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passing tests
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@doserjef
doserjef committed Sep 1, 2024
1 parent 8ba3b50 commit dbd6f76
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Showing 21 changed files with 2 additions and 82 deletions.
2 changes: 0 additions & 2 deletions tests/testthat/test-PGOcc.R
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Expand Up @@ -243,7 +243,6 @@ test_that("default priors, inits, burn, thin work", {
det.formula = ~ 1,
data = data.list,
n.samples = n.samples,
parallel.chains = TRUE,
n.chains = 1,
n.omp.threads = 1,
verbose = FALSE)
Expand Down Expand Up @@ -456,7 +455,6 @@ test_that("verbose prints to the screen", {
data = data.list,
n.samples = 100,
n.omp.threads = 1,
parallel.chains = TRUE,
verbose = TRUE,
n.report = n.report,
n.burn = 1,
Expand Down
4 changes: 2 additions & 2 deletions tests/testthat/test-intMsPGOcc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,7 @@ test_that("verbose prints to the screen", {
det.formula = det.formula,
data = data.list,
n.samples = 100,
parallel.chains = TRUE,
parallel.chains = FALSE,
n.omp.threads = 1,
verbose = TRUE,
n.report = 100,
Expand Down Expand Up @@ -325,7 +325,7 @@ test_that("verbose prints to the screen", {
det.formula = det.formula,
data = data.list,
n.samples = 100,
parallel.chains = TRUE,
parallel.chains = FALSE,
n.omp.threads = 1,
verbose = TRUE,
n.report = 100,
Expand Down
3 changes: 0 additions & 3 deletions tests/testthat/test-intPGOcc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -121,7 +121,6 @@ test_that("default priors, inits, burn, thin, work", {
det.formula = det.formula,
data = data.list,
n.samples = 100,
parallel.chains = TRUE,
n.omp.threads = 1,
verbose = FALSE,
n.chains = 1)
Expand Down Expand Up @@ -288,7 +287,6 @@ test_that("individual data set cv works", {
data = data.list,
inits = inits.list,
n.samples = n.samples,
parallel.chains = TRUE,
priors = prior.list,
n.omp.threads = 1,
verbose = FALSE,
Expand Down Expand Up @@ -485,7 +483,6 @@ out <- intPGOcc(occ.formula = occ.formula,
data = data.list,
inits = inits.list,
n.samples = n.samples,
parallel.chains = TRUE,
priors = prior.list,
n.omp.threads = 1,
verbose = FALSE,
Expand Down
3 changes: 0 additions & 3 deletions tests/testthat/test-lfJSDM.R
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Original file line number Diff line number Diff line change
Expand Up @@ -272,7 +272,6 @@ test_that("default priors, inits, burn, thin work", {
data = data.list,
n.factors = 3,
n.samples = n.samples,
parallel.chains = TRUE,
n.omp.threads = 1,
verbose = FALSE)
expect_s3_class(out, "lfJSDM")
Expand Down Expand Up @@ -637,7 +636,6 @@ test_that("default priors, inits, burn, thin work", {
data = data.list,
n.factors = 3,
n.samples = n.samples,
parallel.chains = TRUE,
n.omp.threads = 1,
verbose = FALSE)
expect_s3_class(out, "lfJSDM")
Expand Down Expand Up @@ -752,7 +750,6 @@ out <- lfJSDM(formula = formula,
n.samples = n.samples,
n.factors = 3,
priors = prior.list,
parallel.chains = TRUE,
n.omp.threads = 1,
verbose = FALSE,
n.report = n.report,
Expand Down
6 changes: 0 additions & 6 deletions tests/testthat/test-lfMsPGOcc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -149,7 +149,6 @@ test_that("verbose prints to the screen", {
data = data.list,
n.samples = 100,
n.omp.threads = 1,
parallel.chains = TRUE,
n.factors = 3,
verbose = TRUE,
n.report = 100,
Expand Down Expand Up @@ -341,7 +340,6 @@ test_that("verbose prints to the screen", {
det.formula = det.formula,
data = data.list,
n.samples = 100,
