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PLOS One logoLink to PLOS One
. 2021 Jun 25;16(6):e0253389. doi: 10.1371/journal.pone.0253389

Comparison of the performances of survival analysis regression models for analysis of conception modes and risk of type-1 diabetes among 1985–2015 Swedish birth cohort

Adeniyi Francis Fagbamigbe 1,2,3,*, Emma Norrman 4,5, Christina Bergh 4,5, Ulla-Britt Wennerholm 4,5, Max Petzold 6
Editor: Y Zhan7
PMCID: PMC8232413  PMID: 34170924

Abstract

The goal is to examine the risk of conception mode-type-1 diabetes using different survival analysis modelling approaches and examine if there are differentials in the risk of type-1 diabetes between children from fresh and frozen-thawed embryo transfers. We aimed to compare the performances and fitness of different survival analysis regression models with the Cox proportional hazard (CPH) model used in an earlier study. The effect of conception modes and other prognostic factors on type-1 diabetes among children conceived either spontaneously or by assisted reproductive technology (ART) and its sub-groups was modelled in the earlier study. We used the information on all singleton children from the Swedish Medical Birth Register hosted by the Swedish National Board of Health and Welfare, 1985 to 2015. The main explanatory variable was the mode of conception. We applied the CPH, parametric and flexible parametric survival regression (FPSR) models to the data at 5% significance level. Loglikelihood, Akaike and Bayesian information criteria were used to assess model fit. Among the 3,138,540 singletons, 47,938 (1.5%) were conceived through ART (11,211 frozen-thawed transfer and 36,727 fresh embryo transfer). In total, 18,118 (0.58%) of the children had type-1 diabetes, higher among (0.58%) those conceived spontaneously than the ART-conceived (0.42%). The median (Interquartile range (IQR)) age at onset of type-1 diabetes among spontaneously conceived children was 10 (14–6) years, 8(5–12) for ART, 6 (4–10) years for frozen-thawed embryo transfer and 9 (5–12) years for fresh embryo transfer. The estimates from the CPH, FPSR and parametric PH models are similar. There was no significant difference in the risk of type-1 diabetes among ART- and spontaneously conceived children; FPSR: (adjusted Hazard Ratio (aHR) = 1.070; 95% Confidence Interval (CI):0.929–1.232, p = 0.346) vs CPH: (aHR = 1.068; 95%CI: 0.927–1.230, p = 0.361). A sub-analysis showed that the adjusted hazard of type-1 diabetes was 37% (aHR = 1.368; 95%CI: 1.013–1.847, p = 0.041) higher among children from frozen-thawed embryo transfer than among children from spontaneous conception. The hazard of type-1 diabetes was higher among children whose mothers do not smoke (aHR = 1.296; 95%CI:1.240–1.354, p<0.001) and of diabetic mothers (aHR = 6.419; 95%CI:5.852–7.041, p<0.001) and fathers (aHR = 8.808; 95%CI:8.221–9.437, p<0.001). The estimates from the CPH, parametric models and the FPSR model were close. This is an indication that the models performed similarly and any of them can be used to model the data. We couldn’t establish that ART increases the risk of type-1 diabetes except when it is subdivided into its two subtypes. There is evidence of a greater risk of type-1 diabetes when conception is through frozen-thawed transfer.

Introduction

An exploratory analysis of age at onset of type-1 diabetes among children born in Sweden between 1985 and 2015 and conceived either spontaneously or by assisted reproductive technology (ART) showed that (i) skewed discrete age distribution because most ART-conceived children are younger (ART is increasing and most children were born in the more recent years), (ii) a probable peak in the risk of type-1 diabetes at 10–14 years of age, (iii) there is an increased risk of developing diabetes in more recent years [1]. The ART was either the standard in-vitro-fertilization (IVF) or intracytoplasmic sperm injection (ICSI) with fresh or frozen-thawed embryo transfer. This study used the Cox proportional hazard (CPH) model to evaluate if the mode of conception (ART vs spontaneous) was associated with an increased risk of type-1 diabetes [1]. However, it is not known whether this method captured the peculiarities of the data. There is a need to investigate if the differences were caused by skewness in age, having more ART-conceived children during the later years when diabetes is more prominent.

There have been contradictions in the reported risk of conception mode-type-1 diabetes in the literature [1–3]. Norrman et al. reported an insignificant risk of Type-1 diabetes by maternal fertility (adjusted hazard ratio (aHR) = 1.07; 95% CI: 0.93–1.23) but significant differences in risk were found between frozen embryo transfer and type-1 diabetes (aHR 1.52; 95% CI: 1.08–2.14 and 1.41; 95% CI: 1.05–1.89) for frozen versus fresh and frozen versus spontaneous conception (SC), respectively in a subgroup analyses of a Swedish data [1]. Using Danish data, Hargreave et al. found that the risk of type-1 diabetes was not significant with conception mode (aHR = 1.01; 95% CI: 0.90–1.13) after adjusting for other covariates [3]. Similarly, Kettner et al. reported no association between fertility treatment and childhood type-1 diabetes mellitus but found that ovulation induction or intrauterine insemination with follicle-stimulating hormone was associated with a higher risk of type-1 diabetes mellitus (aHR = 3.22; 95% CI: 1.20 to 8.64) [2]. The authors found no association with diabetes type-1 diabetes in other types of fertility treatment indications [2]. The data analysed by Hargreave et al. and Kettner et al. were both Danish but differed in sizes with over 1, 550,519 and 565,116 births respectively whereas there were 3,138,540 births in the study by Norrman et al. [1–3]. The study setting, sample sizes and methods of analysis might have caused these contradictions. The reason for these contradictory findings could be that the analyses used in the prior literature depended on the appropriateness of proportional hazards models in the settings. This paper is therefore designed to revisit and assess the effect of ART and its subgroups, on the development of type-1 diabetes. To achieve this, we assessed the fit of a range of different survival analysis regression models in assessing the effect of ART in having type-1 diabetes among a birth cohort in Sweden.

The data used in Norrman et al. presented right-censored data on the onset of type-1 diabetes which makes survival analysis a natural choice of analysis [1]. Survival analysis, also called analysis of time-to-event, is a statistical procedure for a follow-up study in which some subjects may not have experienced the event of interest due to loss to follow up, withdrawal of subjects from the study or the study coming to an end [4, 5]. Besides the estimation of the survival function of such time-to-event, greater interest is the identification of prognostic factors that affects the timings [6–9]. Several methodologies, known as survival regression methods, have been developed to achieve this goal. While some of the models are traditional survival regression models, some are modern [10, 11]. The traditional survival regression models consist of the non-parametric, semi-parametric and parametric models. We describe the assumptions, advantages and disadvantages of these models in the next paragraph.

The Kaplan-Meier estimator is the nonparametric maximum likelihood estimate (NPMLE) of the survivor function when the model is a non-parametric survival model. It does not allow the investigation of the effects of covariates [5]. Hence the effects of risk factors on the time-to-event cannot be estimated. Nonetheless, the Kaplan-Meier estimator allows the exploration of the effect of covariates graphically and by comparison of distinct estimates of the survival function but this gets cumbersome when several covariates are to be investigated together. The CPH model is a semi-parametric regression model and it is the most commonly used survival analysis regression models [12–16]. This model has a unique advantage of not making any assumptions about the shape of the underlying hazard function and can directly use the hazard ratios to make a reliable estimation of the treatment effects [14] but rather assumes that the hazard ratios of the covariates in the model are constant over time [16, 17]. Although the CPH model is very useful and often accurate for a large sample size study, the major criticism against the CPH models is that this assumption is often violated, especially in a very long follow-up study. The CPH model has another disadvantage in that the survival function hence the cumulative hazard function, are continuous with respect to Lebesgue measure [18]. The estimators are, however, step functions rather than being smooth [11, 19].

The parametric models assume that the survival and hazard functions follow a specific distribution in which case the parameters can be estimated. The parametric survival models, such as the exponential and Weibull models in addition to the log-logistic and generalized gamma models are often used to obtain smooth hazard rates and cumulative hazard functions of the risk factors and to extrapolate the survival functions and cumulative functions [5, 20]. A major disadvantage of the parametric models lies in their insufficient flexibility to ensure adequate representation of the data been fitted, and the fact that the cumulative hazard function or survival function may be biased [19]. These inflexibilities often lead to biased estimates for the cumulative hazard and/or survival functions. Moreover, parametric models with complex underlying hazard fail to capture the true (covariate) effects [21, 22].

The Flexible parametric survival regression (FPSR) models were developed by Royston and Parmar in the early 2000s [23] as a more flexible alternative. The FPSR attempted to eliminate the shortcoming of the CPH and the parametric models by building on the strengths of these models. The flexible models are an extension of several parametric survival models [23] and were formulated to relax the assumption of linearity of log time [24]. These flexible models represent the log of the baseline cumulative hazard function with a restricted cubic spline function of the logarithm function of time [4, 21, 24]. The literature is replete with several advantages of the FPSR models [4, 5, 14, 21, 22, 25, 26].

This study is a method paper with an application. The analyses were carried out to assess the effect of ART on the development of type-1 diabetes and compare the performance of the CPH, parametric and the FPSR models in the identification and quantification of the hazards of prognostic factors of the timing of onset of type-1 diabetes among ART (including fresh and frozen embryo transfer) and spontaneously conceived children in Sweden between 1985 and 2015. We ascertained the effect of the differences in age distribution between ART and spontaneously conceived children on the risk of having type-1 diabetes. In this study, we applied and compared the fit and performances of (i) Cox proportional hazard (CPH) models, (ii) The proportional hazard (PH) (Weibull PH, exponential PH and Gompertz PH) and the Accelerated Failure Time (AFT) (Weibull AFT, exponential AFT, log-logistic, lognormal, and the generalized gamma models) parametric survival models and (iii) Royston-Parmar (RP) Flexible parametric survival regression (FPSR) models with a different number of knots. The assumption of the PH can be relaxed in the PH models. The FPSR models have the advantage that the PH assumption can be relaxed rather easily in comparison to the other survival models.

Methods

The data

The data used for this study were collected in Sweden and represent all singleton children (n = 3,138,540) born between 1985 and 2015, excluding singletons conceived after oocyte donation. The data was extracted from the national health data registers hosted by the Swedish National Board of Health and Welfare, linked with several national quality registers and information from Statistics Sweden (SCB). The SCB maintains a constantly updated and quality-checked register from the Swedish National Board of Health and Welfare, and the Swedish National Data Service which ensures the completeness of the data. The national quality registers include registers on morbidity and mortality of children born in Sweden. The SCB did not state any change in the inclusion criteria of morbidities and mortalities over time.

Further details on the data have been reported [1]. Ethical permission was given from the Regional Ethical Committee (bjorn.rydevik@gu.se) at the University of Gothenburg (Dnr 214–12, T422-12, T516-15, T233-16, T300-17, T1144-17, T121-18). The Swedish National Board of Health and Welfare obtained informed written consent from patients to have data/samples from their medical records used in research. We followed the prescribed ethical regulations on confidentiality when the database was accessed in October 2019. The Swedish National Board of Health and Welfare, and Statistics Sweden (SCB) placed ethical restrictions on sharing the data publicly as the data contain potentially identifying or sensitive patient information. The restriction was concurred by the Regional Ethical Committee at the University of Gothenburg, Sweden.

