tests/testthat/testthat_dataOrganize.R
In PhilipMostert/inlabruSDMs: Fit Models Derived from Point Processes to Species Distributions using 'inlabru'
##Load in the necessary data
Check <- dataOrganize$new()
projection <- '+proj=tmerc'
#Make random shape to generate points on
x <- c(16.48438, 17.49512, 24.74609, 22.59277, 16.48438)
y <- c(59.736328125, 55.1220703125, 55.0341796875, 61.142578125, 59.736328125)
xy <- cbind(x, y)
SpatialPoly <- st_sfc(st_polygon(list(xy)), crs = projection)
##Old coordinate names
#Make random points
#Random presence only dataset
PO <- st_as_sf(st_sample(SpatialPoly, 100, crs = projection))
st_geometry(PO) <- 'geometry'
##Add random variable
PO$numvar <- runif(n = nrow(PO))
PO$factvar <- sample(x = c('a','b'), size = nrow(PO), replace = TRUE)
PO$species <- sample(x = c('fish1', 'fish2'), size = nrow(PO), replace = TRUE)
PO$temp <- sample(x = c(1,2), nrow(PO), replace = TRUE)
#Random presence absence dataset
PA <- st_as_sf(st_sample(SpatialPoly, 100, crs = projection))
st_geometry(PA) <- 'geometry'
PA$PAresp <- sample(x = c(0,1), size = nrow(PA), replace = TRUE)
#Add trial name
PA$trial <- sample(x = c(1,2,3), size = nrow(PA), replace = TRUE)
PA$pointcov <- runif(n = nrow(PA))
PA$binommark <- sample(x = 0:1, size = nrow(PA), replace = TRUE)
PA$marktrial <- sample(x = 1:3, size = nrow(PA), replace = TRUE)
PA$species <- sample(x = c('bird1', 'bird2'), nrow(PA), replace = TRUE)
PA$temp <- sample(x = c(1,2), nrow(PA), replace = TRUE)
mesh <- fmesher::fm_mesh_2d_inla(boundary = fmesher::fm_as_segm(SpatialPoly),
max.edge = 2, crs = fmesher::fm_crs(projection))
#iPoints <- inlabru::ipoints(samplers = SpatialPoly, domain = mesh)
iPoints <- fmesher::fm_int(samplers = SpatialPoly, domain = mesh)
spData <- list(PO, PA)
test_that('The internal function makeData returns a list of sf objects as
well as the relevant metadata to be used in the integrated model.', {
Check$makeData(datapoints = spData, datanames = c('PO', 'PA'),
coords = c('long', 'lat'), proj = projection, offsetname = NULL,
pointcovnames = 'pointcov', paresp = 'PAresp', countsresp = 'counts', trialname = 'trial',
speciesname = 'species', marks = c('numvar', 'factvar', 'binommark'), temporalvar = 'temp',
marktrialname = 'marktrial', markfamily = c('uniform', 'multinomial', 'binomial'))
expect_setequal(names(Check$Data), c('PO','PA'))
expect_true(all(unlist(sapply(unlist(Check$Data, recursive = FALSE), function(x) inherits(x, 'sf')))))
##Should create a placeholder variable for the poresp +
#should keep marks +
#should create new variables for the multinomial marks.
expect_setequal(names(Check$Data$PO[[1]]), c("poresp", "numvar", "factvar", 'temp', 'geometry', '._dataset_index_var_.',
"species", "factvar_phi", "factvar_response", 'speciesINDEX_VAR'))
expect_true((all(Check$Data$PO[[1]]$factvar_phi == 1)))
expect_true((all(Check$Data$PO[[1]]$factvar_response == 1)))
expect_true(class(Check$Data$PO[[1]]$factvar) == 'character')
expect_setequal(names(Check$Data$PA[[1]]), c("PAresp", "trial", "binommark", 'temp', 'geometry', '._dataset_index_var_.',
"marktrial", "species", "pointcov", 'speciesINDEX_VAR'))
#Family for PO should be:
# cp for the points;
# uniform for the mark;
# poisson for the multinomial mark.
expect_setequal(Check$Family$PO, c('cp', 'uniform', 'poisson'))
expect_setequal(Check$Family$PA, c('binomial', 'binomial'))
expect_named(Check$dataType, c('PO', 'PA'))
expect_setequal(Check$dataType, c('Present only', 'Present absence'))
##PO has no point covariates;
##PA has pointcov as a pointcovariate
expect_true(is.null(unlist(Check$varsIn$PO)))
expect_true(unlist(Check$varsIn$PA) == 'pointcov')
expect_setequal(Check$Marks$PO, c('numvar', 'factvar'))
expect_setequal(Check$Marks$PA, c('binommark'))
expect_named(Check$marksType$PO, c('numvar', 'factvar'))
expect_named(Check$marksType$PA, c('binommark'))
expect_setequal(Check$marksType$PO, c('Uniform mark', 'Multinomial mark'))
expect_setequal(Check$marksType$PA, c('Binomial mark'))
expect_true('factvar' %in% Check$multinomVars)
expect_true(Check$numObs[1] == nrow(PO))
expect_true(Check$numObs[2] == nrow(PA))
#Ie there are three processes in PO: the points + 2 marks
expect_length(Check$dataSource[[1]], 3)
#Ie there are two processes in PO: the points + 21marks
expect_length(Check$dataSource[[2]],2)
#Remove a dataset name
expect_error(Check$makeData(datapoints = spData, datanames = c('PO'),
coords = colnames(PO@coords), proj = projection,
pointcovnames = 'pointcov', paresp = 'PAresp', countsresp = 'counts', trialname = 'trial',
speciesname = 'species', marks = c('numvar', 'factvar', 'binommark'),
marktrialname = 'marktrial', markfamily = c('uniform', 'multinomial', 'binomial')),
'Number of dataset names needs to equal length of datasets.')
