tests/testthat/test-reli_stats.R
In arcaldwell49/SimplyAgree: Flexible and Robust Agreement and Reliability Analyses
context("agree_test")
testthat::test_that("Simple Use Run Through", {
sf <- matrix(
c(9, 2, 5, 8,
6, 1, 3, 2,
8, 4, 6, 8,
7, 1, 2, 6,
10, 5, 6, 9,
6, 2, 4, 7),
ncol = 4,
byrow = TRUE
)
ratermat1 = ("Rater1 Rater2 Rater3 Rater4
1 1 1 NA 1
2 2 2 3 2
3 3 3 3 3
4 3 3 3 3
5 2 2 2 2
6 1 2 3 4
7 4 4 4 4
8 1 1 2 1
9 2 2 2 2
10 NA 5 5 5
11 NA NA 1 1
12 NA NA 3 NA")
ratermat2 = as.matrix(read.table(textConnection(ratermat1),
header=TRUE,
row.names=1))
expect_error(agree_coef(data = ratermat2,
wide = TRUE,
weighted = TRUE))
expect_error(agree_coef(data = ratermat2,
wide = FALSE,
weighted = TRUE,
col.names = c("Rater1", "Rater2", "Rater3", "Rater4")))
irr1w = agree_coef(data = ratermat2,
wide = TRUE,
weighted = TRUE,
col.names = c("Rater1", "Rater2", "Rater3", "Rater4"))
expect_equivalent(c(0.9753788, .9140007, 0.8649351, 0.8491071),
irr1w$est,
tolerance = .00001)
expect_equivalent(c(1, 1, 1, 1),
irr1w$upper.ci,
tolerance = .01)
expect_equivalent(c(.775, .685, .543, .561),
irr1w$lower.ci,
tolerance = .01)
irr1 = agree_coef(data = ratermat2,
wide = TRUE,
weighted = FALSE,
col.names = c("Rater1", "Rater2", "Rater3", "Rater4"))
expect_equivalent(c(.818,.775,.7611,.743),
irr1$est,
tolerance = .001)
expect_equivalent(c(1, 1, 1, 1),
irr1$upper.ci,
tolerance = .01)
expect_equivalent(c(.5417,.4608,.4243,.4192),
irr1$lower.ci,
tolerance = .01)
colnames(sf) <- paste("J", 1:4, sep = "")
rownames(sf) <- paste("S", 1:6, sep = "")
#sf #example from Shrout and Fleiss (1979)
dat = as.data.frame(sf)
test1 = reli_stats(data = dat,
wide = TRUE,
se_type = "ICC1",
col.names = c("J1", "J2", "J3", "J4"))
test1 = reli_stats(data = dat,
wide = TRUE,
cv_calc = "SEM",
col.names = c("J1", "J2", "J3", "J4"))
test1 = reli_stats(data = dat,
wide = TRUE,
cv_calc = "residuals",
col.names = c("J1", "J2", "J3", "J4"))
test1 = reli_stats(data = dat,
wide = TRUE,
col.names = c("J1", "J2", "J3", "J4"))
test1_aov = reli_aov(data = dat,
wide = TRUE,
col.names = c("J1", "J2", "J3", "J4"))
expect_equivalent(test1$icc$icc, test1$icc$icc)
checktest1 = check(test1)
checktest2 = check(test1_aov)
ptest = print(test1_aov)
ptest2 = plot(test1_aov)
jmvtest2 = jmvreli(data = dat,
vars =c("J1", "J2", "J3", "J4"),
desc = TRUE,
plots = TRUE)
testthat::expect_equivalent(jmvtest2$icctab$asDF$icc,
test1$icc$icc)
testthat::expect_equivalent(jmvtest2$icctab$asDF$lower.ci,
test1$icc$lower.ci)
testthat::expect_equivalent(jmvtest2$icctab$asDF$upper.ci,
test1$icc$upper.ci)
pr_test = print(test1)
p = plot(test1)
df = data.frame(id = c(1,1,1,1,
2,2,2,2,
3,3,3,3,
4,4,4,4,
5,5,5,5,
6,6,6,6),
it = c(1,2,3,4,
1,2,3,4,
1,2,3,4,
1,2,3,4,
1,2,3,4,
1,2,3,4),
va = c(9,2,5,8,
6,1,3,2,
8,4,6,8,
7,1,2,6,
10,5,6,9,
6,2,4,7))
coeftest = agree_coef(wide = FALSE,
data = df,
measure = "va",
item = "it",
id = "id",
weighted = TRUE)
test2 = reli_stats(data = df,
measure = "va",
item = "it",
id = "id")
test2_aov = reli_aov(data = df,
measure = "va",
item = "it",
id = "id")
expect_equivalent(round(test2$icc$icc,4), round(test2_aov$icc$icc,4))
