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unmarkedFrame.R
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unmarkedFrame.R
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# ------------------------ VALIDATION FUNCTIONS --------------------------
validunmarkedFrame <- function(object) {
errors <- character(0)
M <- nrow(object@y)
J <- ncol(object@y)
if(!is.null(object@siteCovs))
if(nrow(object@siteCovs) != M)
errors <- c(errors,
"siteCovData does not have same size number of sites as y.")
if(!is.null(obsCovs(object)) & !is.null(obsNum(object)))
if(nrow(object@obsCovs) != M*obsNum(object))
errors <- c(errors, "obsCovData does not have M*obsNum rows.")
if(length(errors) == 0)
TRUE
else
errors
}
# --------------------------- DATA CLASSES -------------------------------
# Class to hold data for analyses in unmarked.
setClass("unmarkedFrame",
representation(y = "matrix",
obsCovs = "optionalDataFrame",
siteCovs = "optionalDataFrame",
mapInfo = "optionalMapInfo",
obsToY = "optionalMatrix"),
validity = validunmarkedFrame)
## a class for multi-season data
setClass("unmarkedMultFrame",
representation(numPrimary = "numeric",
#data frame in site-major, year-minor order describing siteCovs
yearlySiteCovs = "optionalDataFrame"),
contains="unmarkedFrame")
## a class for distance sampling data
setClass("unmarkedFrameDS",
representation(
dist.breaks = "numeric",
tlength = "numeric",
survey = "character",
unitsIn = "character"),
contains = "unmarkedFrame",
validity = function(object) {
errors <- character(0)
J <- numY(object)
db <- object@dist.breaks
if(J != length(db) - 1)
errors <- c(errors, "ncol(y) must equal length(dist.breaks)-1")
if(db[1] != 0)
errors <- c(errors, "dist.breaks[1] must equal 0")
if(!is.null(obsCovs(object)))
"obsCovs cannot be used with distsamp"
if(length(errors) == 0) TRUE
else errors
})
setClass("unmarkedFrameOccu",
contains = "unmarkedFrame")
setClass("unmarkedFrameOccuFP",
representation(
type = "numeric"),
contains = "unmarkedFrame")
#Multi-state occupancy
setClass('unmarkedFrameOccuMS',
representation(
numStates = "numeric",
phiOrder = "list"),
contains = "unmarkedMultFrame")
#Time-to-detection occupancy
setClass("unmarkedFrameOccuTTD",
representation(
surveyLength = "matrix"),
contains = "unmarkedMultFrame")
setClass("unmarkedFrameOccuMulti",
representation(ylist = "list", fDesign = "matrix"),
contains = "unmarkedFrame",
validity = function(object) {
errors <- character(0)
M <- nrow(object@y)
J <- ncol(object@y)
Ms <- sapply(object@ylist,nrow)
Js <- sapply(object@ylist,ncol)
if(length(unique(Ms)) != 1)
errors <- c(errors, "All species must have same number of sites")
if(length(unique(Js)) != 1)
errors <- c(errors, "All species must have same number of observations")
if(!is.null(object@siteCovs))
if(nrow(object@siteCovs) != M)
errors <- c(errors,
"siteCovData does not have same size number of sites as y.")
if(!is.null(obsCovs(object)) & !is.null(obsNum(object)))
if(nrow(object@obsCovs) != M*obsNum(object))
errors <- c(errors, "obsCovData does not have M*obsNum rows.")