Statistical models

Cox proportional hazard models

The CPH model was developed based on the assumption that hazards are multiplicatively proportional to baseline hazards [27] but without any assumption about the distribution of the hazards.

h(t)=h0(t)eβ1x1+β2x2+⋯βkxk (1)

From Eq (1), coefficients β1, β2,………, βk could be estimated but a direct estimate of the baseline hazard (h0(t)) or its distribution cannot be estimated. The model nonetheless provides an avenue to estimate the baseline cumulative hazard (H0(t)) and baseline survival (S0(t)) which can be used to estimate the h0(t) [19].

The CPH uses maximum partial likelihood methods to estimate coefficients (βi). Numerically, let xi be the row vector of covariates for the time interval (t0i; ti) for the ith observation in a dataset with N subjects (i = 1, 2, 3,………., N). The coefficient (βi) of the covariates (Xi) can be estimated by maximizing the partial log-likelihood function

logL=∑j=1P[∑i∈Pjxiβ−djlog{∑k∈Rjexp(xkβ)}] (2)

where j indexes the ordered failure times t(j), j = 1, 2, ……., P; Pj is the set of Pj observations that fail at t(j); dj is the number of failures at t(j); and Rj is the set of observations k that are at risk at time t(j) (that is, all k such that t(0k) < t(j) ≤ t(k)).

Parametric survival models

As reported in the literature [5, 20], the accelerated failure-time (AFT) models and the multiplicative or proportional hazards (PH) model are the most-used parametric models for adjusting survivor functions for the effects of covariates. The PH models include the Weibull, Gompertz, and exponential while the exponential, Weibull, lognormal, log-logistic, and generalized gamma are the commonest AFT models. In the AFT model, log(t) (the natural logarithm of the survival time) is expressed as a linear function of the covariates which yields a linear model

logtj=Xjβ+zj. (3)

where xj is a vector of the covariates, β is a vector of the regression coefficients, and zj is the error function whose distributional form determines the form of the regression model. For instance, a normal density leads to the lognormal regression model just as the logistic density yields the log-logistic regression. The AFT models applied to change the time scale by a factor of e−xjβ. The time is accelerated if the factor is <1 and decelerated (degraded) if >1. In the PH model, the concomitant covariates have a multiplicative effect on the hazard function and contain the covariates which have a multiplicative effect on the hazard function

h(tj)=h0(t)g(Xj) (4)

for some h0(t) and for g(Xj), a non-negative covariates function. In some cases, g(Xj) is expressed as exjβ. The parametric PH model becomes a CPH model if the function h0(t) is not specified [5, 20].

Flexible parametric survival regression model

These models use restricted cubic splines to model a transformation of the survival function and can be modelled on different scales, including the hazard scale, the odds scale, and the probit scale in flexible parametric survival analyses. We focussed on the hazard scale of the models to ensure that the estimates from the FPSR and CPH models are comparable. This approach has an advantage in that the corresponding function is more stable and the process of capturing the shape of the function is easier [28]. The Weibull model is one of the commonest parametric models for survival data and can be criticized due to its lack of flexibility in the shape of the hazard function. The log cumulative hazard function of Weibull distribution is written as

ln{H(t:x)}=ln(H0(t))+xiβi=lnλ+γln(t)+xiβi (5)

In Eq (5), ln H0(t) is the baseline log cumulative hazard at time point t, λ is the scale parameter, γ is the shape parameter, xi is the covariate and βi is the coefficient of the covariate [28]. The log cumulative hazard function of the FPSR models are based on a log cumulative hazard scale with the use of restricted cubic spline function of the log time to transform the function in Eq (5) is

ln{H(t:x)}=lnH0(t)+xiβi=s(x)+xiβi (6)

In Eq (6), x = ln(t) and s(x) is a restricted cubic spline function with k knots k1, k2,…………….kk and parameters γ0, γ1,…………….γk−1 is expressed as

s(x)=γ0+γ1z1+⋯…………+γk−1zk−1

Where z1 = x = ln(t) and zj(j≥2) are derivable functions that are determined by the numbers and the positions of the knots is computed as

zj=(x−kj)+3−ϕj(x−kj)+3−(1−ϕj)(x−kj)+3j=2,…,k−1

Where ϕj = (kk−kj)/(kk−k1) [4, 19, 23].

The desired complexity of the FSPR models is specified as the number and positions of the knots (connection points) in log time of the spline’s cubic polynomial segments [19]. The k knots, a maximum of 9 knots, has k+1 degrees of freedom (df). The placement of knots is at the centiles (computed as 100/df) of event times. For 4 Knots, the df is 5 and the knots will be located at centiles 20, 40, 60 and 80. The internal knots are bounded by the “boundary knots” which are placed at the minimum and maximum of the distribution of uncensored survival times. The FSPR model reduces to the Weibull model if the number of knots is 0, with γ0 and γ1 as the estimates of its scale and shape parameter respectively. Royston et al. suggested either 1 or 2 knots for smaller (<10,000) datasets and 4 or 5 knots for larger (> = 10,000) datasets [19]. The FSPR model was implemented in Stata using “stpm2” command. The stpm2 can be used with single- or multiple-record or failure survival data on the log cumulative hazard, the log cumulative odds, the probit scales, or on a scale based on theta-value using the Aranda-Ordaz family of link functions [9, 24]. We computed the incidence rate as the probability of having diabetes per person-year and the attributable fraction to assess the excess risk attributable to been conceived with ART compared with spontaneous conception. The survival analysis was performed using Stata 16.0 (Stata-Corp LP, College Station, TX, USA). Microsoft Excel in Office 365 and R Software were used for data visualization.

Dependent variable

The outcome is a paired survival time and indicator of whether the participant had experienced type-1 diabetes or not. For those that had type-1 diabetes, the survival time was their age as of its onset, while the time (age) to type-1 diabetes was censored on the date of the data collection, emigration and death for those with no type-1 diabetes.

Independent variable

Our choice of covariates was informed by Norman et al. [1]. The main explanatory variable in this study is the mode of the conception of the children: spontaneous or ART conception. The types of ART considered in this study are IVF and ICSI with fresh and frozen-thawed embryo transfer. The other independent variables are sex of the child, maternal age, parity, year of birth (birth cohort), mother’s and father’s country of birth, mothers’ smoking status, mothers’ and fathers’ diabetic status, and maternal and paternal education at the birth of the child.

Model selection criteria

The log-likelihood, Akaike information criteria (AIC) [29] and the Bayesian information criteria (BIC) [30] were used to assess the fit of the models. The lower these quantities the better the fitness of the models. The AIC and the BIC are usually computed and compared separately among different models to determine the best fitting model. In all cases, the lower the AIC and BIC, the better the model [14]. Literature suggests that AIC will choose a more complex model irrespective of sample size while BIC is more likely to choose a simpler model [14]. AIC is often preferable in situations when a false negative finding would be considered to be more misleading than a false positive, and BIC is better in situations where a false positive is as misleading as, or more misleading than, a false negative [14]. We used these criteria to assess which of the models been compared was the optimal model.

Results

Among the 3,138,540 children included in the analysis, 98.5% (3,090,602) were conceived spontaneously while 1.5% (47,938) were conceived through ART. Of the 47,938 ART-conceived children, 36,727 were through fresh embryo transfer and 11,211 were from frozen-thawed embryo transfer. About 51.4% of the children were males, nearly half (47.8%) were from mothers aged 30–39 years, 81.7% were from Swedish mothers, from mothers (0.4%) and fathers (0.6%) who were diabetic. In total, 18,118 (0.58%) became type-1 diabetic during the follow-up period comprising 50,936,586 person-years at risk. Among those conceived spontaneously, 0.58% (n = 17,916) became diabetic compared with 0.42% (n = 202) among the ART-conceived (Table 1). The median (Interquartile Range (IQR)) age at onset of type-1 diabetes among spontaneously conceived children was 10 (6–14) years, 8 (5–12) for ART, 9 (5–12) years for fresh embryo transfer and 6 (4–10) years for frozen-thawed embryo transfer. Children conceived by ART had a higher incidence rate of type-1 diabetes compared with those conceived spontaneously. The overall incidence rate of those conceived through ART and spontaneously were 43 and 36 per 100 000 person-years at risk respectively. The highest incidence of type-1 diabetes was found among children whose fathers (320/100,000) and mothers (244/100,000) were diabetic compared with those whose parents were not diabetic (34/100,000 and 35/100,000). The distribution of the incidence of type-1 diabetes by selected children characteristics is presented in Fig 1.

Table 1. Distribution of children’ characteristics and incidence rate of type-1 diabetes.

Characteristics n (%) Prevalence (%) *Median (IQR) years Age **Incidence per 100,000
Conception Mode
Spontaneous 3,090,602 (98.5) 0.58 10(6–14) 36
ART 47,938 (1.5) 0.42 8(5–12) 43
Fresh^ 36.727(1.2) 0.43 9(5–12) 41
Frozen-thawed^ 11,211(0.3) 0.40 6(4–10) 53
Sex
Male 1,613,900 (51.4) 0.62 11(6–15) 38
Female 1,524,640 (48.6) 0.53 9(6–13) 33
Birth Cohort
1985–1990 634,215 (20.2) 0.80 13(9–19) 29
1991–1995 554,632 (17.7) 0.84 12(7–16) 36
1996–2000 426,536 (13.6) 0.80 10(6–14) 44
2001–2005 463,312 (14.8) 0.61 9(5–11) 46
2006–2010 518,879 (16.5) 0.32a a5(3–7) 36
2011–2015 540,966 (17.2) 0.09a a4(2–3) 24
Mother age at birth
<20 44,917 (1.4) 0.55 11(7–16) 30
20/24 465,164 (14.8) 0.61 11(7–16) 33
25/29 1,017,464 (32.4) 0.62 10(6–15) 36
30/39 1,501,187 (47.8) 0.55 10(6–14) 36
40+ 109,808 (3.5) 0.50 9(5–12) 37
Parity
First 1,344,674 (42.8) 0.57 10(6–14) 36
Multi 1,793,866 (57.2) 0.58 10(6–14) 35
Smoking mother
No 2,706,434 (86.2) 0.57 10(6–14) 37
Yes 432,106 (13.8) 0.60 12(7–17) 28
Mothers’ country
Sweden 2,563,910 (81.7) 0.64 10(6–14) 38
Nordic 85,708 (2.7) 0.62 11(7–15) 35
Europe 173,997 (5.5) 0.23 10(6–14) 17
Other 314,486 (10.0) 0.23 8(4–12) 19
Fathers’ country oo ofof birthfodlandgr_
Sweden 2,526,560 (81.2) 0.64 10(6–14) 38
Nordic 79,013 (2.5) 0.62 11(7–15) 35
Europe 190,586 (6.1) 0.23 10(6–14) 17
Other 315,239 (10.1) 0.26 8(5–12) 21
Mothers’ education
< = 9 years 303,360 (9.7) 0.53 11(6–15) 32
10–12 years 1,377,240 (44.2) 0.64 10(6–15) 36
Higher edu<3 years 459,124 (14.7) 0.60 10(6–14) 36
Higher edu> = 3 years 974,777 (31.3) 0.50 9(5–13) 35
Fathers’ education
< = 9 years 440,486 (14.3) 0.58 11(7–15) 31
10–12 years 1,544,336 (50.1) 0.63 10(6–14) 37
Higher edu<3 years 440,789 (14.3) 0.59 10(6–14) 36
Higher edu> = 3 years 659,817 (21.4) 0.47 9(5–14) 34
Type-1 diabetes mother
No 3,125,405 (99.6) 0.56 10(6–14) 35
Yes 13,135 (0.4) 3.56 8(4–12) 244
Type-1 diabetes father
No 3,120,677 (99.4) 0.55 10(6–14) 34
Yes 17,863 (0.6) 4.78 8(5–13) 320
Total 3,138,540 0.58 10(6–14) 36

^subdivisions of ART

*median age at the onset of type-1 diabetes, IQR Interquartile Range

**Incidence per 100,000 person-year

aLimited follow-up time

Fig 1. Distribution of incidence of type-1 diabetes by selected children characteristics.

