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10 Undertaking meta- analysis
81
81
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CT
Study
Dewey 2006
Kefer 2005
Langer 2009
Maintz 2007
Pouleur 2008
MRI
Study
Dewey 2006
Kefer 2005
Langer 2009
Maintz 2007
Pouleur 2008
TP
4
5
62
2
6
32
1
2
25
1
2
15
1
7
16
TP
FN
FP
42
7
2
30
4
9
18
8
15
15
1
1
17
0
17
0.94 [0.85, 0.98]
46
0.94 [0.80, 0.99]
12
0.96 [0.80, 1.00]
40
0.94 [0.70, 1.00]
2
0.94 [0.71, 1.00]
53
Sensitivity (95% CI)
TN
0.86 [0.73, 0.94]
39
0.88 [0.73, 0.97]
9
0.69 [0.48, 0.86]
27
0.94 [0.70, 1.00]
3
1.00 [0.80, 1.00]
43
Sensitivity (95% Cl)
lN
FN
FP
Specificity (95% CI)
0.90 [0.79, 0.97]
0.67 [0.41, 0.87]
0.95 [0.84, 0.99]
0.50 [0.07, 0.93]
0.88 [0.77, 0.95]
Specificity (95% CI)
0.95 [0.83, 0.99]
0.50 [0.26, 0.74]
0.64 [0.48, 0.78]
0.75 [0.19, 0.99]
0.72 [0.59, 0.83]
Sensitivity (95% CI) Specificity (95% Cl)
00.2 0.40.6 0.8100.2 0.40.6 0.
Sensitivity (95% CI) Specificity (95% Cl)
00.2 0.40.6 0.8100.2 0.40.6 0.
Figure10.6.b Forest plot of comparative studies of CT versus MRI for coronary artery disease.
Source: Data taken from Schuetz 2010
Box 10.6.a Large gradient values in SAS for bivariate model parameters for CT and
MRI comparative studies (model without test type covariate)
Parameter Estimates
Standard
Parameter
msens
mspec
s2usens
s2uspec
covsesp
Estimate
2.0000
1.0000
–111E-14
2.21E-11
–108E-15
Error DF t Value Pr > |t| 95% Confidence Limits Gradient
0.4686
0.2041
0.4240
0.01977
0.0236
4.27
3
0.0163
4.90
3
1.0000
–0.00
3
1.0000
0.00
3
3
-
-
0.5086
0.3504
–1.3493
–0.06291
-
3.4914
1.6496
1.3493
0.06291
-
–6.88008
–25.4401
–0.31355
–188.328
–44.9080
-
To assess the effect of test type on sensitivity and specificity, models with and without
the covariate were fitted. The output of fitting a bivariate model without the test type
covariate to the data using Proc NLMIXED in SAS showed that the convergence criterion
was satisfied. However, all the parameter estimates have large gradient values, indicating poor estimation (Box10.6.a). A model may satisfy a convergence criterion but may
be unstable (e.g. changing the starting values results in a change in parameter estimates), or have missing standard errors for one or more parameter estimates. Therefore,
in addition to meeting a convergence criterion, meta- analysts should check for missing
standard errors and if the program output permits, also check that gradient values for
all model parameters are very close to zero before concluding that the analysis has successfully converged.
Several attempts were made to improve estimation of the parameters by specifying
different options for fitting the model (see code in Appendix 9 of the online supplementary material (10.S1 Code for undertaking meta- analysis)). The options included
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10.6 Meta- analysis ofsparse data anda typical data sets
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Box 10.6.b Improved estimation in SAS of bivariate model parameters for CT and
MRI comparative studies by changing model fitting options
Parameter Estimates
Standard
Parameter
msens
mspec
s2usens
s2uspec
covsesp
Estimate
2.2554
1.3083
0.006812
0.4138
–0.03331
Error DF t Value Pr > |t| 95% Confidence Limits Gradient
0.3569
0.3375
0.5582
0.3633
0.1724
0.0080
6.32
3
0.0304
3.88
3
0.9910
0.01
3
0.3374
1.14
3
0.8592
–0.19
3
1.1194
0.2342
–1.7695
–0.7424
–0.5821
3.3913
2.3823
1.7831
1.5701
0.5155
0.000057
0.000543
1.70698
–0.02091
–0.21665
increasing the number of quadrature points; changing the optimization technique from
the default quasi- Newton technique to the Newton- Raphson technique; trying different
starting values, e.g. using a grid search; and setting boundary constraints for the variance parameters (i.e. variance ≥ 0). Imposing boundary constraints can reduce the risk
of convergence problems. If boundary constraints are triggered for variance parameters, then estimation of these parameters is truncated at zero. The same options
explored here for fitting the bivariate model can be applied when fitting the HSROC
model in SAS. For the CT versus MRI example, trying each of the options separately
failed to improve estimation of the bivariate model parameters and there were error
and/or warning messages. Finally, setting boundary constraints for the variance parameters and using a different set of starting values resulted in more reliable parameter
estimates (Box10.6.b).