expect_equivalent(test1_aov$icc$icc, test2_aov$icc$icc)
test3_chi = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi")
test3_chi = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi",
cv_calc = "resid")
test3_chi = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi",
cv_calc = "SEM")
test3 = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "perc",
replicates = 49)
test3_aov = reli_aov(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "perc",
replicates = 49)
testthat::expect_equivalent(round(test3$icc$icc,4),
round(test3_aov$icc$icc,4))
testthat::expect_equivalent(round(test3$var_comp$percent,4),
round(test3_aov$var_comp$percent,4))
test3_aov = reli_aov(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi")
test3_aov = reli_aov(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi",
cv_calc = "resid")
test3_aov = reli_aov(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi",
cv_calc = "SEM")
pr_test = print(test3)
p = plot(test3)
pr_test = print(test2)
p = plot(test2)
testthat::expect_equal(test1$icc,
test2$icc)
testthat::expect_equal(test1$anova,
test2$anova)
testthat::expect_equal(test1$var_comp,
test2$var_comp)
testthat::expect_equal(test1$cv,
test2$cv)
testthat::expect_equal(test1$SEM,
test2$SEM)
testthat::expect_equal(test1$SEE,
test2$SEE)
testthat::expect_equal(test1$SEP,
test2$SEP)
df2 = data.frame(
id = c(
1,1,
3,3,
4,4,
5,5,
6,6,
7,7,
9,9,
10,10,
12,12,
13,13,
14,14
),
time = c(
0,1,
0,1,
0,1,
0,1,
0,1,
0,1,
0,1,
0,1,
0,1,
0,1,
0,1
),
fam_trial =
c(1,2,
1,2,
1,2,
1,2,
1,2,
1,2,
1,2,
1,2,
1,2,
1,2,
1,2),
dyspnea = c(
7,8,
7,7,
4,4,
8,6,
5,3,
7,5,
3,3,
5,6,
1,3,
3,4,
4,8
),
headache = c(
0,0,
8,7.5,
0.5,4,
2.5,3.5,
0,0,
1.5,1,
0,1,
1.5,1,
0.5,0,
0,0,
4.5,6.5
)
)
df2$id = as.factor(df2$id)
df2$fam_trial = as.factor(df2$fam_trial)
coeftest2 = agree_coef(wide = FALSE,
data = df2,
measure = "dyspnea",
item = "fam_trial",
id = "id",
weighted = TRUE)
coeftest3 = agree_coef(wide = FALSE,
data = df2,
measure = "headache",
item = "fam_trial",
id = "id",
weighted = TRUE)
### increase coverage calcs ----
test3 = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
cv_calc = "SEM",
other_ci = TRUE,
type = "perc",
replicates = 59)
test3 = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
cv_calc = "residuals",
other_ci = TRUE,
type = "perc",
replicates = 59)
test3 = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
se_type = "ICC2",
other_ci = TRUE,
type = "perc",
replicates = 59)
})
test_that("Weir dataset A",{
df_a = data.frame(
x = c(146, 148, 170, 90, 157, 156, 176, 205),
y = c(140, 152, 152, 99, 145, 153, 167, 218)
)
test_a = reli_aov(data = df_a,
col.names = c("x", "y"),
wide = TRUE)
#testlmer = reli_stats(data = df_a,
# col.names = c("x", "y"),
# wide = TRUE)
expect_equal(round(test_a$SEM$estimate,1),
7.6) # page 236 paragraph 1
test_a = reli_aov(data = df_a,
col.names = c("x", "y"),
wide = TRUE,
se_type = "ICC3")
expect_equal(round(test_a$SEP$estimate,1),
10.2) # page 236 2nd column
expect_equal(round(test_a$SEE$estimate,1),
7.1) # page 236 2nd column
})
