International Journal of Mathematical, Engineering and Management SciencesVol. 3, No. 2, 90–112, 2018
ISSN: 2455-7749

Causal-Effect Analysis using Bayesian LiNGAM Comparing with
Correlation Analysis in Function Point Metrics and Effort
Masanari Kondo*, Osamu Mizuno†
Kyoto Institute of Technology
Kyoto, Japan
E-mails: *m-kondo@se.is.kit.ac.jp, †o-mizuno@kit.ac.jp†
Corresponding author

Eun-Hye Choi†
National Institute of Advanced Industrial Science and Technology (AIST)
Ikeda, Osaka, Japan
E-mail: e.choi@aist.go.jp(Received March 31, 2017; Accepted September 27, 2017)

Abstract
Software effort estimation is a critical task for successful software development, which is necessary for appropriately
managing software task assignment and schedule and consequently producing high quality software. Function Point(FP) metrics are commonly used for software effort estimation. To build a good effort estimation model, independent
explanatory variables corresponding to FP metrics are required to avoid a multicollinearity problem. For this reason,previous studies have tackled analyzing correlation relationships between FP metrics. However, previous results on therelationships have some inconsistencies. To obtain evidences for such inconsistent results and achieve more effective
effort estimation, we propose a novel analysis, which investigates causal-effect relationships between FP metrics andeffort. We use an advanced linear non-Gaussian acyclic model called BayesLiNGAM for our causal-effect analysis, andcompare the correlation relationships with the causal-effect relationships between FP metrics. In this paper, we report
several new findings including the most effective FP metric for effort estimation investigated by our analysis using two
datasets.
Keywords- Software effort estimation, Function point (FP) metrics, Causal-effect analysis, Correlation analysis, Linear
non-Gaussian acyclic model (LiNGAM), BayesLiNGAM.

1. Introduction
Software effort estimation is an important task in software development, which predicts anecessary development cost to meet a scheduled deadline of software release. In real industrial
situations, however, many software projects fail on accurate effort estimation, and thus exceed
cost and the scheduled deadline. For instance, the chaos report (The Standish Group, 1994) points
out that on average 89% of companies are exceeding the estimated costs. In addition, Molokken
and Jorgensen (2003) report that the development time delay reaches approx. 30% and up to 40%of the scheduled time.
To address such problems and achieve more accurate effort estimation, many effort estimation
models have been studied so far (Wen et al., 2012). Effort estimation models are often regression
models (e.g. linear regression models), and use metrics to estimate efforts. Among such metrics,
the most widely-used ones are FP (Function Point) metrics.
On the other hand, Kitchenham et al. (2007) indicate that some studies show inconsistent resultsin effort estimation. For instance, Jeffery et al. (2000) report that using Cross-Company Datasets
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ISSN: 2455-7749(CC) are worse than using Within-Company Datasets (WC) in effort estimation. Differently from(Jeffery et al., 2000), Briand et al. (1999) and Mendes et al. (2005) report that CC is as good as
WC. Kitchenham et al. (2007) present a systematic review to summarize such reports. However,it cannot determine which of WC or CC is better.
To remedy the inconsistencies among the results of different researchers, it is important to analyze
the relationships among metrics for effort estimation. The reason is that in an effort estimation
model (e.g. a linear regression model) using metrics, we get a misleading result due to themulticollinearity problem (Farrar and Glauber, 1967) if explanation variables corresponding to themetrics (e.g. FP metrics) are not independent. So far, a lot of studies (Kitchenham and Känsälä,
1993; Jeffery and Stathis, 1996; Lokan, 1999; Uzzafer, 2016) have investigated the relationships
between FP metrics using correlation analysis. However, they have also reported inconsistent
results that the explanation variables can be either dependent or independent (Jeffery and Stathis,
1996; Kitchenham and Känsälä, 1993).
In this paper, we propose a novel analysis that investigates causal-effect relationships between FP
metrics and effort in addition to correlations between FP metrics. Causal-effect relationships could
provide us additional information on relationships among metrics such that a certain correlation isa spurious correlation, and some metrics do not have a correlation, however, have causal-effectrelationships with other metrics. In our study, we assume that FP metrics and effort are modeledusing a Linear Non-Gaussian Acyclic Model (LiNGAM) (Shimizu et al., 2006). In particular, we
adopt an advanced LiNGAM called BayesLiNGAM (Hoyer and Hyttinen, 2009) to identify thecausal-effect relationships between FP metrics and effort.
We address the following three research questions and obtain findings for each of them:
RQ1. Are correlation coefficients between FP metrics in our dataset similar to those inprevious research?
The correlation coefficients in our dataset are similar to the majority results in previous
research. Previous researches (Kitchenham and Känsälä, 1993; Jeffery and Stathis, 1996;
Lokan, 1999; Uzzafer, 2016) investigate relationships between FP metrics, however, they havereported inconsistent results. Thus, we investigate the correlation in our datasets.

RQ2. How many bootstrap samples should we use?
A sufficient sample size is 100. BayesLiNGAM occasionally extracts wrong causal-effectrelationships. To overcome this deficiency, we adopt a general random resampling approach,called bootstrap sampling (Efron, 1992). Thus, we investigate this RQ to select the sufficientnumber of samples for bootstrap sampling.