#Remove a mark family
expect_error(Check$makeData(datapoints = spData, datanames = c('PO','PA'),
coords = colnames(PO@coords), proj = projection,
pointcovnames = 'pointcov', paresp = 'PAresp', countsresp = 'counts', trialname = 'trial',
speciesname = 'species', marks = c('numvar', 'factvar', 'binommark'),
marktrialname = 'marktrial', markfamily = c('uniform', 'multinomial')),
"Number of marks needs to equal the number of mark families.")
})
test_that('makeSpecies is able to split the data up by species.', {
Check$makeSpecies(speciesname = 'species')
expect_setequal(names(Check$Data$PO), c('PO_fish1', 'PO_fish2'))
expect_setequal(names(Check$Data$PA), c('PA_bird1', 'PA_bird2'))
expect_setequal(Check$SpeciesInData$PO, c('fish1', 'fish2'))
expect_setequal(Check$SpeciesInData$PA, c('bird1', 'bird2'))
#When converting factors to numeric, we expect them to be ordered alphabetically
## So bird1 and bird2 should get 1 and 2; fish1 and fish2 should get 3 and 4
expect_true(all(unlist(Check$speciesNumeric$species$PO)%in%c(3,4)))
expect_true(all(unlist(Check$speciesNumeric$species$PA)%in%c(1,2)))
#ie multiply the length of process by #species = 2
expect_length(Check$dataSource[[1]], 3 * 2)
expect_length(Check$dataSource[[2]], 2 * 2)
})
test_that('makeMultinom is able to organize and create usable multinomial data for INLA', {
#This function was implicitly checked with makeSpecies?
Check$makeMultinom(multinomVars = Check$multinomVars, return = 'marks', oldVars = NULL)
expect_setequal(unlist(Check$multinomIndex$factvar$PO),c('a','b'))
#No factor var present in PA, so should expect NA
expect_true(all(is.na(unlist(Check$multinomIndex$factvar$PA))))
expect_true(all(as.numeric(factor(unlist(Check$multinomIndex$factvar$PO))) == unlist(Check$multinomNumeric$factvar$PO)))
#The factor variable should now be numeric in the data; the index is stored in multinoIndex
expect_true(all(sapply(Check$Data$PO, function(x) class(x$factvar) == 'numeric')))
})
test_that('makeFormulas is able to make the correct formulas for the different processes
based on their response variables, and the available covariates.', {
#Spatcovs is the names of the spatial covariates
#specnesname is the name of the species variable
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', markintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = TRUE, speciesspatial = 'individual',
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesindependent = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_setequal(names(Check$Formulas), c('PO', 'PA'))
expect_setequal(names(Check$Formulas$PO), c('fish1','fish2'))
expect_setequal(names(Check$Formulas$PA), c('bird1','bird2'))
expect_setequal(names(Check$Formulas$PO$fish1), c('geometry', 'numvar', 'factvar_response'))
expect_setequal(names(Check$Formulas$PO$fish2), c('geometry', 'numvar', 'factvar_response'))
expect_setequal(names(Check$Formulas$PA$bird1), c('PAresp', 'binommark'))
expect_setequal(names(Check$Formulas$PA$bird2), c('PAresp', 'binommark'))
expect_equal(deparse1(Check$Formulas$PO$fish1$geometry$LHS),
'geometry ~ .')
expect_equal(deparse1(Check$Formulas$PO$fish1$numvar$LHS),
'numvar ~ .')
expect_equal(deparse1(Check$Formulas$PO$fish1$factvar_response$LHS),
'factvar_response ~ .')
expect_equal(deparse1(Check$Formulas$PA$bird1$PAresp$LHS),
'PAresp ~ .')
expect_equal(deparse1(Check$Formulas$PA$bird1$binommark$LHS),
'binommark ~ .')
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("fish1_spatcovs", "fish1_PO_spatial", "shared_spatial", "fish1_intercept"))
expect_setequal(Check$Formulas$PO$fish1$numvar$RHS,
c("fish1_spatcovs", "numvar_intercept", "numvar_spatial", 'PO_numvar_spatial'))
expect_setequal(Check$Formulas$PO$fish1$factvar_response$RHS,
c("fish1_spatcovs",
"factvar_spatial", "factvar", "factvar_phi", 'PO_factvar_response_spatial'))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("bird1_spatcovs", "bird1_PA_spatial", "shared_spatial", "bird1_intercept", "pointcov"))
expect_setequal(Check$Formulas$PA$bird2$binommark$RHS,
c("bird2_spatcovs", "binommark_spatial", "binommark_intercept", 'PA_binommark_spatial'))
##Change terms
#Set spatial and intercept to FALSE
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', temporalname = 'temp', speciesintercept = NULL, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = FALSE, speciesspatial = NULL,
marks = c('numvar', 'factvar', 'binommark'), markintercept = FALSE, speciesindependent = FALSE,
spatial = NULL, intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("fish1_spatcovs"))
expect_setequal(Check$Formulas$PO$fish1$numvar$RHS,
c("fish1_spatcovs", 'PO_numvar_spatial'))
expect_setequal(Check$Formulas$PO$fish1$factvar_response$RHS,
c("fish1_spatcovs", "factvar", "factvar_phi", 'PO_factvar_response_spatial'))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("bird1_spatcovs", "pointcov"))
expect_setequal(Check$Formulas$PA$bird2$binommark$RHS,
c("bird2_spatcovs", 'PA_binommark_spatial'))
##Change terms
#Set spatcovs to NULL
Check$makeFormulas(spatcovs = NULL, speciesname = 'species', marksspatial = TRUE, speciesspatial = 'individual',
paresp = 'PAresp', countresp = 'counts', markintercept = FALSE, speciesindependent = FALSE,
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesintercept = FALSE, speciesenvironment = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("fish1_PO_spatial", "shared_spatial", "fish1_intercept"))
expect_setequal(Check$Formulas$PO$fish1$numvar$RHS,
c("numvar_spatial", 'PO_numvar_spatial'))
expect_setequal(Check$Formulas$PO$fish1$factvar_response$RHS,
c("factvar_spatial", "factvar", "factvar_phi", 'PO_factvar_response_spatial'))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("bird1_PA_spatial", "shared_spatial", "bird1_intercept", "pointcov"))
expect_setequal(Check$Formulas$PA$bird2$binommark$RHS,
c("binommark_spatial", 'PA_binommark_spatial'))
##Try copy model
Check$makeFormulas(spatcovs = NULL, speciesname = 'species', marksspatial = TRUE, speciesspatial = 'individual',
paresp = 'PAresp', countresp = 'counts', markintercept = FALSE, speciesindependent = FALSE,
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesintercept = FALSE, speciesenvironment = TRUE,
spatial = 'copy', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_setequal(Check$Formulas$PO$fish2$geometry$RHS,
c('PO_spatial',"fish2_PO_spatial", "fish2_intercept"))
