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Fixed bug in schnabel CI result in mrClosed()
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@droglenc
droglenc committed May 3, 2018
1 parent b6bf6d7 commit 61b4814
Showing 1 changed file with 38 additions and 18 deletions.
56 changes: 38 additions & 18 deletions R/mrClosed.R
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Original file line number Diff line number Diff line change
Expand Up @@ -182,13 +182,15 @@
#' @rdname mrClosed
#' @export
mrClosed <- function(M=NULL,n=NULL,m=NULL,R=NULL,
method=c("Petersen","Chapman","Ricker","Bailey","Schnabel","SchumacherEschmeyer"),
method=c("Petersen","Chapman","Ricker","Bailey",
"Schnabel","SchumacherEschmeyer"),
labels=NULL,chapman.mod=TRUE) {
method <- match.arg(method)
if (method %in% c("Petersen","Chapman","Ricker","Bailey")) {
if (!is.null(R)) {
## R not in single methods. If nothing else, throw error
if (is.null(c(M,n,m))) STOP("'R' not used in single census methods;\n must supply 'M', 'n', and 'm'.")
if (is.null(c(M,n,m)))
STOP("'R' not used in single census methods;\n must supply 'M', 'n', and 'm'.")
## Otherwise warn that it will be ignored
WARN("'R' not used in single census methods and will be ignored.")
}
Expand All @@ -206,26 +208,30 @@ iMRCSingle <- function(M,n,m,method,labels) {
# initial checks
if (is.null(M)) STOP("'M' is missing; must be from 'capHistSum()' or value(s).")
if (is.CapHist(M)) {
if (!is.null(m) | !is.null(n)) WARN("'m' and 'n' ignored when 'M' from capHistSum().")
if (!is.null(m) | !is.null(n))
WARN("'m' and 'n' ignored when 'M' from capHistSum().")
m <- M$sum$m
n <- M$sum$n
M <- M$sum$M
} else {
if (is.null(n) | is.null(m)) STOP("One or both of 'n' or 'm' is missing without 'M' from capHistSum().")
if (is.null(n) | is.null(m))
STOP("One or both of 'n' or 'm' is missing without 'M' from capHistSum().")
# Make sure that the vectors are of the same size
lengths <- c(length(M),length(n),length(m))
if (any(diff(lengths)!=0)) STOP("'M', 'n', or 'm' vectors must be same length.")
}
# Make sure that recapture number makes sense relative to sample size
if (any((n-m)<0)) {
if (length(n)==1) STOP("Can't have more recaptures (m) then total individuals (n).")
else STOP("Row ",which((n-m)<0)," has more recaptures (m) then total individuals (n).")
else STOP("Row ",which((n-m)<0),
" has more recaptures (m) then total individuals (n).")
}
# If no labels then assign letters, if labels then make sure size is correct
if (is.null(labels)) {
if (length(M)>1) labels <- LETTERS[seq_along(M)]
} else {
if (length(M) != length(labels)) STOP("'labels' must be same length as 'M', 'n', and 'm'.")
if (length(M) != length(labels))
STOP("'labels' must be same length as 'M', 'n', and 'm'.")
}
# handle modifications for simplicity of calculation below
switch(method,
Expand All @@ -250,15 +256,17 @@ iMRCSingle <- function(M,n,m,method,labels) {
#===========================================================================
#' @rdname mrClosed
#' @export
summary.mrClosed1 <- function(object,digits=0,incl.SE=FALSE,incl.all=TRUE,verbose=FALSE,...) {
summary.mrClosed1 <- function(object,digits=0,incl.SE=FALSE,
incl.all=TRUE,verbose=FALSE,...) {
# Put descriptive label of input values at top of output if the user asked for it.
if(verbose) {
if (is.null(object$labels)) message("Used ",object$methodLbl," with M=",
object$M,", n=",object$n,
", and m=",object$m,".\n")
else {
message("Used ",object$methodLbl," with observed inputs (by group) of:")
tmp <- paste0(" ",object$labels,": M=",object$M,", n=",object$n,", and m=",object$m)
tmp <- paste0(" ",object$labels,": M=",object$M,", n=",object$n,
", and m=",object$m)
for (i in tmp) message(i)
}
}
Expand Down Expand Up @@ -311,8 +319,10 @@ iMRCSingleVar <- function(object) {
#===========================================================================
#' @rdname mrClosed
#' @export
confint.mrClosed1 <- function(object,parm=NULL,level=conf.level,conf.level=0.95,digits=0,
type=c("suggested","binomial","hypergeometric","normal","Poisson"),
confint.mrClosed1 <- function(object,parm=NULL,level=conf.level,conf.level=0.95,
digits=0,
type=c("suggested","binomial","hypergeometric",
"normal","Poisson"),
bin.type=c("wilson","exact","asymptotic"),
poi.type=c("exact","daly","byar","asymptotic"),
incl.all=TRUE,verbose=FALSE,...) {
Expand Down Expand Up @@ -443,13 +453,15 @@ iMRCMultiple <- function(M,n,m,R,method,chapman.mod) {
} else {
## Results not from capHistSum and values of M provided.
# check if M is a vector
if (!is.vector(M)) STOP("If given, 'M' must be a vector or from 'capHistSum()`.")
if (!is.vector(M))
STOP("If given, 'M' must be a vector or from 'capHistSum()`.")
