Difference between revisions of "OpasnetUtils/Drafts"

library(OpasnetUtils)

ograph <- function( # Määritellään yleisfunktio peruskuvaajan piirtämiseen.
	ovariable, 
	x, 
	y = character(), 
	type = character(), 
	other = character(),
	fill = NA, 
	...
) {
	if(class(ovariable) == "ovariable")  {
		if(nrow(ovariable@output) == 0) ovariable <- EvalOutput(ovariable)
		data <- ovariable@output
		title <- ovariable@name
		if(length(y) == 0) y <- paste(title, "Result", sep = "")
	} else {
		data <- ovariable
		title <- character()
		if(length(y) == 0) y <- "Result"
	}
	if(length(type) == 0) {
		if("Iter" %in% colnames(data)) type <- geom_boxplot() else type <- geom_bar(stat = "identity")
	}
	out <- ggplot(data, aes_string(x = x, y = y, fill = fill)) # Määritellään kuvan sarakkeet
	out <- out + type
	out <- out + theme_grey(base_size=24) # Fontin kokoa suurennetaan
	out <- out + labs(
			title	= title,
			y = paste(unique(data[[paste(title, "Yksikkö", sep = "")]]), sep = "", collapse = ", ")
		)
	out <- out + theme(axis.text.x = element_text(angle = 90, hjust = 1)) # X-akselin tekstit käännetään niin että mahtuvat
	if(length(other) != 0) out <- out + other
	return(out)
}

# fillna takes a data.frame and fills the cells with NA with each level in that column.
# object is the data.frame, marginals is a vector of columns (either column names or positions) that are to be filled.
# This version of fillna accepts column positions (as the previous version) and also column names in marginals.

fillna <- function (object, marginals) {
	a <- dropall(object)
	if(!is.numeric(marginals)) marginals <- match(marginals, colnames(object))
	for (i in marginals) {
		a[[i]] <- as.factor(a[[i]])
		a1 <- a[!is.na(a[[i]]), ]
		a2 <- a[is.na(a[[i]]), ][-i]
		addition <- data.frame(A = levels(a[[i]]))
		colnames(addition) <- colnames(a)[i]
		a2 <- merge(addition, a2)
		a <- rbind(a1, a2)
	}
	return(a)
}

## collapsemarg is a placeholder for a better functionality within CollapseMarginals.
## It takes an ovariable, and summarises all indices in cols using tapply and a user-defined function.
## However, you can also use function "pick" to select locations defined in a list picks found in indices cols.
## Function "unkeep" simply drops the unkept indices without any other operation.
## The output is an ovariable with the same name as the input.
## This was first created for [[:op_fi:Radonin terveysvaikutukset]]

collapsemarg <- function(variable, cols, fun = "sum", picks = list(), ...) { # cols is a character vector, while probs is a list
	out <- dropall(variable@output)
	marginals <- colnames(out)[variable@marginal]

	if(tolower(fun) == "unkeep") { # The function must be a string, otherwise this row will fail.
		out <- out[!colnames(out) %in% cols]
	} else {
		if(tolower(fun) == "pick") {
			for(i in cols) {
				out <- out[out[[i]] %in% picks[[match(i, cols)]] , ]
			}
			cols <- "" # Those locations that were picked are still marginals.
		} else {
			margtemp <- colnames(out)[colnames(out) %in% marginals & !colnames(out) %in% cols] 
			# You must leave at least one index.

			out <- as.data.frame(as.table(tapply(result(variable), out[margtemp], fun)))
			out <- out[!is.na(out$Freq) , ]

			colnames(out)[colnames(out) == "Freq"] <- ifelse(
				length(variable@name) == 0, 
				"Result", 
				paste(variable@name, "Result", sep = "")
			)
		}
	}

	variable@output <- out
	variable@marginal <- colnames(out) %in% marginals & ! colnames(out) %in% cols
	
