Change from unmarkedFitCOP to unmarkedFitOccuCOP

9 files changed, 33 insertions, 33 deletions

diff --git a/R/occuCOP.R b/R/occuCOP.R
index 6879576..ec27b58 100644
--- a/R/occuCOP.R
+++ b/R/occuCOP.R
@@ -49,8 +49,8 @@ setClass(
   }
 )
 
-## unmarkedFitCOP class ----
-setClass("unmarkedFitCOP",
+## unmarkedFitOccuCOP class ----
+setClass("unmarkedFitOccuCOP",
          representation(removed_obs = "matrix",
                         formlist = "list"),
          contains = "unmarkedFit")
@@ -331,13 +331,13 @@ setMethod("[", c("unmarkedFrameOccuCOP", "missing", "numeric", "missing"),
 
 
 ## fl_getY ----
-setMethod("fl_getY", "unmarkedFitCOP", function(fit, ...){
+setMethod("fl_getY", "unmarkedFitOccuCOP", function(fit, ...){
   getDesign(getData(fit), fit@formlist)$y
 })
 
 
 ## predict_inputs_from_umf ----
-setMethod("predict_inputs_from_umf", "unmarkedFitCOP",
+setMethod("predict_inputs_from_umf", "unmarkedFitOccuCOP",
           function(object, type, newdata, na.rm, re.form = NULL) {
             designMats = getDesign(umf = newdata,
                                    formlist = object@formlist,
@@ -351,14 +351,14 @@ setMethod("predict_inputs_from_umf", "unmarkedFitCOP",
 
 
 ## get_formula ----
-setMethod("get_formula", "unmarkedFitCOP", function(object, type, ...) {
+setMethod("get_formula", "unmarkedFitOccuCOP", function(object, type, ...) {
   fl <- object@formlist
   switch(type, psi = fl$psiformula, lambda = fl$lambdaformula)
 })
 
 
 ## get_orig_data ----
-setMethod("get_orig_data", "unmarkedFitCOP", function(object, type, ...){
+setMethod("get_orig_data", "unmarkedFitOccuCOP", function(object, type, ...){
   clean_covs <- clean_up_covs(object@data, drop_final=FALSE)
   datatype <- switch(type, psi = 'site_covs', lambda = 'obs_covs')
   clean_covs[[datatype]]
@@ -366,7 +366,7 @@ setMethod("get_orig_data", "unmarkedFitCOP", function(object, type, ...){
 
 
 ## getP ----
-setMethod("getP", "unmarkedFitCOP", function(object) {
+setMethod("getP", "unmarkedFitOccuCOP", function(object) {
   data <- object@data
   M = nrow(getY(data))
   J = ncol(getY(data))
@@ -380,7 +380,7 @@ setMethod("getP", "unmarkedFitCOP", function(object) {
 
 
 ## fitted ----
-setMethod("fitted", "unmarkedFitCOP", function(object) {
+setMethod("fitted", "unmarkedFitOccuCOP", function(object) {
   data <- object@data
   M = nrow(getY(data))
   J = ncol(getY(data))
@@ -396,7 +396,7 @@ setMethod("fitted", "unmarkedFitCOP", function(object) {
 
 
 ## residuals ----
-setMethod("residuals", "unmarkedFitCOP", function(object) {
+setMethod("residuals", "unmarkedFitOccuCOP", function(object) {
   y <- getY(object@data)
   e <- fitted(object)
   r <- y - e
@@ -405,7 +405,7 @@ setMethod("residuals", "unmarkedFitCOP", function(object) {
 
 
 ## plot ----
-setMethod("plot", c(x = "unmarkedFitCOP", y = "missing"), function(x, y, ...) {
+setMethod("plot", c(x = "unmarkedFitOccuCOP", y = "missing"), function(x, y, ...) {
   y <- getY(x)
   r <- residuals(x)
   e <- fitted(x)
@@ -433,7 +433,7 @@ setMethod("plot", c(x = "unmarkedFitCOP", y = "missing"), function(x, y, ...) {
 