The gradient for the variance of the random effects for logit(sensitivity) is large
(1.70698), and there is concern about the analysis. Since the estimate of the variance of
logit(sensitivity) is close to zero (s2usens = 0.006812) and given the previous observation
about limited heterogeneity in the sensitivity estimates for CT, simplifying the model by
removing either a variance or covariance parameter may be a reasonable strategy. Such
an analysis will be explored in Section10.6.2.
When the bivariate model was fitted to this data set in Stata using meqrlogit (see
Appendix 11 of the online supplementary material (10.S1 Code for undertaking metaanalysis)), the results were similar to those obtained using SAS and all the gradient values were close to zero (Box10.6.c). In Stata, the default optimization technique for
meqrlogit and xtmelogit is a Newton- Raphson technique. Starting values are
determined by the commands and are not specified by the user.
As stated in Section10.2.3, it is not possible to increase the number of quadrature points
used by glmer to fit a bivariate model in R. Different optimization options can be explored
simultaneously using the allFit function (see code in Appendix 14 of the online
supplementary material (10.S1 Code for undertaking meta- analysis)). The options are
(1) bound optimization by quadratic approximation (BOBYQA); (2) an algorithm derived
from BOBYQA named NLOPT_LN_BOBYQA in Box10.6.d; (3) limited memory Broyden–
Fletcher–Goldfarb–Shanno bound- constrained (L- BFGS- B) optimization; (4) Nelder- Mead
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10 Undertaking meta- analysis
.2104002
2.335581
5
nterval]
1.972165
2
]
=0
0
=1
0
4
0
4
=5
=20
-53.173887
1
1.528322
338.5475
study_id:
nterval]
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Box 10.6.c Estimation in Stata of bivariate model parameters for CT and MRI
comparative studies (model without test type covariate)
Iteration 3:
loglikelihood=
Gradientvector (length= .000245):
eq1:eq1:lns1_1_1: lns1_1_2: atr1_1_1_2:
sens spec _cons_cons _cons
r1 .0000374 .0000781 .0000129 .0002278 -.0000219
Mixed-effectslogistic regressionNumberofobs
Binomialvariable:n
Group variable: study_id Number of groups
Obs per group:
min=
avg= 4.
max=
Integration points= 5Waldchi2(2)
Log likelihood =-53.173887Prob>chi2
true Coef.Std.Err.zP>|z|[95%Conf. Interval
sens 2.249856.204119 11.020.000 1.849792.64992
spec 1.308397.33866343.860.000 .6446286
Random-effectsParameters Estimate Std. Err. [95% Conf.I
study_id: Unstructured
var(sens) .001594.01471322.22e-11114638.
var(spec) .4178528 .366883.074757
cov(sens,spec) -.0258082.1205167-.2620166
Using option stddev to output standard deviations and correlation instead of the
variances and covariance above gives the following output.
Random-effectsParameters Estimate Std. Err. [95% Conf.I
Unstructured
sd(sens) .0399259 .1842611 4.71e-06
sd(spec) .6464237 .2837953 .2734133
corr(sens,spec) -1 .0011101 -1
45.1
.000
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10.6 Meta- analysis ofsparse data anda typical data sets
2
~ , with .