Fig 1

Test of equality of incidence rates of type-1 diabetes

The overall difference in unadjusted incidence rate between the children conceived spontaneously and by ART was 0.000791 (95% CI: 0.000019–0.000139, incidence rate ratio was 1.222589 (95% CI: 1.058–1.40448), attributable fraction exposed was 0.18206 (95% CI: 0.05568–0.28799). The two tail hypothesis test that the incidence rates for each of the groups are not different was significant (p = 0.0058) (Not shown in the Tables).

Distribution of the hazard and survival functions under different distributions

On the choice of the survival regression analysis to be adopted, we first explored the CPH model. As shown in Fig 2 (left panel), the assumption of proportionality was not violated. In the same way, a test of non-proportionality of Kaplan Meier survival curves of the observed and predicted ART estimates at various ages of the children was not significant (Fig 2: right panel).

Fig 2. Proportionality of survival curves of onset of type-1 diabetes among ART and spontaneously conceived children.

Fig 2

In Fig 3, we present the survival and hazard functions of developing type-1 diabetes by modes of conception using the Kaplan Meier, smoothed, CPH and the FSPR models. In all, survivorship was higher among the spontaneously conceived children compared with those conceived through ART. In the same way, the hazard of type-1 diabetes was higher among those conceived through ART compared with those that were spontaneously conceived.

Fig 3. Comparison of hazard and survival functions under different survival regression models.

Fig 3

In Fig 4, we compared the hazard and survival functions of the flexible models at different degrees of freedom (knots/splines). The functions appear more realistic and flexible at higher degrees of freedom than the Weibull distribution. The greatest flexibility was noticeable at df = 6. The lower panel of Fig 4 shows the predicted incidence of diabetes using the flexible model.

Fig 4. Comparing the hazard and survival functions of the flexible models at different knots/splines.

Fig 4

Comparison of the models

The statistics of all the model selection criteria considered in this study (the loglikelihood, the AIC and the BIC) are shown in Table 2. The AIC and BIC of the FPSR models, the statistics obtained from the parametric models including the Weibull AFT, exponential AFT, log-logistic, lognormal, and the generalized gamma models were only slightly higher than that of the FPSR models. Among the FPSR models evaluated at different degrees of freedom, the largest loglikelihood, the lowest AIC and the lowest BIC were at 6 degrees of freedom (df = 6). Although the model fits are similar for all the models, the FPSR has the lowest values for each of the criteria. This is further supported by the significance of restricted cubic splines (rcs) of each covariate otherwise called the slope of the hazard curve within each of the knots generated at 6 degrees of freedom (Table 2).

Table 2. Comparison of the loglikelihood, AIC and BIC of the models considered.

Model ll(null) ll(model) df AIC BIC
CPH CPH -260143.50* -257910* 27 515873.50 516222.80
Parametric PH Gompertz -121461.50 -118977 29 238012.30 238387.40
Weibull -121176.60 -118547 29 237151.30 237526.40
Exponential -121462.00 -118992 28 238039.70 238401.80
Parametric AFT Weibull -121176.60 -118547 29 237151.30 237526.40
Exponential -121462.00 -118992 28 238039.70 238401.80
Lognormal -120706.30 -118199 29 236455.40 236830.50
Loglogistic -121167.20 -118534 29 237125.40 237500.50
FPSR df = 1 -120890.80 -118547 29 237151.30 237526.40
df = 2 -120890.80 -117781 30 235621.20 236009.20
df = 3 -120890.80 -117598 31 235258.00 235659.00
df = 4 -120890.80 -117525 32 235114.20 235528.10
df = 5 -120890.80 -117512 33 235090.60 235517.50
df = 6 -120890.80 -117497 34 235062.50 235502.30

AIC Akaike Information Criteria BIC Bayesian Information Criteria df degrees of freedom ll loglikelihood PH Proportional Hazard AFT Accelerated Failure Rate

*partial likelihood

Table 3 shows the coefficients of the covariates included in the adjusted models and their respective standard errors (s.e). In all, the estimates from the CPH model, the parametric PH models and the FPSR model at different degrees of freedom were similar and generally lower than the estimates from the parametric AFT models.

Table 3. Coefficients of the covariates from the fitted models.

CPH Parametric PH (β(s.e)) Parametric AFT (β(s.e)) Flexible Model (β(s.e))
Characteristics β(s.e) Gompertz Weibull Exponential Weibull Exponential Lognormal Loglogistic df = = 2 df = = 4 df = = 5 df = = 6
ART 0.07(0.077) 0.07(0.077) 0.06(0.077) 0.07(0.077) 0.06(0.054) 0.06(0.067) 0.05(0.057) 0.06(0.054) 0.07(0.077) 0.07(0.077) 0.07(0.077) 0.07(0.078)
Sex
Male 0.16(0.018) 0.16(0.018) 0.16(0.018) 0.16(0.018) 0.13(0.011) 0.16(0.013) 0.12(0.011) 0.13(0.011) 0.16(0.018) 0.16(0.018) 0.16(0.018) 0.17(0.018)
Birth Cohort (1985–1990)
1991–1995 0.16(0.024) 0.29(0.028) 0.24(0.026) 0.26(0.027) 0.23(0.013) 0.24(0.016) 0.23(0.014) 0.23(0.013) 0.21(0.025) 0.16(0.024) 0.16(0.024) 0.16(0.024)
1996–2000 0.26(0.030) 0.54(0.039) 0.43(0.035) 0.46(0.037) 0.43(0.012) 0.43(0.015) 0.41(0.013) 0.43(0.012) 0.37(0.033) 0.28(0.031) 0.28(0.031) 0.29(0.031)
2001–2005 0.26(0.033) 0.65(0.048) 0.46(0.039) 0.51(0.043) 0.52(0.012) 0.46(0.015) 0.48(0.013) 0.52(0.012) 0.39(0.038) 0.33(0.035) 0.32(0.035) 0.32(0.035)
2006–2010 0.21(0.039) 0.56(0.055) 0.26(0.038) 0.32(0.044) 0.44(0.015) 0.26(0.023) 0.39(0.016) 0.44(0.015) 0.28(0.042) 0.31(0.043) 0.32(0.043) 0.33(0.044)
2011–2015 0.08(0.056) 0.34(0.073) 0.15(0.042) 0.07(0.047) 0.27(0.031) 0.15(0.056) 0.28(0.028) 0.27(0.031) 0.31(0.070) 0.31(0.070) 0.31(0.070) 0.31(0.070)
Maternal age(<20)
20/24 0.07(0.073) 0.07(0.073) 0.07(0.073) 0.07(0.073) 0.05(0.051) 0.07(0.063) 0.06(0.053) 0.05(0.051) 0.07(0.073) 0.07(0.073) 0.07(0.073) 0.07(0.073)
25/29 0.09(0.073) 0.09(0.073) 0.09(0.073) 0.09(0.073) 0.07(0.050) 0.09(0.061) 0.08(0.052) 0.07(0.050) 0.09(0.073) 0.09(0.073) 0.09(0.073) 0.09(0.073)
30/39 0.10(0.074) 0.10(0.074) 0.10(0.074) 0.10(0.074) 0.08(0.050) 0.10(0.061) 0.09(0.051) 0.08(0.050) 0.10(0.074) 0.10(0.074) 0.10(0.074) 0.10(0.074)
40+ 0.14(0.091) 0.14(0.091) 0.14(0.091) 0.14(0.091) 0.11(0.057) 0.14(0.069) 0.13(0.058) 0.11(0.057) 0.14(0.091) 0.14(0.092) 0.14(0.091) 0.14(0.091)
Parity(> = 2)
First 0.01(0.016) 0.01(0.016) 0.01(0.016) 0.01(0.016) 0.01(0.013) 0.01(0.016) 0.01(0.014) 0.01(0.013) 0.01(0.016) 0.01(0.016) 0.01(0.016) 0.01(0.016)
Mother Smokes
No 0.26(0.029) 0.26(0.029) 0.26(0.029) 0.26(0.029) 0.21(0.015) 0.26(0.017) 0.23(0.015) 0.21(0.015) 0.26(0.029) 0.26(0.029) 0.26(0.029) 0.26(0.029)
Mother Country (Europa)
Sweden 0.45(0.092) 0.45(0.091) 0.45(0.092) 0.45(0.092) 0.36(0.033) 0.45(0.037) 0.36(0.032) 0.36(0.033) 0.45(0.091) 0.45(0.091) 0.45(0.091) 0.45(0.091)
Nordic 0.47(0.116) 0.47(0.116) 0.46(0.116) 0.46(0.116) 0.37(0.040) 0.46(0.046) 0.38(0.040) 0.37(0.040) 0.47(0.116) 0.47(0.116) 0.47(0.116) 0.47(0.116)
Other 0.10(0.067) 0.10(0.067) 0.10(0.067) 0.10(0.067) 0.08(0.063) 0.10(0.081) 0.07(0.061) 0.08(0.063) 0.10(0.067) 0.10(0.067) 0.10(0.067) 0.10(0.067)
Father Country (Europa)
Sweden 0.57(0.099) 0.57(0.099) 0.57(0.099) 0.57(0.099) 0.45(0.028) 0.57(0.032) 0.45(0.028) 0.45(0.028) 0.57(0.099) 0.57(0.099) 0.57(0.099) 0.56(0.100)
Nordic 0.56(0.127) 0.56(0.127) 0.56(0.127) 0.56(0.127) 0.45(0.037) 0.56(0.041) 0.45(0.037) 0.45(0.037) 0.57(0.127) 0.57(0.127) 0.57(0.127) 0.57(0.127)
Other 0.32(0.096) 0.32(0.096) 0.32(0.096) 0.32(0.096) 0.26(0.043) 0.32(0.051) 0.26(0.042) 0.26(0.043) 0.32(0.096) 0.32(0.096) 0.32(0.096) 0.32(0.096)
Mother education(>3 yr)
< = 9 years 0.14(0.036) 0.13(0.036) 0.13(0.036) 0.13(0.036) 0.11(0.023) 0.13(0.028) 0.12(0.024) 0.11(0.023) 0.13(0.036) 0.14(0.036) 0.14(0.036) 0.14(0.036)
10–12 years 0.08(0.022) 0.08(0.021) 0.08(0.022) 0.08(0.022) 0.06(0.015) 0.08(0.018) 0.07(0.016) 0.06(0.015) 0.08(0.022) 0.08(0.022) 0.08(0.022) 0.08(0.022)
Higher edu<3 years 0.02(0.025) 0.02(0.025) 0.02(0.025) 0.02(0.025) 0.02(0.019) 0.02(0.024) 0.02(0.020) 0.02(0.019) 0.02(0.025) 0.02(0.025) 0.02(0.025) 0.02(0.025)
Father education(>3 yr)
< = 9 years 0.02(0.030) 0.02(0.023) 0.02(0.023) 0.02(0.023) 0.02(0.023) 0.02(0.029) 0.01(0.024) 0.02(0.023) 0.02(0.030) 0.02(0.030) 0.02(0.030) 0.02(0.030)
10–12 years 0.09(0.025) 0.09(0.025) 0.09(0.025) 0.09(0.025) 0.07(0.017) 0.09(0.021) 0.07(0.018) 0.07(0.017) 0.09(0.025) 0.09(0.025) 0.09(0.025) 0.09(0.025)
Higher edu<3 years 0.04(0.028) 0.04(0.028) 0.05(0.028) 0.05(0.028) 0.04(0.021) 0.05(0.026) 0.04(0.022) 0.04(0.021) 0.04(0.028) 0.04(0.028) 0.04(0.028) 0.04(0.028)
Mother Diabetic 1.86(0.302) 1.86(0.304) 1.86(0.302) 1.86(0.302) 1.48(0.009) 1.86(0.007) 1.74(0.009) 1.50(0.009) 1.86(0.303) 1.86(0.303) 1.86(0.303) 1.86(0.303)
Father Diabetic 2.17(0.309) 2.18(0.311) 2.17(0.309) 2.17(0.309) 1.73(0.005) 2.17(0.004) 2.07(0.005) 1.76(0.005) 2.18(0.310) 2.18(0.310) 2.18(0.310) 2.19(0.312)