if(length(errors) == 0)
TRUE
else
errors
})
setClass("unmarkedFramePCount",
contains = "unmarkedFrame")
setClass("unmarkedFrameMPois",
representation(
samplingMethod = "character",
piFun = "character"),
contains = "unmarkedFrame")
setClass("unmarkedFrameG3",
contains = "unmarkedMultFrame")
setClass("unmarkedFramePCO",
representation(primaryPeriod = "matrix"),
contains = "unmarkedMultFrame")
setClass("unmarkedFrameGMM",
representation(
piFun = "character",
samplingMethod = "character"),
contains = "unmarkedFrameG3")
setClass("unmarkedFrameGDS",
representation(
dist.breaks = "numeric",
tlength = "numeric",
survey = "character",
unitsIn = "character"),
contains = "unmarkedFrameG3")
setClass("unmarkedFrameGPC",
contains = "unmarkedFrameG3")
setClass("unmarkedFrameMMO",
representation(primaryPeriod = "matrix"),
contains = "unmarkedFrameGMM")
## Andy 12/27/2015
setClass("unmarkedFrameDSO",
representation(primaryPeriod = "matrix"),
contains = "unmarkedFrameGDS")
# ------------------------------- CONSTRUCTORS ---------------------------
#Convert covs provided as list of matrices/dfs to data frame
covsToDF <- function(covs, name, obsNum, numSites){
if(is.null(covs)) return(covs)
if(inherits(covs, "data.frame")){
if(nrow(covs) != (obsNum * numSites)){
stop("Incorrect number of rows in ", name, " data frame", call.=FALSE)
}
return(covs)
}
if(is.null(names(covs)) | any(is.na(names(covs))) | any(names(covs)=="")){
stop("All elements of list provided to ", name, " argument must be named", call.=FALSE)
}
lapply(covs, function(x){
if(!inherits(x, c("matrix", "data.frame")))
stop(paste("At least one element of", name, "is not a matrix or data frame."))
if(ncol(x) != obsNum | nrow(x) != numSites)
stop(paste("At least one element of", name, "has incorrect number of dimensions."))
})
data.frame(lapply(covs, function(x) as.vector(t(x))))
}
# Constructor for unmarkedFrames.
unmarkedFrame <- function(y, siteCovs = NULL, obsCovs = NULL, mapInfo,
obsToY) {
if(!missing(obsToY)){
obsNum <- nrow(obsToY)
} else {
obsNum <- ncol(y)
}
if(is.null(obsNum) & inherits(obsCovs, "list"))
obsNum <- ncol(obsCovs[[1]]) #??
obsCovs <- covsToDF(obsCovs, "obsCovs", obsNum, nrow(y))
if(inherits(y, c("data.frame", "cast_matrix")))
y <- as.matrix(y)
if(missing(obsToY)) obsToY <- NULL
if(missing(mapInfo)) mapInfo <- NULL
umf <- new("unmarkedFrame", y = y, obsCovs = obsCovs, siteCovs = siteCovs,
mapInfo = mapInfo, obsToY = obsToY)
umf <- umf_to_factor(umf)
return(umf)
}
unmarkedFrameDS <- function(y, siteCovs = NULL, dist.breaks, tlength,
survey, unitsIn, mapInfo = NULL)
{
if(missing(survey))
stop("survey argument must be specified")
if(missing(tlength) & survey == "point")
tlength <- rep(NA_real_, nrow(y))
if((survey=="line") & (length(tlength) != nrow(y)))
stop("tlength should be a vector with length(tlength)==nrow(y)")
if(length(dist.breaks) != ncol(y)+1){
stop(paste("dist.breaks should have",ncol(y)+1,"values"))
}
umfds <- new("unmarkedFrameDS", y = y, obsCovs = NULL,
siteCovs = siteCovs, dist.breaks = dist.breaks,
tlength = tlength, survey = survey, unitsIn = unitsIn,
obsToY = matrix(1, 1, ncol(y)))
umfds <- umf_to_factor(umfds)
return(umfds)
}
unmarkedFrameOccu <- function(y, siteCovs = NULL, obsCovs = NULL, mapInfo)
{
J <- ncol(y)
umf <- unmarkedFrame(y, siteCovs, obsCovs, obsToY = diag(J),
mapInfo = mapInfo)
umf <- as(umf, "unmarkedFrameOccu")
umf
}
unmarkedFrameOccuFP <- function(y, siteCovs = NULL, obsCovs = NULL, type, mapInfo)
{
J <- ncol(y)
umf <- unmarkedFrame(y, siteCovs, obsCovs, obsToY = diag(J),
mapInfo = mapInfo)
umf <- as(umf, "unmarkedFrameOccuFP")
umf@type <- type
umf
}
unmarkedFrameOccuMulti <- function(y, siteCovs = NULL, obsCovs = NULL,
maxOrder, mapInfo = NULL)
{
ylist <- y
#Fix non-matching missing observations in ylist
na_list <- lapply(ylist, function(x) is.na(x))
sum_na <- sapply(na_list, sum)
if(any(sum_na[1] != sum_na)){
warning("Missing obs do not match among species. Converting some obs to NAs so they match.")