parallel.chains = TRUE,
n.factors = 3,
n.omp.threads = 1,
verbose = TRUE,
Expand Down Expand Up @@ -718,7 +716,6 @@ test_that("default priors, inits, burn, thin work", {
det.formula = det.formula,
data = data.list,
n.samples = n.samples,
parallel.chains = TRUE,
n.factors = 3,
n.omp.threads = 1,
verbose = FALSE)
Expand Down Expand Up @@ -1069,7 +1066,6 @@ out <- lfMsPGOcc(occ.formula = occ.formula,
data = data.list,
inits = inits.list,
n.samples = n.samples,
parallel.chains = TRUE,
n.factors = 3,
priors = prior.list,
n.omp.threads = 1,
Expand Down Expand Up @@ -1347,7 +1343,6 @@ test_that("default priors, inits, burn, thin work", {
det.formula = det.formula,
data = data.list,
n.samples = n.samples,
parallel.chains = TRUE,
n.factors = 3,
n.omp.threads = 1,
verbose = FALSE)
Expand Down Expand Up @@ -1598,7 +1593,6 @@ test_that("verbose prints to the screen", {
det.formula = det.formula,
data = data.list,
n.samples = 100,
parallel.chains = TRUE,
n.factors = 3,
n.omp.threads = 1,
verbose = TRUE,
Expand Down
4 changes: 0 additions & 4 deletions tests/testthat/test-msPGOcc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -256,7 +256,6 @@ out <- msPGOcc(occ.formula = occ.formula,
inits = inits.list,
n.samples = n.samples,
priors = prior.list,
parallel.chains = TRUE,
n.omp.threads = 1,
verbose = FALSE,
n.report = n.report,
Expand Down Expand Up @@ -325,7 +324,6 @@ test_that("default priors, inits, burn, thin work", {
data = data.list,
n.samples = n.samples,
n.omp.threads = 1,
parallel.chains = TRUE,
verbose = FALSE)
expect_s3_class(out, "msPGOcc")
})
Expand Down Expand Up @@ -519,7 +517,6 @@ test_that("missing value error handling works", {
expect_error(msPGOcc(occ.formula = occ.formula,
det.formula = det.formula,
data = tmp.data,
parallel.chains = TRUE,
n.samples = n.samples,
n.omp.threads = 1,
verbose = FALSE))
Expand Down Expand Up @@ -684,7 +681,6 @@ out <- msPGOcc(occ.formula = occ.formula,
data = data.list,
inits = inits.list,
n.samples = n.samples,
parallel.chains = TRUE,
priors = prior.list,
n.omp.threads = 1,
verbose = FALSE,
Expand Down
5 changes: 0 additions & 5 deletions tests/testthat/test-sfJSDM-NNGP.R
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Original file line number Diff line number Diff line change
Expand Up @@ -167,7 +167,6 @@ test_that("all correlation functions work", {
n.batch = n.batch,
batch.length = batch.length,
accept.rate = 0.43,
parallel.chains = TRUE,
priors = prior.list,
cov.model = "gaussian",
tuning = list(phi = 0.3),
Expand Down Expand Up @@ -402,7 +401,6 @@ test_that("default priors, inits, burn, thin work", {
n.batch = n.batch,
batch.length = batch.length,
accept.rate = 0.43,
parallel.chains = TRUE,
cov.model = "exponential",
tuning = tuning.list,
n.factors = 3,
Expand Down Expand Up @@ -497,7 +495,6 @@ test_that("verbose prints to the screen", {
inits = inits.list,
n.batch = n.batch,
batch.length = batch.length,
parallel.chains = TRUE,
accept.rate = 0.43,
priors = prior.list,
cov.model = "exponential",
Expand Down Expand Up @@ -754,7 +751,6 @@ test_that("all correlation functions work", {
inits = inits.list,
n.batch = n.batch,
batch.length = batch.length,
parallel.chains = TRUE,
accept.rate = 0.43,
priors = prior.list,
cov.model = "spherical",
Expand Down Expand Up @@ -990,7 +986,6 @@ test_that("random effect gives error when non-numeric", {
data = data.list,
inits = inits.list,
n.batch = n.batch,
parallel.chains = TRUE,
batch.length = batch.length,
n.factors = 3,
accept.rate = 0.43,
Expand Down
5 changes: 0 additions & 5 deletions tests/testthat/test-sfMsPGOcc-NNGP.R