RQ3. What are causal-effect relationships between FP metrics and Effort?
The strengths of the causal-effect relationships are similar to those of the correlation
relationships, however, the directions of the causal-effect relationships depend on datasets.

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The main contributions of our paper are as follows: We present the first investigation of the causal-effect relationships between FP metrics andeffort using two datasets.
 We show that the causal-effect relationships can provide additional relationships between FP
metrics and effort.
From our results, the correlation coefficients in our dataset are similar to the majority results inprevious research. In addition, the existence of the causal-effect relationships is similar to that of
the correlation relationships, however, the directions of the causal-effect relationships depend on
datasets. Interface, one of the FP metrics, often does not have strong correlation coefficients andcausal-effect relationships with other FP metrics. However, interestingly, Interface has the causaleffect relationships to effort. This means Interface is an independent metric. Therefore, if we use
Interface as an explained variable for an effort estimation model, Interface does not cause a
multicollinearity problem. In addition, other FP metrics except Interface have both the causaleffect relationships and the correlation relationships with each other. Those metrics may lead a
multicollinearity problem.
The organization of this paper is as follows: Section 2 introduces related work andBayesLiNGAM. Section 3 explains the experimental setup and used datasets. Section 4 presents
research questions and answers. Section 5 gives discussions on questions arise from theexperiment results. Section 6 describes threats to validity. Section 7 presents a conclusion andfuture work.

2. Background
2.1 Motivating Example
To analyze a relationship between factor (e.g. FP metrics) using only a correlation coefficient
involves a risk. We describe a risk using the following example: In the software development, aproject sometimes falls into a runaway status (Takagi et al., 2005). An expert developer who hasa long experience is often employed to extinguish a runaway project. Then, the high effort projects
that fall into a runaway status and the projects that the expert developer belongs to are strongly
correlated, when we analyze if an effort of a project that the expert developer belongs to is either
high or low. Such a correlation can lead a misunderstanding such that the project requires a higheffort due to the expert developer, and thus we may take a wrong solution (e.g. removing the expert
developer from the project).
Therefore, it is risky to determine the reason of a high effort project using a correlation analysis
only. If we investigate a causal-effect relationship between the expert developer and the high effort
projects, we may not conclude the wrong solution. This is a motivation to use not only a correlation
analysis but also a causal-effect analysis in our approach.

2.2 Related Work2.2.1 Effort Estimation
Software effort (shortly, effort) is a measure to indicate whole working time for the softwaredevelopment. So far, various studies (Molokken and Jorgensen, 2003; Wen et al., 2012; Jorgensen
and Shepperd, 2007) have proposed effort estimation approaches. FP metrics (Albrecht and
Gaffney, 1983) are common metrics to build an effort estimation model, which are provided by
the International Function Point Users Group (IFPUG) to measure the size of software. For

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instance, Albrecht is the first person who developed a methodology of FP metrics in IBM and(Albrecht and Gaffney, 1983) originally propose adopting FP metrics for effort estimation. Ahn etal. (2003) present adopting FP metrics for effort estimation of software maintenance.
FP metrics measure five elementary function types to estimate a size of software; two data
functions types — internal logical files (File) and external interface files (Interface) — and threetransactional function types — external inputs (Input), external outputs (Output), and externalinquiries (Enquiry). These function types are used as explanatory variables for an effort estimation
model in a hypothesis that large-sized software requires large effort (Abran et al., 2002).
In general, the estimation model (e.g. a regression model) needs an assumption that explanatory
variables are independent (Farrar and Glauber, 1967). To confirm the assumption, many studies(Lokan, 1999; Jeffery and Stathis, 1996; Kitchenham and Känsälä, 1993; Uzzafer, 2016) havereported correlations between FP metrics. For instance, Kitchenham and Känsälä (1993) report FP
metrics have correlations with each other, and are not well-formed. In addition, Lokan (Lokan,1999) indicates that results of existing research have an inconsistency.
In this paper, we first perform a correlation analysis that means, we calculate correlation
coefficients between FP metrics in our datasets, to compare with previous research. We next
calculate causal-effect relationships between FP metrics and effort for a more detailed analysis.
Finally, Kitchenham and Känsälä (1993) and Jeffery and Stathis (1996) report Pearson correlation
coefficients between FP metrics and Effort. For instance, Kitchenham and Känsälä analyze thecoefficients and use stepwise multivariate regression to build the effort estimation model. Jeffery
and Stathis report the coefficients between FP metrics and Effort, and those between Unadjusted
Function Points (UFP) and Effort. There are some inconsistent results between Kitchenham et al.
and Jeffery and Stathis differently from their work, in this paper, we use Kendall’s t B (Sprent andSmeeton, 2016) to analyze correlation coefficients between FP metrics, and focus on causal-effectrelationships between FP metrics and Effort.