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("PO_spatial", "fish1_intercept", "fish1_PO_spatial"))
expect_setequal(Check$Formulas$PA$bird2$PAresp$RHS,
c("PA_spatial", "bird2_intercept", 'pointcov', "bird2_PA_spatial"))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("PA_spatial", "bird1_intercept", "pointcov", "bird1_PA_spatial"))
##Make random species intercept terms
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', markintercept = TRUE, speciesintercept = TRUE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = TRUE, speciesspatial = 'individual',
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesindependent = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_setequal(Check$Formulas$PO$fish2$geometry$RHS,
c('shared_spatial',"fish2_PO_spatial", "species_intercepts", 'fish2_spatcovs'))
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("shared_spatial", "fish1_PO_spatial", "species_intercepts", 'fish1_spatcovs'))
expect_setequal(Check$Formulas$PA$bird2$PAresp$RHS,
c("shared_spatial", "species_intercepts", "bird2_PA_spatial", 'bird2_spatcovs', 'pointcov'))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("shared_spatial", "species_intercepts", "bird1_PA_spatial", 'bird1_spatcovs', 'pointcov'))
#Check biasFormula
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', markintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = TRUE, speciesspatial = 'individual',
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesindependent = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = ~ biasVar, covariateformula = NULL)
#Bias only in PO
expect_setequal(Check$Formulas$PO$fish2$geometry$RHS,
c("fish2_spatcovs", "shared_spatial", "fish2_intercept", "fish2_PO_spatial", "Bias__Effects__Comps"))
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("fish1_spatcovs", "shared_spatial", "fish1_intercept", "fish1_PO_spatial", "Bias__Effects__Comps"))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("bird1_spatcovs", "shared_spatial", "bird1_intercept", "pointcov","bird1_PA_spatial"))
expect_setequal(Check$Formulas$PA$bird2$PAresp$RHS,
c("bird2_spatcovs", "shared_spatial", "bird2_intercept", "pointcov","bird2_PA_spatial"))
#Check covariateFormula
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', markintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = TRUE, speciesspatial = 'individual',
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesindependent = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = ~ cov + I(cov^2))
expect_setequal(Check$Formulas$PO$fish2$geometry$RHS,
c("fish2_Fixed__Effects__Comps", "shared_spatial", "fish2_intercept", "fish2_PO_spatial"))
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("fish1_Fixed__Effects__Comps", "shared_spatial", "fish1_intercept", "fish1_PO_spatial"))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("bird1_Fixed__Effects__Comps", "shared_spatial", "bird1_intercept", "pointcov","bird1_PA_spatial"))
expect_setequal(Check$Formulas$PA$bird2$PAresp$RHS,
c("bird2_Fixed__Effects__Comps", "shared_spatial", "bird2_intercept", "pointcov","bird2_PA_spatial"))
#Check replicate
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', markintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = TRUE, speciesspatial = 'replicate',
marks = NULL, temporalname = 'temp', speciesindependent = FALSE,
spatial = 'correlate', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_true(all(unlist(lapply(unlist(unlist(Check$Formulas, recursive = FALSE), recursive = FALSE), function(x) 'shared_spatial' %in% x$RHS))))
})
#Change back to original
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', marksspatial = TRUE, speciesintercept = TRUE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', markintercept = TRUE, speciesspatial = 'individual',
marks = NULL, temporalname = 'temp', speciesindependent = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
test_that('makeComponents is able to make the correct components for all the processes
based on the predictors and spatial effects available.', {
comps <- Check$makeComponents(spatial = 'shared', intercepts = FALSE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = 'temp', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(comps,c("shared_spatial(main = geometry, model = shared_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"numvar_spatial(main = geometry, model = numvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))" ,
"factvar_spatial(main = geometry, model = factvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"binommark_spatial(main = geometry, model = binommark_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"PO_numvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PO_factvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PA_binommark_spatial(main = geometry, copy = \"shared_spatial\")",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"fish2_intercept(1)",
"fish1_intercept(1)",
"bird2_intercept(1)",
"bird1_intercept(1)",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"numvar_intercept(1)",
"binommark_intercept(1)"))
## Change arguments
#spatial and intercepts == FALSE
comps2 <- Check$makeComponents(spatial = NULL, intercepts = FALSE, datanames = c('PO','PA'), speciesintercept = NULL, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), marksspatial = FALSE, offsetname = NULL,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksintercept = FALSE, speciesindependent = FALSE,
speciesname = 'species', covariatenames = 'spatcovs', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(comps2,c("fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)"))
#Check replicate
compsrep <- Check$makeComponents(spatial = NULL, intercepts = FALSE, datanames = c('PO','PA'), speciesintercept = NULL, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), marksspatial = FALSE, offsetname = NULL,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksintercept = FALSE, speciesindependent = FALSE,
speciesname = 'species', covariatenames = 'spatcovs', speciesspatial = 'replicate',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsrep,c("speciesShared(main = geometry, model = speciesField, group = speciesSpatialGroup, control.group = list(model = \"iid\"))",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)"))
#checkComponents with a copy model