0
B
## nloptwrap.NLOPT_LN_BOBYQA
0.03977226
0.6429241
–0.9999665
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Box 10.6.d Estimation in R of bivariate model parameters for CT and MRI comparative studies (model without test type covariate)
ss$fixef
##
## bobyqa
## Nelder_Mead
## nlminbwrap
## nmkbw
## optimx.L-BFGS-B
## nloptwrap.NLOPT_LN_NELDERMEAD
## nloptwrap.NLOPT_LN_BOBYQA
ss$sdcor ## table of random effect SDs and correlations
##
## bobyqa
## Nelder_Mead
## nlminbwrap
## nmkbw
## optimx.L-BFGS-B
## nloptwrap.NLOPT_LN_NELDERMEAD
## table of fixed effects
sens
2.249866
2.249865
2.249866
2.249880
2.249866
2.249860
2.249818
Study_ID.sens
1.308946
1.308946
1.308946
1.309040
1.308946
1.308935
1.308969
0.03989542
0.03989567
0.03989607
0.03977192
0.03989560
0.03990032
spec
Study_ID.spec.sens
0.6429813
0.6429822
0.6429808
0.6429379
0.6429822
0.6429883
Study_ID.spec
–1.0000000
–1.0000000
–1.0000000
–0.9999521
–1.0000000
–0.9999998
method; (5) Nelder- Mead simplex algorithm (NLOPT_LN_NELDERMEAD in Box10.6.d);
(6) nonlinear minimization with box constraints (nlminb); and (7) Nelder- Mead algorithm
for derivative- free optimization (nmkb). In this example, the seven optimization options
in the red box produced similar results (Box10.6.d). The help files of the functions and
commands in different software packages are a useful source of information on the quadrature and optimization options available for model estimation.
10.6.2 Simplifying hierarchical models
Hierarchical models can be simplified by removing parameters from the regression equation and editing the covariance structure. Prior to simplifying the models, plot the data on
forest and SROC plots to assess heterogeneity visually and to gain a better understanding
of the data (e.g. all or most studies report 100% sensitivity and/or specificity with no indication of a threshold effect). If the bivariate model described in Chapter9, Section9.4.1, is
simplified by assuming that the covariance or correlation is zero (i.e. an independent variance–covariance structure), the model reduces to two univariate random- effects logistic
regression models for sensitivity and specificity as follows:
Ai A A
N
Bi B
0
(10.7)
2
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10 Undertaking meta- analysis
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Study
Zar 2019
Nicol 2018
Sabi 2018
FP
TP
0
108
31
0
206
64
2
22
TN
FN
51
97
105
67
Sensitivity (95% Cl)
0.22 [0.16, 0.30]
0.24 [0.19, 0.29]
0.25 [0.16, 0.35]
Specificity (95% Cl)
1. 00 [0.93, 1. 00]
1. 00 [0.96, 1. 00]
0.98 [0.93, 1. 00]
Sensitivity (95% CI) Specificity (95% Cl)
00.2 0.40.6 0.8100.2 0.40.6 0.
Figure10.6.c Forest plot of Xpert Ultra against a composite reference standard. Studies on the
plot are sorted by sensitivity and then by specificity. Source: Adapted from Kay 2020
If there is little or no observed variation in sensitivity and/or specificity, these univariate models can be further simplified by dropping one or both variance parameters.
Without the variance parameters, the models reduce to fixed- effect logistic regression
models. For example, a Cochrane Review included three studies that assessed Xpert
Ultra against a composite reference standard using sputum specimens from children
(Kay 2020). The estimates of sensitivity and specificity were similar in the three studies
(Figure10.6.c). Given the small number of studies and lack of heterogeneity, a fixed-
effect
meta- analysis was considered appropriate. In Stata the meqrlogit or xtmelogit
command cannot be used for fitting fixed- effect logistic regression models; instead use
the blogit command (see code in Appendix 15 of the online supplementary material
(10.S1 Code for undertaking meta- analysis)).
For the IOC example introduced in Section10.6, when the covariance matrix for the
random effects for logit(sensitivity) and logit(specificity) was unstructured (model A)–
i.e. no constraints imposed so that the variances and covariance were uniquely estimated– the variances were poorly estimated, especially the variance parameter for the
logit(sensitivity) of IOC. It is unsurprising that the variances were poorly estimated
given the small number of studies and sparse data. Alternative models were investigated, as shown in Table10.6.a. In model B, the exchangeable covariance structure estimated a common variance and a covariance for the random effects of the logit(sensitivity)
and logit(specificity). The independent covariance structure used in model C estimated
distinct variances for the random effects, but the covariance was assumed to be zero
(i.e. two separate univariate random- effects logistic regression models). In model D the
variance parameter for logit(sensitivity) was dropped and so there was no covariance.
Stata code for the four models is in Appendix 16 of the online supplementary material
(10.S1 Code for undertaking meta- analysis).