2.2.2 Causal Discovery
A causal-effect relationship is an important relationship in an engineering to estimate and solve anindustrial problem. To solve the industrial problem needs to decide if each metric is either an
explanatory variable or an objective variable to build an estimation model. The causal-effectrelationship can support the decision.
In addition, if we find out causal-effect relationships correctly, we can control values of arbitrary
metrics using an interpretation (Pearl, 2002). The interpretation is that when a variable in a certain
probability model is changed by a disturbance effect, we can observe an effect for the wholeprobability model by considering a direct effect by the variable (Pearl, 2002). Consequently, in theinterpretation, we can consider the probability model whose variable can be intentionally changed
by a disturbance effect, although a correlation is a result of analyzing data, and cannot consider achange by a disturbance effect.
To identify causal-effect relationships, we typically use a counterfactual thinking or structuralcausal models (Holland et al., 1985; Robins, 1986; Hernán, 2004; Heinze-Deml et al., 2017; Pfister
et al., 2017; Shimizu et al., 2006; Hoyer and Hyttinen, 2009). Counterfactual thinking uses acontrary fact. For instance, in counterfactual thinking, we consider two facts to identify causal93

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effect relationships: she did well on exam because she was coached by her teacher, and she did
not well on exam because was not coached by her teacher. Then, we compare these two facts to
identify that the study is causal to the result of the exam or not for her. However, it is difficult tocompare the two facts (Holland et al., 1985). Structural causal models are defined on numericalmodels. For instance, Shimizu et al. (2006) use Linear, Non-Gaussian, Acyclic Model to solve
causal discovery.
In this paper, we use a type of structural causal models. The proposed approach uses a Directed
Acyclic Graph (DAG) (Pearl, 2002) to describe causal-effect relationships between factors(metrics). To identify DAG is difficult, however, Shimizu et al. (2006) report that DAG is
identifiable when we assume a non-Gaussian disturbance density instead of Gaussian for DAG.

Fig. 1. Example causal-effect relationships among chocolate consumption, Nobel laureates and GDP

Finally, we illustrate two more motivating examples in the causal discovery. Messerli (Messerli,2012) studies correlation relationships between chocolate consumption and Nobel laureates; there
is a strong linear correlation (r=0.791, p-value<0.0001). If we only use the correlation analysis,
we should eat more chocolate to get Nobel laureates. However, if we use the causal discovery, we
can find out other results (Fig. 1). Causal-effect relationships between factors are represented in
DAG, a structural causal model. From Fig. 1, eating much chocolate does not cause Nobel
laureates, and therefore, does not produce Nobel laureates. On the other hand, improving GDP cancause both Nobel laureates and eating much chocolate, since GDP is causal to Nobel laureates andchocolate consumption (interpretation).
The other causal discovery example is the study by Green et al. (2017). They report causal-effectrelationships between social transitions (e.g. getting job) and both smoking and drinking. In
addition, causal discovery is often applied to medical field (e.g. finding the adverse effects ofdrugs) (Kleinberg, and Hripcsak, 2011).

2.3 Linear Non-Gaussian Acyclic Models (LiNGAM)
Previously, it has been considered that causal-effect relationships cannot be extracted from only
observed data that have no time information. However, recent studies (Shimizu et al., 2006) show

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that causal-effect relationships can be extracted from only observed data under certain
assumptions. One of such assumptions is the use of a Linear Non-Gaussian Acyclic Model(LiNGAM). LiNGAM is a data-generating model satisfying the following three properties:
1.

A Directed Acyclic Graph (DAG) represents a one-to-one mapping between observed
variables.

2.

The value assigned to each variable xi is a linear function of the values already assigned to
the variables, plus a disturbance (noise) term ei , and plus a constant term ci , that isxi b x  e  c ,ijk ( j )k (i )

j

i

(1)

i

where k(i) is a causal order. LiNGAM calculates all possible causal orders. Thus, if we consider
many variables, the number of causal orders is explosively increased. We’ll discuss more detailsof this problem in discussion section 5.6.
3.

The disturbances ei are all continuous random variables. The ei are generated by nonGaussian distribuions of non-zero variances. The ei are independent of each other, i.e.

p(ei , , en )  i pi (ei ) .
2.4 Bayesian Discovery of Linear Acyclic Causal Models
In our approach, we extract causal-effect relationships by using the simple Bayesian inference on
LiNGAM (BayesLiNGAM) (Hoyer and Hyttinen, 2009). BayesLiNGAM calculates posterior
probabilities of possible DAGs from only given data. Posterior probabilities are calculated asfollows:

P(Gm | D) 
where
D=

p(D | Gm )P(Gm )
,
p(D)