}
any_na <- Reduce(function(x,y) x|y, na_list)
ylist <- lapply(ylist, function(x){
x[any_na] <- NA
x})
y <- ylist[[1]]
J <- ncol(y)
if(is.null(names(ylist)))
names(ylist) <- paste('sp',1:length(ylist),sep='')
obsCovs <- covsToDF(obsCovs, "obsCovs", J, nrow(y))
#f design matrix guide
S <- length(ylist)
z <- expand.grid(rep(list(1:0),S))[,S:1]
colnames(z) <- names(ylist)
if(missing(maxOrder)) maxOrder <- S
if(maxOrder == 1){
fDesign <- as.matrix(z)
} else {
fDesign <- model.matrix(as.formula(paste0("~.^",maxOrder,"-1")),z)
}
attr(fDesign,'assign') <- NULL
zinds <- apply(z,1,function(x) paste(x,collapse=''))
rownames(fDesign) <- paste('psi[',zinds,']',sep='')
colnames(fDesign) <- paste('f',1:ncol(fDesign),'[',
colnames(fDesign),']',sep='')
umfmo <- new("unmarkedFrameOccuMulti", y=y, ylist = ylist, fDesign=fDesign,
obsCovs = obsCovs, siteCovs = siteCovs, obsToY = diag(J))
umfmo <- umf_to_factor(umfmo)
return(umfmo)
}
unmarkedFramePCount <- function(y, siteCovs = NULL, obsCovs = NULL, mapInfo)
{
J <- ncol(y)
umf <- unmarkedFrame(y, siteCovs, obsCovs, obsToY = diag(J),
mapInfo = mapInfo)
umf <- as(umf, "unmarkedFramePCount")
umf
}
unmarkedFrameMPois <- function(y, siteCovs = NULL, obsCovs = NULL, type,
obsToY, mapInfo, piFun)
{
if(!missing(type)) {
switch(type,
removal = {
obsToY <- matrix(1, ncol(y), ncol(y))
obsToY[col(obsToY) < row(obsToY)] <- 0
#obsToY <- diag(ncol(y))
#obsToY[upper.tri(obsToY)] <- 1
piFun <- "removalPiFun"
},
double = {
#obsToY <- matrix(c(1, 0, 0, 1, 1, 1), 2, 3)
obsToY <- matrix(1, 2, 3)
piFun <- "doublePiFun"
},
depDouble = {
obsToY <- matrix(1, 2, 2)
piFun <- "depDoublePiFun"
if(ncol(y) != 2){
stop("y must have exactly 2 columns when type = 'depDouble'",
call.=FALSE)
}
})
} else {
if(missing(obsToY))
stop("obsToY is required for multinomial-Poisson data with no specified type.")
type <- "userDefined"
}
umf <- unmarkedFrame(y, siteCovs, obsCovs, obsToY = obsToY,
mapInfo = mapInfo)
umf <- as(umf, "unmarkedFrameMPois")
umf@piFun <- piFun
umf@samplingMethod <- type
umf
}
# This function constructs an unmarkedMultFrame object.
unmarkedMultFrame <- function(y, siteCovs = NULL, obsCovs = NULL,
numPrimary, yearlySiteCovs = NULL)
{
J <- ncol(y)
umf <- unmarkedFrame(y, siteCovs, obsCovs, obsToY = diag(J))
umf <- as(umf, "unmarkedMultFrame")
if(ncol(umf@y) %% numPrimary != 0){
stop("Unequal number of secondary periods in each primary period", call.=FALSE)
}
umf@numPrimary <- numPrimary
umf@yearlySiteCovs <- covsToDF(yearlySiteCovs, "yearlySiteCovs",
numPrimary, nrow(y))
umf <- umf_to_factor(umf)
umf
}
# Construct a unmarkedFrameOccuMS object (multistate occupancy)
unmarkedFrameOccuMS <- function(y, siteCovs = NULL, obsCovs = NULL,
numPrimary = 1, yearlySiteCovs = NULL)
{
umf <- unmarkedMultFrame(y, siteCovs, obsCovs, numPrimary, yearlySiteCovs)
umf <- as(umf, "unmarkedFrameOccuMS")
umf@numStates <- max(y,na.rm=T) + 1
if(umf@numStates<3){
stop("<3 occupancy states detected. Use occu() or colext() instead.")