Modelling the risk factors of type-1 diabetes

The estimates from each of the model were similar. We have used the estimates from the FPSR model at 6 degrees of freedom to interpret the adjusted determinants of timing of the onset of type-1 diabetes among the children. The age of the children was used as a timescale to correct for the problem associated with lesser exposure time among the late entries. Although insignificant, the adjusted hazard of type-1 diabetes was 7% higher (adjusted Hazard Ratio (aHR) = 1.070; 95% Confidence Interval (CI): 0.929–1.232, p = 0.346)) among children conceived through ART than those conceived spontaneously while controlling for other variables. A sub-analysis with emphasis on whether the transferred embryo was fresh or frozen-thawed transferred while controlling for other covariates showed that the hazard of type-1 diabetes was 37% (aHR = 1.368; 95% CI: 1.013–1.847, p = 0.041) higher among frozen-thawed transfer compared with those conceived spontaneously. Inversely, the hazard of type-1 diabetes was higher among frozen-thawed embryo transfer than fresh embryo transfer (aHR = 1.407; 95% CI: 1.007–1.965, p = 0.046; not shown in the Tables). While controlling for other variables, the hazard of type-1 diabetes was about 17% (aHR = 1.171; 95% CI: 1.137–1.206, p<0.001) higher among males than the females. The adjusted hazard of type-1 diabetes was significantly associated with the birth cohort of the children. The younger the children the higher the hazard of type-1 diabetes. For instance, those born in 1991–1995 had 18%, 1996–2000 (33%), 2001–2005 (38%), 2006–2010 (38%) and 2011–2015 (36%) higher hazard of type-1 diabetes than those in 1985–1990 birth cohort.

The hazard of type-1 diabetes was higher among children whose mothers do not smoke (aHR = 1.296; 95% CI: 1.240–1.354, p<0.001) than those whose mother smokes. The adjusted hazard of type-1 diabetes was 60% higher among children of both Swedish and other Nordic mothers than those of other European mothers while the hazard was about 76% higher among the children of both Swedish and other Nordic fathers than those of other European fathers. The hazard of type-1 diabetes increased with a lower level of paternal and maternal education. The highest hazard of type-1 diabetes was found among children whose parents were diabetic. Children of diabetic mothers and fathers were about 6 times (aHR = 6.419; 95% CI: 5.852–7.041, p<0.001) and 9 times (aHR = 8.808; 95% CI: 8.221–9.437, p<0.001) respectively more likely to be diabetic than those whose parents were not diabetic as shown in Table 4. However, maternal age and the parity of the index child were not significantly associated with the risk of type-1 diabetes. The visualization of the adjusted hazard ratios is presented in Fig 5.

Table 4. Adjusted prognostic factors of type-1 diabetes among the studied Swedish cohort from CPH and FPSR model with 6 degrees of freedom.

FPSR Model (df = 6) CPH Model
Characteristics aHR (95% CI) p-value aHR (95% CI) p-value
Conception Mode
Spontaneous 1.000
ARTa 1.070(0.929–1.232) 0.346 1.068(0.927–1.230) 0.361
Spontaneous 1.000
Freshb 1.010(0.862–1.184) 0.902 1.008(0.860–1.182) 0.917
Frozen-thawedb 1.368(1.013–1.847) 0.041 1.361(1.011–1.834) 0.044
Sex
Female 1.000
Male 1.171(1.137–1.206) 0.000 1.171(1.137–1.206) 0.000
Birth Cohort
1985–1990 1.000
1991–1995 1.179(1.132–1.228) 0.000 1.168(1.121–1.217) 0.000
1996–2000 1.332(1.273–1.395) 0.000 1.297(1.240–1.358) 0.000
2001–2005 1.380(1.313–1.451) 0.000 1.297(1.234–1.363) 0.000
2006–2010 1.382(1.299–1.470) 0.000 1.234(1.160–1.311) 0.000
2011–2015 1.359(1.228–1.504) 0.000 1.085(0.981–1.199) 0.114
Maternal age (years)
<20 1.000
20/24 1.073(0.940–1.226) 0.296 1.074(0.940–1.226) 0.295
25/29 1.093(0.958–1.246) 0.186 1.093(0.958–1.246) 0.185
30/39 1.104(0.967–1.260) 0.143 1.104(0.967–1.260) 0.142
40+ 1.151(0.985–1.345) 0.076 1.151(0.985–1.345) 0.076
Parity
> = 2 1.000
First 1.007(0.975–1.040) 0.677 1.007(0.975–1.039) 0.688
Smoking mother
Yes
No 1.296(1.240–1.354) 0.000 1.295(1.239–1.353) 0.000
Mother Country
Europa 1.000
Sweden 1.567(1.397–1.757) 0.000 1.569(1.399–1.759) 0.000
Nordic 1.596(1.384–1.841) 0.000 1.594(1.382–1.839) 0.000
Other 0.908(0.786–1.048) 0.187 0.907(0.785–1.047) 0.182
Father Country
Europa 1.000
Sweden 1.767(1.583–1.972) 0.000 1.769(1.585–1.975) 0.000
Nordic 1.760(1.527–2.028) 0.000 1.759(1.526–2.027) 0.000
Other 1.380(1.204–1.582) 0.000 1.378(1.203–1.580) 0.000
Mother Education
Higher edu> = 3 years 1.000
< = 9 years 1.145(1.076–1.219) 0.000 1.145(1.076–1.219) 0.000
10–12 years 1.082(1.041–1.125) 0.000 1.082(1.041–1.125) 0.000
Higher edu<3 years 1.024(0.976–1.074) 0.327 1.025(0.977–1.075) 0.320
Father Education
Higher edu> = 3 years 1.000
< = 9 years 1.022(0.965–1.082) 0.458 1.023(0.966–1.084) 0.431
10–12 years 1.094(1.046–1.144) 0.000 1.095(1.047–1.145) 0.000
Higher edu<3 years 1.045(0.991–1.102) 0.105 1.046(0.992–1.103) 0.099
Mother Diabetic 6.419(5.852–7.041) 0.000 6.405(5.839–7.026) 0.000
Father Diabetic 8.808(8.221–9.437) 0.000 8.789(8.203–9.417) 0.000

aHR adjusted Hazard Ratio, CPH Cox Proportional Hazard FSPR Flexible Parametric Survival Regression

_rcs Spline variables for the log baseline cumulative hazard Estimates from the FPSR model are significant but are not presented.

a,b fitted in separate models alongside the covariates

Fig 5. The hazard ratios of the prognostic factors of type-1 diabetes among the studied Swedish cohort.

Fig 5

Discussions

This study was designed to compare the performance of different survival models in examining the risk of type-1 diabetes viz-a-viz mode of conception and assess if there are differentials in the risk of type-1 diabetes between children from fresh or frozen-thawed embryo transfers. In all, the models considered in this study are comparable as far as modelling the effect of conception modes on the risk of diabetes is concerned. While there were no significant differences in the risk of diabetes between children conceived spontaneously and by ART, the risk differed significantly among children from fresh and frozen-thawed embryo transfers. The measures of goodness of fit of models considered in this study were relatively lower in the flexible models. However, rather than likelihoods, the CPH model uses a different procedure and returns partial likelihood, which is also lower than the likelihood of the other models. Similarly, the AIC and the BIC which are measures of information lost by each of the models were more favourable to the flexible models. Similar approaches have been used to identify better models in the literature [31, 32]. Besides having the lowest information lost, the flexible model fitted the data most but this did not lead to large differences between the estimates from the models. At higher degrees of freedom, the flexible model fitted the data most and also showed that the occurrence of type-1 diabetes is not proportional to the baseline hazard but that the risk changed severally as the children grew older. We have applied the proportional hazard and other parametric, as well as the flexible parametric models to the data. A major strength of the flexible parametric model is its ability to account for non-proportional hazards, hence individual non-PH models were not explored in this study. However, the estimates from the flexible parametric and CPH models are similar when the proportional hazard assumptions were not violated.

The estimates from the adjusted hazard ratios from the CPH model was close to those obtained from the parametric PH and the flexible models. Lambert et al. had stated that rather than just a comparison of the AIC or BIC, it is a strength to draw conclusions from the estimates that do not change largely when different reasonable models are chosen [32]. Therefore, we can conclude that although the FPSR provided a relatively better model fit, the estimates from all the models considered in the current study are similar. With such, any of the models could be used. Among the FPSR models evaluated at different degrees of freedom, the loglikelihood, as well as the AIC and the BIC unanimously identified the 5-knot (6 degrees of freedom) flexible model as the best model. Our finding agreed with the recommendation of Royston et al., that flexible models with 5 or 6 degrees freedom will be more ideal for a sample size greater than 10,000 [19].

Nonetheless, the parameter estimates from the flexible and the CPH model are very close, despite the wide differences in all the measures of model fitness adopted in this study. These similarities underscore the strength of the CPH model when a “large” sample is followed up for a sufficiently “long” time [14]. There are possibilities that the proportional assumption could be violated, especially in a long follow-up study of this nature. Bower et al affirmed the need to account for non-proportionality, if present, to get an insight into the natural history of the disease and biological process, and to make accurate predictions [14]. Rutherford et al. emphasized that the flexible models provide a more accurate estimate of complex hazard functions as well as unbiased estimates of hazard ratios than the parametric models [22]. The flexible model has a unique advantage of providing a direct estimate of relative and absolute effects besides the quantification of differences between survival and hazard functions using a time scale of interest [33–35].

However, literature has suggested that AFT models are better alternatives to the CPH in the analysis of time to event data, especially when there is no permanent effect in the context of the follow-up period [36–39]. The AFT models assume that the effect of a covariate is either to accelerate or decelerate the life course of an outcome, say diabetes type-1, by some constant. Whereas, the CPH model assumes that the hazard functions for any two patients with baseline x vectors x1 and x2 are constrained to be proportional, upon which the estimation method is based [37–39]. Additionally, Lambert et al remarked that, unlike a CPH model, regression parameter estimates from AFT models are robust to neglected covariates and less affected by the chosen probability distribution [36].

Although the hazard of type-1 diabetes was higher among children conceived through ART than those conceived spontaneously in the bivariable analysis, we found no significant difference in the hazard of type-1 diabetes among the two groups of children in the adjusted models. This finding is corroborated in the literature by recent Danish studies [2, 3]. However, a further sub-group analysis controlling for other variables showed that the children conceived from frozen-thawed transfer had a significantly higher hazard of type-1 diabetes than those from fresh embryo transfer and children from spontaneous conception. This is in agreement with the previous study on the same cohort by Norrman et al. who reported a higher risk of type-1 diabetes among children from frozen-thawed embryo transfer than those from fresh embryo transfer (aHR: 1.52; 95% CI: 1.08–2.14) and those conceived spontaneously (aHR: 1.41; 95% CI: 1.05–1.89) [1]. This implies that the type of ART adopted is associated with the risk of type-1 diabetes.