(2)

is the different possible DAGs, and N is the number of data samples.
is the observed dataset. Here P(D) is a constant that simply normalizes the

distribution. P(Gm ) is the prior probability distribution over DAGs and incorporates any domain
knowledge that we have. When we do not have any knowledge, we assume a uniform priorprobability distribution over all DAGs. The marginal likelihoods are calculated as follows:p(D | Gm )   p(D | q , Gm ) p(q | Gm )dq ,(3)

where q consists of all the parameters (i.e. the coefficients bij , the constants ci , and the
disturbance densities pi (ei ) ). p(q | Gm ) is calculated when we assume three assumptions that bij
is a standard Gaussian distribution with zero-mean and unit variance, ci is zero, and pi (ei ) models
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a parameterization of the densities. pi (ei ) implements the two quite basic parameterizations: a
simple two-parameter exponential family distribution combining the Gaussian and Laplace
distributions, and a finite mixture of Gaussian density family. The integral is calculated by the
Laplace approximation. We use this approach (Hoyer and Hyttinen, 2009) for our experiment.
Here we need to compute an approximation to (3). By the definition of LiNGAM (Hoyer andHyttinen, 2009), p(D | q , Gm ) is transformed top(D | q , Gm )   pi (xi ib x  c ).

ij j
k ( j )k (i )(4)iFig. 2. Example extraction of a causal-effect relationship by BayesLiNGAM

2.5 Outputs of BayesLiNGAM
We describe outputs of BayesLiNGAM to understand analyzed data. Fig. 2 shows an example ofan output of BayesLiNGAM. First, we input two observed variables, Metric A and Metric B, toBayesLiNGAM. Each variable has N samples data. Then, BayesLiNGAM calculates posterior
probabilities of causal-effect relationships to the all possible combinations of metrics. Posterior
probabilities provide us which causal-effect relationship has the strongest possibility. In thisexample, two metrics have three possible combinations of metrics; Metric A is a cause of Metric
B, Metric B is a cause of Metric A, and no cause.

Table 1. Description of analyzed projects

3. Experimental Setup
For experiments, we use two types of datasets called China Dataset and Finnish Dataset. Table 1
summarizes the number of samples, the number of all metrics, and the metrics adopted in our
analysis for each dataset.

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3.1 China Dataset
China dataset is a dataset in PROMISE data repository (Menzies, et al., 2016) obtained from 499
software development projects. It has 19 metrics. Among them, we use five FP metrics—Interface,
Output, Enquiry, Input, File—and a metric for effort, Effort.

(a) China dataset(b) Finnish dataset

Fig. 3. Histograms for effort(a) China dataset(b) Finnish dataset

Fig. 4. Boxplots for FP metrics

3.2 Finnish Software Effort Dataset
Finnish Software Effort Data Set (Sigweni et al., 2015) is a dataset obtained from many companies
in Finland. It has 46 metrics. Among them, we use the mostly used five FP metrics — IntFP,
OutFP, InqFP, InpFP, EntFP — and a metric for effort, Worksup.

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The metrics have different names but have same meaning in China dataset and Finnish dataset. In
this paper, we translate the names of FP metrics for Finnish dataset into the names of thecorresponding FP metrics for China dataset as follows: IntFP corresponds to Interface, OutFP
corresponds to Output, InqFP corresponds to Enquiry, InpFP corresponds to Input, EntFP
corresponds to File, and Worksup corresponds to Effort.
There are some different points between China and Finnish datasets. For instance, China dataset
has many smaller projects with smaller efforts than Finnish dataset does. Finnish dataset has manylarger projects with larger efforts than China dataset does. Fig. 3 shows histograms of values ofEffort in both China and Finnish datasets. We can observe China dataset has more projects thanFinnish dataset in small effort values, and Finnish dataset has more projects than China dataset inlarge effort values. Note that China dataset has approx. 100 more projects than Finnish dataset has.

Table 2. Pearson’s moment coefficient of skewness

In addition, values of FP metrics are similar in China and Finnish dataset. Each FP metric isskewness data, and they have many outliers. Fig. 4 shows boxplots of FP metrics in China andFinnish dataset. Each boxplot has a median value not located in the center of a box. Table 2 shows
Pearson’s moment coefficient of skewness (skewness) (You, 2016). The skewness is ameasurement of symmetry as follows:(4)

In summary, all values in Table 2 are positive values, and therefore, it is reasonable to support that
FP metrics are skew in these datasets.

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4. Results
4.1 RQ1: Are correlation coefficients between FP metrics in our dataset similar to
those in previous research?
4.1.1 Motivation
We first need to analyze and confirm the correlation coefficients between FP metrics for ourdatasets. As mentioned before, Lokan (Lokan, 1999) reports that correlation coefficients between
FP metrics have inconsistency in previous results. For instance, Kitchenham and Känsälä (1993)
report that Output is significantly correlated with Input, Inquiries and Files. However, Jeffery andStathis (1996) report that they have no significant correlation.
We use Kendall’s t B (Sprent and Smeeton, 2016) to analyze the correlation coefficients between
FP metrics for our datasets. Kendall’s t B is the t B version of Kendall’s t that takes ties into
accounts. Kendall’s t is used to measure a correlation for ordinal data, which is also used in theprevious studies compared with ours.