compsCopy <- Check$makeComponents(spatial = 'copy', intercepts = FALSE, datanames = c('PO','PA'), speciesintercept = NULL, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), marksspatial = FALSE, offsetname = NULL,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksintercept = FALSE, speciesindependent = FALSE,
speciesname = 'species', covariatenames = 'spatcovs', speciesspatial = 'individual', temporalname = NULL,
covariateclass = 'numeric', numtime = NULL, copymodel = "list(beta = list(fixed = FALSE))",
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsCopy,c("PO_spatial(main = geometry, model = PO_field)",
"PA_spatial(main = geometry, copy = \"PO_spatial\", hyper = list(beta = list(fixed = FALSE)))",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"pointcov",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)"))
#Species random effects
compsRandom <- Check$makeComponents(spatial = 'shared', intercepts = TRUE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = TRUE, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = 'temp', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsRandom,
c("shared_spatial(main = geometry, model = shared_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"numvar_spatial(main = geometry, model = numvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))" ,
"factvar_spatial(main = geometry, model = factvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"binommark_spatial(main = geometry, model = binommark_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"PO_intercept(1)",
"PA_intercept(1)",
"PO_factvar_spatial(main = geometry, copy = \"shared_spatial\")" ,
"PO_numvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PA_binommark_spatial(main = geometry, copy = \"shared_spatial\")",
"species_intercepts(main = species, model = \"iid\", constr = TRUE, hyper = list(prec = list(prior = \"loggamma\", param = c(1, 5e-05))))",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"numvar_intercept(1)",
"binommark_intercept(1)"))
#Species but dataset intercepts
compsData <- Check$makeComponents(spatial = 'shared', intercepts = TRUE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = NULL, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = 'temp', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsData,
c("shared_spatial(main = geometry, model = shared_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"numvar_spatial(main = geometry, model = numvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))" ,
"factvar_spatial(main = geometry, model = factvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"binommark_spatial(main = geometry, model = binommark_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"PO_numvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PO_factvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PA_binommark_spatial(main = geometry, copy = \"shared_spatial\")",
'PO_intercept(1)', 'PA_intercept(1)',
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"numvar_intercept(1)",
"binommark_intercept(1)"))
#Check biasFormula
compsBias <- Check$makeComponents(spatial = 'shared', intercepts = FALSE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = 'temp', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = ~ BiasCov, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsBias,
c("shared_spatial(main = geometry, model = shared_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"numvar_spatial(main = geometry, model = numvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))" ,
"factvar_spatial(main = geometry, model = factvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"binommark_spatial(main = geometry, model = binommark_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"fish2_intercept(1)",
"fish1_intercept(1)",
"bird2_intercept(1)",
"bird1_intercept(1)",
"PO_numvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PO_factvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PA_binommark_spatial(main = geometry, copy = \"shared_spatial\")",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"numvar_intercept(1)",
"binommark_intercept(1)",
"Bias__Effects__Comps(main = ~BiasCov - 1, model = \"fixed\")",
"Bias__Effects__Comps(main = ~BiasCov - 1, model = \"fixed\")",
"Bias__Effects__Comps(main = ~BiasCov - 1, model = \"fixed\")",
"Bias__Effects__Comps(main = ~BiasCov - 1, model = \"fixed\")"))
#Check covariateFormula
compsCov <- Check$makeComponents(spatial = 'shared', intercepts = FALSE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = 'temp', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = ~ Var + I(Var^2), marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsCov,
c("shared_spatial(main = geometry, model = shared_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"numvar_spatial(main = geometry, model = numvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))" ,
"factvar_spatial(main = geometry, model = factvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"binommark_spatial(main = geometry, model = binommark_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_Fixed__Effects__Comps(main = ~fish2_Var + I(fish2_Var^2) - 1, model = \"fixed\")",
"fish1_Fixed__Effects__Comps(main = ~fish1_Var + I(fish1_Var^2) - 1, model = \"fixed\")",
"bird1_Fixed__Effects__Comps(main = ~bird1_Var + I(bird1_Var^2) - 1, model = \"fixed\")",
"bird2_Fixed__Effects__Comps(main = ~bird2_Var + I(bird2_Var^2) - 1, model = \"fixed\")",
"pointcov",
"fish2_intercept(1)",
"fish1_intercept(1)",
"bird2_intercept(1)",
"bird1_intercept(1)",
"PO_numvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PO_factvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PA_binommark_spatial(main = geometry, copy = \"shared_spatial\")",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"numvar_intercept(1)",
"binommark_intercept(1)"))
compsCorrel <- Check$makeComponents(spatial = 'correlate', intercepts = FALSE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
marks = NULL, temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = NULL, speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL)
expect_setequal(compsCorrel, c("shared_spatial(main = geometry, model = shared_field, group = ._dataset_index_var_., control.group = list(model = \"exchangeable\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"pointcov",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"fish2_intercept(1)",
"fish1_intercept(1)",
"bird1_intercept(1)",
"bird2_intercept(1)" ))
})
PhilipMostert/inlabruSDMs documentation built on April 14, 2025, 11:39 a.m.
