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######################################
## dropall pudottaa data.framesta pois kaikki faktorien sellaiset levelit, joita ei käytetä.
## parametrit: x = data.frame
dropall <- function(x){
isFac <- NULL
for (i in 1:dim(x)[2]){isFac[i] = is.factor(x[ , i])}
for (i in 1:length(isFac)){
x[, i] <- x[, i][ , drop = TRUE]
}
return(x)
}
########################################
#########################################
## PTable muuntaa arvioinnin todennäköisyystaulun sopivaan muotoon arviointia varten.
## Parametrit: P = todennäköisyystaulu Opasnet-kannasta kaivettuna.
## n = iteraatioiden lukumäärä Monte Carlossa
## Todennäköisyystaulun sarakkeiden on oltava: Muuttuja, Selite, Lokaatio, P
## Tuotteena on Monte Carloa varten tehty taulu, jonka sarakkeina ovat
## n (iteraatio) ja kaikki todennäköisyystaulussa olleet selitteet, joiden riveille on arvottu
## lokaatiot niiden todennäköisyyksien mukaisesti, jotka todennäköisyystaulussa oli annettu.
PTable <- function(P, n) {
Pt <- unique(P[,c("Muuttuja", "Selite")])
Pt <- data.frame(Muuttuja = rep(Pt$Muuttuja, n), Selite = rep(Pt$Selite, n), obs = rep(1:n, each = nrow(Pt)), P = runif(n*nrow(Pt), 0, 1))
for(i in 2:nrow(P)){P$Result[i] <- P$Result[i] + ifelse(P$Muuttuja[i] == P$Muuttuja[i-1] & P$Selite[i] == P$Selite[i-1], P$Result[i-1], 0)}
P <- merge(P, Pt)
P <- P[P$P <= P$Result, ]
Pt <- as.data.frame(as.table(tapply(P$Result, as.list(P[, c("Muuttuja", "Selite", "obs")]), min)))
colnames(Pt) <- c("Muuttuja", "Selite", "obs", "Result")
Pt <- Pt[!is.na(P$Result), ]
P <- merge(P, Pt)
P <- P[, !colnames(P) %in% c("Result", "P", "Muuttuja")]
P <- reshape(P, idvar = "obs", timevar = "Selite", v.names = "Lokaatio", direction = "wide")
colnames(P) <- ifelse(substr(colnames(P), 1, 9) == "Lokaatio.", substr(colnames(P), 10,30), colnames(P))
return(P)
}
######################################
## opasnet.data downloads a file from Finnish Opasnet wiki, English Opasnet wiki, or Opasnet File.
## Parameters: filename is the URL without the first part (see below), wiki is "opasnet_en", "opasnet_fi", or "M-files".
## If table is TRUE then a table file for read.table function is assumed; all other parameters are for this read.table function.
opasnet.data <- function(filename, wiki = "opasnet_en", table = FALSE, ...)
{
if (wiki == "opasnet_en") {
file <- paste("http://en.opasnet.org/en-opwiki/images/", filename, sep = "")
}
if (wiki == "opasnet_fi") {
file <- paste("http://fi.opasnet.org/fi_wiki/images/", filename, sep = "")
}
if (wiki == "M-files") {
file <- paste("http://http://fi.opasnet.org/fi_wiki/extensions/mfiles/", filename, sep = "")
}
#if(table == TRUE) {
#file <- re#ad.table(file, header = FALSE, sep = "", quote = "\"'",
# dec = ".", row.names, col.names,
# as.is = !stringsAsFactors,
# na.strings = "NA", colClasses = NA, nrows = -1,
# skip = 0, check.names = TRUE, fill = !blank.lines.skip,
# strip.white = FALSE, blank.lines.skip = TRUE,
# comment.char = "#",
# allowEscapes = FALSE, flush = FALSE,
# stringsAsFactors = default.stringsAsFactors(),
# fileEncoding = "", encoding = "unknown")
#return(file)
#}
#else {return(ge#tURL(file))}
}
############ tidy: a function that cleans the tables from Opasnet Base
# data is a table from op_baseGetData function
# obs: if TRUE, keep obs column in output.
tidy <- function (data, obs = FALSE) {
data$Result <- ifelse(!is.na(data$Result.Text), as.character(data$Result.Text), data$Result)
if("Observation" %in% colnames(data)){test <- data$Observation != "Description"} else {test <- TRUE}
if("Havainto" %in% colnames(data)){test <- data$Havainto != "kuvaus"}
if(obs) {remove <- c("id", "Result.Text")} else {remove <- c("id", "obs", "Result.Text")}
data <- data[test, !colnames(data) %in% remove]
if(sum(is.na(as.numeric(as.character(data$Result)))) == 0) {data$Result <- as.numeric(as.character(data$Result))}
return(data)
}
############### Bring parts of summary table
# data is the summary table.
summary.bring <- function(data){
data <- data[, !colnames(data) %in% c("id", "obs")]
pages <- levels(data$Page)
## temp contains the additional information that is not on the actual data table.
temp <- data[data$Observation != "Description", !colnames(data) %in% c("Result", "Observation")]
temp <- reshape(temp, idvar = "Page", timevar = "Index", direction = "wide")
colnames(temp) <- ifelse(substr(colnames(temp), 1, 12) == "Result.Text.", substr(colnames(temp), 13, 50), colnames(temp))
## Get all data tables one at a time and combine them.
for(i in 1:length(pages)){
out <- op_baseGetData("opasnet_base", pages[i])
out <- tidy(out)
cols <- colnames(out)[!colnames(out) %in% c("Observation", "Result")]
out <- reshape(out, timevar = "Observation", idvar = cols, direction = "wide")
colnames(out) <- ifelse(substr(colnames(out), 1, 7) == "Result.", substr(colnames(out), 8, 50), colnames(out))
nam <- colnames(temp)[colnames(temp) != "Page"][1] # nam is needed in the case that the next line drops the colname
out <- merge(temp[temp$Page == pages[i], colnames(temp) != "Page"], out)
colnames(out)[colnames(out) == "x"] <- nam
## Check that all data tables have all the same columns before you combine them with rbind.
if(i == 1){out2 <- out} else {
addcol <- colnames(out2)[!colnames(out2) %in% colnames(out)]
if(length(addcol) > 0) {
temp <- as.data.frame(array("*", dim = c(1,length(addcol))))
colnames(temp) <- addcol
out <- merge(out, temp)}
addcol <- colnames(out)[!colnames(out) %in% colnames(out2)]
if(length(addcol) > 0) {
temp <- as.data.frame(array("*", dim = c(1,length(addcol))))
colnames(temp) <- addcol
out2 <- merge(out2, temp)}
## Combine data tables.
out2 <- rbind(out2, out)}
}
return(out2)
}
##########
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