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Original file line number Diff line number Diff line change
Expand Up @@ -205,7 +205,6 @@ test_that("all correlation functions work", {
det.formula = det.formula,
data = data.list,
inits = inits.list,
parallel.chains = TRUE,
n.batch = n.batch,
batch.length = batch.length,
accept.rate = 0.43,
Expand Down Expand Up @@ -414,7 +413,6 @@ out <- sfMsPGOcc(occ.formula = occ.formula,
data = data.list,
inits = inits.list,
n.batch = n.batch,
parallel.chains = TRUE,
batch.length = batch.length,
accept.rate = 0.43,
priors = prior.list,
Expand Down Expand Up @@ -501,7 +499,6 @@ test_that("all correlation functions work", {
det.formula = det.formula,
data = data.list,
inits = inits.list,
parallel.chains = TRUE,
n.batch = n.batch,
batch.length = batch.length,
accept.rate = 0.43,
Expand Down Expand Up @@ -758,7 +755,6 @@ test_that("default priors, inits, burn, thin work", {
det.formula = det.formula,
data = data.list,
n.batch = n.batch,
parallel.chains = TRUE,
batch.length = batch.length,
accept.rate = 0.43,
cov.model = "exponential",
Expand Down Expand Up @@ -1389,7 +1385,6 @@ test_that("all correlation functions work", {
data = data.list,
inits = inits.list,
n.batch = n.batch,
parallel.chains = TRUE,
batch.length = batch.length,
accept.rate = 0.43,
priors = prior.list,
Expand Down
3 changes: 0 additions & 3 deletions tests/testthat/test-spIntPGOcc-NNGP.R
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Original file line number Diff line number Diff line change
Expand Up @@ -194,7 +194,6 @@ test_that("verbose prints to the screen", {
data = data.list,
n.batch = n.batch,
batch.length = batch.length,
parallel.chains = TRUE,
accept.rate = 0.43,
cov.model = "exponential",
tuning = tuning.list,
Expand Down Expand Up @@ -249,7 +248,6 @@ test_that("all correlation functions work", {
n.batch = 40,
batch.length = batch.length,
cov.model = "matern",
parallel.chains = TRUE,
priors = list(nu.unif = c(0.5, 2)),
tuning = list(phi = 0.5, nu = 0.5),
NNGP = TRUE,
Expand Down Expand Up @@ -538,7 +536,6 @@ test_that("default priors and inits work", {
data = data.list,
n.batch = n.batch,
batch.length = batch.length,
parallel.chains = TRUE,
accept.rate = 0.43,
cov.model = "exponential",
tuning = tuning.list,
Expand Down
5 changes: 0 additions & 5 deletions tests/testthat/test-spMsPGOcc-NNGP.R
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Original file line number Diff line number Diff line change
Expand Up @@ -197,7 +197,6 @@ test_that("all correlation functions work", {
det.formula = det.formula,
data = data.list,
inits = inits.list,
parallel.chains = TRUE,
n.batch = n.batch,
batch.length = batch.length,
accept.rate = 0.43,
Expand Down Expand Up @@ -501,7 +500,6 @@ test_that("default priors, inits, burn, thin work", {
data = data.list,
n.batch = n.batch,
batch.length = batch.length,
parallel.chains = TRUE,
accept.rate = 0.43,
cov.model = "exponential",
tuning = tuning.list,
Expand Down Expand Up @@ -842,7 +840,6 @@ test_that("default priors, inits, burn, thin work", {
det.formula = det.formula,
data = data.list,
n.batch = n.batch,
parallel.chains = TRUE,
batch.length = batch.length,
accept.rate = 0.43,
cov.model = "exponential",
Expand Down Expand Up @@ -1182,7 +1179,6 @@ test_that("default priors, inits, burn, thin work", {
out <- spMsPGOcc(occ.formula = occ.formula,
det.formula = det.formula,
data = data.list,
parallel.chains = TRUE,
n.batch = n.batch,
batch.length = batch.length,
accept.rate = 0.43,
Expand Down Expand Up @@ -1525,7 +1521,6 @@ test_that("default priors, inits, burn, thin work", {