4.1.2 Approach
Kendall’s t B observes the rank correlation, and therefore, can calculate correlation coefficientseven when projects have outliers or skewed data. Since China and Finnish datasets have manyoutliers and skewed FP metrics, Kendall’s t B is effective for evaluation.
In addition, we do not perform preprocessing to data since Kendall’s t B is a non-parametric test,
and we do not need to assume a distribution of data.
Correlation coefficients for our datasets are compared with those in the previous research. We
collect the results of previous research are collected from the literature by Lokan (Lokan, 1999).
Lokan employs results of correlation coefficients by Kitchenham and Känsälä (1993) and Jeffery
and Stathis (1996). In addition, correlation coefficients are compared by a statistical test. Nullhypothesis of the statistical test is that a correlation coefficient between two FP metrics has not acorrelation.

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Table 3. Results of Kendall’s t and p-values in previous research and our correlation analysis

4.1.3 Results
The correlation coefficients between FP metrics by our analysis are similar to those in the previous
results by Kitchenham and Känsälä (1993) and Lokan (Lokan, 1999). Table 3 shows thecorrelation coefficients between FP metrics for three previous studies and two new results for ourdatasets with respect to Kendall’s t B . In our results, Interface shows weak correlation with otherFP metrics ( t B ranges from 0.02 to 0.21). The results of Kitchenham and Känsälä, and Lokan also
show weak correlation with other FP metrics ( t B ranges from -0.02 to 0.31). Output, Enquiry, andInput show relatively stronger correlation with other FP metrics and it is similar in the results ofKitchenham and Känsälä, and Lokan. Therefore, we can say that our other correlation coefficientsare very similar to the results by Kitchenham and Känsälä, and Lokan, although our results havesome differences from the results by Kitchenham and Känsälä, and Lokan, where correlations
between FP metrics are statistically significant except the pairs of Interface and Enquiry, andInterface and Input.
For our datasets, we agree with the results by Kitchenham and Känsälä (1993) and Lokan (Lokan,1999) on the correlation coefficients between FP metrics. On the other hand, we disagree with theresult by Jeffery and Stathis (1996) on the correlation coefficients.

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Fig. 5. Our experiment procedure for RQ2 (focusing on two metrics)

4.2 RQ2: How many bootstrap samples should we use?
4.2.1 Motivation
In our analysis, we adopt BayesLiNGAM, which is an approach for extracting causal-effectrelationships, however, occasionally extracts wrong causal-effect relationships. To overcome thisdeficiency, in our previous work (Kondo and Mizuno, 2016), we created 15 new datasets from one
original dataset by conducting 15 times extracting 150 samples by random sampling. We analyzed
the new 15 datasets by BayesLiNGAM, and conducted majority voting to decide which causaleffect relationship is true. However, there is no evidence to decide the number of new datasets, 15.
To get an evidence for the sufficient number of new datasets, in this paper, we adopt a general
random re-sampling approach, bootstrap sampling (Efron, 1992), to a phase creating new datasets.
This approach provides us a heuristic solution of how many new datasets are sufficient by plotting
distribution and confirming if the distribution is smooth or not.

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4.2.2 Approach
Bootstrap sampling is a procedure to estimate a sampling distribution of a model to verify themodel performance in general (Efron, 1992). The sampling distribution is generated by plotting
performances of the model using bootstrap samples. Bootstrap samples are generated by a repeatedmethod extracting N samples allowing overlapping by random sampling from an original datasetthat has N samples. Bootstrap sampling can be used in outputs of the model are underspecified toevaluate a performance of the model in general.
Fig. 5 shows the procedure of our experiments that using BayesLiNGAM, extracts causal-effectrelationships. The procedure is as follows:
1. We create two sets (China and Finnish datasets) that consist of M datasets that consist of N
samples. M means the number of bootstrap samples, and N means the sample size of a dataset(i.e. 499 and 407), respectively.
2. The posterior probabilities of three causal-effect relationships between pairs of metrics arecalculated from the M datasets by BayesLiNGAM for China and Finnish datasets,
respectively.
3. We plot three posterior probabilities of causal-effect relationships using M datasets, andcheck the distributions.
Here, we define smoothness of the distribution. We define that a distribution of the causal-effectrelationships is smooth if it satisfies either of the following two conditions under the following
assumption.
Assumption:
 We only consider the distribution of the causal-effect relationships that are calculated using
more than a half of bootstrap samples.
Conditions: Absolute differences of the posterior probabilities (values of x-axis) of the mode and thoseof the second mode are less than or equal to 5 and greater than or equal to 50.
 Differences of the numbers of the mode entities (values of y-axis) and those of the second
mode entities are greater than or equal to 10.
The assumption aims at removing the distributions of causal-effect relationships that are notcalculated on over a half of bootstrap samples. We suppose such causal-effect relationships might
not true.
The first condition aims at picking up the distributions that have similar posterior probabilities ordifferent ones between the mode and the second mode. For instance, if the difference of posterior
probabilities between the mode and the second mode are very close (i.e., the difference is less thanor equal to 5), it is reasonable that these values consist of one same distribution and are in a peakof the same distribution. On the other hand, the probabilities are very far from each other (i.e., thedifference is greater than or equal to 50), it is reasonable that these values have a different
distribution. Otherwise (if the first condition does not hold), the values possibly consist of a
distribution having two peaks (e.g. mixture model).
The second condition considers the value of the y-axis of a distribution. If the value differences ofy-axes between the mode and the second mode are small (i.e., the second condition does not hold),
and the first condition does not hold, it is reasonable that they consist of a distribution having two102