}
#Create guide for phi formula order
S <- umf@numStates
#Multinomial
vals <- paste0('phi[',rep(0:(S-1),each=S),'->',rep(0:(S-1),S),']')
vals <- matrix(vals,nrow=S)
diag(vals) <- NA
phi_mult <- c(na.omit(as.vector(vals)))
#Cond binom
phi_cb <- c(paste0('phi[',0:(S-1),']'),paste0('R[',0:(S-1),']'))
umf@phiOrder <- list(multinomial=phi_mult,cond_binom=phi_cb)
umf
}
#Construct a unmarkedFrameOccuTTD object (time-to-detection occupancy)
unmarkedFrameOccuTTD <- function(y, surveyLength, siteCovs = NULL, obsCovs = NULL,
numPrimary = 1, yearlySiteCovs = NULL)
{
#Convert vector y to 1 col matrix
if(is.null(dim(y))) y <- matrix(y, ncol=1)
#Check if surveyLength input is correct
if(length(surveyLength)>1 & is.null(dim(surveyLength))){
surveyLength <- matrix(surveyLength, ncol=1)
}
if(length(surveyLength)==1){
surveyLength <- matrix(surveyLength, nrow=nrow(y), ncol=ncol(y))
} else if(!identical(dim(surveyLength), dim(y))){
stop("surveyLength must be a single value or have same dimensions as y",
call. = FALSE)
}
#Check if numPrimary makes sense
if((ncol(y) %% numPrimary) != 0){
stop(paste("Uneven number of secondary periods in each primary period.",
"You can pad with columns of NAs if necessary."),call.=FALSE)
}
#Build umf
umf <- unmarkedMultFrame(y, siteCovs, obsCovs, numPrimary, yearlySiteCovs)
umf <- as(umf, "unmarkedFrameOccuTTD")
umf@surveyLength <- surveyLength
umf
}
# This function constructs an unmarkedMultFrame object.
unmarkedFrameGMM <- function(y, siteCovs = NULL, obsCovs = NULL, numPrimary,
yearlySiteCovs = NULL, type, obsToY, piFun)
{
J <- ncol(y) / numPrimary
if(!missing(type)) {
if(!type %in% c("removal", "double", "depDouble"))
stop("if specifying type, it should either be 'removal', 'double', or 'depDouble'")
switch(type,
removal = {
obsToY <- diag(J)
obsToY[upper.tri(obsToY)] <- 1
obsToY <- kronecker(diag(numPrimary), obsToY)
piFun <- "removalPiFun"
},
double = {
obsToY <- matrix(1, 2, 3)
obsToY <- kronecker(diag(numPrimary), obsToY)
piFun <- "doublePiFun"
},
depDouble = {
if(J!=2){
stop("y must have exactly 2 columns per primary period", call.=FALSE)
}
obsToY <- matrix(1, 2, 2)
obsToY <- kronecker(diag(numPrimary), obsToY)
piFun <- "depDoublePiFun"
})
} else {
### 2/4/2019 ... cat("this is a test message",fill=TRUE)
type <- "userDefined"
# ncol(obsToY) should be ncol(y) (numPrimary*J)
if(missing(obsToY))
stop("obsToY is required for gmultmix data with no specified type.")
if(ncol(obsToY) == J){
obsToY <- kronecker(diag(numPrimary), obsToY)
}
if(ncol(obsToY) == ncol(y)){
# this is a good situation
}
if(ncol(obsToY) != ncol(y) & ncol(obsToY) != J){
stop("obsToY wrong dimension.")
}
}
umf <- unmarkedFrame(y, siteCovs, obsCovs, obsToY = obsToY)
umf <- as(umf, "unmarkedMultFrame")
umf@numPrimary <- numPrimary
umf@yearlySiteCovs <- covsToDF(yearlySiteCovs, "yearlySiteCovs",
numPrimary, nrow(y))
umf <- as(umf, "unmarkedFrameGMM")
umf@piFun <- piFun
umf@samplingMethod <- type
umf <- umf_to_factor(umf)