The current study established a higher risk of type-1 diabetes in the offspring of diabetic parents. Children of diabetic mothers were about 540% at higher risk of type-1 diabetes compared with children whose mothers are not diabetic. A similar pattern but a higher likelihood of risk (780%) was found among children whose fathers were diabetic. This finding aligns with the findings of previous studies [40, 41]. Diabetic parents pose a higher risk of type-1 diabetes to their children independent of the conception method. This is plausible as a systematic review has reported a 51% significant increase in diabetes mellitus among parents who conceived by ART compared with those who conceived spontaneously [42].

The sex of the children was significantly associated with the age at the onset of type-1 diabetes. The males were at higher risk of type-1 diabetes than females. Further research is necessary to understand the biological configuration of males that put them at higher risk of type-1 diabetes. Our study is however corroborated by earlier researches which showed that about three-fifths of children who developed type-1 diabetes were boys [43].

The median age at onset of type-1 diabetes among diabetic children was 10 years (Interquartile range: 6–14 years). There appears to be a generational shift in the age at the onset of type-1 diabetes among the children. The increase in the risk of type-1 diabetes in the studied population was linear with the lowest risk among the children born between 1985 and 1990 and highest (about 36% on average) among the birth cohorts of 2001–2005, 2006–2010, and 2011–2015. Our finding is at variance with the results of the Danish study which found no association between risk of type-1 diabetes and birth cohorts [3]. Although not reported in the results, our stratified birth cohort analysis showed that covariate effects remain constant over different cohorts.

We found a higher preponderance of type-1 diabetes among children whose mothers do not smoke compared with those whose mothers smoke. This finding is at variance with findings of a comparative study on the associations of parental smoking during pregnancy and childhood-onset of type-1 diabetes in the Norwegian Mother and Child Cohort Study and the Danish National Birth Cohort by Magnues et al. [44]. Magnus et al. reported that in both cohorts, maternal smoking beyond gestational week 12 was inversely associated with type-1 diabetes” and that “in the Norwegian register-based cohort, children of mothers who still smoked at the end of pregnancy had a lower risk of type-1 diabetes” [44]. The authors noted that their findings were in contrast to teratogens operating very early during development, but similar to what has been reported earlier for effects of maternal smoking on birth weight [45]. There could be pathways to the modification of the effect of smoking on diabetes. One such is the effect of low birth weight. Reduced risk of type-1 diabetes in children with low birth weight has been reported and low birth weight is more prevalent among smoking mothers [46].

The country of birth of the parents significantly predicted the risk of type-1 diabetes with higher risks among children of Swedish and other Nordic mothers and fathers compared with children whose either parent is born outside the Nordic countries. Existing literature had suggested that people from certain countries are more likely to be diabetic than others [1, 47–51]. Studies have shown a higher preponderance of type-1 diabetes in the Scandinavian countries [1, 49, 50]. Although the reasons for these differences are yet to be well articulated in the literature.

Educational attainment of parents was significantly associated with the risk of type-1 diabetes among the children. The risk of type-1 diabetes was higher among children of those who had a lower level of paternal and maternal education. Educational attainment could be associated with the amount of information at the disposal of parents which may or may not predispose a child to type-1 diabetes. Maternal age and the parity of the index child were not significant predictors of type-1 diabetes.

Strength and limitations of the study

Our study has a major strength of a detailed analysis and comparison of the fit and performance of a different range of regression models including the semi-parametric proportional hazard, parametric proportional hazard and accelerated failure time models as well as the flexible model at different degrees of freedom to arrive at our conclusions. Also, we have used a large dataset that consists of over three million births spanning over 30 years of follow-up and nearly 19,000 cases from high validity registries. Hence, the estimated risks of type-1 diabetes were made with high statistical precision. Furthermore, our study is based on Swedish nationwide population-based registries, we, therefore, used data with almost complete coverage with no sampling or recall bias, leading to high generalizability, no loss to follow up, and almost complete ascertainment of type-1 diabetes cases. Besides, we adjusted for several potential confounders including the sex of the children, parental type-1 diabetes status, and country of birth of the parents. One of the limitations of our study was the limited time of exposure for those born after 2000. Some data were missing hence we may not have accounted for some confounders. The control group consisted of all non-ART singletons. A better control group might have been children to subfertile couples conceiving spontaneously. However, such a control group is almost impossible to identify.

Conclusion

Our estimates from the different regression models including the semi-parametric proportional hazard, parametric proportional hazard models and the flexible model at different degrees of freedom were similar. This is an indication that the models performed similarly and any of them can be used to model the data. For the Swedish birth data used in the current study, we did not find any significant differences among the performances of the regression methods. There may be a need for a similar comparative analysis of Danish data used by Hargreave et al. and Kettner et al. [2, 3] so as to ascertain that the contradictions in their findings were not due to the methods of analysis. As shown in this study, for a very large sample followed up for a long time, the CPH model provided a comparative estimate with the FPSR model. Any of the models, especially the Cox semi-parametric model, parametric proportional hazard models and the flexible model at higher degrees of freedom are appropriate in modelling the risk of type-1 diabetes among ART and spontaneously-conceived children.

The results from our large population-based nationwide data were generally reliable, indicating that mode of conception could affect the risk of type-1 diabetes among the children especially when they are from frozen-thawed embryo transfer. Although we found no significant difference in the risk of type-1 diabetes among ART and spontaneously conceived children generally, our sub-analysis showed that children from frozen-thawed embryo transfer had a higher risk than other children. This is of some concern in view of the increasing number of frozen cycles all around the world. Estimates suggest that some 390,000 babies are now born each year globally through assisted fertility techniques including IVF and ICSI while the total number of ART children have exceeded eight million by 2019 [52, 53].

It’s hard to generalise these findings to other settings. Although the considered models performed similarly in this specific setting, there’s no guarantee that this will be the case with other data sources or diseases or other settings.

Acknowledgments

The authors appreciate the logistic supports provided by the Consortium for Advanced Research and Training in Africa (CARTA) to AFF to visit the University of Gothenburg as part of his fellowship at the University of Warwick. The data analysis was done during the visit.

Abbreviations

AFT

Accelerated Failure Time

AIC

Akaike information criteria

aHR

adjusted Hazard Ratio

ART

assisted reproductive technology

BIC

Bayesian information criteria

CI

Confidence Interval

CPH

Cox Proportional Hazard

FPSR

Flexible parametric survival regression

ICSI

Intracytoplasmic sperm injection

IQR

Interquartile range

IVF

In-Vitro-Fertilization

PH

Proportional hazard

RP

Royston-Parmar

SB

Statistics Sweden

SC

Spontaneous conception

Data Availability

Ethical permission was given from the Regional Ethical Committee (bjorn.rydevik@gu.se) at the University of Gothenburg (Dnr 214-12, T422-12, T516-15, T233-16, T300-17, T1144-17, T121-18). The Swedish National Board of Health and Welfare obtained informed written consent from patients to have data/samples from their medical records used in research. We followed the prescribed ethical regulations on confidentiality when the database was accessed in October 2019. The Swedish National Board of Health and Welfare, and Statistics Sweden (SCB) placed ethical restrictions on sharing the data publicly as the data contain potentially identifying or sensitive patient information. The restriction was concurred to by the Regional Ethical Committee at the University of Gothenburg, Sweden.

Funding Statement

The author(s) received no specific funding for this work.

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Decision Letter 0

Y Zhan

Transfer Alert

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9 Feb 2021

PONE-D-21-00472

Conception modes and risk of Type-1 diabetes among 1985-2015 Swedish birth cohort: How robust are the survival analysis regression models?

PLOS ONE

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Reviewer #1: The authors of this study attempt to address two questions, 1) how does mode of conception affect the risk of type I diabetes in children, and 2) which survival model is best for the assessment of this association.

Main comments

The combination of the two above aims does not flow in my opinion, and is not adequately motivated. Who is the target audience of this paper? The medical research question of interest, seems to be relevant and interesting (although not my field of work), but the comparison of survival analysis models does not add to the current body of work in this area. Even if this did add to the question of “which is the best survival analysis model?” (which I’m not convinced has a definite answer), the comparison of methods here is undertaken in a situation where we do not know the underlying true answer to the question of interest. It is therefore, very difficult to determine which of the models is the best fitting. Furthermore, the selection of the best model according to the AIC and BIC is of course useful, but does not concretely determine which of the models fitted is the best model for the data. The AIC and BIC can indicate that different models are the better fitting model, and should be used as a guide for model selection along with knowledge about the specific subject area. In my opinion, the model selection process described in this paper, to some extent is what most researchers do in the background without presenting such results, but rather describe that they have chosen, say, a flexible parametric survival model based on the AIC and BIC.

For the above reasons, I would suggest that the authors of the paper focus on the research question of interest, i.e., the association between type I diabetes mode of conception, and refrain from presenting the comparison of survival analysis models in this paper.

Independent of the above comments, I think that some work could be done in the structuring of the paper to ensure a logical progression through the manuscript to help the reader’s understanding. The description of the survival analysis models in the introduction needs some more careful editing (see specific comments for examples), and I would suggest that detailed descriptions are instead presented in the methods section. There are results presented with no corresponding description in the methods section; the authors give detailed mathematical descriptions of the models they are going to fit, but no actual description of the models used for the analysis, i.e. how were certain variables modelled? Attributable fraction results are presented in the results with no description of what the measure is in the methods section. Another example is that the AIC and the BIC are described well, but the paper is lacking a sentence stating “We used these criteria to assess which of the above described models was the optimal model.” Additionally, some of the language used in the introduction is very non-specific; examples include the terms “adequate representation”, or “building on their strengths”. I would suggest the paper needs editing before it is at the standard for publication.

Specific comments

1. Ensure that initialisations are defined (e.g. SC, NPMLE)

2. Avoid the use contractions: “doesn’t” in the introduction

3. Add reference for Lebesgue measure

4. Some of the models are described as being proportional hazards models, and whilst the Cox model is most commonly called the Cox Proportional Hazards Model, the assumption of proportional hazards (PH) can be relaxed in these models and in the other models described.

5. Related, were non-proportional hazards models fitted? If not, why the focus on this in the description of the models? Perhaps the authors wanted to highlight an advantage of the flexible parametric survival models (that the PH assumption can be relaxed rather easily in comparison to the other survival models), but then this needs to be stated. If PHs are mentioned then a more thorough description would be a good idea to help the reader.

6. Line 118: Smooth hazard ratios should be smooth hazard rates.

7. Description of flexible parametric models (FPM) in the introduction: restricted cubic splines (RCS) do not need to model log time. In fact, when considering attained age as the time scale, restricted cubic splines are often used to model the untransformed time scale.

8. It is not clear to me why the comparison between the use of RCS in FPMs is compared to a linear function of log time in the introduction.

9. When presenting survival analyses, the timescale and event of interest are often presented alongside the exposure of interest and any confounding variables. I would suggest describing the analysis in this way instead of dependent/independent variables.

10. Related, a description to link the motivation behind the age distribution problems described in the introduction, and how this was dealt with in your analysis is needed (I think you did this by using age as the timescale?)

11. When incidence rates are so low, present them per 1,000 person-years (for example)

12. Was there missing data? If so, how much? How did you deal with this?

13. Figures need some cleaning up: ensure consistency between grayscale and colour figures, x-axes should be consistently named.

