tests/testthat/testErrors.R
In slequime/nosoi: A Forward Agent-Based Transmission Chain Simulator
context("Other error messages")
test_that("Error messages on NosoiSim", {
t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_exit_param1 <- function(x){rnorm(x,mean = 10,sd=2)}
p_Exit_fct <- function(t,pExit.param1){plogis(t,pExit.param1,2)}
proba <- function(t,p_max,t_incub){
if(t <= t_incub){p=0}
if(t >= t_incub){p=p_max}
return(p)
}
time_contact = function(t){round(rnorm(1, 3, 1), 0)}
expect_error(
test.nosoiC <- nosoiSim(type="triple", popStructure="none",
length=40,
max.infected=100,
init.individuals=3,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit = list(pExit.param1=p_exit_param1)
),
"Type of transmission should be 'single' or 'dual'-host."
)
expect_error(
test.nosoiC <- nosoiSim(type="single", popStructure="multiple",
length=40,
max.infected=100,
init.individuals=3,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit = list(pExit.param1=p_exit_param1)
),
"Unrecognized parameters for population structure, should be 'none,'discrete' or 'continuous'."
)
})
test_that("Error messages on SanityCheck", {
t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_exit_param1 <- function(x){rnorm(x,mean = 10,sd=2)}
p_Exit_fct <- function(t,pExit.param1){plogis(t,pExit.param1,2)}
proba <- function(t,p_max,t_incub){
if(t <= t_incub){p=0}
if(t >= t_incub){p=p_max}
return(p)
}
time_contact = function(t){round(rnorm(1, 3, 1), 0)}
expect_error(
nosoiSim(type="single", popStructure="none",
length=1,
max.infected=100,
init.individuals=3,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit = list(pExit.param1=p_exit_param1)
),
"You must specify a length (in time units) for your simulation (bigger than 1).",fixed=TRUE
)
expect_error(
test.nosoiC <- nosoiSim(type="single", popStructure="none",
length=100,
max.infected=NA,
init.individuals=3,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit = list(pExit.param1=p_exit_param1)
),
"You must specify a maximum number of infected hosts (bigger than 1).",fixed=TRUE
)
expect_error(
test.nosoiC <- nosoiSim(type="single", popStructure="none",
length=100,
max.infected=100,
init.individuals=NA,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit = list(pExit.param1=p_exit_param1)
),
"The transmission chain should be started by 1 or more (integer) individuals.",fixed=TRUE
)
})
test_that("Error messages on MatrixSanityCheck", {
t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_Move_fct <- function(t){return(0.1)}
p_Exit_fct <- function(t,current.in){
if(current.in=="A"){return(0)}
if(current.in=="B"){return(0.5)}
if(current.in=="C"){return(1)}}
proba <- function(t,p_max,t_incub){
if(t <= t_incub){p=0}
if(t >= t_incub){p=p_max}
return(p)
}
time_contact = function(t){round(rnorm(1, 3, 1), 0)}
transition.matrix = matrix(c(0,0.2,0.4,0.5,0,0.6,0.5,0.8,0),nrow = 3, ncol = 3,dimnames=list(c("A","B","C"),c("A","B","C")))
set.seed(805)
expect_error(
test.nosoiA <- nosoiSim(type="dual", popStructure="discrete",
length.sim=20,
max.infected.A=1000,
max.infected.B=1000,
init.individuals.A=1,
init.individuals.B=0,
init.structure.A="D",
init.structure.B=NA,
structure.matrix.A=transition.matrix,
structure.matrix.B=transition.matrix,
pExit.A=p_Exit_fct,
param.pExit.A=NA,
timeDep.pExit.A=FALSE,
diff.pExit.A=TRUE,
pMove.A=p_Move_fct,
param.pMove.A=NA,
timeDep.pMove.A=FALSE,
diff.pMove.A=FALSE,
nContact.A=time_contact,
param.nContact.A=NA,
timeDep.nContact.A=FALSE,
diff.nContact.A=FALSE,
pTrans.A=proba,
param.pTrans.A=list(p_max=p_max_fct,
t_incub=t_incub_fct),
timeDep.pTrans.A=FALSE,
diff.pTrans.A=FALSE,
prefix.host.A="H",
pExit.B=p_Exit_fct,
param.pExit.B=NA,
timeDep.pExit.B=FALSE,
diff.pExit.B=TRUE,
pMove.B=p_Move_fct,
param.pMove.B=NA,
timeDep.pMove.B=FALSE,
diff.pMove.B=FALSE,
nContact.B=time_contact,
param.nContact.B=NA,
timeDep.nContact.B=FALSE,
diff.nContact.B=FALSE,
pTrans.B=proba,
param.pTrans.B=list(p_max=p_max_fct,
t_incub=t_incub_fct),
timeDep.pTrans.B=FALSE,
diff.pTrans.B=FALSE,
prefix.host.B="V"),
"init.structure should be a state present in structure.matrix.")
