Change name to plotEffects

7 files changed, 56 insertions, 42 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index cabf60b..5a04732 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: unmarked
-Version: 1.2.5.9010
-Date: 2022-12-29
+Version: 1.2.5.9011
+Date: 2023-03-07
 Type: Package
 Title: Models for Data from Unmarked Animals
 Authors@R: c(
@@ -46,7 +46,7 @@ Collate: 'classes.R' 'unmarkedEstimate.R' 'mapInfo.R' 'unmarkedFrame.R'
     'unmarkedCrossVal.R' 'piFun.R' 'vif.R' 'makePiFun.R' 'posteriorSamples.R'
     'nmixTTD.R'
     'gdistremoval.R'
-    'plotMarginal.R'
+    'plotEffects.R'
     'mixedModelTools.R'
     'power.R' 
     'simulate.R'
diff --git a/NAMESPACE b/NAMESPACE
index 34a99c6..7273ce1 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -51,7 +51,7 @@ exportMethods(backTransform, coef, confint, coordinates, fitted, getData,
               "siteCovs<-", summary, update, vcov, yearlySiteCovs,
               "yearlySiteCovs<-", "[", smoothed, projected, nonparboot, logLik,
               LRT, ranef, bup, crossVal, posteriorSamples, sigma, randomTerms, 
-              optimizePenalty, unmarkedPowerList, plotMarginalData, plotMarginal)
+              optimizePenalty, unmarkedPowerList, plotEffectsData, plotEffects)
 
 S3method("print", "unmarkedPostSamples")
 
diff --git a/R/plotMarginal.R b/R/plotEffects.R
index 14bbd74..f5be1d8 100644
--- a/R/plotMarginal.R
+++ b/R/plotEffects.R
@@ -1,8 +1,10 @@
 type_to_covs <- function(umf, type){
-  if(type %in% c("state")){
+  if(type %in% c("state","psi","lam","lambda","sigma","dist")){
     return(methods::slot(umf, "siteCovs"))
-  } else if(type %in% c("det")){
+  } else if(type %in% c("det","rem","fp","b")){
     return(methods::slot(umf, "obsCovs"))
+  } else if(type %in% c("phi","transition","col","ext","gamma","omega","iota")){
+    return(methods::slot(umf, "yearlySiteCovs"))
   }
   return(NULL)
 }
@@ -11,7 +13,7 @@ get_base_newdata <- function(umf, type){
   covs <- type_to_covs(umf, type)
   out <- lapply(covs, function(x){
     if(is.numeric(x)){
-      return(mean(x, na.rm=TRUE))
+      return(median(x, na.rm=TRUE))
     } else if(is.factor(x)){
       return(factor(levels(x)[1], levels=levels(x)))
     }  else {
@@ -33,9 +35,9 @@ get_cov_seq <- function(covariate, umf, type){
   }
 }
 
-setGeneric("plotMarginalData", function(object, ...) standardGeneric("plotMarginalData"))
+setGeneric("plotEffectsData", function(object, ...) standardGeneric("plotEffectsData"))
 
-setMethod("plotMarginalData", "unmarkedFit",
+setMethod("plotEffectsData", "unmarkedFit",
   function(object, type, covariate, level=0.95, ...){
 
   umf <- umf_to_factor(object@data)
@@ -53,13 +55,13 @@ setMethod("plotMarginalData", "unmarkedFit",
   pr
 })
 
-setGeneric("plotMarginal", function(object, ...) standardGeneric("plotMarginal"))
+setGeneric("plotEffects", function(object, ...) standardGeneric("plotEffects"))
 
-setMethod("plotMarginal", "unmarkedFit",
+setMethod("plotEffects", "unmarkedFit",
   function(object, type, covariate, level=0.95, ...){
 
   # Get data for plot
-  plot_data <- plotMarginalData(object, type, covariate, level, ...)
+  plot_data <- plotEffectsData(object, type, covariate, level, ...)
 
   # Is covariate a factor?
   is_factor <- is.factor(plot_data$covariateValue)
diff --git a/man/plotMarginal.Rd b/man/plotEffects.Rd
index 0be5bbc..d176d43 100644
--- a/man/plotMarginal.Rd
+++ b/man/plotEffects.Rd
@@ -1,22 +1,22 @@
-\name{plotMarginal}
-\alias{plotMarginal}
-\alias{plotMarginal-methods}
-\alias{plotMarginal,unmarkedFit-method}
-\alias{plotMarginalData}
-\alias{plotMarginalData-methods}
-\alias{plotMarginalData,unmarkedFit-method}
+\name{plotEffects}
+\alias{plotEffects}
+\alias{plotEffects-methods}
+\alias{plotEffects,unmarkedFit-method}
+\alias{plotEffectsData}
+\alias{plotEffectsData-methods}
+\alias{plotEffectsData,unmarkedFit-method}
 
 \title{Plot marginal effects of covariates in unmarked models}
 
-\description{This function generates a plot visualizing the marginal effects
- of a given covariate on a parameter (e.g. occupancy, abundance) in an unmarked 
+\description{This function generates a plot visualizing the effects
+ of a single covariate on a parameter (e.g. occupancy, abundance) in an unmarked 
  model. If the covariate is numeric, the result is a line plot with an error
  ribbon where the x-axis is the range of the covariate and the y-axis is the 
  predicted parameter value. If the covariate is an R factor (i.e., categorical),
  the x-axis instead contains each unique value of the covariate. 
 