14. Figure 3: there is no description of the smoother used for the smoothed hazard estimates. “Stpm2” will not be clear for readers who are not familiar with FPM and/or Stata.

15. Figure 4, third panel: which degrees of freedom are presented?

16. I think the results you rely on are from the FPM with 6 degrees of freedom. This is quite a high number. Given the subject area, is the hazard function presented in figure 3 with 6 degrees of freedom reasonable to the authors?

17. Table 3: all the coefficient estimates need not be presented, only the exposure of interest and a description that the estimates were adjusted for the other variables. In particular, since the estimates for the restricted cubic spline coefficients are so often misinterpreted (and actually never presented in the context of answering a medical research question) I would suggest to remove these.

Reviewer #2: The advantages of this study are 1) compared statistical methods for exploring effects of different conception modes on a long-term outcome (Type 1 diabetes), using observational data from a nationwide register in Sweden with almost 31 years follow-up; 2) the authors are familiar with applications of parametric, flexible parametric and semi-parametric regression models to time-to-event data analysis. Sharing the codes would benefit the STATA users who want to do these similar comparisons.

Here are some comments for improvement:

1) In multivariable analysis, the adjustment was mad for child’s sex as well. Did the authors consider sex as a potential confounder or only an independent predictor for the outcome? It seems like sex of child was not associated with conception modes.

2) There is space to improve abstract: e.g. the second sentence repeated the information of the first sentence. As seen, the same cohort (data) had been applied in the Reference paper 1 for the same research question, both with hazard ratios as the association measure. Some conclusions were also similar. The authors could emphasize on the comparisons of methods and presenting corresponding results, presenting less similar conclusions as Ref 1 in this study.

3) Time-to-event was defined from baby born (i.e time zero) that has been accepted in literature. However, conception modes were determined at the beginning of pregnancy. There were a time window of gestational age that might differed between ART and spontaneous conception, due to ART being a risk factor of preterm birth. Then baby with ART would early expose to risk of type 1 diabetes (T1D). How the authors consider the following question: whether there is potential bias by gestational age?

4) Using singleton births from the same mothers, there might be more or less intra-correlation, especially for T1D showing familial aggregation, which could be discussed by the authors why didn’t take it account in this study.

5) Check the text carefully, e.g. minor typos: “Royston-Palmar” should be Royston-Parmar in several places.

Reviewer #3: The manuscript by Fagbamigbe et al. describes the results of an observational study on the association between conception mode and the risk of type-I diabetes using data from the Swedish birth register. Furthermore, they aim to compare the results of different survival models in their settings, with the hypothesis that using inappropriate models might explain contradictory findings that have been reported in the literature.

I think the applied analysis of the manuscript is interesting (nice work), but the more methodological parts need some extra work, as I feel the authors don’t fully accomplish what they aimed to do. In particular, I would like to see a more detailed comparison of the modelling approaches being studied, to show the effect of misspecifying a model or choosing a not-flexible-enough model for time to event data; statistical Monte Carlo simulation might even help selling the message as well.

More detailed comments (section by section) follow.

# Introduction

- Line 102/103: The Kaplan-Meier estimator can actually be used to investigate the effect of covariates, as you could in principle stratify the analysis (see e.g. the results of sts graph, by(covariate) in Stata) and still get distinct estimates of the survival function. Please reword that sentence. Having said that, of course this gets cumbersome when several covariates are to be investigated together, and therefore I agree that regression models are helpful in those settings.

- Line 119/122: I am not sure what the authors mean with the sentence “...and the fact that the cumulative hazard function or survival function may not be unbiased”. Please clarify.

# Flexible parametric survival regression model

- Please add a citation for software that is not part of Stata itself, e.g. the stpm2 Stata package used to fit the FPMs (https://www.stata-journal.com/article.html?article=st0165); it’s academic output by academic researchers, who need to seek funding to continue developing and supporting such packages.

# Results

- Some captions in Figure 1 are cropped away (e.g. the bottom panel, I feel like text ends abruptly), was there an issue with the online submission process or something like that? Also, several numbers overlap (e.g. panel b and d) making the graph really hard to read. Would it be possible to improve on that?

- Incidence rates per 1-person-year and per 100000-person-years are both presented, I think the former should be removed (as it is redundant and much harder to grasp compared to the same metric rescaled to 100000-person-years)

- How was the test for the equality of incidence rates conducted? Are the estimated measures fully unadjusted? It’s not clear from the text, please clarify.

- The log-log plot from figure 2 doesn’t show such a strong violation of the proportionality assumption, especially with such a large sample size; has that been tested further using other methods? How is the panel on the right testing the proportionality assumption?

- Are the hazard comparisons from fully adjusted models and non-parametric estimates? If so, please be careful that interpretation might not be the same and they might not be directly comparable.

- I wouldn’t say that the baseline hazard function looks more realistic with 6 df, as it is expected for it to be “more wobbly” with more degrees of freedom: please reword.

- When comparing the AIC/BIC/likelihood of the models, the Cox model returns a very different value: that is because the model uses (and returns) partial likelihood, therefore it is not possible to compare its value (nor AIC or BIC) to those of parametric and fully parametric model. This section needs to be re-written to fix this issue.

- In the same section, you see that AFT and PH models with the same baseline hazard distribution yield exactly the same fitted likelihood value: that is because they are equivalent, just with different parametrisations. This is not discussed at all in the manuscript, and it is particularly important as model coefficients from AFT and PH models have different interpretation.

- The authors are over-interpreting the significance tests for the coefficients of the spline for the baseline hazard function in FPMs, which don’t really have any meaningful interpretation (not directly, at least).

- The authors said they were comparing “robustness” of different methods, but such comparison is not present (they only compare a FPM with 6 df and a Cox model). I was expecting at least a comparison of the fitted coefficients from all models included in the comparison, to assess how estimates would change by choosing a not-flexible-enough model.

- When adjusting (and interpreting) for calendar year in the analysis, isn’t the interpretation of it just the effect of time (e.g. older cohorts have had more time to develop diabetes, and hence a higher risk)?

The higher risk for smoking mothers was surprising, as well as the difference with parents of non-nordic heritage. Any further insight on that?

- Can the observed effect of having diabetic parents be just genetics (and heritability of the trait)? I am not an expert on the topic, so it might be a silly comment (I apologise if so).

- The model estimates from FPM (6 df) and the CPH are very similar, but this is not news - there are several papers (e.g. the one by Rutherford et al cited by the authors) that show that model coefficients are insensitive to the choice of number of degrees of freedom (as long as enough flexibility is allowed). The Cox model fully solves the problem by not modelling the baseline hazard at all, so it’s not surprising that the two are so close to each other.

# Discussion

- The section on AIC/BIC needs to be re-written, the CPH with partial likelihood cannot be directly compared to the other methods that use full likelihood.

- The conclusion that “estimates from all models considered are similar” is not supported by data presented in the manuscipt, as I could only see estimates from FPM (6 df) and CPH.

- Line 388/389, model-based predictions are not showed in the manuscript, this sentence is not supported by data/plots in the ms.

- Line 399/400: it’s hard to say that ART -> type I diabetes without a study in a proper causal framework, I would suggest toning down that conclusion.

- Some comments on calendar time and genetics from the previous section apply here as well.

# Conclusion

- It is hard to conclude that the analysis method didn’t matter: (1) model estimates from other models are not showed, and (2) there might still be time-dependent effects or interactions that have not been studied thoroughly here. In fact, it would be nice to study time-dependent effects of e.g. treatment and so on (given the sample size), maybe as future research?

# Some typos and language

- Line 75, page 3, I would remove the *a* from the “Using a Danish data…” sentence;

- Line 90, page 4, I think it should be *subgroups* instead of *subgroup*;

- The word “determinate variable” is used throughout the ms, I find it a bit unusual even though I understand what the authors mean with that?

- I find the paper hard to read/follow at times (but it might just be me!), I wonder if the language could be simplified to improve readability of the ms?

Reviewer #4: General comment:

This paper investigates different statistical modelling approaches to assess if conception mode from ART influences risk of type 1 diabetes in children. Data comes from the Swedish Medical Birth Registry including births 1985-2015, an impressive thirty years study period. The paper has two aims, 1) to assess the medical research question regarding ART and type 1 diabetes and 2) to assess the methodological question by comparing different methods, which is a very nice combination and a good example of applied statistics research. However, this can be a challenge to combine, and the paper lacks some clarity and structure. I think the authors need to decide whether they are writing a medical paper with some advanced methods or if they are writing a methods paper with an application.

Main comments:

1. My main concern is that the authors have not utilized the strength of the FPSR, which is the straight-forward possibility to include non-proportional hazards. If indeed it was the intention to utilize the FPSR to explore interesting patterns of association for ART and type 1 diabetes in the data, it is unclear why this possibility was not pursued. As it is, the CPH and FPSR are nearly identical proportional hazards models and no benefit of the FPSR can be made, other than also obtaining absolute rates and survival measures directly from the model without additional post-estimation as for CPH. Fig 2 (right) also clearly shows non-proportional hazards (with very little effect of ART prior to age 12, and with stronger effect after age 12), yet the authors fit two proportional hazards models.

2. Methods, The data, row 219-225: The Data section needs to be extended, for example the data sources need to be explicitly spelled out, including what quality registers and register information from Statistics Sweden. What are the completeness of these data sources? Have the inclusion criteria changed over time? From which register was type 1 diabetes obtained, which diagnosis codes, etc. If the aim is to write a medical paper, then I think the data section should be first in the methods section, and then followed by the statistical methods section. If the aim is to write a methodological paper then the data section can be less.

3. Table 2: Why is the Log-likelihood so much higher for the CPH? Were all models fitted with the same covariates (i.e. same linear predictor of covariate effects), apart from the difference in baseline hazard parameterisation?

4. Table 3: The birth cohort effect does not make sense. The FPSR and CPH should yield similar results, if they are proportional hazards models with similar adjustment factors. Please clarify why the models give such different results.

Minor comments:

5. Abstract: In the results it is stated “hazard” of type 1 diabetes, but are the authors not estimating incidence rates of diabetes? Maybe clarify which disease measure is estimated rather than using the generic term hazard.

6. Introd: Can be shortened, and some text around previous literature can be moved to Discussion, I think.

7. Intro row 102: Explain term NPMLE.

8. Intro row 104: KM curves can be estimated by risk factor groups (covariates), but it is difficult to adjust for multiple confounders simultaneously (however, the curves can be standardized, as a form of adjustment). Standardization is mainly used for one to two variables at the time. Please clarify.

9. Does the methods section require all the formula given, or can it be simplified and referenced to original papers instead?

10. Methods: I don’t understand the “……………………………..(1)” notation in the formulas. Also notation “(i = 1, ………., N)” should perhaps be “(i=1,2,…,N)”. I don’t understand the notation “j= 1; : : : ;P;” or the notation “… … … … … .” or the notation “+ ⋯… … … …+”.

11. Methods row 187: “Odd scale” should be “odds scale” I think?

12. Methods row 210: The sentence “The position of the internal knots is usually in centiles computed as 100/df.” The placement of knots are at the centiles of event times, I believe.

13. Methods, Dependent variable, row 227: I don’t understand the sentence “The dependent variable is the censored timing (age) of the onset of type-1 diabetes among children. The time was censored on the date of the data collection, emigration and death.” In survival analysis the outcome is two-dimensional and defined by a survival time (with a start and an end), and an event indicator. Please clarify. What does “date of data collection” mean? Is this the date of extraction from the registers?

14. Results: How was the attributable fraction calculated, please explain in the methods section and give a reference.

15. Results, row 270-274: I don’t understand the added value of this section. Why is inference made on crude unadjusted rates? This is better done in adjusted models further down in the results section.