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##Load in the necessary data
Check <- dataOrganize$new()
projection <- '+proj=tmerc'
#Make random shape to generate points on
x <- c(16.48438, 17.49512, 24.74609, 22.59277, 16.48438)
y <- c(59.736328125, 55.1220703125, 55.0341796875, 61.142578125, 59.736328125)
xy <- cbind(x, y)
SpatialPoly <- st_sfc(st_polygon(list(xy)), crs = projection)
##Old coordinate names
#Make random points
#Random presence only dataset
PO <- st_as_sf(st_sample(SpatialPoly, 100, crs = projection))
st_geometry(PO) <- 'geometry'
##Add random variable
PO$numvar <- runif(n = nrow(PO))
PO$factvar <- sample(x = c('a','b'), size = nrow(PO), replace = TRUE)
PO$species <- sample(x = c('fish1', 'fish2'), size = nrow(PO), replace = TRUE)
PO$temp <- sample(x = c(1,2), nrow(PO), replace = TRUE)
#Random presence absence dataset
PA <- st_as_sf(st_sample(SpatialPoly, 100, crs = projection))
st_geometry(PA) <- 'geometry'
PA$PAresp <- sample(x = c(0,1), size = nrow(PA), replace = TRUE)
#Add trial name
PA$trial <- sample(x = c(1,2,3), size = nrow(PA), replace = TRUE)
PA$pointcov <- runif(n = nrow(PA))
PA$binommark <- sample(x = 0:1, size = nrow(PA), replace = TRUE)
PA$marktrial <- sample(x = 1:3, size = nrow(PA), replace = TRUE)
PA$species <- sample(x = c('bird1', 'bird2'), nrow(PA), replace = TRUE)
PA$temp <- sample(x = c(1,2), nrow(PA), replace = TRUE)
mesh <- fmesher::fm_mesh_2d_inla(boundary = fmesher::fm_as_segm(SpatialPoly),
max.edge = 2, crs = fmesher::fm_crs(projection))
#iPoints <- inlabru::ipoints(samplers = SpatialPoly, domain = mesh)
iPoints <- fmesher::fm_int(samplers = SpatialPoly, domain = mesh)
spData <- list(PO, PA)
test_that('The internal function makeData returns a list of sf objects as
well as the relevant metadata to be used in the integrated model.', {
Check$makeData(datapoints = spData, datanames = c('PO', 'PA'),
coords = c('long', 'lat'), proj = projection, offsetname = NULL,
pointcovnames = 'pointcov', paresp = 'PAresp', countsresp = 'counts', trialname = 'trial',
speciesname = 'species', marks = c('numvar', 'factvar', 'binommark'), temporalvar = 'temp',
marktrialname = 'marktrial', markfamily = c('uniform', 'multinomial', 'binomial'))
expect_setequal(names(Check$Data), c('PO','PA'))
expect_true(all(unlist(sapply(unlist(Check$Data, recursive = FALSE), function(x) inherits(x, 'sf')))))
##Should create a placeholder variable for the poresp +
#should keep marks +
#should create new variables for the multinomial marks.
expect_setequal(names(Check$Data$PO[[1]]), c("poresp", "numvar", "factvar", 'temp', 'geometry', '._dataset_index_var_.',
"species", "factvar_phi", "factvar_response", 'speciesINDEX_VAR'))
expect_true((all(Check$Data$PO[[1]]$factvar_phi == 1)))
expect_true((all(Check$Data$PO[[1]]$factvar_response == 1)))
expect_true(class(Check$Data$PO[[1]]$factvar) == 'character')
expect_setequal(names(Check$Data$PA[[1]]), c("PAresp", "trial", "binommark", 'temp', 'geometry', '._dataset_index_var_.',
"marktrial", "species", "pointcov", 'speciesINDEX_VAR'))
#Family for PO should be:
# cp for the points;
# uniform for the mark;
# poisson for the multinomial mark.
expect_setequal(Check$Family$PO, c('cp', 'uniform', 'poisson'))
expect_setequal(Check$Family$PA, c('binomial', 'binomial'))
expect_named(Check$dataType, c('PO', 'PA'))
expect_setequal(Check$dataType, c('Present only', 'Present absence'))
##PO has no point covariates;
##PA has pointcov as a pointcovariate
expect_true(is.null(unlist(Check$varsIn$PO)))
expect_true(unlist(Check$varsIn$PA) == 'pointcov')
expect_setequal(Check$Marks$PO, c('numvar', 'factvar'))
expect_setequal(Check$Marks$PA, c('binommark'))
expect_named(Check$marksType$PO, c('numvar', 'factvar'))
expect_named(Check$marksType$PA, c('binommark'))
expect_setequal(Check$marksType$PO, c('Uniform mark', 'Multinomial mark'))
expect_setequal(Check$marksType$PA, c('Binomial mark'))
expect_true('factvar' %in% Check$multinomVars)
expect_true(Check$numObs[1] == nrow(PO))
expect_true(Check$numObs[2] == nrow(PA))
#Ie there are three processes in PO: the points + 2 marks
expect_length(Check$dataSource[[1]], 3)
#Ie there are two processes in PO: the points + 21marks
expect_length(Check$dataSource[[2]],2)
#Remove a dataset name
expect_error(Check$makeData(datapoints = spData, datanames = c('PO'),
coords = colnames(PO@coords), proj = projection,
pointcovnames = 'pointcov', paresp = 'PAresp', countsresp = 'counts', trialname = 'trial',
speciesname = 'species', marks = c('numvar', 'factvar', 'binommark'),
marktrialname = 'marktrial', markfamily = c('uniform', 'multinomial', 'binomial')),
'Number of dataset names needs to equal length of datasets.')
#Remove a mark family
expect_error(Check$makeData(datapoints = spData, datanames = c('PO','PA'),
coords = colnames(PO@coords), proj = projection,
pointcovnames = 'pointcov', paresp = 'PAresp', countsresp = 'counts', trialname = 'trial',
speciesname = 'species', marks = c('numvar', 'factvar', 'binommark'),
marktrialname = 'marktrial', markfamily = c('uniform', 'multinomial')),
"Number of marks needs to equal the number of mark families.")
})
test_that('makeSpecies is able to split the data up by species.', {
Check$makeSpecies(speciesname = 'species')
expect_setequal(names(Check$Data$PO), c('PO_fish1', 'PO_fish2'))
expect_setequal(names(Check$Data$PA), c('PA_bird1', 'PA_bird2'))
expect_setequal(Check$SpeciesInData$PO, c('fish1', 'fish2'))
expect_setequal(Check$SpeciesInData$PA, c('bird1', 'bird2'))
#When converting factors to numeric, we expect them to be ordered alphabetically
## So bird1 and bird2 should get 1 and 2; fish1 and fish2 should get 3 and 4
expect_true(all(unlist(Check$speciesNumeric$species$PO)%in%c(3,4)))
expect_true(all(unlist(Check$speciesNumeric$species$PA)%in%c(1,2)))
#ie multiply the length of process by #species = 2
expect_length(Check$dataSource[[1]], 3 * 2)
expect_length(Check$dataSource[[2]], 2 * 2)
})
test_that('makeMultinom is able to organize and create usable multinomial data for INLA', {
#This function was implicitly checked with makeSpecies?