To check the robustness of the assumptions about the variances of the random
effects, the estimates of sensitivity and specificity were also compared between models
(Table10.6.a). The analytical approach adopted was based on the reasoning that it is
inappropriate to overfit models by estimating too many parameters from few studies,
and to simplify models when parameter estimates cannot be reliably estimated. The
validity of this approach has been investigated in a simulation study that concluded
that simpler hierarchical models are valid in situations with few studies or sparse data
(Takwoingi 2017). For estimating summary sensitivity and specificity, simplifying the
bivariate model to univariate random- effects logistic regression models is appropriate.
For estimating a summary curve, an HSROC model without the shape parameter (i.e. a
symmetrical curve) can be used. If there is very little or no observed heterogeneity,
fixed- effect equivalents of the models can be applied.
The output of the bivariate model fitted to the CT and MRI comparative studies in
Stata (Box10.6.c) and R (Box10.6.d) show that the correlation of the logits was
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10.6 Meta- analysis ofsparse data anda typical data sets
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Table10.6.a Parameter andsummary estimates forIOC frommodels withdierent variance–covariance
structure
Parameter Models
A: Unstructured
variance–covariance
structure
Mean logit
sensitivity (SE)
Mean logit
specificity (SE)
Variance of random
effects for logit
sensitivity (SE)
Variance of random
effects for logit
specificity (SE)
Correlation of the
logits (SE)
Sensitivity (95% CI) 99.9 (14.1, to 100) 98.8 (83.1 to 99.9) 99.8 (42.3 to 100) 94.4 (88.7 to 97.3)
Specificity (95% CI) 98.5 (95.8 to 99.4) 99.2 (94.5 to 99.9) 98.5 (95.6 to 99.5) 98.5 (95.6 to 99.5)
7.06 (4.53) 4.43 (1.45) 6.12 (3.2) 2.82 (0.39)
4.15 (0.52) 4.80 (1.00) 4.19 (0.57) 4.19 (0.57)
16.7 (26.9) 2.85 (2.71) 9.74 (12.7) 0
0.25 (0.54) 2.85 (2.71) 0.34 (0.67) 0.34 (0.67)
–0.73 (0.98) 0.03 (0.76) 0 0
B: Exchangeable
variance–covariance
structure
C: Independent
variance–covariance
structure
D: Fixed effects for
sensitivity of IOC
estimated on the boundary of the parameter space as –1 (see Section10.6.1). Therefore,
simplifying the model to two univariate random- effects logistic regression models for
sensitivity and specificity, by removing the correlation or covariance parameter, seems
a reasonable first step (see SAS code in Appendix 9 of the online supplementary material (10.S1 Code for undertaking meta- analysis)). The output of fitting this model in SAS
shows that the boundary constraint for the variance of logit(sensitivity) was triggered
(see Active BC column in (i) in Box10.6.e). Thus the next step is to simplify further by
also removing this variance parameter, i.e. assume a fixed effect for sensitivity. Covariate
terms can now be added to this model to compare the sensitivity and specificity of CT
and MRI (see SAS code in Appendix 9 of the online supplementary material (10.S1 Code
for undertaking meta-
analysis)). The difficulty encountered in the analysis of CT and
MRI when using Proc NLMIXED in SAS was not experienced when using Stata (see
code in Appendix 11 of the online supplementary material (10.S1 Code for undertaking
meta- analysis)) and R (Appendix 14 of the online supplementary material (10.S1 Code
for undertaking meta- analysis)). It is possible for the analysis of sparse data to be problematic in one program and not as problematic in another program due to differences
in the implementation of the programs.
Univariate models can also be used for investigating heterogeneity or for test comparisons when the rationale for simplifying hierarchical models is not due to the number of studies or convergence issues. A univariate random- effects logistic meta- regression
model that allowed for a separate variance term for the random effects of logit(sensitivity)
for each test was used in the main meta- analysis comparing the accuracy of nine firsttrimester serum test strategies for Down syndrome screening (Alldred 2015). The analysis
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10 Undertaking meta- analysis
2
~ ,.