16. Results: Row 278: The log rank test is not a test of proportional hazards assumption, I think. Please clarify.

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PLoS One. 2021 Jun 25;16(6):e0253389. doi: 10.1371/journal.pone.0253389.r002

Author response to Decision Letter 0


21 Feb 2021

The Editor

PLOS ONE

Attn: Yiqiang Zhan

Academic Editor

PLOS ONE

PONE-D-21-00472

Conception modes and risk of Type-1 diabetes among 1985-2015 Swedish birth cohort: How robust are the survival analysis regression models?

Dear Dr. Fagbamigbe,

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

________________________________________

Reviewer #1: The authors of this study attempt to address two questions, 1) how does mode of conception affect the risk of type I diabetes in children, and 2) which survival model is best for the assessment of this association.

Main comments

The combination of the two above aims does not flow in my opinion, and is not adequately motivated. Who is the target audience of this paper? The medical research question of interest, seems to be relevant and interesting (although not my field of work), but the comparison of survival analysis models does not add to the current body of work in this area. Even if this did add to the question of “which is the best survival analysis model?” (which I’m not convinced has a definite answer), the comparison of methods here is undertaken in a situation where we do not know the underlying true answer to the question of interest. It is therefore, very difficult to determine which of the models is the best fitting. Furthermore, the selection of the best model according to the AIC and BIC is of course useful, but does not concretely determine which of the models fitted is the best model for the data. The AIC and BIC can indicate that different models are the better fitting model, and should be used as a guide for model selection along with knowledge about the specific subject area. In my opinion, the model selection process described in this paper, to some extent is what most researchers do in the background without presenting such results, but rather describe that they have chosen, say, a flexible parametric survival model based on the AIC and BIC.

For the above reasons, I would suggest that the authors of the paper focus on the research question of interest, i.e., the association between type I diabetes mode of conception, and refrain from presenting the comparison of survival analysis models in this paper.

THANK YOU. WE AGREE WITH OUR REVIEWERS COMMENT, BUT THE AIM IS TO BE ABLE TO EVALUATE THE MODEL THAT FIT THE DATA TO AN EXTENT. OUR WORK IS A METHOD PAPER WITH AN APPLICATION. WE TOTALLY UNDERSTAND AND AGREE THAT THAT THERE MAY NOT BE THE “ULTIMATE BEST” MODEL BECAUSE IT IS IMPRACTICABLE TO CONSIDER ALL MODELS. HOWEVER, WE FEEL THAT THE MODELS SHOULD BE RETAINED, ESPECIALLY AS THE OTHER REVIEWERS ARE COMFORTABLE WITH IT.

Independent of the above comments, I think that some work could be done in the structuring of the paper to ensure a logical progression through the manuscript to help the reader’s understanding. The description of the survival analysis models in the introduction needs some more careful editing (see specific comments for examples), and I would suggest that detailed descriptions are instead presented in the methods section. There are results presented with no corresponding description in the methods section; the authors give detailed mathematical descriptions of the models they are going to fit, but no actual description of the models used for the analysis, i.e. how were certain variables modelled? Attributable fraction results are presented in the results with no description of what the measure is in the methods section. Another example is that the AIC and the BIC are described well, but the paper is lacking a sentence stating “We used these criteria to assess which of the above described models was the optimal model.” Additionally, some of the language used in the introduction is very non-specific; examples include the terms “adequate representation”, or “building on their strengths”. I would suggest the paper needs editing before it is at the standard for publication.

WE APPRECIATE THESE CRITICAL AND CONSTRUCTIVE SUGGESTIONS. WE HAVE TAKEN ALL THE SUGGESTIONS

Specific comments

1. Ensure that initialisations are defined (e.g. SC, NPMLE):

THANK YOU, THIS HAS BEEN ADDED

2. Avoid the use contractions: “doesn’t” in the introduction:

THANK YOU, THIS HAS BEEN ADDED

3. Add reference for Lebesgue measure;

THIS HAS BEEN ADDED

4. Some of the models are described as being proportional hazards models, and whilst the Cox model is most commonly called the Cox Proportional Hazards Model, the assumption of proportional hazards (PH) can be relaxed in these models and in the other models described.

WE AGREE. THANK YOU. IT HAS BEEN ADDED

5. Related, were non-proportional hazards models fitted? If not, why the focus on this in the description of the models? Perhaps the authors wanted to highlight an advantage of the flexible parametric survival models (that the PH assumption can be relaxed rather easily in comparison to the other survival models), but then this needs to be stated. If PHs are mentioned then a more thorough description would be a good idea to help the reader.

THANK YOU. WE HAVE REVIEWED THIS

6. Line 118: Smooth hazard ratios should be smooth hazard rates.

THANK YOU. IT HAS BEEN CORRECTED

7. Description of flexible parametric models (FPM) in the introduction: restricted cubic splines (RCS) do not need to model log time. In fact, when considering attained age as the time scale, restricted cubic splines are often used to model the untransformed time scale.

THANK YOU. IT HAS BEEN CORRECTED

8. It is not clear to me why the comparison between the use of RCS in FPMs is compared to a linear function of log time in the introduction.

THE UNNECESSARY PHRASE HAS BEEN EXPUNGED

9. When presenting survival analyses, the timescale and event of interest are often presented alongside the exposure of interest and any confounding variables. I would suggest describing the analysis in this way instead of dependent/independent variables.

THANK YOU. IT HAS BEEN CORRECTED IN THE MANUSCRIPT

10. Related, a description to link the motivation behind the age distribution problems described in the introduction, and how this was dealt with in your analysis is needed (I think you did this by using age as the timescale?)

YES THE CHILDREN AGE WERE USED AS THE TIME SCALE

11. When incidence rates are so low, present them per 1,000 person-years (for example)

WE RECOGNISED NTHIS AND WE ALREADY PROVIDED THE RATES PER 100,000 PERSON-YEAR IN THE LAST COLUMN OF TABLE 1

12. Was there missing data? If so, how much? How did you deal with this?

THERE ARE NO MISSING DATA

13. Figures need some cleaning up: ensure consistency between grayscale and colour figures, x-axes should be consistently named.

THANK YOU. WE HAVE REPRODUCED THE FIGURES AND HARMONIZED THE LABELS

14. Figure 3: there is no description of the smoother used for the smoothed hazard estimates. “Stpm2” will not be clear for readers who are not familiar with FPM and/or Stata.

THANK YOU, WE HAVE PROVIDED ADDITIONAL INFORMATION ON STPM2

15. Figure 4, third panel: which degrees of freedom are presented?

THIS ARE THE DEGREES OF FREEDOM FOR THE DIFFERENIT KNOTS IN THE FLEXIBLE MODEL

16. I think the results you rely on are from the FPM with 6 degrees of freedom. This is quite a high number. Given the subject area, is the hazard function presented in figure 3 with 6 degrees of freedom reasonable to the authors?

YES, WE DIDN’T PRODUCE ANY GRAPH IN FIGURE 3 WITH 6 DEGREES OF FREEDOM, RATHER WITH 3 DEGREES OF FREEDOM. THE FIGURE 3 SHOWED EXPLORATORY ON THE AVERAGE LEVEL. THE COMPARISON OF THE DEGREES OF FREEDOM WERE SHOWED IN FIGURE4 WHERE 6 DEGREES FREEDOM WAS FOUND TO BE BETTER THAN OTHERS.

17. Table 3: all the coefficient estimates need not be presented, only the exposure of interest and a description that the estimates were adjusted for the other variables. In particular, since the estimates for the restricted cubic spline coefficients are so often misinterpreted (and actually never presented in the context of answering a medical research question) I would suggest to remove these.

THANK YOU. WE HAVE REMOVED THE RESTRICTED CUBIC SPLINE COEFFICIENTS TO AVOID MISINTERPRETED BUT RETAINED THE OTHER COVARIATES BECAUSE THERE ARE NECESSARY TO ENSURE THAT READERS UNDERSTAND THE EFFECTS OF THESSE COVARIATES

Reviewer #2: The advantages of this study are 1) compared statistical methods for exploring effects of different conception modes on a long-term outcome (Type 1 diabetes), using observational data from a nationwide register in Sweden with almost 31 years follow-up; 2) the authors are familiar with applications of parametric, flexible parametric and semi-parametric regression models to time-to-event data analysis. Sharing the codes would benefit the STATA users who want to do these similar comparisons.

THANK YOU. WE CAN PROVIDE THE CODES

Here are some comments for improvement:

1) In multivariable analysis, the adjustment was mad for child’s sex as well. Did the authors consider sex as a potential confounder or only an independent predictor for the outcome? It seems like sex of child was not associated with conception modes.

NO, WE CONSIDERED SEX. AS SHOWN IN TABLE 2, THE RISK OF dm WAS 17% HIGHER AMONG THE MALES THAN THE FEMALES

2) There is space to improve abstract: e.g. the second sentence repeated the information of the first sentence. As seen, the same cohort (data) had been applied in the Reference paper 1 for the same research question, both with hazard ratios as the association measure. Some conclusions were also similar. The authors could emphasize on the comparisons of methods and presenting corresponding results, presenting less similar conclusions as Ref 1 in this study.

THANK YOU. IT HAS BEEN CORRECTED

3) Time-to-event was defined from baby born (i.e time zero) that has been accepted in literature. However, conception modes were determined at the beginning of pregnancy. There were a time window of gestational age that might differed between ART and spontaneous conception, due to ART being a risk factor of preterm birth. Then baby with ART would early expose to risk of type 1 diabetes (T1D). How the authors consider the following question: whether there is potential bias by gestational age?

NO, THE DATA OWNERS DID NOT CAPTURE THIS IMPORTANT INFORMATION.

4) Using singleton births from the same mothers, there might be more or less intra-correlation, especially for T1D showing familial aggregation, which could be discussed by the authors why didn’t take it account in this study.

AGAIN, THIS INFORMATION WAS NOT PROVIDED IN THE DATA REGISTER

5) Check the text carefully, e.g. minor typos: “Royston-Palmar” should be Royston-Parmar in several places.

THANK YOU. THIS AND ITS OTHER INSTANCES, HAVE BEEN CORRECTED

Reviewer #3: The manuscript by Fagbamigbe et al. describes the results of an observational study on the association between conception mode and the risk of type-I diabetes using data from the Swedish birth register. Furthermore, they aim to compare the results of different survival models in their settings, with the hypothesis that using inappropriate models might explain contradictory findings that have been reported in the literature.

I think the applied analysis of the manuscript is interesting (nice work), but the more methodological parts need some extra work, as I feel the authors don’t fully accomplish what they aimed to do. In particular, I would like to see a more detailed comparison of the modelling approaches being studied, to show the effect of misspecifying a model or choosing a not-flexible-enough model for time to event data; statistical Monte Carlo simulation might even help selling the message as well.

More detailed comments (section by section) follow.

# Introduction

- Line 102/103: The Kaplan-Meier estimator can actually be used to investigate the effect of covariates, as you could in principle stratify the analysis (see e.g. the results of sts graph, by(covariate) in Stata) and still get distinct estimates of the survival function. Please reword that sentence. Having said that, of course this gets cumbersome when several covariates are to be investigated together, and therefore I agree that regression models are helpful in those settings.

THANK YOU. THIS HAS BEEN CORRECTED

- Line 119/122: I am not sure what the authors mean with the sentence “...and the fact that the cumulative hazard function or survival function may not be unbiased”. Please clarify.