umf
}
# This function constructs an unmarkedMultFrame object.
unmarkedFrameDSO <- function(y, siteCovs=NULL, yearlySiteCovs=NULL, numPrimary,
primaryPeriod, dist.breaks, tlength, survey,
unitsIn)
{
J <- ncol(y) / numPrimary
obsToY <- matrix(1, 1, J)
obsToY <- kronecker(diag(numPrimary), obsToY)
if(missing(siteCovs))
siteCovs <- NULL
M <- nrow(y)
T <- numPrimary
if(missing(primaryPeriod))
primaryPeriod <- matrix(1:T, M, T, byrow=TRUE)
if(nrow(primaryPeriod) != M | ncol(primaryPeriod) != T)
stop("Dimensions of primaryPeriod matrix should be MxT")
if(any(primaryPeriod < 0, na.rm=TRUE))
stop("Negative primaryPeriod values are not allowed.")
if(any(is.na(primaryPeriod)))
stop("Missing values are not allowed in primaryPeriod.")
if(!identical(typeof(primaryPeriod), "integer")) {
mode(primaryPeriod) <- "integer"
warning("primaryPeriod values have been converted to integers")
}
#######well fuck, not sure why this needs to be this way:
#obsToY = diag(J*T)
### This is from unmarkedFramePCO
umf <- unmarkedFrame(y = y, siteCovs = siteCovs, obsToY = obsToY)
umf <- as(umf, "unmarkedMultFrame")
umf@numPrimary <- numPrimary
if(inherits(yearlySiteCovs, "list")) {
yearlySiteVars <- names(yearlySiteCovs)
for(i in seq(length(yearlySiteVars))) {
if(!inherits(yearlySiteCovs[[i]], c("matrix","data.frame")))
stop("At least one element of yearlySiteCovs is not a matrix or data frame.")
if(ncol(yearlySiteCovs[[i]]) != numPrimary |
nrow(yearlySiteCovs[[i]]) != nrow(y))
stop("At least one matrix in yearlySiteCovs has incorrect number of dimensions.")
}
yearlySiteCovs <- data.frame(lapply(yearlySiteCovs, function(x)
as.vector(t(x))))
}
if(identical(survey, "point")) {
if(!missing(tlength))
stop("tlength cannot be specified with point transect data")
tlength <- rep(1, nrow(y))
}
if(identical(survey, "line")) {
if(length(tlength) != nrow(y)) {
stop("tlength should be a vector with length(tlength)==nrow(y)")
}
}
if(length(dist.breaks) != J+1){
stop(paste("dist.breaks should have",J+1,"values"))
}
umf@yearlySiteCovs <- yearlySiteCovs
umf <- as(umf, "unmarkedFrameDSO")
umf@dist.breaks <- dist.breaks
umf@survey <- survey
umf@unitsIn <- unitsIn
umf@tlength <- tlength
umf@primaryPeriod <- primaryPeriod
umf <- umf_to_factor(umf)
umf
}
unmarkedFrameGDS<- function(y, siteCovs, numPrimary,
yearlySiteCovs, dist.breaks, survey, unitsIn, tlength)
{
J <- ncol(y) / numPrimary
obsToY <- matrix(1, 1, J)
obsToY <- kronecker(diag(numPrimary), obsToY)
if(missing(siteCovs))
siteCovs <- NULL
umf <- unmarkedFrame(y = y, siteCovs = siteCovs, obsToY = obsToY)
umf <- as(umf, "unmarkedMultFrame")
umf@numPrimary <- numPrimary
if(missing(yearlySiteCovs))
yearlySiteCovs <- NULL
umf@yearlySiteCovs <- covsToDF(yearlySiteCovs, "yearlySiteCovs",
numPrimary, nrow(y))
if(identical(survey, "point")) {
if(!missing(tlength))
stop("tlength cannot be specified with point transect data")
tlength <- rep(1, nrow(y))
}
if(identical(survey, "line")) {
if(length(tlength) != nrow(y)) {
stop("tlength should be a vector with length(tlength)==nrow(y)")
}
}
if(length(dist.breaks) != J+1){
stop(paste("dist.breaks should have",J+1,"values"))
}
umf <- as(umf, "unmarkedFrameGDS")
umf@dist.breaks <- dist.breaks
umf@survey <- survey
umf@unitsIn <- unitsIn
umf@tlength <- tlength
umf <- umf_to_factor(umf)