Check$makeMultinom(multinomVars = Check$multinomVars, return = 'marks', oldVars = NULL)
expect_setequal(unlist(Check$multinomIndex$factvar$PO),c('a','b'))
#No factor var present in PA, so should expect NA
expect_true(all(is.na(unlist(Check$multinomIndex$factvar$PA))))
expect_true(all(as.numeric(factor(unlist(Check$multinomIndex$factvar$PO))) == unlist(Check$multinomNumeric$factvar$PO)))
#The factor variable should now be numeric in the data; the index is stored in multinoIndex
expect_true(all(sapply(Check$Data$PO, function(x) class(x$factvar) == 'numeric')))
})
test_that('makeFormulas is able to make the correct formulas for the different processes
based on their response variables, and the available covariates.', {
#Spatcovs is the names of the spatial covariates
#specnesname is the name of the species variable
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', markintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = TRUE, speciesspatial = 'individual',
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesindependent = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_setequal(names(Check$Formulas), c('PO', 'PA'))
expect_setequal(names(Check$Formulas$PO), c('fish1','fish2'))
expect_setequal(names(Check$Formulas$PA), c('bird1','bird2'))
expect_setequal(names(Check$Formulas$PO$fish1), c('geometry', 'numvar', 'factvar_response'))
expect_setequal(names(Check$Formulas$PO$fish2), c('geometry', 'numvar', 'factvar_response'))
expect_setequal(names(Check$Formulas$PA$bird1), c('PAresp', 'binommark'))
expect_setequal(names(Check$Formulas$PA$bird2), c('PAresp', 'binommark'))
expect_equal(deparse1(Check$Formulas$PO$fish1$geometry$LHS),
'geometry ~ .')
expect_equal(deparse1(Check$Formulas$PO$fish1$numvar$LHS),
'numvar ~ .')
expect_equal(deparse1(Check$Formulas$PO$fish1$factvar_response$LHS),
'factvar_response ~ .')
expect_equal(deparse1(Check$Formulas$PA$bird1$PAresp$LHS),
'PAresp ~ .')
expect_equal(deparse1(Check$Formulas$PA$bird1$binommark$LHS),
'binommark ~ .')
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("fish1_spatcovs", "fish1_PO_spatial", "shared_spatial", "fish1_intercept"))
expect_setequal(Check$Formulas$PO$fish1$numvar$RHS,
c("fish1_spatcovs", "numvar_intercept", "numvar_spatial", 'PO_numvar_spatial'))
expect_setequal(Check$Formulas$PO$fish1$factvar_response$RHS,
c("fish1_spatcovs",
"factvar_spatial", "factvar", "factvar_phi", 'PO_factvar_response_spatial'))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("bird1_spatcovs", "bird1_PA_spatial", "shared_spatial", "bird1_intercept", "pointcov"))
expect_setequal(Check$Formulas$PA$bird2$binommark$RHS,
c("bird2_spatcovs", "binommark_spatial", "binommark_intercept", 'PA_binommark_spatial'))
##Change terms
#Set spatial and intercept to FALSE
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', temporalname = 'temp', speciesintercept = NULL, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = FALSE, speciesspatial = NULL,
marks = c('numvar', 'factvar', 'binommark'), markintercept = FALSE, speciesindependent = FALSE,
spatial = NULL, intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("fish1_spatcovs"))
expect_setequal(Check$Formulas$PO$fish1$numvar$RHS,
c("fish1_spatcovs", 'PO_numvar_spatial'))
expect_setequal(Check$Formulas$PO$fish1$factvar_response$RHS,
c("fish1_spatcovs", "factvar", "factvar_phi", 'PO_factvar_response_spatial'))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("bird1_spatcovs", "pointcov"))
expect_setequal(Check$Formulas$PA$bird2$binommark$RHS,
c("bird2_spatcovs", 'PA_binommark_spatial'))
##Change terms
#Set spatcovs to NULL
Check$makeFormulas(spatcovs = NULL, speciesname = 'species', marksspatial = TRUE, speciesspatial = 'individual',
paresp = 'PAresp', countresp = 'counts', markintercept = FALSE, speciesindependent = FALSE,
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesintercept = FALSE, speciesenvironment = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("fish1_PO_spatial", "shared_spatial", "fish1_intercept"))
expect_setequal(Check$Formulas$PO$fish1$numvar$RHS,
c("numvar_spatial", 'PO_numvar_spatial'))
expect_setequal(Check$Formulas$PO$fish1$factvar_response$RHS,
c("factvar_spatial", "factvar", "factvar_phi", 'PO_factvar_response_spatial'))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("bird1_PA_spatial", "shared_spatial", "bird1_intercept", "pointcov"))
expect_setequal(Check$Formulas$PA$bird2$binommark$RHS,
c("binommark_spatial", 'PA_binommark_spatial'))
##Try copy model
Check$makeFormulas(spatcovs = NULL, speciesname = 'species', marksspatial = TRUE, speciesspatial = 'individual',
paresp = 'PAresp', countresp = 'counts', markintercept = FALSE, speciesindependent = FALSE,
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesintercept = FALSE, speciesenvironment = TRUE,
spatial = 'copy', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_setequal(Check$Formulas$PO$fish2$geometry$RHS,
c('PO_spatial',"fish2_PO_spatial", "fish2_intercept"))
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("PO_spatial", "fish1_intercept", "fish1_PO_spatial"))
expect_setequal(Check$Formulas$PA$bird2$PAresp$RHS,
c("PA_spatial", "bird2_intercept", 'pointcov', "bird2_PA_spatial"))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("PA_spatial", "bird1_intercept", "pointcov", "bird1_PA_spatial"))
##Make random species intercept terms
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', markintercept = TRUE, speciesintercept = TRUE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = TRUE, speciesspatial = 'individual',
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesindependent = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_setequal(Check$Formulas$PO$fish2$geometry$RHS,
c('shared_spatial',"fish2_PO_spatial", "species_intercepts", 'fish2_spatcovs'))
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("shared_spatial", "fish1_PO_spatial", "species_intercepts", 'fish1_spatcovs'))
expect_setequal(Check$Formulas$PA$bird2$PAresp$RHS,
c("shared_spatial", "species_intercepts", "bird2_PA_spatial", 'bird2_spatcovs', 'pointcov'))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("shared_spatial", "species_intercepts", "bird1_PA_spatial", 'bird1_spatcovs', 'pointcov'))
#Check biasFormula
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', markintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = TRUE, speciesspatial = 'individual',