2
Ak
(i) Model without covariance parameter
(ii) Model without
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Box 10.6.e Simplifying the bivariate model to univariate random- effects logistic
regression models for CT and MRI comparative studies (model without covariate)
Parameter
msens
mspec
s2usens
s2uspec
Estimate
2.2385
1.3122
0
0.4111
covariance parameter and variance parameter for logit (sensitivity)
Fit Statistics
-2 Log Likelihood
AIC (smaller is better)
AICC (smaller is better)
BIC (smaller is better)
Parameter Estimates
Standard
Error DF t Value Pr > |t|95% Confidence Limits Gradient Active BC
0.0014
11.46
0.1953
0.3363
0.3602
3
0.0299
3.90
3
1.14
-
0.3366
3
-
3
106.4
114.4
117.1
112.9
0.000407
1.6168
0.2418
-
–0.7353
2.8602
–0.00025
2.3825
1.81131
1.5575
-
–8.11E-6
-
Lower BC
included all studies that used a 5% FPR threshold. Equation10.8 expressed only for
logit(sensitivity) was thus extended as follows:
where μ
kth test; μA estimates the mean logit(sensitivity) for the index test used as the referent
test (note not the reference standard); μA+vAZk estimates the mean logit(sensitivity)
for the kth test; and
Fit Statistics
-2 Log Likelihood
AIC (smaller is better)
AICC (smaller is better)
BIC (smaller is better)
Parameter Estimates
2.2385
1.3122
0.4111
Standard
Error DF t Value Pr > |t|95% Confidence Limits Gradient
0.0003
11.46
0.1953
0.3363
0.3602
4
0.0175
3.90
4
0.3174
1.14
4
N vZ
Aik A A k Ak
Parameter
msens
mspec
s2uspec
Estimate
is the logit(sensitivity) for the kth test within the ith study; Zk represents the
Aik
106.4
112.4
113.9
111.3
0.000012
1.6961
0.3784
–0.5890
2.7809
2.2460
1.4112
–0.00012
–0.00004
(10.8)
is the variance of logit(sensitivity) for the kth test. The Stata
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10.7 Meta- analysis withmultiple thresholds per study
90
Sensitivity (95% CI)
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A
80
70
60
50
40
30
20
10
2 (160/1144)
Figure10.6.d Sensitivity at a 5% false positive rate for nine first- trimester serum test strategies
for Down syndrome screening. Sensitivity is presented as percentages. Each circle represents the
summary sensitivity for a test strategy and the size of each circle is proportional to the number of
Down syndrome cases. The estimates are shown with 95% confidence intervals. The test strategies
are ordered on the plot according to decreasing detection rate. The number of studies, cases and
women included for each test strategy are shown on the horizontal axis. A = Age, PlGF, PAPPfree ßhCG; B = Age, PAPP- A, free ßhCG and AFP; C = Age, ADAM 12, PAPP- A and freeßhCG; D = Age,
PAPP- A and free ßhCG; E = Age, PAPP- A; F = PAPP- A; G = Age, free ßhCG and AFP; H = Age, free ßhCG; I =
Free ßhCG. Source: Adapted from Alldred 2015
B
2 (116 /2705)
C
2 (74/1222)
D
(1037/49827)
E
5 (359/3491)
F
4 (325/2837)
G
3 (157/2992)
H
7 (460/5893)
A and
I
4 (390/4280)
code and output of the parameter estimates are in Appendix 17 of the online supplementary material (10.S1 Code for undertaking metathe summary estimates of sensitivity obtained, including their 95% confidence intervals, at the 5% FPR. The test combinations were ordered on the plot according to
decreasing sensitivity. The plot shows that the single- test strategies with and without
maternal age (PAPP- A alone, free βhCG alone, PAPP- A and maternal age, and free βhCG
and maternal age) have the worst performance, whereas thetriple- test strategies
(ADAM 12, PAPP- A, free βhCG and maternal age; PAPP- A, free βhCG, AFP and maternal
age) have the highest performance.
10.7 Meta- analysis withmultiple thresholds per study
As noted in Chapter9, Section9.4.5, some studies may report sensitivity and specificity
at more than one threshold, because the results of the index test are ordinal categories or continuous measurements (see Chapter4). The development of methods that
analysis). Figure 10.6.d shows
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10 Undertaking meta- analysis
i i it it
i i it it
sp
it
se
it
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allow for the inclusion of multiple thresholds from each included study is an active
area ofresearch (Zapf 2021). This section describes and demonstrates implementation of the Steinhauser (2016) and Jones(2019) approaches introduced in Chapter9,
Section9.4.5. Both models performed similarly when evaluated empirically using
data for a subset of published thresholds as well as all relevant thresholds from an
individual participant data set of 45 studies (Benedetti 2020). The models are for
tests that produce a continuous, numerical result. It is assumed that each study
reports sensitivity and specificity at one or more numerical threshold values.