arcaldwell49/SimplyAgree documentation built on March 26, 2024, 2:26 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
context("agree_test")
testthat::test_that("Simple Use Run Through", {
sf <- matrix(
c(9, 2, 5, 8,
6, 1, 3, 2,
8, 4, 6, 8,
7, 1, 2, 6,
10, 5, 6, 9,
6, 2, 4, 7),
ncol = 4,
byrow = TRUE
)
ratermat1 = ("Rater1 Rater2 Rater3 Rater4
1 1 1 NA 1
2 2 2 3 2
3 3 3 3 3
4 3 3 3 3
5 2 2 2 2
6 1 2 3 4
7 4 4 4 4
8 1 1 2 1
9 2 2 2 2
10 NA 5 5 5
11 NA NA 1 1
12 NA NA 3 NA")
ratermat2 = as.matrix(read.table(textConnection(ratermat1),
header=TRUE,
row.names=1))
expect_error(agree_coef(data = ratermat2,
wide = TRUE,
weighted = TRUE))
expect_error(agree_coef(data = ratermat2,
wide = FALSE,
weighted = TRUE,
col.names = c("Rater1", "Rater2", "Rater3", "Rater4")))
irr1w = agree_coef(data = ratermat2,
wide = TRUE,
weighted = TRUE,
col.names = c("Rater1", "Rater2", "Rater3", "Rater4"))
expect_equivalent(c(0.9753788, .9140007, 0.8649351, 0.8491071),
irr1w$est,
tolerance = .00001)
expect_equivalent(c(1, 1, 1, 1),
irr1w$upper.ci,
tolerance = .01)
expect_equivalent(c(.775, .685, .543, .561),
irr1w$lower.ci,
tolerance = .01)
irr1 = agree_coef(data = ratermat2,
wide = TRUE,
weighted = FALSE,
col.names = c("Rater1", "Rater2", "Rater3", "Rater4"))
expect_equivalent(c(.818,.775,.7611,.743),
irr1$est,
tolerance = .001)
expect_equivalent(c(1, 1, 1, 1),
irr1$upper.ci,
tolerance = .01)
expect_equivalent(c(.5417,.4608,.4243,.4192),
irr1$lower.ci,
tolerance = .01)
colnames(sf) <- paste("J", 1:4, sep = "")
rownames(sf) <- paste("S", 1:6, sep = "")
#sf #example from Shrout and Fleiss (1979)
dat = as.data.frame(sf)
test1 = reli_stats(data = dat,
wide = TRUE,
se_type = "ICC1",
col.names = c("J1", "J2", "J3", "J4"))
test1 = reli_stats(data = dat,
wide = TRUE,
cv_calc = "SEM",
col.names = c("J1", "J2", "J3", "J4"))
test1 = reli_stats(data = dat,
wide = TRUE,
cv_calc = "residuals",
col.names = c("J1", "J2", "J3", "J4"))
test1 = reli_stats(data = dat,
wide = TRUE,
col.names = c("J1", "J2", "J3", "J4"))
test1_aov = reli_aov(data = dat,
wide = TRUE,
col.names = c("J1", "J2", "J3", "J4"))
expect_equivalent(test1$icc$icc, test1$icc$icc)
checktest1 = check(test1)
checktest2 = check(test1_aov)
ptest = print(test1_aov)
ptest2 = plot(test1_aov)
jmvtest2 = jmvreli(data = dat,
vars =c("J1", "J2", "J3", "J4"),
desc = TRUE,
plots = TRUE)
testthat::expect_equivalent(jmvtest2$icctab$asDF$icc,
test1$icc$icc)
testthat::expect_equivalent(jmvtest2$icctab$asDF$lower.ci,
test1$icc$lower.ci)
testthat::expect_equivalent(jmvtest2$icctab$asDF$upper.ci,
test1$icc$upper.ci)
pr_test = print(test1)
p = plot(test1)
df = data.frame(id = c(1,1,1,1,
2,2,2,2,
3,3,3,3,
4,4,4,4,
5,5,5,5,
6,6,6,6),
it = c(1,2,3,4,
1,2,3,4,
1,2,3,4,
1,2,3,4,
1,2,3,4,
1,2,3,4),
va = c(9,2,5,8,
6,1,3,2,
8,4,6,8,
7,1,2,6,
10,5,6,9,
6,2,4,7))
coeftest = agree_coef(wide = FALSE,
data = df,
measure = "va",
item = "it",
id = "id",
weighted = TRUE)
test2 = reli_stats(data = df,
measure = "va",
item = "it",
id = "id")
test2_aov = reli_aov(data = df,
measure = "va",
item = "it",
id = "id")
expect_equivalent(round(test2$icc$icc,4), round(test2_aov$icc$icc,4))