 
 ## get_umf_components ----
-setMethod("get_umf_components", "unmarkedFitCOP",
+setMethod("get_umf_components", "unmarkedFitOccuCOP",
   function(object, formulas, guide, design, ...){
     sc <- generate_data(formulas$psi, guide, design$M)
     oc <- generate_data(formulas$lambda, guide, design$J*design$M)
@@ -443,7 +443,7 @@ setMethod("get_umf_components", "unmarkedFitCOP",
 
 
 ## simulate_fit ----
-setMethod("simulate_fit", "unmarkedFitCOP",
+setMethod("simulate_fit", "unmarkedFitOccuCOP",
   function(object, formulas, guide, design, ...){
     # Generate covariates and create a y matrix of zeros
     parts <- get_umf_components(object, formulas, guide, design, ...)
@@ -462,7 +462,7 @@ setMethod("simulate_fit", "unmarkedFitCOP",
 
 
 ## simulate ----
-setMethod("simulate", "unmarkedFitCOP",
+setMethod("simulate", "unmarkedFitOccuCOP",
   function(object, nsim = 1, seed = NULL, na.rm = TRUE){
   # set.seed(seed) 
   # Purposefully not implemented
@@ -494,14 +494,14 @@ setMethod("simulate", "unmarkedFitCOP",
 
 
 ## nonparboot ----
-setMethod("nonparboot", "unmarkedFitCOP",
+setMethod("nonparboot", "unmarkedFitOccuCOP",
   function(object, B = 0, keepOldSamples = TRUE, ...) {
-  stop("Not currently supported for unmarkedFitCOP", call.=FALSE)
+  stop("Not currently supported for unmarkedFitOccuCOP", call.=FALSE)
 })
 
 
 ## ranef ----
-setMethod("ranef", "unmarkedFitCOP", function(object, ...) {
+setMethod("ranef", "unmarkedFitOccuCOP", function(object, ...) {
   # Sites removed (srm) and sites kept (sk)
   srm <- object@sitesRemoved
   if (length(srm) > 0) {
@@ -942,7 +942,7 @@ occuCOP <- function(data,
   