# check if M has an NA in first position
if (is.na(M[1])) {
WARN("NA for first sample of 'M' was ignored.")
M[1] <- 0
}
if (is.null(n) | is.null(m)) STOP("One or both of 'n' or 'm' is missing without 'M' from capHistSum().")
if (is.null(n) | is.null(m))
STOP("One or both of 'n' or 'm' is missing without 'M' from capHistSum().")
else if (!is.null(R)) WARN("Only need one of 'M' or 'R'. 'R' is ignored.")
R <- n
R[length(R)] <- 0
Expand Down Expand Up @@ -505,7 +517,8 @@ summary.mrClosed2 <- function(object,digits=0,verbose=FALSE,...) {
# Put descriptive label of input values at top of output if the user asked for it.
if(verbose) {
msg <- paste0("Used ",object$methodLbl)
ifelse(object$chapman.mod,msg <- paste(msg,"with Chapman modification.\n"),msg <- paste0(msg,".\n"))
ifelse(object$chapman.mod,msg <- paste(msg,"with Chapman modification.\n"),
msg <- paste0(msg,".\n"))
message(msg)
}
# Put the PE into a matrix to return
Expand All @@ -519,12 +532,15 @@ summary.mrClosed2 <- function(object,digits=0,verbose=FALSE,...) {
#===========================================================================
#' @rdname mrClosed
#' @export
confint.mrClosed2 <- function(object,parm=NULL,level=conf.level,conf.level=0.95,digits=0,
confint.mrClosed2 <- function(object,parm=NULL,level=conf.level,conf.level=0.95,
digits=0,
type=c("suggested","normal","Poisson"),
poi.type=c("exact","daly","byar","asymptotic"),
verbose=FALSE,...) {
# Initial Checks
type <- match.arg(type)
## This is needed so that only one poisson type is used
poi.type <- match.arg(poi.type)
parm <- iCI.CheckParm(parm)
if (conf.level<=0 | conf.level>=1) STOP("'conf.level' must be between 0 and 1")
# Construct the confidence intervals
Expand All @@ -534,7 +550,8 @@ confint.mrClosed2 <- function(object,parm=NULL,level=conf.level,conf.level=0.95,
ci <- iCI2.MRCSchnabel(object,conf.level,type,poi.type,verbose,...)
},
SchumacherEschmeyer= {
if (type=="Poisson") WARN("'type' changed to 'normal' for Schumacher-Eschmeyer method.")
if (type=="Poisson")
WARN("'type' changed to 'normal' for Schumacher-Eschmeyer method.")
type <- "normal"
ci <- iCI2.MRCSchumacher(object,conf.level,type,verbose,...)
}
Expand Down Expand Up @@ -576,7 +593,8 @@ iCI2.MRCSchnabel <- function(object,conf.level,type,poi.type,...) {
# Change if chapman modification was used
ifelse(object$chapman.mod,N.poi <- object$sum.nM/(ci1+1),
N.poi <- object$sum.nM/ci1)
ci <- rbind(N.poi[2:1])
# CIs come out backwards so switch them
ci <- rbind(N.poi[,2:1])
}
ci
}
Expand All @@ -602,8 +620,10 @@ plot.mrClosed2 <- function(x,pch=19,col.pt="black",
xlab="Marked in Population",
ylab="Prop. Recaptures in Sample",
loess=FALSE,lty.loess=2,lwd.loess=1,
col.loess="gray20",trans.loess=10,span=0.9,...) { # nocov start
col.loess="gray20",trans.loess=10,span=0.9,...) {
# nocov start
graphics::plot(x$M,x$m/x$n,pch=pch,col=col.pt,xlab=xlab,ylab=ylab,...)
# add loess line if asked for
if (loess) iAddLoessLine(x$m/x$n,x$M,lty.loess,lwd.loess,col.loess,trans.loess,span=span)
if (loess) iAddLoessLine(x$m/x$n,x$M,lty.loess,lwd.loess,col.loess,
trans.loess,span=span)
} # nocov end

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