We first define a common notation for both models. Study i=1, ..., I provides data
on sensitivity and specificity at threshold values Cit, where t=1, ..., Ti. Both models
accommodate varying numbers of, and different sets of, thresholds across studies
and the possibility that some studies report accuracy data at only a single threshold
(i.e.T
equals 1).
i
10.7.1 Meta- analysis ofmultiple thresholds withR
The Steinhauser approach for meta- analysis of multiple thresholds creates a link between
the range of thresholds and the respective pairs of sensitivity and specificity (Steinhauser
2016). The model is a two- stage random- effects model. At the study level, the reported
specificity estimates across thresholds provide an estimate of the cumulative distribution
function (cdf) of continuous test results among individuals without the target condition.
Likewise, the set of sensitivity estimates across reported thresholds provides an estimate
of the cdf of test results among individuals with the target condition. At the meta- analytical
level, the model fits the data for both groups and all available thresholds over all studies.
Based on a chosen parametric model, for example a logistic model, it provides estimates
of the two cdfs for the two groups across all studies, accounting for the between- study
heterogeneity and across- study correlation between groups.
The general model, here assuming an underlying logistic distribution for the logtransformed continuous test results, is given by
where
and
denote the observed values of specificity and sensitivity at threshold Cit
in study i, α1 and α0 are fixed intercepts, and β1 and β0 are fixed slopes for the individuals
with and without the target condition. The terms a0i, a1i, b0i, b1i denote random intercepts
and slopes. These are assumed to follow a multivariate normal distribution, reflecting the
correlation across studies. The terms ϵit and δit represent within- study random errors. The
parameters are estimated using weighted least squares, where each data point is weighted
with the inverse variance of the respective logit- transformed proportion.
The model provides estimates of the average distribution functions for both study
groups. This allows derivation of a model- based SROC curve. If, in addition, criteria
for selecting a threshold can be specified– in this case maximization of the Youden
index (defined as sensitivity + specificity– 1), which applies if false negatives and
false positives are of equal importance – an estimate of this threshold can be
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sp a b C
00 00
it
se a b C
it
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10.7 Meta- analysis withmultiple thresholds per study
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obtained from the model. Alternatively, a larger or smaller weight can be specified
(for details, see later), implemented in the R package diagmeta (Rücker 2020).
The practical use of diagmeta version 0.5-0 is demonstrated using an example
provided with the diagmeta package. The data are from a meta- analysis of the diagnostic accuracy of fractional exhaled nitric oxide (FeNO) for diagnosis of asthma (Schneider
2017). First, the diagmeta package must be installed on the user’s platform from the
CRAN repository:
install.packages("diagmeta")
After the package has been installed, it must be made available in the working
space using the command library(diagmeta). Load the FENO data using
data(Schneider2017)and examine the data structure using the command
View(Schneider2017), which provides the full data table. Alternatively, the first
few lines of the table can be examined using the command head(Schneider2017),
which produces the output in Box10.7.a.
The first number in each row is a row number automatically provided by R (not given in
the data set). The second column (study_id) is the study identifier, here a number; the
third and fourth columns provide study author and year of publication. All the visible lines
belong to the same study, Arora 2006, with a study ID of 1. The ‘group’ column is empty for
this study (it refers to a later study, Malinovschi 2012, which provides data in three substudies). The ‘cutpoint’ column contains the threshold for FeNO measured in ppb. The last
four columns (tpos, fneg, fpos and tneg) give the numbers of true positive (TP), false negative (FN), false positive (FP) and true negative (TN) results (2×2data), if the value in the
‘cutpoint’ column is used to determine test positivity. Because larger values indicate
asthma (thetarget condition), the numbers of (true or false) positives must decrease with
increasing threshold, whereas the numbers of (true or false) negatives increase with the
threshold within a study. Note that it is also possible to start from individual participant
data with a given study ID, true status of the participant and individual marker value. This
type of data can be transformed to the format needed using the function IPD2diag().
The main function of diagmeta is also called diagmeta(). To see the arguments
required by diagmeta(), look at the help file using help(diagmeta) or look directly
at the arguments using args(diagmeta)to give the
output presented in Box10.7.b.
Box 10.7.a Subset of fractional exhaled nitric oxide data for diagnosis of asthma
study_id author year group cutpoint tpos fneg fpos tneg
1 1 Arora 2006 6 133 5 34 0
2 1 Arora 2006 7 131 7 33 1
3 1 Arora 2006 8 130 8 31 3
4 1 Arora 2006 9 127 11 30 4
5 1 Arora 2006 10 119 19 28 6
6 1 Arora 2006 11 115 23 26 8
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