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peaks. For instance, Fig. 6(c) shows a distribution not smooth, because the posterior probabilities
between the mode and second mode are close and the value difference of y-axes is small.
Here, we need to decide a disturbance density pi (ei ) for BayesLiNGAM. This density is used to
calculate the marginal likelihood for BayesLiNGAM. The density indicates an occurrence
distribution of a disturbance term. We adopt a finite mixture of Gaussian density (MoG) since it
provides better performance than the Gaussian and Laplace distributions (Hoyer and Hyttinen,2009). As the number of mixtures of MoG, we choose five from our experience (Kondo and
Mizuno, 2016).
We compare two bootstrap sample sizes, 15 and 100. The upper restriction is 100 in our
experiment. Tantithamthavorn et al. (2017) state that 100 is a sufficient value for bootstrap
sampling. Thus, we employ the same upper restriction.

(a) No causal-effect relationship(b) Output is causal to Enquiry(c) Enquiry is causal to Output

Fig. 6. Distributions of posterior probabilities between Output and Enquiry in China dataset when thenumber of bootstrap samples is 15(a) No causal-effect relationship(b) Interface is causal to Enquiry(c) Enquiry is causal to Interface

Fig. 7. Distributions of posterior probabilities between Interface and Enquiry in Finnish dataset when thenumber of bootstrap samples is 15

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ISSN: 2455-7749(a) No causal-effect relationship(b) Output is causal to Enquiry(c) Enquiry is causal to Output

Fig. 8. Distributions of posterior probabilities between Output and Enquiry in China dataset when thenumber of bootstrap samples is 100(a) No causal-effect relationship(b) Interface is causal to Enquiry(c) Enquiry is causal to Interface

Fig. 9. Distributions of posterior probabilities between Interface and Enquiry in Finnish dataset when thenumber of bootstrap samples is 100

Fig. 10. Our experiment procedure for RQ3 (focusing on two metrics).

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4.2.3 Results
As the number of bootstrap samples, 15 is not enough for bootstrap sampling, since the sampling
distribution for bootstrap sampling using 15 samples is not smooth. Figs. 6 and 7 show threesampling distributions of posterior probabilities where M is 15 for China (between Output andEnquiry) and Finnish (Interface and Enquiry) datasets. For instance, Fig. 6(c) for “Enquiry iscausal to Output” does not show a smooth sampling distribution.
From our results, the sufficient number of bootstrap samples is 100 to do bootstrap sampling.
When bootstrap sampling uses 100 samples, the sampling distribution is smooth. Figs. 8 and 9
show three sampling distributions of posterior probabilities where M is 100 for China and Finnish
datasets. For instance, Fig. 8(c) for “Enquiry is causal to Output” shows a smooth sampling
distribution.
Figs. 8(b) and 9(b) also do not show a clear distribution. However, posterior probabilities are
distributed to about 0 or 100, and the numbers of datasets in y-axis are similarly between 0 and
100 of posterior probabilities. Thus, it is reasonable to support BayesLiNGAM that cannot identify
this causal-effect relationship into one posterior probability, and shows two types of posterior
probabilities of causal-effect relationships. More details will be discussed in Section 5.1.
As the number of bootstrap samples, 100 is sufficient to do bootstrap sampling. In addition,
BayesLiNGAM cannot decide one posterior probability of the causal-effect relationship in somecases.

4.3 RQ3: What are causal-effect relationships between FP metrics and Effort?
4.3.1 Motivation
The knowledge of correct causal-effect relationships can contribute to building more accurate
estimation models necessary for software development in the industrial problem. However, so far,the causal-effect relationships between FP metrics and Effort for effort estimation have not yet
been analyzed.

4.3.2 Approach
To extract causal-effect relationships, we adopt BayesLiNGAM using bootstrap sampling where
the number of bootstrap samples sets to 100 from the answer of RQ2.
Fig. 10 shows the flow of our experiments. The procedure is as follows:
1. We create two sets (Finnish and China datasets) that consist of 100 datasets that consist of N
data. N means the size of a dataset (i.e. 499 and 407), respectively.
2. The 100 causal-effect relationships between pairs of metrics are calculated from the 100
datasets by BayesLiNGAM for China and Finnish datasets, respectively.
3. The causal-effect relationships between pairs of metrics are determined by the majority
voting of the 100 causal-effect relationships. These causal-effect relationships are referred toas #1. The second-largest ones are referred to as #2.
4. #1 and #2 denote the possibilities of causal-effect relationships

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Table 4. Results of upper two causal-effect relationships (mixture: 5) and Kendall’s t and p-values for
China dataset. Upper triangular indicates causal-effect relationships. Lower triangular matrix indicatescorrelation coefficients

Table 5. Results of upper two causal-effect relationships (mixture: 5) and Kendall’s t and p-values for
Finnish dataset. Upper triangular indicates causal-effect relationships. Lower triangular matrix indicatescorrelation coefficients