   # Create unmarkedFit object--------------------------------------------------
   umfit <- new(
-    "unmarkedFitCOP",
+    "unmarkedFitOccuCOP",
     fitType = "occuCOP",
     call = match.call(),
     formula = as.formula(paste(
diff --git a/man/fitted-methods.Rd b/man/fitted-methods.Rd
index 98e343b..7ef7ede 100644
--- a/man/fitted-methods.Rd
+++ b/man/fitted-methods.Rd
@@ -16,7 +16,7 @@
 \alias{fitted,unmarkedFitGDR-method}
 \alias{fitted,unmarkedFitDailMadsen-method}
 \alias{fitted,unmarkedFitGOccu-method}
-\alias{fitted,unmarkedFitCOP-method}
+\alias{fitted,unmarkedFitOccuCOP-method}
 \title{Methods for Function fitted in Package `unmarked'}
 \description{Extracted fitted values from a fitted model.
 }
diff --git a/man/getP-methods.Rd b/man/getP-methods.Rd
index ba26ee6..7a3b87e 100644
--- a/man/getP-methods.Rd
+++ b/man/getP-methods.Rd
@@ -18,7 +18,7 @@
 \alias{getP,unmarkedFitMMO-method}
 \alias{getP,unmarkedFitGDR-method}
 \alias{getP,unmarkedFitGOccu-method}
-\alias{getP,unmarkedFitCOP-method}
+\alias{getP,unmarkedFitOccuCOP-method}
 \title{Methods for Function getP in Package `unmarked'}
 \description{
 Methods for function \code{getP} in Package `unmarked'. These methods return a matrix of the back-transformed detection parameter (\eqn{p} the detection probability or \eqn{\lambda} the detection rate, depending on the model). The matrix is of dimension MxJ, with M the number of sites and J the number of sampling periods; or of dimension MxJT for models with multiple primary periods T.
@@ -29,6 +29,6 @@ Methods for function \code{getP} in Package `unmarked'. These methods return a m
 \item{\code{signature(object = "unmarkedFitDS")}}{A fitted model object}
 \item{\code{signature(object = "unmarkedFitMPois")}}{A fitted model object}
 \item{\code{signature(object = "unmarkedFitGMM")}}{A fitted model object}
-\item{\code{signature(object = "unmarkedFitCOP")}}{With \code{unmarkedFitCOP} the object of a model fitted with \code{occuCOP}. Returns a matrix of \eqn{\lambda} the detection rate.}
+\item{\code{signature(object = "unmarkedFitOccuCOP")}}{With \code{unmarkedFitOccuCOP} the object of a model fitted with \code{occuCOP}. Returns a matrix of \eqn{\lambda} the detection rate.}
 }}
 \keyword{methods}
diff --git a/man/nonparboot-methods.Rd b/man/nonparboot-methods.Rd
index 7dd2c54..40dd72f 100644
--- a/man/nonparboot-methods.Rd
+++ b/man/nonparboot-methods.Rd
@@ -18,7 +18,7 @@
 \alias{nonparboot,unmarkedFitNmixTTD-method}
 \alias{nonparboot,unmarkedFitGDR-method}
 \alias{nonparboot,unmarkedFitDailMadsen-method}
-\alias{nonparboot,unmarkedFitCOP-method}
+\alias{nonparboot,unmarkedFitOccuCOP-method}
 
 \title{ Nonparametric bootstrapping in unmarked }
 \description{
diff --git a/man/occuCOP.Rd b/man/occuCOP.Rd
index 1693b25..f0b5be0 100644
--- a/man/occuCOP.Rd
+++ b/man/occuCOP.Rd
@@ -91,7 +91,7 @@ occuCOP(data,
   
 }
 
-\value{\code{unmarkedFitCOP} object describing the model fit. See the \code{\linkS4class{unmarkedFit}} classes.}
+\value{\code{unmarkedFitOccuCOP} object describing the model fit. See the \code{\linkS4class{unmarkedFit}} classes.}
 