	return(variable)
}

MyPointKML <- function( # The function creates a KML fille from a SpatialPointsDataFrame object.
	obj = NULL, # Spatial object with the data. A SpatialPointsDataFrame.
	kmlname = "", # Name of the KML fille (does this show on the map?)
	kmldescription = "", # Description of the KML fille (does this show on the map?)
	name = NULL, # Name for each datapoint (vector with the same length as data in obj).
	description = "", # Descrtion of each datapoint (vector with the same length as data in obj).
	icon = "http://maps.google.com/mapfiles/kml/pal4/icon24.png", # Icon shown on pin (?)
	col=NULL # I don't know what this does.
) {
    if (is.null(obj)) 
        return(list(header = c("<?xml version=\"1.0\" encoding=\"UTF-8\"?>", 
            "<kml xmlns=\"http://earth.google.com/kml/2.2\">", 
            "<Document>", paste("<name>", kmlname, "</name>", 
                sep = ""), paste("<description><![CDATA[", kmldescription, 
                "]]></description>", sep = "")), footer = c("</Document>", 
            "</kml>")))
    if (class(obj) != "SpatialPointsDataFrame") 
        stop("obj must be of class 'SpatialPointsDataFrame' [package 'sp']")
    if (is.null(name)) {
        name = c()
        for (i in 1:nrow(obj)) name <- append(name, paste("site", 
            i))
    }
    if (length(name) < nrow(obj)) {
        if (length(name) > 1) 
            warning("kmlPoints: length(name) does not match nrow(obj). The first name will be replicated.")
        name <- rep(name, nrow(obj))
    }
    if (length(description) < nrow(obj)) {
        if (length(description) > 1) 
            warning("kmlPoints: length(description) does not match nrow(obj). The first description will be replicated.")
        description <- rep(description, nrow(obj))
    }
    if (length(icon) < nrow(obj)) {
        if (length(icon) > 1) 
            warning("kmlPoints: length(icon) does not match nrow(obj). Only the first one will be used.")
        icon <- icon[1]
    }

	# This is some kind of a colour definition
	
	col2kmlcolor <- function(col) 
		paste(rev(sapply(
			col2rgb(col, TRUE), 
			function(x) sprintf("%02x", x))
		), collapse = "")
	
    kml <- kmlStyle <- ""
    
	# Create the KML fille.
	
	kmlHeader <- c("<?xml version=\"1.0\" encoding=\"UTF-8\"?>","<kml xmlns=\"http://earth.google.com/kml/2.2\">", "<Document>")
    kmlFooter <- c("</Document>", "</kml>")
    
	# Create rows to the KML fille from data in obj.
	
    for (i in 1:nrow(obj)) {
        point <- obj[i, ]
        pt_name <- name[i]
        pt_description <- description[i]
        pt_style <- paste("#style", ifelse(length(icon) == 1, 1, i), sep = "")
        kml <- append(kml, "<Placemark>")
        kml <- append(kml, paste("  <description><![CDATA[",pt_description, "]]></description>", sep = ""))
	#kml <- append(kml, "<Style><IconStyle>")
	#kml <- append(kml, paste("<color>", col2kmlcolor(col[i]), "</color>", sep =""))
	#kml <- append(kml, paste("  <Icon><href>", icon, "</href></Icon>", sep = ""))
	#kml <- append(kml, "<scale>0.300000</scale>")
	#kml <- append(kml, "</IconStyle></Style>")
        kml <- append(kml, "  <Point>")
        kml <- append(kml, "    <coordinates>")
        kml <- append(kml, paste(point@coords[1], point@coords[2], sep = ","))
        kml <- append(kml, "    </coordinates>")
        kml <- append(kml, "  </Point>")
        kml <- append(kml, "</Placemark>")
    }
    
    return(paste(paste(c(kmlHeader, kmlStyle, kml, kmlFooter), sep = "", collapse = "\n"), collapse="\n", sep = ""))
}

ova2spat <- function( # This function converts an ovariable into a SpatialPointsDataFrame.
	ovariable, # An evaluated ovariable that has coordinate indices.
	coords, # The names of the coordinate indices as a character vector, first x then y.
	proj4string # Projection identifier or specification as character string. See http://spatialreference.org/
) {
	temp <- ovariable@output
	
	# Transform coordinates into numeric format.
	
	for(i in coords) { 
		if(is(temp[[i]], "factor"))    temp[[i]] <- levels(temp[[i]])[temp[[i]]]
		if(is(temp[[i]], "character")) temp[[i]] <- as.numeric(temp[[i]])
	}
	
	# Define the coordinate points first, then add other ovariable output to it.
	
	sp <- SpatialPoints(temp[coords], CRS(proj4string))
	out <- SpatialPointsDataFrame(sp, temp[!colnames(temp) %in% coords])

	#Transform the projection to longitude-latitude system.
	
	epsg4326String <- CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +no_defs")
	out <- spTransform(out,epsg4326String)

	return(out)
}

objects.store(ograph, fillna, collapsemarg, MyPointKML, ova2spat)

cat("The following objects are stored: ograph, fillna, collapsemarg, MyPointKML, ova2spat.\n")