})
test_that("Error messages on RasterSanityCheck", {
library(raster)
#Generating a raster for the movement
set.seed(860)
test.raster <- raster(nrows=100, ncols=100, xmn=-50, xmx=50, ymn=-50,ymx=50)
test.raster[] <- runif(10000, -80, 180)
test.raster <- focal(focal(test.raster, w=matrix(1, 5, 5), mean), w=matrix(1, 5, 5), mean)
# plot(test.raster)
bad.raster <- "raster"
t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_Move_fct <- function(t){return(0.1)}
sdMove_fct = function(t,current.env.value){return(100/(current.env.value+1))}
p_Exit_fct <- function(t){return(0.08)}
proba <- function(t,p_max,t_incub){
if(t <= t_incub){p=0}
if(t >= t_incub){p=p_max}
return(p)
}
time_contact = function(t){round(rnorm(1, 3, 1), 0)}
start.pos <- c(0,0)
bad.start.pos <- c(100,100)
expect_error(nosoiSim(type="single", popStructure="continuous",
length=200,
max.infected=500,
init.individuals=1,
init.structure=start.pos,
structure.raster=bad.raster,
pMove=p_Move_fct,
param.pMove=NA,
diff.sdMove=TRUE,
sdMove=sdMove_fct,
param.sdMove=NA,
attracted.by.raster=TRUE,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit=NA),
"structure.raster must be a raster (class RasterLayer).", fixed=TRUE)
expect_error(nosoiSim(type="single", popStructure="continuous",
length=200,
max.infected=500,
init.individuals=1,
init.structure=bad.start.pos,
structure.raster=test.raster,
pMove=p_Move_fct,
param.pMove=NA,
diff.sdMove=TRUE,
sdMove=sdMove_fct,
param.sdMove=NA,
attracted.by.raster=TRUE,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit=NA),
"Your starting position (init.structure) should be on the raster.", fixed=TRUE)
set.seed(805)
expect_error(
nosoiSim(type="dual", popStructure="continuous",
length.sim=200,
max.infected.A=500,
max.infected.B=500,
init.individuals.A=1,
init.individuals.B=0,
init.structure.A=bad.start.pos,
init.structure.B=NA,
structure.raster.A=test.raster,
structure.raster.B=test.raster,
pExit.A=p_Exit_fct,
param.pExit.A=NA,
timeDep.pExit.A=FALSE,
diff.pExit.A=FALSE,
pMove.A=p_Move_fct,
param.pMove.A=NA,
timeDep.pMove.A=FALSE,
diff.pMove.A=FALSE,
diff.sdMove.A=TRUE,
sdMove.A=sdMove_fct,
param.sdMove.A=NA,
attracted.by.raster.A=TRUE,
nContact.A=time_contact,
param.nContact.A=NA,
timeDep.nContact.A=FALSE,
diff.nContact.A=FALSE,
pTrans.A=proba,
param.pTrans.A=list(p_max=p_max_fct,