expect_equivalent(test1_aov$icc$icc, test2_aov$icc$icc)
test3_chi = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi")
test3_chi = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi",
cv_calc = "resid")
test3_chi = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi",
cv_calc = "SEM")
test3 = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "perc",
replicates = 49)
test3_aov = reli_aov(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "perc",
replicates = 49)
testthat::expect_equivalent(round(test3$icc$icc,4),
round(test3_aov$icc$icc,4))
testthat::expect_equivalent(round(test3$var_comp$percent,4),
round(test3_aov$var_comp$percent,4))
test3_aov = reli_aov(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi")
test3_aov = reli_aov(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi",
cv_calc = "resid")
test3_aov = reli_aov(data = df,
measure = "va",
item = "it",
id = "id",
other_ci = TRUE,
type = "chi",
cv_calc = "SEM")
pr_test = print(test3)
p = plot(test3)
pr_test = print(test2)
p = plot(test2)
testthat::expect_equal(test1$icc,
test2$icc)
testthat::expect_equal(test1$anova,
test2$anova)
testthat::expect_equal(test1$var_comp,
test2$var_comp)
testthat::expect_equal(test1$cv,
test2$cv)
testthat::expect_equal(test1$SEM,
test2$SEM)
testthat::expect_equal(test1$SEE,
test2$SEE)
testthat::expect_equal(test1$SEP,
test2$SEP)
df2 = data.frame(
id = c(
1,1,
3,3,
4,4,
5,5,
6,6,
7,7,
9,9,
10,10,
12,12,
13,13,
14,14
),
time = c(
0,1,
0,1,
0,1,
0,1,
0,1,
0,1,
0,1,
0,1,
0,1,
0,1,
0,1
),
fam_trial =
c(1,2,
1,2,
1,2,
1,2,
1,2,
1,2,
1,2,
1,2,
1,2,
1,2,
1,2),
dyspnea = c(
7,8,
7,7,
4,4,
8,6,
5,3,
7,5,
3,3,
5,6,
1,3,
3,4,
4,8
),
headache = c(
0,0,
8,7.5,
0.5,4,
2.5,3.5,
0,0,
1.5,1,
0,1,
1.5,1,
0.5,0,
0,0,
4.5,6.5
)
)
df2$id = as.factor(df2$id)
df2$fam_trial = as.factor(df2$fam_trial)
coeftest2 = agree_coef(wide = FALSE,
data = df2,
measure = "dyspnea",
item = "fam_trial",
id = "id",
weighted = TRUE)
coeftest3 = agree_coef(wide = FALSE,
data = df2,
measure = "headache",
item = "fam_trial",
id = "id",
weighted = TRUE)
### increase coverage calcs ----
test3 = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
cv_calc = "SEM",
other_ci = TRUE,
type = "perc",
replicates = 59)
test3 = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
cv_calc = "residuals",
other_ci = TRUE,
type = "perc",
replicates = 59)
test3 = reli_stats(data = df,
measure = "va",
item = "it",
id = "id",
se_type = "ICC2",
other_ci = TRUE,
type = "perc",
replicates = 59)
})
test_that("Weir dataset A",{
df_a = data.frame(
x = c(146, 148, 170, 90, 157, 156, 176, 205),
y = c(140, 152, 152, 99, 145, 153, 167, 218)
)
test_a = reli_aov(data = df_a,
col.names = c("x", "y"),
wide = TRUE)
#testlmer = reli_stats(data = df_a,
# col.names = c("x", "y"),
# wide = TRUE)
expect_equal(round(test_a$SEM$estimate,1),
7.6) # page 236 paragraph 1
test_a = reli_aov(data = df_a,
col.names = c("x", "y"),
wide = TRUE,
se_type = "ICC3")
expect_equal(round(test_a$SEP$estimate,1),
10.2) # page 236 2nd column
expect_equal(round(test_a$SEE$estimate,1),
7.1) # page 236 2nd column
})
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