4.3.3 Results
Table 4 shows for China dataset, the directions of causal-effect relationships and the number ofdatasets which indicate the directions for #1 and #2 in an upper triangular matrix, and thecorrelation coefficients in a lower triangular matrix. The symbol “→” means a row metric is causal
to a column metric. The symbol “←” means a column metric is causal to a row metric. “None”
means there is no causal-effect relationship between a row metric and a column metric. The
number in brackets means the number of bootstrap samples. For instance, look at the cells forInterface and Output in Table 4. None for #1 indicates there is no causal-effect relationshipbetween Interface and Output. The number in the bracket, 46, indicates this result is calculated
from 46 bootstrap samples. → for #2 indicates Interface is causal to Output. This result is
calculated from 41 bootstrap samples.
In China dataset, when FP metrics and Effort have small correlation coefficients, there are
low possibilities of causal-effect relationships, and when FP metrics and Effort have strong
correlation coefficients, there are high possibilities of causal-effect relationships. Causaleffect relationships and correlation coefficients have a relationship. For instance, Interface has
small correlation coefficients with other metrics except Effort, and it has low possibilities for acausal-effect relationship with other metrics except Effort. In addition, Output has a smaller
correlation coefficient with Enquiry than with other metrics, and it also has a low possibility for acausal-effect relationship with Enquiry.

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Table 5 also shows the causal-effect relationships and the correlation coefficients in Finnish
dataset. Finnish dataset has the similar results with China dataset except for Interface andthe pair of Output and File. Causal-effect relationships between Interface and other metrics for
Finnish dataset are different with those for China dataset. For instance, #1 and #2 are different.
Causal-effect relationships between Output and File are also different.
In China dataset, causal-effect relationships are similar to correlation coefficients. On the other
hand, in Finnish dataset, causal-effect relationships are similar to correlation coefficients,
however, some metrics have different directions of causal-effect relationships with China dataset.
Thus, the causal-effect relationships for some metrics possibly depend on datasets.

Table 6. The number of datasets on causal-effect relationships between Interface and Input in Finnish dataset

5. Discussion and Findings
In this section, we give discussions on questions arise from and the findings from the results of
our analysis.

5.1 The sampling distributions for a few causal-effect relationships have two different
distributions by bootstrap sampling using 100 samples.
The sampling distributions by bootstrap sampling sometimes have two different distributions (i.e.
they do not satisfy the first and the second conditions for smooth distributions in Section 4.2.2).
For example, “Output is causal to Enquiry” and “Interface is causal to Enquiry” as shown in Figs.
8 and 9 have two different distributions. Bootstrap sampling typically generates a sampling
distribution, and therefore, these results are unusual.
However, this circumstance does not affect identifying a causal-effect relationship byBayesLiNGAM based on bootstrap sampling. The pairs of metrics that are involved in such cases
have a clear difference between possibilities of causal-effect relationships. For instance, thesampling distribution of “Output is causal to Enquiry” in China dataset has two different
distributions. Nevertheless, the sampling distribution of no causal-effect relationship for the pairof metrics is smooth and has many datasets achieving high posterior probabilities, as in Figs. 8(a)and 8(b). In addition, the pair of metrics has a high difference between #1 and #2 as shown in
Table 4.

5.2 A few causal-effect relationships have a small difference between #1 and #2.
Identifying a causal-effect relationship is difficult when a difference between #1 and #2 is small
since we could not identify which causal-effect relationships are likelihood in bootstrap sampling.
For instance, the difference between Interface and Output is small both for China and Finnish
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datasets. BayesLiNGAM cannot always indicate the correct causal-effect relationships for suchcases. Investigating a further decision method would be useful to support such a case that thedifference between #1 and #2 is small, and thus it is difficult to identify a causal-effect relationshipby BayesLiNGAM.

5.3 BayesLiNGAM sometimes cannot extract a posterior probability for a causaleffect relationship.
We have conducted bootstrap sampling, however, BayesLiNGAM cannot calculate a posterior
probability for a few datasets (bootstrap samples). Table 6 shows the example of the number ofdatasets between Interface and Input in Finnish dataset. BayesLiNGAM successfully calculatescausal-effect relationships for 93 datasets, but fails the calculation for 7 datasets. Nevertheless, we
can identify a causal-effect relationship, since we can get the calculation results for almost alldatasets. In particular, it is more important to identify a causal-effect relationship than to calculate
and identify all posterior probabilities of bootstrap datasets.

5.4 Causal-effect relationships can explain inconsistent results between WC and CC.
Kitchenham et al. (2007) indicate that some studies show inconsistent results on whether there aredifferences between WC and CC to estimate effort or not. Our results indicate that causal-effectrelationships are different depending on datasets. The differences of causal-effect relationships
across both WC and CC can lead to such inconsistent results since different causal-effectrelationships have different tendencies. Therefore, the proposed method can be used to analyze
relationships across metrics of WC and CC, and to compare estimation results across WC and CC.
If WC has inconsistent causal-effect relationships like our results, and metrics of CC are also
inconsistency, we can find out one reason why sometimes WC is better than CC, and for othertimes, WC is as well as CC. If WC has consistent causal-effect relationships and CC does not haveconsistent causal-effect relationships, it indicates that sometimes CC is as well as WC, however,CC includes worse points than WC does.