t_incub=t_incub_fct),
timeDep.pTrans.A=FALSE,
diff.pTrans.A=FALSE,
prefix.host.A="H",
pExit.B=p_Exit_fct,
param.pExit.B=NA,
timeDep.pExit.B=FALSE,
diff.pExit.B=FALSE,
pMove.B=NA,
param.pMove.B=NA,
timeDep.pMove.B=FALSE,
diff.pMove.B=FALSE,
diff.sdMove.B=FALSE,
sdMove.B=NA,
param.sdMove.B=NA,
attracted.by.raster.B=FALSE,
nContact.B=time_contact,
param.nContact.B=NA,
timeDep.nContact.B=FALSE,
diff.nContact.B=FALSE,
pTrans.B=proba,
param.pTrans.B=list(p_max=p_max_fct,
t_incub=t_incub_fct),
timeDep.pTrans.B=FALSE,
diff.pTrans.B=FALSE,
prefix.host.B="V"),
"Your starting position (init.structure) should be on the raster.",fixed=TRUE)
expect_error(
test.nosoiA <- nosoiSim(type="single", popStructure="discrete",
length=100,
max.infected=200,
init.individuals=1,
init.structure="A",
structure.matrix=transition.matrix,
pMove=p_Move_fct,
param.pMove=NA,
diff.nContact=FALSE,
hostCount.nContact=TRUE,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit=NA
),
"diff.nContact should be TRUE to use hostCount.nContact.")
})
test_that("Error messages on drawBernouilli", {
test = data.frame(A=0.5,B=0.6,C=0.1)
expect_error(drawBernouilli(test),
"Function 'drawBernouilli' should be applied to a vector.")
})
slequime/nosoi documentation built on Feb. 15, 2024, 3:31 p.m.
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context("Other error messages")
test_that("Error messages on NosoiSim", {
t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_exit_param1 <- function(x){rnorm(x,mean = 10,sd=2)}
p_Exit_fct <- function(t,pExit.param1){plogis(t,pExit.param1,2)}
proba <- function(t,p_max,t_incub){
if(t <= t_incub){p=0}
if(t >= t_incub){p=p_max}
return(p)
}
time_contact = function(t){round(rnorm(1, 3, 1), 0)}
expect_error(
test.nosoiC <- nosoiSim(type="triple", popStructure="none",
length=40,
max.infected=100,
init.individuals=3,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit = list(pExit.param1=p_exit_param1)
),
"Type of transmission should be 'single' or 'dual'-host."
)
expect_error(
test.nosoiC <- nosoiSim(type="single", popStructure="multiple",
length=40,
max.infected=100,
init.individuals=3,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit = list(pExit.param1=p_exit_param1)
),
"Unrecognized parameters for population structure, should be 'none,'discrete' or 'continuous'."