 \references{
 
diff --git a/man/ranef-methods.Rd b/man/ranef-methods.Rd
index d24ed2a..1eb0704 100644
--- a/man/ranef-methods.Rd
+++ b/man/ranef-methods.Rd
@@ -21,7 +21,7 @@
 \alias{ranef,unmarkedFitGDR-method}
 \alias{ranef,unmarkedFitDailMadsen-method}
 \alias{ranef,unmarkedFitGOccu-method}
-\alias{ranef,unmarkedFitCOP-method}
+\alias{ranef,unmarkedFitOccuCOP-method}
 \title{ Methods for Function \code{ranef} in Package \pkg{unmarked} }
 \description{
 Estimate posterior distributions of the random variables (latent
diff --git a/man/simulate-methods.Rd b/man/simulate-methods.Rd
index 2678812..21bd377 100644
--- a/man/simulate-methods.Rd
+++ b/man/simulate-methods.Rd
@@ -19,7 +19,7 @@
 \alias{simulate,unmarkedFitGDR-method}
 \alias{simulate,unmarkedFitDailMadsen-method}
 \alias{simulate,unmarkedFitGOccu-method}
-\alias{simulate,unmarkedFitCOP-method}
+\alias{simulate,unmarkedFitOccuCOP-method}
 \alias{simulate,character-method}
 \title{Methods for Function simulate in Package `unmarked'}
 \description{
diff --git a/man/unmarkedFit-class.Rd b/man/unmarkedFit-class.Rd
index f7da3b0..d8b1aea 100644
--- a/man/unmarkedFit-class.Rd
+++ b/man/unmarkedFit-class.Rd
@@ -18,7 +18,7 @@
 \alias{plot,unmarkedFit,missing-method}
 \alias{plot,unmarkedFitOccuMulti,missing-method}
 \alias{plot,unmarkedFitGDR,missing-method}
-\alias{plot,unmarkedFitCOP,missing-method}
+\alias{plot,unmarkedFitOccuCOP,missing-method}
 \alias{profile,unmarkedFit-method}
 \alias{residuals,unmarkedFit-method}
 \alias{residuals,unmarkedFitOccu-method}
@@ -27,7 +27,7 @@
 \alias{residuals,unmarkedFitOccuMulti-method}
 \alias{residuals,unmarkedFitOccuTTD-method}
 \alias{residuals,unmarkedFitGDR-method}
-\alias{residuals,unmarkedFitCOP-method}
+\alias{residuals,unmarkedFitOccuCOP-method}
 \alias{update,unmarkedFit-method}
 \alias{update,unmarkedFitColExt-method}
 \alias{update,unmarkedFitGMM-method}
diff --git a/tests/testthat/test_occuCOP.R b/tests/testthat/test_occuCOP.R
index 54445bb..ca880bd 100644
--- a/tests/testthat/test_occuCOP.R
+++ b/tests/testthat/test_occuCOP.R
@@ -236,7 +236,7 @@ test_that("occuCOP can fit simple models", {
   expect_error(occuCOP(data = umf, na.rm = "no", psistarts = 0, lambdastarts = 0, L1=T))
 
   # Looking at at COP model outputs ----
-  expect_is(fit_default, "unmarkedFitCOP")
+  expect_is(fit_default, "unmarkedFitOccuCOP")
   expect_equivalent(coef(fit_default), c(0.13067954, 0.06077929), tol = 1e-5)
   
   ## backTransform
@@ -364,7 +364,7 @@ test_that("We can simulate COP data", {
   
   # With no covariates
   expect_no_error(simulate(
-    "COP",
+    "occuCOP",
     formulas = list(psi =  ~ 1, lambda =  ~ 1),
     coefs = list(
       psi = c(intercept = 0),
@@ -375,7 +375,7 @@ test_that("We can simulate COP data", {
   
   # With quantitative covariates
   expect_no_error(simulate(
-    "COP",
+    "occuCOP",
     formulas = list(psi =  ~ elev, lambda =  ~ rain),
     coefs = list(
       psi = c(intercept = qlogis(.5), elev = -0.5),
@@ -386,7 +386,7 @@ test_that("We can simulate COP data", {
   
   # With guides
   expect_no_error(simulate(
-    "COP",
+    "occuCOP",
     formulas = list(psi =  ~ elev, lambda =  ~ rain),
     coefs = list(
       psi = c(intercept = qlogis(.5), elev = -0.5),
@@ -398,7 +398,7 @@ test_that("We can simulate COP data", {
   
   # With qualitative covariates
   expect_no_error(umf <- simulate(
-    "COP",
+    "occuCOP",
     formulas = list(psi =  ~ elev + habitat, lambda =  ~ 1),
     coefs = list(
       psi = c(
@@ -413,7 +413,7 @@ test_that("We can simulate COP data", {
     guide = list(habitat = factor(levels = c("A", "B", "C")))
   ))
   
-  # From unmarkedFitCOP ----
+  # From unmarkedFitOccuCOP ----
   expect_no_error(umfit <- occuCOP(
     umf,
     psiformula =  ~ habitat,
@@ -428,7 +428,7 @@ test_that("occuCOP can fit and predict models with covariates", {
   # Simulate data with covariates ----
   set.seed(123)
   expect_no_error(umf <- simulate(
-    "COP",
+    "occuCOP",
     formulas = list(psi =  ~ elev + habitat, lambda =  ~ rain),
     coefs = list(
       psi = c(