OpasnetUtils/Drafts
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Question
Which functions are so useful that they should be taken into OpasnetUtils package? This page contains draft function which will be included when they are good enough and found important.
Answer
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_style <- paste("#style", ifelse(length(icon) == 1, 1, i), sep = "")
kml <- append(kml, "<Placemark>")
kml <- append(kml, paste(
" <description><![CDATA[",
name[i],
": ",
description[i],
"]]></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)
}
# MyRmap is a function for creating static Google maps as png.
# It is based on MyMap function without the "file destination" parameter
# Requires RgoogleMaps package
MyRmap <- function (
shp, # a spatial data object
plotvar, # Name of the column that has the values to be illustrated on the map
pch = 19, # Shape of the point (19: circle)
cex = 0.3, # Size of the point
legend_title = "", # Title of the legend
legend_position = "topleft",
numbins = 8, # Number of colour bins in graph
center, # center of the map
size = c(640, 480), # size of the map. This produces the right dimensions in Opasnet.
MINIMUMSIZE = FALSE,
RETURNIMAGE = TRUE,
GRAYSCALE = FALSE,
NEWMAP = TRUE,
zoom,
verbose = 1,
...
) {
plotvar <- shp[[plotvar]]
plotclr <- brewer.pal(numbins, "Spectral")
classes <- classIntervals(plotvar, numbins, style = "quantile")
colcode <- findColours(classes, plotclr)
latR <- shp@coords[ , 2]
lonR <- shp@coords[ , 1]
#get the bounding box:
bb <- qbbox(lat = latR, lon = lonR)
if (missing(zoom))
zoom <- min(MaxZoom(latR, lonR, size))
if (missing(center)) {
lat.center <- mean(latR)
lon.center <- mean(lonR)
}
else {
lat.center <- center[1]
lon.center <- center[2]
}
if (MINIMUMSIZE) {
ll <- LatLon2XY(latR[1], lonR[1], zoom) # I think the latR and lonR are used here differently than how they
ur <- LatLon2XY(latR[2], lonR[2], zoom) # are used elsewhere. Thus, if MINIMUMSIZE = TRUE, you may see problems.
cr <- LatLon2XY(lat.center, lon.center, zoom)
ll.Rcoords <- Tile2R(ll, cr)
ur.Rcoords <- Tile2R(ur, cr)
if (verbose > 1) {
cat("ll:")
print(ll)
print(ll.Rcoords)
cat("ur:")
print(ur)
print(ur.Rcoords)
cat("cr:")
print(cr)
}
size[1] <- 2 * max(c(ceiling(abs(ll.Rcoords$X)), ceiling(abs(ur.Rcoords$X)))) + 1
size[2] <- 2 * max(c(ceiling(abs(ll.Rcoords$Y)), ceiling(abs(ur.Rcoords$Y)))) + 1
if (verbose) cat("new size: ", size, "\n")
}
MyMap <- GetMap(
center = c(lat.center, lon.center),
zoom = zoom,
size = size,
RETURNIMAGE = RETURNIMAGE,
GRAYSCALE = GRAYSCALE,
verbose = verbose,
...
)
PlotOnStaticMap(MyMap) # Plot an empty map.
PlotOnStaticMap( # Plot the data points on the map.
MyMap,
lat = latR,
lon = lonR,
pch = pch,
cex = cex,
col = colcode,
add = T
)
legend( # Plot the legend on the map.
legend_position,
legend = names(attr(colcode, "table")),
title = legend_title,
fill = attr(colcode, "palette"),
cex = 1.0,
bty = "y",
bg = "white"
)
}
objects.store(ograph, fillna, collapsemarg, MyPointKML, ova2spat, MyRmap)
cat("The following objects are stored: ograph, fillna, collapsemarg, MyPointKML, ova2spat, MyRmap.\n")
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See also
- OpasnetUtils/Ograph, a previous code, now depreciated.
References
Related files
<mfanonymousfilelist></mfanonymousfilelist>
