From 9f5b8442f9044bb7bc580eb5bf001d2c1fde8146 Mon Sep 17 00:00:00 2001 From: Ken Kellner Date: Wed, 13 Dec 2023 09:00:30 -0500 Subject: Change from unmarkedFitCOP to unmarkedFitOccuCOP --- R/occuCOP.R | 34 +++++++++++++++++----------------- man/fitted-methods.Rd | 2 +- man/getP-methods.Rd | 4 ++-- man/nonparboot-methods.Rd | 2 +- man/occuCOP.Rd | 2 +- man/ranef-methods.Rd | 2 +- man/simulate-methods.Rd | 2 +- man/unmarkedFit-class.Rd | 4 ++-- tests/testthat/test_occuCOP.R | 14 +++++++------- 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( -- cgit v1.2.3