umf
}
# This function constructs an object.
unmarkedFrameGPC <- function(y, siteCovs=NULL, obsCovs=NULL, numPrimary,
yearlySiteCovs=NULL) {
if(numPrimary < 2)
stop("numPrimary must be >1. Use pcount of numPrimary=1")
J <- ncol(y) / numPrimary
obsToY <- diag(J*numPrimary)
if(missing(siteCovs))
siteCovs <- NULL
umf <- unmarkedFrame(y = y, siteCovs = siteCovs, obsCovs = obsCovs,
obsToY = obsToY)
umf <- as(umf, "unmarkedMultFrame")
umf@numPrimary <- numPrimary
if(missing(yearlySiteCovs))
yearlySiteCovs <- NULL
umf@yearlySiteCovs <- covsToDF(yearlySiteCovs, "yearlySiteCovs",
numPrimary, nrow(y))
umf <- as(umf, "unmarkedFrameGPC")
umf <- umf_to_factor(umf)
umf
}
unmarkedFramePCO <- function(y, siteCovs = NULL, obsCovs = NULL,
yearlySiteCovs = NULL, mapInfo, numPrimary, primaryPeriod)
{
M <- nrow(y)
T <- numPrimary
J <- ncol(y) / T
if(missing(primaryPeriod))
primaryPeriod <- matrix(1:T, M, T, byrow=TRUE)
if(nrow(primaryPeriod) != M | ncol(primaryPeriod) != T)
stop("Dimensions of primaryPeriod matrix should be MxT")
if(any(primaryPeriod < 0, na.rm=TRUE))
stop("Negative primaryPeriod values are not allowed.")
if(any(is.na(primaryPeriod)))
stop("Missing values are not allowed in primaryPeriod.")
if(!identical(typeof(primaryPeriod), "integer")) {
mode(primaryPeriod) <- "integer"
warning("primaryPeriod values have been converted to integers")
}
ya <- array(y, c(M, J, T))
yt.na <- apply(!is.na(ya), c(1,3), any)
yt.na <- which(!yt.na)
d.na <- which(is.na(primaryPeriod))
if(!all(d.na %in% yt.na))
stop("primaryPeriod values must be supplied for all non-missing values of y")
increasing <- function(x) {
x <- x[!is.na(x)]
all(order(x) == 1:length(x))
}
if(!all(apply(primaryPeriod, 1, increasing)))
stop("primaryPeriod values must increase over time for each site")
obsCovs <- covsToDF(obsCovs, "obsCovs", J*T, M)
umf <- unmarkedFrame(y, siteCovs, obsCovs, obsToY = diag(J*T))
umf <- as(umf, "unmarkedMultFrame")
umf@numPrimary <- numPrimary
umf@yearlySiteCovs <- covsToDF(yearlySiteCovs, "yearlySiteCovs",
numPrimary, nrow(y))
umf <- as(umf, "unmarkedFramePCO")
umf@primaryPeriod <- primaryPeriod
# There is no obsToY function
umf <- umf_to_factor(umf)
return(umf)
}
unmarkedFrameMMO <- function(y, siteCovs = NULL, obsCovs = NULL,
yearlySiteCovs = NULL, numPrimary, type, primaryPeriod)
{
M <- nrow(y)
T <- numPrimary
J <- ncol(y) / T
if(missing(primaryPeriod))
primaryPeriod <- matrix(1:T, M, T, byrow=TRUE)
if(nrow(primaryPeriod) != M | ncol(primaryPeriod) != T)
stop("Dimensions of primaryPeriod matrix should be MxT")
if(any(primaryPeriod < 0, na.rm=TRUE))
stop("Negative primaryPeriod values are not allowed.")
if(any(is.na(primaryPeriod)))
stop("Missing values are not allowed in primaryPeriod.")
