library(vortexR)
library(vortexRdata)
context("test fit_regression")
test_that("fit-regressin", {
# Using Pacioni et al. example data. See ?pac.run.lhs and ?pac.lhs for more
# details.
data(pac.run.lhs, pac.lhs)
# Remove base scenario from .stdat data
pac.lhs.no.base <- pac.lhs[!pac.lhs$scen.name == "ST_LHS(Base)", ]
# Use function lookup_table to obtain correct parameter values at year 0
lkup.ST_LHS <- lookup_table(data=pac.lhs.no.base, project="Pacioni_et_al",
scenario="ST_LHS",
pop="Population 1",
SVs=c("SV1", "SV2", "SV3", "SV4", "SV5", "SV6",
"SV7"),
save2disk=FALSE)
# Remove base scenario from .run output in long format
lrun.ST_LHS.no.base <- pac.run.lhs[[2]][
!pac.run.lhs[[2]]$Scenario == "ST_LHS(Base)",
]
reg <- fit_regression(data=lrun.ST_LHS.no.base, lookup=lkup.ST_LHS,
census=FALSE,
project="Pacioni_et_al", scenario="ST_LHS", popn=1,
param="N", vs=c("SV1", "SV2", "SV3"), l=2, ncand=30,
save2disk=FALSE)
expect_is(reg, "glmulti")
coefs <- coef(reg@objects[[1]])
expect_true(round(0.0038677, 6)==round(coefs["SV1"], 6))
reg.prop <- fit_regression(data=lrun.ST_LHS.no.base, lookup=lkup.ST_LHS,
census=FALSE,
project="Pacioni_et_al", scenario="ST_LHS", popn=1,
param="GeneDiv", vs=c("SV1", "SV2", "SV3"), l=2, ncand=30,
save2disk=FALSE)
expect_is(reg.prop, "glmulti")
coefs <- coef(reg.prop@objects[[1]])
expect_true(round(1.663474e-04, 6)==round(coefs["SV1"], 6))
reg.prop2 <- fit_regression(data=lrun.ST_LHS.no.base, lookup=lkup.ST_LHS,
census=FALSE,
links = c("logit", "probit", "cauchit", "loglog"),
project="Pacioni_et_al", scenario="ST_LHS", popn=1,
param="GeneDiv", vs=c("SV1", "SV2", "SV3"), l=2,
ncand=30,
save2disk=FALSE)
coefs <- coef(reg.prop2@objects[[1]])
expect_true(round(0.0002583495, 6)==round(coefs["SV1"], 6))
})
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