE, local = TRUE),
+          envir = namespace)
+    cache_module(namespace)
+    namespace
+}
+
+exhibit_namespace = function (namespace, name, parent) {
+    exported_functions = lsf.str(namespace)
+    # Skip one parent environment because this module is hooked into the chain
+    # between the calling environment and its ancestor, thus sitting in its
+    # local object search path.
+    structure(list2env(sapply(exported_functions, get, envir = namespace),
+                       parent = parent.env(parent)),
+              name = paste('module', name, sep = ':'),
+              path = module_path(namespace),
+              class = c('module', 'environment'))
+}
+
+export_operators = function (namespace, parent) {
+    # `$` cannot be overwritten, but it is generic so S3 variants of it can be
+    # defined. We therefore test it as well.
+    ops = c('+', '-', '*', '/', '^', '**', '&', '|', ':', '::', ':::', '$', '=',
+            '<-', '<<-', '==', '<', '<=', '>', '>=', '!=', '~', '&&', '||')
+
+    is_predefined = function (f) f %in% ops
+
+    is_op = function (f) {
+        prefix = strsplit(f, '\\.')[[1]][1]
+        is_predefined(prefix) || grepl('^%.*%$', prefix)
+    }
+
+    operators = Filter(is_op, lsf.str(namespace))
+    name = module_name(namespace)
+    # Skip one parent environment because this module is hooked into the chain
+    # between the calling environment and its ancestor, thus sitting in its
+    # local object search path.
+    op_env = structure(list2env(sapply(operators, get, envir = namespace),
+                                parent = parent.env(parent)),
+                       name = paste('operators', name, sep = ':'),
+                       path = module_path(namespace),
+                       class = c('module', 'environment'))
+
+    if (identical(parent, .GlobalEnv))
+        attach(op_env, name = environmentName(op_env))
+    else
+        parent.env(parent) = op_env
+}
+
+#' Unload a given module
+#'
+#' Unset the module variable that is being passed as a parameter, and remove the
+#' loaded module from cache.
+#' @param module reference to the module which should be unloaded
+#' @note Any other references to the loaded modules remain unchanged, and will
+#' still work. However, subsequently importing the module again will reload its
+#' source files, which would not have happened without \code{unload}.
+#' Unloading modules is primarily useful for testing during development, and
+#' should not be used in production code.
+#'
+#' \code{unload} does not currently detach environments.
+#' @seealso \code{import}
+#' @seealso \code{reload}
+#' @export
+unload = function (module) {
+    stopifnot(inherits(module, 'module'))
+    module_ref = as.character(substitute(module))
+    rm(list = module_path(module), envir = .loaded_modules)
+    # unset the module reference in its scope, i.e. the caller’s environment or
+    # some parent thereof.
+    rm(list = module_ref, envir = parent.frame(), inherits = TRUE)
+}
+
+#' Reload a given module
+#'
+#' Remove the loaded module from the cache, forcing a reload. The newly reloaded
+#' module is assigned to the module reference in the calling scope.
+#' @param module reference to the module which should be unloaded
+#' @note Any other references to the loaded modules remain unchanged, and will
+#' still work. Reloading modules is primarily useful for testing during
+#' development, and should not be used in production code.
+#'
+#' \code{reload} does not work correctly with attached environments.
+#' @seealso \code{import}
+#' @seealso \code{unload}
+#' @export
+reload = function (module) {
+    stopifnot(inherits(module, 'module'))
+    module_ref = as.character(substitute(module))
+    module_path = module_path(module)
+    module_name = module_name(module)
+    rm(list = module_path, envir = .loaded_modules)
+    #' @TODO Once we have `attach`, need also to take care of the search path
+    #' and whatnot.
+    mod_ns = do_import(module_name, module_path)
+    module_parent = parent.frame()
+    mod_env = exhibit_namespace(mod_ns, module_ref, module_parent)
+    assign(module_ref, mod_env, envir = module_parent, inherits = TRUE)
+}