det.formula = det.formula,
data = data.list,
n.batch = n.batch,
parallel.chains = TRUE,
batch.length = batch.length,
accept.rate = 0.43,
cov.model = "exponential",
Expand Down
3 changes: 0 additions & 3 deletions tests/testthat/test-spPGOcc-NNGP.R
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Original file line number Diff line number Diff line change
Expand Up @@ -108,7 +108,6 @@ test_that("default priors and inits work", {
det.formula = det.formula,
data = data.list,
n.batch = 40,
parallel.chains = TRUE,
batch.length = batch.length,
cov.model = "exponential",
tuning = tuning.list,
Expand Down Expand Up @@ -158,7 +157,6 @@ test_that("all correlation functions work", {
out <- spPGOcc(occ.formula = occ.formula,
det.formula = det.formula,
data = data.list,
parallel.chains = TRUE,
n.batch = 40,
batch.length = batch.length,
cov.model = "matern",
Expand Down Expand Up @@ -355,7 +353,6 @@ test_that("default priors and inits work", {
det.formula = det.formula,
data = data.list,
n.batch = 40,
parallel.chains = TRUE,
batch.length = batch.length,
cov.model = "exponential",
tuning = tuning.list,
Expand Down
4 changes: 0 additions & 4 deletions tests/testthat/test-stMsPGOcc.R
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Original file line number Diff line number Diff line change
Expand Up @@ -176,7 +176,6 @@ test_that("all correlation functions work", {
out <- stMsPGOcc(occ.formula = occ.formula,
det.formula = det.formula,
data = data.list,
parallel.chains = TRUE,
inits = inits.list,
n.batch = n.batch,
batch.length = batch.length,
Expand Down Expand Up @@ -447,7 +446,6 @@ test_that("default priors, inits, burn, thin work", {
det.formula = det.formula,
data = data.list,
n.batch = n.batch,
parallel.chains = TRUE,
n.factors = n.factors,
ar1 = FALSE,
batch.length = batch.length,
Expand Down Expand Up @@ -495,7 +493,6 @@ test_that("all correlation functions work", {
out <- stMsPGOcc(occ.formula = occ.formula,
det.formula = det.formula,
data = data.list,
parallel.chains = TRUE,
inits = inits.list,
n.batch = n.batch,
batch.length = batch.length,
Expand Down Expand Up @@ -766,7 +763,6 @@ test_that("default priors, inits, burn, thin work", {
det.formula = det.formula,
data = data.list,
n.batch = n.batch,
parallel.chains = TRUE,
n.factors = n.factors,
ar1 = FALSE,
batch.length = batch.length,
Expand Down
4 changes: 0 additions & 4 deletions tests/testthat/test-stPGOcc-NNGP.R
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Original file line number Diff line number Diff line change
Expand Up @@ -186,7 +186,6 @@ test_that("default priors and inits work", {
data = data.list,
n.batch = 40,
batch.length = batch.length,
parallel.chains = TRUE,
cov.model = "exponential",
tuning = tuning.list,
NNGP = TRUE,
Expand Down Expand Up @@ -448,7 +447,6 @@ out <- stPGOcc(occ.formula = occ.formula,
data = data.list,
inits = inits.list,
batch.length = batch.length,
parallel.chains = TRUE,
n.batch = n.batch,
priors = prior.list,
accept.rate = 0.43,
Expand Down Expand Up @@ -564,7 +562,6 @@ test_that("all correlation functions work", {
out <- stPGOcc(occ.formula = occ.formula,
det.formula = det.formula,
data = data.list,
parallel.chains = TRUE,
n.batch = 40,
batch.length = batch.length,
cov.model = "gaussian",
Expand Down Expand Up @@ -908,7 +905,6 @@ test_that("default priors and inits work", {
det.formula = det.formula,
data = data.list,
n.batch = 40,
parallel.chains = TRUE,
batch.length = batch.length,
cov.model = "exponential",
tuning = tuning.list,
Expand Down
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