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesindependent = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = ~ biasVar, covariateformula = NULL)
#Bias only in PO
expect_setequal(Check$Formulas$PO$fish2$geometry$RHS,
c("fish2_spatcovs", "shared_spatial", "fish2_intercept", "fish2_PO_spatial", "Bias__Effects__Comps"))
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("fish1_spatcovs", "shared_spatial", "fish1_intercept", "fish1_PO_spatial", "Bias__Effects__Comps"))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("bird1_spatcovs", "shared_spatial", "bird1_intercept", "pointcov","bird1_PA_spatial"))
expect_setequal(Check$Formulas$PA$bird2$PAresp$RHS,
c("bird2_spatcovs", "shared_spatial", "bird2_intercept", "pointcov","bird2_PA_spatial"))
#Check covariateFormula
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', markintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = TRUE, speciesspatial = 'individual',
marks = c('numvar', 'factvar', 'binommark'), temporalname = 'temp', speciesindependent = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = ~ cov + I(cov^2))
expect_setequal(Check$Formulas$PO$fish2$geometry$RHS,
c("fish2_Fixed__Effects__Comps", "shared_spatial", "fish2_intercept", "fish2_PO_spatial"))
expect_setequal(Check$Formulas$PO$fish1$geometry$RHS,
c("fish1_Fixed__Effects__Comps", "shared_spatial", "fish1_intercept", "fish1_PO_spatial"))
expect_setequal(Check$Formulas$PA$bird1$PAresp$RHS,
c("bird1_Fixed__Effects__Comps", "shared_spatial", "bird1_intercept", "pointcov","bird1_PA_spatial"))
expect_setequal(Check$Formulas$PA$bird2$PAresp$RHS,
c("bird2_Fixed__Effects__Comps", "shared_spatial", "bird2_intercept", "pointcov","bird2_PA_spatial"))
#Check replicate
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', markintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', marksspatial = TRUE, speciesspatial = 'replicate',
marks = NULL, temporalname = 'temp', speciesindependent = FALSE,
spatial = 'correlate', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
expect_true(all(unlist(lapply(unlist(unlist(Check$Formulas, recursive = FALSE), recursive = FALSE), function(x) 'shared_spatial' %in% x$RHS))))
})
#Change back to original
Check$makeFormulas(spatcovs = 'spatcovs', speciesname = 'species', marksspatial = TRUE, speciesintercept = TRUE, speciesenvironment = TRUE,
paresp = 'PAresp', countresp = 'counts', markintercept = TRUE, speciesspatial = 'individual',
marks = NULL, temporalname = 'temp', speciesindependent = FALSE,
spatial = 'shared', intercept = FALSE, pointcovs = 'pointcov', biasformula = NULL, covariateformula = NULL)
test_that('makeComponents is able to make the correct components for all the processes
based on the predictors and spatial effects available.', {
comps <- Check$makeComponents(spatial = 'shared', intercepts = FALSE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = 'temp', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(comps,c("shared_spatial(main = geometry, model = shared_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"numvar_spatial(main = geometry, model = numvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))" ,
"factvar_spatial(main = geometry, model = factvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"binommark_spatial(main = geometry, model = binommark_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"PO_numvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PO_factvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PA_binommark_spatial(main = geometry, copy = \"shared_spatial\")",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"fish2_intercept(1)",
"fish1_intercept(1)",
"bird2_intercept(1)",
"bird1_intercept(1)",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"numvar_intercept(1)",
"binommark_intercept(1)"))
## Change arguments
#spatial and intercepts == FALSE
comps2 <- Check$makeComponents(spatial = NULL, intercepts = FALSE, datanames = c('PO','PA'), speciesintercept = NULL, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), marksspatial = FALSE, offsetname = NULL,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksintercept = FALSE, speciesindependent = FALSE,
speciesname = 'species', covariatenames = 'spatcovs', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(comps2,c("fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)"))
#Check replicate
compsrep <- Check$makeComponents(spatial = NULL, intercepts = FALSE, datanames = c('PO','PA'), speciesintercept = NULL, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), marksspatial = FALSE, offsetname = NULL,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksintercept = FALSE, speciesindependent = FALSE,
speciesname = 'species', covariatenames = 'spatcovs', speciesspatial = 'replicate',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsrep,c("speciesShared(main = geometry, model = speciesField, group = speciesSpatialGroup, control.group = list(model = \"iid\"))",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)"))
#checkComponents with a copy model
compsCopy <- Check$makeComponents(spatial = 'copy', intercepts = FALSE, datanames = c('PO','PA'), speciesintercept = NULL, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), marksspatial = FALSE, offsetname = NULL,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksintercept = FALSE, speciesindependent = FALSE,
speciesname = 'species', covariatenames = 'spatcovs', speciesspatial = 'individual', temporalname = NULL,
covariateclass = 'numeric', numtime = NULL, copymodel = "list(beta = list(fixed = FALSE))",
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsCopy,c("PO_spatial(main = geometry, model = PO_field)",
"PA_spatial(main = geometry, copy = \"PO_spatial\", hyper = list(beta = list(fixed = FALSE)))",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"pointcov",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)"))
#Species random effects
compsRandom <- Check$makeComponents(spatial = 'shared', intercepts = TRUE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = TRUE, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = 'temp', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsRandom,
c("shared_spatial(main = geometry, model = shared_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"numvar_spatial(main = geometry, model = numvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))" ,