)
})
test_that("Error messages on SanityCheck", {
t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_exit_param1 <- function(x){rnorm(x,mean = 10,sd=2)}
p_Exit_fct <- function(t,pExit.param1){plogis(t,pExit.param1,2)}
proba <- function(t,p_max,t_incub){
if(t <= t_incub){p=0}
if(t >= t_incub){p=p_max}
return(p)
}
time_contact = function(t){round(rnorm(1, 3, 1), 0)}
expect_error(
nosoiSim(type="single", popStructure="none",
length=1,
max.infected=100,
init.individuals=3,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit = list(pExit.param1=p_exit_param1)
),
"You must specify a length (in time units) for your simulation (bigger than 1).",fixed=TRUE
)
expect_error(
test.nosoiC <- nosoiSim(type="single", popStructure="none",
length=100,
max.infected=NA,
init.individuals=3,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit = list(pExit.param1=p_exit_param1)
),
"You must specify a maximum number of infected hosts (bigger than 1).",fixed=TRUE
)
expect_error(
test.nosoiC <- nosoiSim(type="single", popStructure="none",
length=100,
max.infected=100,
init.individuals=NA,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit = list(pExit.param1=p_exit_param1)
),
"The transmission chain should be started by 1 or more (integer) individuals.",fixed=TRUE
)
})
test_that("Error messages on MatrixSanityCheck", {
t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_Move_fct <- function(t){return(0.1)}
p_Exit_fct <- function(t,current.in){
if(current.in=="A"){return(0)}
if(current.in=="B"){return(0.5)}
if(current.in=="C"){return(1)}}
proba <- function(t,p_max,t_incub){
if(t <= t_incub){p=0}
if(t >= t_incub){p=p_max}
return(p)
}
time_contact = function(t){round(rnorm(1, 3, 1), 0)}
transition.matrix = matrix(c(0,0.2,0.4,0.5,0,0.6,0.5,0.8,0),nrow = 3, ncol = 3,dimnames=list(c("A","B","C"),c("A","B","C")))
set.seed(805)
expect_error(
test.nosoiA <- nosoiSim(type="dual", popStructure="discrete",
length.sim=20,
max.infected.A=1000,
max.infected.B=1000,
init.individuals.A=1,
init.individuals.B=0,
init.structure.A="D",
init.structure.B=NA,
structure.matrix.A=transition.matrix,
structure.matrix.B=transition.matrix,
pExit.A=p_Exit_fct,
param.pExit.A=NA,
timeDep.pExit.A=FALSE,
diff.pExit.A=TRUE,
pMove.A=p_Move_fct,
param.pMove.A=NA,
timeDep.pMove.A=FALSE,
diff.pMove.A=FALSE,
nContact.A=time_contact,
param.nContact.A=NA,
timeDep.nContact.A=FALSE,
diff.nContact.A=FALSE,
pTrans.A=proba,
param.pTrans.A=list(p_max=p_max_fct,
t_incub=t_incub_fct),
timeDep.pTrans.A=FALSE,
diff.pTrans.A=FALSE,
prefix.host.A="H",
pExit.B=p_Exit_fct,
param.pExit.B=NA,
timeDep.pExit.B=FALSE,
diff.pExit.B=TRUE,
pMove.B=p_Move_fct,
param.pMove.B=NA,
timeDep.pMove.B=FALSE,
diff.pMove.B=FALSE,
nContact.B=time_contact,
param.nContact.B=NA,
timeDep.nContact.B=FALSE,
diff.nContact.B=FALSE,
pTrans.B=proba,
param.pTrans.B=list(p_max=p_max_fct,
t_incub=t_incub_fct),
timeDep.pTrans.B=FALSE,
diff.pTrans.B=FALSE,
prefix.host.B="V"),
"init.structure should be a state present in structure.matrix.")