if(!identical(typeof(primaryPeriod), "integer")) {
mode(primaryPeriod) <- "integer"
warning("primaryPeriod values have been converted to integers")
}
ya <- array(y, c(M, J, T))
yt.na <- apply(!is.na(ya), c(1,3), any)
yt.na <- which(!yt.na)
d.na <- which(is.na(primaryPeriod))
if(!all(d.na %in% yt.na))
stop("primaryPeriod values must be supplied for all non-missing values of y")
increasing <- function(x) {
x <- x[!is.na(x)]
all(order(x) == 1:length(x))
}
if(!all(apply(primaryPeriod, 1, increasing)))
stop("primaryPeriod values must increase over time for each site")
umf <- unmarkedFrameGMM(y, siteCovs, obsCovs, numPrimary, yearlySiteCovs,
type)
umf <- as(umf, "unmarkedFrameMMO")
umf@primaryPeriod <- primaryPeriod
umf
}
################ SHOW METHODS ############################################
setMethod("show", "unmarkedFrame", function(object)
{
df <- as(object, "data.frame")
cat("Data frame representation of unmarkedFrame object.\n")
print(df)
})
setMethod("show", "unmarkedMultFrame",
function(object)
{
df <- as(object, "data.frame")
cat("Data frame representation of unmarkedFrame object.\n")
print(df)
})
setMethod("show", "unmarkedFrameOccuMulti", function(object)
{
df <- as(object, "data.frame")
cat("Data frame representation of unmarkedFrame object.\n")
cat("Only showing observation matrix for species 1.\n")
print(df)
})
setMethod("show", "unmarkedFrameOccuTTD", function(object)
{
df <- as(object, "data.frame")
sl <- object@surveyLength
if(ncol(sl)>1){
colnames(sl) <- paste0('surveyLength',1:ncol(sl))
} else {
colnames(sl) <- 'surveyLength'
}
df <- cbind(df, sl)
cat("Data frame representation of unmarkedFrame object.\n")
print(df)
})
############################ EXTRACTORS ##################################
# Extractor for site level covariates
setGeneric("siteCovs", function(object,...) standardGeneric("siteCovs"))
setMethod("siteCovs", "unmarkedFrame", function(object) {
return(object@siteCovs)
})
setGeneric("yearlySiteCovs", function(object,...)
standardGeneric("yearlySiteCovs"))
setMethod("yearlySiteCovs", "unmarkedMultFrame", function(object) {
return(object@yearlySiteCovs)
})
setGeneric("obsCovs", function(object,...) standardGeneric("obsCovs"))
setMethod("obsCovs", "unmarkedFrame", function(object, matrices = FALSE) {
M <- numSites(object)
R <- obsNum(object)
if(matrices) {
value <- list()
for(i in seq(length=length(object@obsCovs))){
value[[i]] <- matrix(object@obsCovs[,i], M, R, byrow = TRUE)
}
names(value) <- names(object@obsCovs)
} else {
value <- object@obsCovs
}
return(value)
})
setGeneric("obsNum", function(object) standardGeneric("obsNum"))
setMethod("obsNum", "unmarkedFrame", function(object) nrow(object@obsToY))
setGeneric("numSites", function(object) standardGeneric("numSites"))
setMethod("numSites", "unmarkedFrame", function(object) nrow(object@y))
setGeneric("numY", function(object) standardGeneric("numY"))
setMethod("numY", "unmarkedFrame", function(object) ncol(object@y))
setGeneric("obsToY", function(object) standardGeneric("obsToY"))
setMethod("obsToY", "unmarkedFrame", function(object) object@obsToY)
setGeneric("obsCovs<-", function(object, value)
standardGeneric("obsCovs<-"))
setReplaceMethod("obsCovs", "unmarkedFrame", function(object, value) {
if(inherits(object, "unmarkedFrameDS"))
stop("unmarkedFrameDS objects cannot have obsCovs")
object@obsCovs <- as.data.frame(value)
object
})
setGeneric("siteCovs<-", function(object, value)
standardGeneric("siteCovs<-"))
setReplaceMethod("siteCovs", "unmarkedFrame", function(object, value) {
object@siteCovs <- as.data.frame(value)
object
})
setGeneric("yearlySiteCovs<-",
function(object, value) standardGeneric("yearlySiteCovs<-"))
setReplaceMethod("yearlySiteCovs", "unmarkedMultFrame",
function(object, value) {
object@yearlySiteCovs <- as.data.frame(value)
object
})
setGeneric("obsToY<-", function(object, value) standardGeneric("obsToY<-"))