"factvar_spatial(main = geometry, model = factvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"binommark_spatial(main = geometry, model = binommark_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"PO_intercept(1)",
"PA_intercept(1)",
"PO_factvar_spatial(main = geometry, copy = \"shared_spatial\")" ,
"PO_numvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PA_binommark_spatial(main = geometry, copy = \"shared_spatial\")",
"species_intercepts(main = species, model = \"iid\", constr = TRUE, hyper = list(prec = list(prior = \"loggamma\", param = c(1, 5e-05))))",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"numvar_intercept(1)",
"binommark_intercept(1)"))
#Species but dataset intercepts
compsData <- Check$makeComponents(spatial = 'shared', intercepts = TRUE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = NULL, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = 'temp', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsData,
c("shared_spatial(main = geometry, model = shared_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"numvar_spatial(main = geometry, model = numvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))" ,
"factvar_spatial(main = geometry, model = factvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"binommark_spatial(main = geometry, model = binommark_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"PO_numvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PO_factvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PA_binommark_spatial(main = geometry, copy = \"shared_spatial\")",
'PO_intercept(1)', 'PA_intercept(1)',
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"numvar_intercept(1)",
"binommark_intercept(1)"))
#Check biasFormula
compsBias <- Check$makeComponents(spatial = 'shared', intercepts = FALSE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = 'temp', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = ~ BiasCov, covariateformula = NULL, marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsBias,
c("shared_spatial(main = geometry, model = shared_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"numvar_spatial(main = geometry, model = numvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))" ,
"factvar_spatial(main = geometry, model = factvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"binommark_spatial(main = geometry, model = binommark_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"pointcov",
"fish2_intercept(1)",
"fish1_intercept(1)",
"bird2_intercept(1)",
"bird1_intercept(1)",
"PO_numvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PO_factvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PA_binommark_spatial(main = geometry, copy = \"shared_spatial\")",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"numvar_intercept(1)",
"binommark_intercept(1)",
"Bias__Effects__Comps(main = ~BiasCov - 1, model = \"fixed\")",
"Bias__Effects__Comps(main = ~BiasCov - 1, model = \"fixed\")",
"Bias__Effects__Comps(main = ~BiasCov - 1, model = \"fixed\")",
"Bias__Effects__Comps(main = ~BiasCov - 1, model = \"fixed\")"))
#Check covariateFormula
compsCov <- Check$makeComponents(spatial = 'shared', intercepts = FALSE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
marks = c('numvar', 'factvar', 'binommark'), temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = 'temp', speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = ~ Var + I(Var^2), marksCopy = list(PO = c('numvar', 'factvar'), PA = 'binommark'))
expect_setequal(compsCov,
c("shared_spatial(main = geometry, model = shared_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"numvar_spatial(main = geometry, model = numvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))" ,
"factvar_spatial(main = geometry, model = factvar_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"binommark_spatial(main = geometry, model = binommark_field, group = temp, ngroup = 2, control.group = list(model = \"ar1\"))",
"fish2_Fixed__Effects__Comps(main = ~fish2_Var + I(fish2_Var^2) - 1, model = \"fixed\")",
"fish1_Fixed__Effects__Comps(main = ~fish1_Var + I(fish1_Var^2) - 1, model = \"fixed\")",
"bird1_Fixed__Effects__Comps(main = ~bird1_Var + I(bird1_Var^2) - 1, model = \"fixed\")",
"bird2_Fixed__Effects__Comps(main = ~bird2_Var + I(bird2_Var^2) - 1, model = \"fixed\")",
"pointcov",
"fish2_intercept(1)",
"fish1_intercept(1)",
"bird2_intercept(1)",
"bird1_intercept(1)",
"PO_numvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PO_factvar_spatial(main = geometry, copy = \"shared_spatial\")",
"PA_binommark_spatial(main = geometry, copy = \"shared_spatial\")",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"numvar_intercept(1)",
"binommark_intercept(1)"))
compsCorrel <- Check$makeComponents(spatial = 'correlate', intercepts = FALSE, datanames = c('PO','PA'), marksintercept = TRUE, speciesintercept = FALSE, speciesenvironment = TRUE,
marks = NULL, temporalmodel = deparse(list(model = "ar1")), speciesindependent = FALSE,
multinomnames = 'factvar', pointcovariates = 'pointcov', marksspatial = TRUE, offsetname = NULL,
speciesname = 'species', covariatenames = 'spatcovs', temporalname = NULL, speciesspatial = 'individual',
covariateclass = 'numeric', numtime = 2, copymodel = Check$.__enclos_env__$private$copyModel,
biasformula = NULL, covariateformula = NULL)
expect_setequal(compsCorrel, c("shared_spatial(main = geometry, model = shared_field, group = ._dataset_index_var_., control.group = list(model = \"exchangeable\"))",
"fish2_PO_spatial(main = geometry, model = fish2_PO_field)",
"fish1_PO_spatial(main = geometry, model = fish1_PO_field)",
"bird1_PA_spatial(main = geometry, model = bird1_PA_field)",
"bird2_PA_spatial(main = geometry, model = bird2_PA_field)",
"fish2_spatcovs(main = fish2_spatcovs, model = \"numeric\")",
"fish1_spatcovs(main = fish1_spatcovs, model = \"numeric\")",
"bird1_spatcovs(main = bird1_spatcovs, model = \"numeric\")",
"bird2_spatcovs(main = bird2_spatcovs, model = \"numeric\")",
"pointcov",
"factvar(main = factvar, model = \"iid\",constr = FALSE, fixed=TRUE)",
"factvar_phi(main = factvar_phi, model = \"iid\", initial = -10, fixed = TRUE)",
"fish2_intercept(1)",
"fish1_intercept(1)",
"bird1_intercept(1)",
"bird2_intercept(1)" ))
})
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