  All covariates in the model besides the one being plotted are held either at
- their mean value (if they are numeric) or at their reference level (if they
+ their median value (if they are numeric) or at their reference level (if they
  are factors).
 
  Some types of unmarked models may require additional arguments, which are passed
@@ -25,15 +25,15 @@
  call in order to work properly.
 
  If you want to customize a plot, the easiest approach is to get data 
- formatted for plotting using \code{plotMarginalData}, and use that. If
- you want to see and/or modify the code used by \code{plotMarginal} to generate
- the default plots, run \code{getMethod("plotMarginal", "unmarkedFit")} in
+ formatted for plotting using \code{plotEffectsData}, and use that. If
+ you want to see and/or modify the code used by \code{plotEffects} to generate
+ the default plots, run \code{getMethod("plotEffects", "unmarkedFit")} in
  the R console.
 }
 
 \usage{
-\S4method{plotMarginal}{unmarkedFit}(object, type, covariate, level=0.95, ...)
-\S4method{plotMarginalData}{unmarkedFit}(object, type, covariate, level=0.95, ...)
+\S4method{plotEffects}{unmarkedFit}(object, type, covariate, level=0.95, ...)
+\S4method{plotEffectsData}{unmarkedFit}(object, type, covariate, level=0.95, ...)
 }
 
 \arguments{
@@ -46,7 +46,7 @@
     for some \code{unmarkedFit} types such as \code{unmarkedFitOccuMulti}}
 } 
 
-\value{A plot (\code{plotMarginal} or a data frame (\code{plotMarginalData})
+\value{A plot (\code{plotEffects} or a data frame (\code{plotEffectsData})
   containing values to be used in a plot.
 }
 
@@ -87,14 +87,14 @@ umf <- unmarkedFrameOccu(y=y, siteCovs=dat_occ, obsCovs=dat_p)
 (fm <- occu(~x2 ~x1 + group, umf))
 
 # Plot marginal effects of various covariates
-plotMarginal(fm, "state", "x1")
-plotMarginal(fm, "state", "group")
-plotMarginal(fm, "det", "x2")
+plotEffects(fm, "state", "x1")
+plotEffects(fm, "state", "group")
+plotEffects(fm, "det", "x2")
 
 # Get raw data used for a plot
-plotMarginalData(fm, "state", "group")
+plotEffectsData(fm, "state", "group")
 
-# See code used by plotMarginal so you can edit it yourself and customize the plot
-methods::getMethod("plotMarginal", "unmarkedFit")
+# See code used by plotEffects so you can edit it yourself and customize the plot
+methods::getMethod("plotEffects", "unmarkedFit")
 }
 }
diff --git a/tests/testthat/test_gdistremoval.R b/tests/testthat/test_gdistremoval.R
index 8f453a5..3e205fb 100644
--- a/tests/testthat/test_gdistremoval.R
+++ b/tests/testthat/test_gdistremoval.R
@@ -343,6 +343,12 @@ test_that("gdistremoval can fit models",{
   expect_is(fl, "unmarkedFitList")
   ms <- modSel(fl)
   expect_is(ms, "unmarkedModSel")
+
+  #plotEffects
+  pdf(NULL)
+  plotEffects(fit, 'lambda', "sc1")
+  plotEffects(fit, 'rem', 'oc1')
+  dev.off()
 })
 
 test_that("gdistremoval predict method works",{
diff --git a/tests/testthat/test_occuTTD.R b/tests/testthat/test_occuTTD.R
index f152cde..0af27a8 100644
--- a/tests/testthat/test_occuTTD.R
+++ b/tests/testthat/test_occuTTD.R
@@ -382,6 +382,10 @@ test_that("occuTTD can fit a dynamic model",{
   expect_equivalent(dim(s[[1]]), c(100,4))
   r <- residuals(fit)
   expect_equivalent(dim(r), c(100,4))
+  pdf(NULL)
+  plotEffects(fit, 'psi', 'elev')
+  plotEffects(fit, 'col', 'forest')
+  dev.off()
 
   #Check ranef
   r <- ranef(fit)
diff --git a/tests/testthat/test_plotMarginal.R b/tests/testthat/test_plotEffects.R
index fcbfe2a..3aea3ec 100644
--- a/tests/testthat/test_plotMarginal.R
+++ b/tests/testthat/test_plotEffects.R
@@ -1,4 +1,4 @@
-context("plotMarginal")
+context("plotEffects")
 
 skip_on_cran()
 
@@ -30,15 +30,17 @@ umf <- unmarkedFrameOccu(y=y, siteCovs=dat_occ, obsCovs=dat_p)
 
 fm <- occu(~x2 ~x1 + group, umf)
 
-test_that("plotMarginal works", {
+test_that("plotEffects works", {
+  
+  pdf(NULL)
+  plotEffects(fm, "state", "x1")
+  plotEffects(fm, "state", "group")
+  plotEffects(fm, "det", "x2")
+  dev.off()
 
-  plotMarginal(fm, "state", "x1")
-  plotMarginal(fm, "state", "group")
-  plotMarginal(fm, "det", "x2")
+  expect_error(plotEffects(fm, "state", "x2"))
 
-  expect_error(plotMarginal(fm, "state", "x2"))
-
-  dat <- plotMarginalData(fm, "state", "group")
+  dat <- plotEffectsData(fm, "state", "group")
 
   expect_true(inherits(dat, "data.frame"))
   expect_equal(nrow(dat), 5)