setReplaceMethod("obsToY", "unmarkedFrame", function(object, value) {
object@obsToY <- value
object
})
setGeneric("getY", function(object) standardGeneric("getY"))
setMethod("getY", "unmarkedFrame", function(object) object@y)
setGeneric("coordinates", function(object) standardGeneric("coordinates"))
setMethod("coordinates", "unmarkedFrame", function(object) {
object@mapInfo@coordinates
})
setGeneric("projection", function(object) standardGeneric("projection"))
setMethod("projection", "unmarkedFrame", function(object) {
object@mapInfo@projection
})
################################### SUMMARY METHODS ######################
setMethod("summary", "unmarkedFrame", function(object,...) {
cat("unmarkedFrame Object\n\n")
cat(nrow(object@y), "sites\n")
cat("Maximum number of observations per site:",obsNum(object),"\n")
mean.obs <- mean(rowSums(!is.na(getY(object))))
cat("Mean number of observations per site:",round(mean.obs,2),"\n")
cat("Sites with at least one detection:",
sum(apply(getY(object), 1, function(x) any(x > 0, na.rm=TRUE))),
"\n\n")
cat("Tabulation of y observations:")
print(table(object@y, exclude=NULL))
if(!is.null(object@siteCovs)) {
cat("\nSite-level covariates:\n")
print(summary(object@siteCovs))
}
if(!is.null(object@obsCovs)) {
cat("\nObservation-level covariates:\n")
print(summary(object@obsCovs))
}
})
setMethod("summary", "unmarkedFrameDS", function(object, ...)
{
cat("unmarkedFrameDS Object\n\n")
cat(object@survey, "-transect survey design", "\n", sep="")
cat(paste("Distance class cutpoints (", object@unitsIn, "): ", sep=""),
object@dist.breaks, "\n\n")
cat(nrow(object@y), "sites\n")
cat("Maximum number of distance classes per site:", ncol(getY(object)), "\n")
mean.dc <- mean(rowSums(!is.na(getY(object))))
cat("Mean number of distance classes per site:", round(mean.dc, 2), "\n")
cat("Sites with at least one detection:",
sum(apply(getY(object), 1, function(x) any(x > 0, na.rm=TRUE))), "\n\n")
cat("Tabulation of y observations:")
print(table(object@y, exclude=NULL))
if(!is.null(object@siteCovs)) {
cat("\nSite-level covariates:\n")
print(summary(object@siteCovs))
}
if(!is.null(object@obsCovs)) {
warning("Observation-level covariates cannot be used by distsamp()")
}
})
setMethod("summary", "unmarkedMultFrame", function(object,...) {
cat("unmarkedFrame Object\n\n")
cat(nrow(object@y), "sites\n")
cat("Maximum number of observations per site:",ncol(object@y),"\n")
mean.obs <- mean(rowSums(!is.na(getY(object))))
cat("Mean number of observations per site:",round(mean.obs,2),"\n")
cat("Number of primary survey periods:", object@numPrimary, "\n")
cat("Number of secondary survey periods:",
obsNum(object) / object@numPrimary, "\n")
cat("Sites with at least one detection:",
sum(apply(getY(object), 1, function(x) any(x > 0, na.rm=TRUE))),
"\n\n")
cat("Tabulation of y observations:")
print(table(object@y, exclude=NULL))
if(!is.null(object@siteCovs)) {
cat("\nSite-level covariates:\n")
print(summary(object@siteCovs))
}
if(!is.null(object@obsCovs)) {
cat("\nObservation-level covariates:\n")
print(summary(object@obsCovs))
}
if(!is.null(object@yearlySiteCovs)) {
cat("\nYearly-site-level covariates:\n")
print(summary(object@yearlySiteCovs))
}
})
setMethod("summary", "unmarkedFrameOccuMulti", function(object,...) {
cat("unmarkedFrame Object\n\n")
cat(nrow(object@y), "sites\n")
cat(length(object@ylist), "species:", names(object@ylist),"\n")
cat("Maximum number of observations per site:",obsNum(object),"\n")
mean.obs <- sapply(object@ylist,function(x) mean(rowSums(!is.na(x))))
cat("Mean number of observations per site:\n")
invisible(sapply(1:length(mean.obs), function(x)
cat(paste(names(mean.obs)[x],': ',mean.obs[x],' ',sep='')))); cat("\n")
s.one <- sapply(object@ylist,function(x) sum(rowSums(x,na.rm=T)>0))
cat("Sites with at least one detection:\n")
invisible(sapply(1:length(s.one), function(x)