5.5 Interface and Output are the best independent explanatory variables for effort
estimation and controlling effort, respectively.
RQ3 is to investigate the directions of causal-effect relationships between FP metrics, and thosein FP metrics and Effort. From results, the causal-effect relationships between FP metrics areinconsistent, and therefore, it is difficult to discuss general findings. On the other hand, causaleffect relationships between FP metrics and Effort have consistent results. FP metrics is causal toEffort metrics in both datasets. Therefore, it is reasonable that every metric can be useful toestimate effort as an independent explanatory variable. We only consider multicollinearity
problem. From this viewpoint, Interface often has neither the causal-effect relationships nor thecorrelation relationships with other FP metrics. Therefore, this is one of the best independent
explanatory variables for effort estimation.
In addition, we can use the interpretation to control effort using FP metrics since FP metrics havecausal-effect relationships for effort. In particular, Output metric is a valuable metric using theinterpretation, since #1 value for Output is high in every dataset.

5.6 How many metrics to which BayesLiNGAM can be applied?
In this paper, using BayesLiNGAM, we only investigate relationships between two metrics of FP
metrics and Effort. BayesLiNGAM can be applied to any number of metrics. However, there is a108

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computational problem such that the number of DAGs (also the number of combinations of causaleffect relationships considered) and thus the calculation time increased explosively with thenumber of metrics. Indeed, the implementation of BayesLiNGAM used in our experiment shows
us a notification that indicates there are too many inputs if we use over five metrics. To overcome
this problem, Hoyer and Hyttinen (2009) propose an alternative approach, which uses the greedy
search. Hoyer and Hyttinen (2009). report that their approach can be applied to estimate causaleffect relationships with over six metrics while reducing the calculation time. Investigating causaleffect relationships among more than two metrics could be an interesting future work.

5.7 How do we decide which correlation relationships or causal-effect relationships
to believe?
In general, causal-effect relationships are better relationships than correlation relationships. Thisis because correlation relationships are sometimes spurious correlations as shown in Fig. 1.
Therefore, if there are conflicting results between causal-effect analysis and correlation analysis,
we should confirm whether correlation relationships are not spurious correlations.

6. Threats to Validity
6.1 Construct Validity
We use Kendall’s t for calculating correlation coefficients instead of Pearson correlation
coefficients. Kendall’s t is also adopted in previous studies, and is more powerful to skewed dataand outliers, and our datasets are skewed and have many outliers. Thus, it is valid to adopt
Kendall’s t to calculate correlation coefficients.
For using BayesLiNGAM, we assume that the disturbance density is a finite mixture of Gaussian
density and the number of mixture is five. That means that we approximate population of data asa five mixture of Gaussian density.
For experimental analysis, we use two datasets, China and Finnish datasets, which have been
adopted previous studies on effort estimation (Sigweni et al., 2016; Bettenburg et al., 2012). Thus,
it is valid to use these datasets.

6.2 External Validity
Correlation coefficients between FP metrics already have been investigated in previous studies,and our results are similar to the majority of previous results. Therefore, results of correlation
coefficients are general.
Results of causal-effect relationships are also general since we adopt two types of datasets, andadopt bootstrap sampling. Bootstrap sampling supports providing a general result.

6.3 Reliability
We use BayesLiNGAM (open at https://www.cs.helsinki.fi/group/neuroinf/lingam/bayeslingam/)that was implemented by Hoyer and Hyttinen who originally proposed BayesLiNGAM. Thus,
reliability of results of BayesLiNGAM is high.
In addition, we provide all data and scripts that are used for our study at https://se.is.kit.ac.jp/~mkondo/BayesLiNGAM.tar.bz2. Thus, anyone can easily conduct and confirm our analysis.

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7. Conclusion
In this paper, we presented a causal-effect analysis between FP metrics and effort using
BayesLiNGAM. Using the proposed analysis, we can investigate the directions of causal-effectrelationships among the metrics. Therefore, our analysis can support building a good effort
estimation model.
From the results of our analysis using two datasets, we confirmed that causal-effect relationships
between FP metrics are similar to correlation relationships between them, and most of causaleffect relationships have same directions. However, a few causal-effect relationships havedifferent directions in difference datasets.
We also confirmed that when FP metrics and effort have a correlation, they also have causal-effectrelationships. Thus, correlations between FP metrics and effort are not spurious correlations.
In addition, from our results, Interface, one of the mostly used FP metrics, does not have strong
correlation coefficients and causal-effect relationships with other FP metrics. This result indicatesthat Interface is the best FP metric to build an effort estimation model since it then does not cause
a multicollinearity problem.
Our future work includes extracting new features from original features (e.g. metrics) to solve themulticollinearity problem. We could make the new features that can overcome themulticollinearity problem by integrating correlated features. Although a stepwise regression
approach (Mendes and Mosley, 2001) is already proposed to remove correlated features, we plan
to make the new features that contribute to the performance improvement of an objective task. In
particular, we are interested in adopting a neural network approach.

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