})
test_that("Error messages on RasterSanityCheck", {
library(raster)
#Generating a raster for the movement
set.seed(860)
test.raster <- raster(nrows=100, ncols=100, xmn=-50, xmx=50, ymn=-50,ymx=50)
test.raster[] <- runif(10000, -80, 180)
test.raster <- focal(focal(test.raster, w=matrix(1, 5, 5), mean), w=matrix(1, 5, 5), mean)
# plot(test.raster)
bad.raster <- "raster"
t_incub_fct <- function(x){rnorm(x,mean = 5,sd=1)}
p_max_fct <- function(x){rbeta(x,shape1 = 5,shape2=2)}
p_Move_fct <- function(t){return(0.1)}
sdMove_fct = function(t,current.env.value){return(100/(current.env.value+1))}
p_Exit_fct <- function(t){return(0.08)}
proba <- function(t,p_max,t_incub){
if(t <= t_incub){p=0}
if(t >= t_incub){p=p_max}
return(p)
}
time_contact = function(t){round(rnorm(1, 3, 1), 0)}
start.pos <- c(0,0)
bad.start.pos <- c(100,100)
expect_error(nosoiSim(type="single", popStructure="continuous",
length=200,
max.infected=500,
init.individuals=1,
init.structure=start.pos,
structure.raster=bad.raster,
pMove=p_Move_fct,
param.pMove=NA,
diff.sdMove=TRUE,
sdMove=sdMove_fct,
param.sdMove=NA,
attracted.by.raster=TRUE,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit=NA),
"structure.raster must be a raster (class RasterLayer).", fixed=TRUE)
expect_error(nosoiSim(type="single", popStructure="continuous",
length=200,
max.infected=500,
init.individuals=1,
init.structure=bad.start.pos,
structure.raster=test.raster,
pMove=p_Move_fct,
param.pMove=NA,
diff.sdMove=TRUE,
sdMove=sdMove_fct,
param.sdMove=NA,
attracted.by.raster=TRUE,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit=NA),
"Your starting position (init.structure) should be on the raster.", fixed=TRUE)
set.seed(805)
expect_error(
nosoiSim(type="dual", popStructure="continuous",
length.sim=200,
max.infected.A=500,
max.infected.B=500,
init.individuals.A=1,
init.individuals.B=0,
init.structure.A=bad.start.pos,
init.structure.B=NA,
structure.raster.A=test.raster,
structure.raster.B=test.raster,
pExit.A=p_Exit_fct,
param.pExit.A=NA,
timeDep.pExit.A=FALSE,
diff.pExit.A=FALSE,
pMove.A=p_Move_fct,
param.pMove.A=NA,
timeDep.pMove.A=FALSE,
diff.pMove.A=FALSE,
diff.sdMove.A=TRUE,
sdMove.A=sdMove_fct,
param.sdMove.A=NA,
attracted.by.raster.A=TRUE,
nContact.A=time_contact,
param.nContact.A=NA,
timeDep.nContact.A=FALSE,
diff.nContact.A=FALSE,
pTrans.A=proba,
param.pTrans.A=list(p_max=p_max_fct,
t_incub=t_incub_fct),
timeDep.pTrans.A=FALSE,
diff.pTrans.A=FALSE,
prefix.host.A="H",
pExit.B=p_Exit_fct,
param.pExit.B=NA,
timeDep.pExit.B=FALSE,
diff.pExit.B=FALSE,
pMove.B=NA,
param.pMove.B=NA,
timeDep.pMove.B=FALSE,
diff.pMove.B=FALSE,
diff.sdMove.B=FALSE,
sdMove.B=NA,
param.sdMove.B=NA,
attracted.by.raster.B=FALSE,
nContact.B=time_contact,
param.nContact.B=NA,
timeDep.nContact.B=FALSE,
diff.nContact.B=FALSE,
pTrans.B=proba,
param.pTrans.B=list(p_max=p_max_fct,
t_incub=t_incub_fct),
timeDep.pTrans.B=FALSE,
diff.pTrans.B=FALSE,
prefix.host.B="V"),
"Your starting position (init.structure) should be on the raster.",fixed=TRUE)
expect_error(
test.nosoiA <- nosoiSim(type="single", popStructure="discrete",
length=100,
max.infected=200,
init.individuals=1,
init.structure="A",
structure.matrix=transition.matrix,
pMove=p_Move_fct,
param.pMove=NA,
diff.nContact=FALSE,
hostCount.nContact=TRUE,
nContact=time_contact,
param.nContact=NA,
pTrans = proba,
param.pTrans = list(p_max=p_max_fct,
t_incub=t_incub_fct),
pExit=p_Exit_fct,
param.pExit=NA
),
"diff.nContact should be TRUE to use hostCount.nContact.")
})
test_that("Error messages on drawBernouilli", {
test = data.frame(A=0.5,B=0.6,C=0.1)
expect_error(drawBernouilli(test),
"Function 'drawBernouilli' should be applied to a vector.")
})
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