THANK YOU. THIS HAS BEEN CLARIFIED

# Flexible parametric survival regression model

- Please add a citation for software that is not part of Stata itself, e.g. the stpm2 Stata package used to fit the FPMs (https://www.stata-journal.com/article.html?article=st0165); it’s academic output by academic researchers, who need to seek funding to continue developing and supporting such packages.

THANK YOU. WE AGREE, IT WAS PORIGINALLY CITED AS REF 18, WE HAVE NOW INSERTED STPM2 AND CITED IT ACCORDINGLY AS REF 19.

# Results

- Some captions in Figure 1 are cropped away (e.g. the bottom panel, I feel like text ends abruptly), was there an issue with the online submission process or something like that? Also, several numbers overlap (e.g. panel b and d) making the graph really hard to read. Would it be possible to improve on that?

THANK YOU, WE HAVE CORRECTED THE GRAPHS

- Incidence rates per 1-person-year and per 100000-person-years are both presented, I think the former should be removed (as it is redundant and much harder to grasp compared to the same metric rescaled to 100000-person-years)

THANK YOU, WE FELT WE SHOULDN’T RETAIN ONLY ONE BUT THE FORMER IS NECESSARY TO UNDERSTAND AND COMPARE WITH MOST OF THE HAZARD GRAPHS WHILE THE LATER IS NECESSARY FOR COMPREHENSION

- How was the test for the equality of incidence rates conducted? Are the estimated measures fully unadjusted? It’s not clear from the text, please clarify.

THANK YOU, THE ESTIMATED MEASURES FOR EQUALITY OF INCIDENCE RATES WERE NOT ADJUSTED FOR COVARIATES

- The log-log plot from figure 2 doesn’t show such a strong violation of the proportionality assumption, especially with such a large sample size; has that been tested further using other methods? How is the panel on the right testing the proportionality assumption?

WE AGREE, IT DOESN’T SHOW A STRONG VIOLATION BUT ITS PRESENCE. THE RIGHT PANEL SHOWS AN ALTERNATIVE TEST OF NON-PROPORTIONALITY OF KAPLAN MEIER SURVIVAL CURVES OF THE OBSERVED AND PREDICTED ART ESTIMATES AT VARIOUS AGES OF THE CHILDREN

- Are the hazard comparisons from fully adjusted models and non-parametric estimates? If so, please be careful that interpretation might not be the same and they might not be directly comparable.

- I wouldn’t say that the baseline hazard function looks more realistic with 6 df, as it is expected for it to be “more wobbly” with more degrees of freedom: please reword.

- When comparing the AIC/BIC/likelihood of the models, the Cox model returns a very different value: that is because the model uses (and returns) partial likelihood, therefore it is not possible to compare its value (nor AIC or BIC) to those of parametric and fully parametric model. This section needs to be re-written to fix this issue.

THE HAZARD COMPARISONS ARE FROM UNADJUSTED MODELS AND NON-PARAMETRIC ESTIMATES. WE HAVE REWORDED THE STATEMENT ON THE COMPARISON OF THE DIFFERENT HAZARD FUNCTIONS AT DIFFERENT DEGREES OF FREEDOM. WE HAVE ALSO IMPROVED ON THE STATEMENT ON THE CPH LIKELIHOOD

- In the same section, you see that AFT and PH models with the same baseline hazard distribution yield exactly the same fitted likelihood value: that is because they are equivalent, just with different parametrisations. This is not discussed at all in the manuscript, and it is particularly important as model coefficients from AFT and PH models have different interpretation.

- The authors are over-interpreting the significance tests for the coefficients of the spline for the baseline hazard function in FPMs, which don’t really have any meaningful interpretation (not directly, at least).

WE HAVE EXPLAINED THE SIMILARITY IN THE LIKELIHOOD OF THE AFT AND PH MODLES AND ALSO REMOVED UNNECESSARY INTERPRETATION OF THE SPLINE

- The authors said they were comparing “robustness” of different methods, but such comparison is not present (they only compare a FPM with 6 df and a Cox model). I was expecting at least a comparison of the fitted coefficients from all models included in the comparison, to assess how estimates would change by choosing a not-flexible-enough model.

OUR COMPARISON WERE STEP-WISE, WE FIRST USED THE AIC AND BIC TO SELECT MODELS AND THEN PRESENTED THE ESTIMATES OF THE SELECTED MODELS

- When adjusting (and interpreting) for calendar year in the analysis, isn’t the interpretation of it just the effect of time (e.g. older cohorts have had more time to develop diabetes, and hence a higher risk)?

The higher risk for smoking mothers was surprising, as well as the difference with parents of non-nordic heritage. Any further insight on that?

- Can the observed effect of having diabetic parents be just genetics (and heritability of the trait)? I am not an expert on the topic, so it might be a silly comment (I apologise if so).

YES, WE USED THE CHILDREN AGE AS THE TIMESCALE TO CONTROL FOR THE DIFFERENCES IN EXPOSURE. THERE ARE INSIGHTS INTO WHY CHILDREN OF SMOKING MOTHERS AS WELL AS PARENTS OF NON-NORDIC HERITAGE HAD HIGHER RISK OF DM. YES, SOME LITERATURE HAVE ESTABLISHED HERITABILITY OF THE DM TRAIT (SPURR ET AL AND WHINCUP ET AL).

- The model estimates from FPM (6 df) and the CPH are very similar, but this is not news - there are several papers (e.g. the one by Rutherford et al cited by the authors) that show that model coefficients are insensitive to the choice of number of degrees of freedom (as long as enough flexibility is allowed). The Cox model fully solves the problem by not modelling the baseline hazard at all, so it’s not surprising that the two are so close to each other.

THANK YOU

# Discussion

- The section on AIC/BIC needs to be re-written, the CPH with partial likelihood cannot be directly compared to the other methods that use full likelihood.

- The conclusion that “estimates from all models considered are similar” is not supported by data presented in the manuscipt, as I could only see estimates from FPM (6 df) and CPH.

- Line 388/389, model-based predictions are not showed in the manuscript, this sentence is not supported by data/plots in the ms.

- Line 399/400: it’s hard to say that ART -> type I diabetes without a study in a proper causal framework, I would suggest toning down that conclusion.

- Some comments on calendar time and genetics from the previous section apply here as well.

WE AGREE WITH ALL THE COMMENTS AND HAVE REPHRASED THE STATEMENT ON AIC/BIC. THE CONCLUSION OF EQUALITY OF ESTIMATES FROM THE DIFFERENT MODELS HAVE BEEN EXPUNGED. THE STATEMENT ON MODEL-BASED PREDICTIONS HAVE BEEN REVISED. THE WRONG STATEMENT HAS BEEN REMOVED. THE WORD “AFFECT” HAS BEEN MODIFIED TO READ “ASSOCIATED”.

# Conclusion

- It is hard to conclude that the analysis method didn’t matter: (1) model estimates from other models are not showed, and (2) there might still be time-dependent effects or interactions that have not been studied thoroughly here. In fact, it would be nice to study time-dependent effects of e.g. treatment and so on (given the sample size), maybe as future research?

THANK YOU. WE TOTALLY AGREE THAT THE STUDY OF TIME-DEPENDENT EFFECTS SUCH AS TREATMENT AND SO ON ARE WORTHY OF FUTURE RESEARCH PROVIDED THE DATA COULD BE MADE AVAILABLE

# Some typos and language

- Line 75, page 3, I would remove the *a* from the “Using a Danish data…” sentence;

- Line 90, page 4, I think it should be *subgroups* instead of *subgroup*;

- The word “determinate variable” is used throughout the ms, I find it a bit unusual even though I understand what the authors mean with that?

- I find the paper hard to read/follow at times (but it might just be me!), I wonder if the language could be simplified to improve readability of the ms?

THANK YOU, WE HAVE CORRECTED THE HIGHLIGHTED TYPOS AND CARRIED OUT A LANGUAGE EDIT

Reviewer #4: General comment:

This paper investigates different statistical modelling approaches to assess if conception mode from ART influences risk of type 1 diabetes in children. Data comes from the Swedish Medical Birth Registry including births 1985-2015, an impressive thirty years study period. The paper has two aims, 1) to assess the medical research question regarding ART and type 1 diabetes and 2) to assess the methodological question by comparing different methods, which is a very nice combination and a good example of applied statistics research. However, this can be a challenge to combine, and the paper lacks some clarity and structure. I think the authors need to decide whether they are writing a medical paper with some advanced methods or if they are writing a methods paper with an application.

Main comments:

1. My main concern is that the authors have not utilized the strength of the FPSR, which is the straight-forward possibility to include non-proportional hazards. If indeed it was the intention to utilize the FPSR to explore interesting patterns of association for ART and type 1 diabetes in the data, it is unclear why this possibility was not pursued. As it is, the CPH and FPSR are nearly identical proportional hazards models and no benefit of the FPSR can be made, other than also obtaining absolute rates and survival measures directly from the model without additional post-estimation as for CPH. Fig 2 (right) also clearly shows non-proportional hazards (with very little effect of ART prior to age 12, and with stronger effect after age 12), yet the authors fit two proportional hazards models.

WE DID PURSUED THE USE OF FPSR TO EXPLORE INTERESTING PATTERNS OF ASSOCIATION FOR ART AND TYPE 1 DIABETES IN THE DATA AND OUR CONCLUSION.

2. Methods, The data, row 219-225: The Data section needs to be extended, for example the data sources need to be explicitly spelled out, including what quality registers and register information from Statistics Sweden. What are the completeness of these data sources? Have the inclusion criteria changed over time? From which register was type 1 diabetes obtained, which diagnosis codes, etc. If the aim is to write a medical paper, then I think the data section should be first in the methods section, and then followed by the statistical methods section. If the aim is to write a methodological paper then the data section can be less.

WE HAVE UPDATED THE DATA SECTION AND MOVED IT TO THE BEGINNING OF THE METHODOLOGY AS SUGGESTED. WE DIDN’T HAVE ACCESS TO THE REGISTERS, RATHER THE NEEDED DATA WERE CURLED OUT FOR US

3. Table 2: Why is the Log-likelihood so much higher for the CPH? Were all models fitted with the same covariates (i.e. same linear predictor of covariate effects), apart from the difference in baseline hazard parameterisation?

YES, WE FITTED THE MODELS WITH SAME COVARIATES, THE HIGHER LIKELIHOOD WAS DUE TO HOW CPH MODEL COMPUTES THE LIKELIHOOD. IT RETURNS PARTIAL LIKELIHOOD. WE HAVE NOTED THIS IN THE MANUSCRIPT.

4. Table 3: The birth cohort effect does not make sense. The FPSR and CPH should yield similar results, if they are proportional hazards models with similar adjustment factors. Please clarify why the models give such different results.

THE FPSR AND CPH WERE MODELED WITH SIMILAR ADJUSTMENT FACTORS. THE ASSUMPTIONS OF THE MODELS COULD HAVE CAUSED THE THIN DIFFERENCES

Minor comments:

5. Abstract: In the results it is stated “hazard” of type 1 diabetes, but are the authors not estimating incidence rates of diabetes? Maybe clarify which disease measure is estimated rather than using the generic term hazard.

WE ESTIMATED THE HAZARD FROM THE MODELS, SO IT IS RIGHT TO USE HAZARD

6. Introd: Can be shortened, and some text around previous literature can be moved to Discussion, I think.

7. Intro row 102: Explain term NPMLE.

IT HAS BEEN EXPLAINED AS NONPARAMETRIC MAXIMUM LIKELIHOOD ESTIMATE

8. Intro row 104: KM curves can be estimated by risk factor groups (covariates), but it is difficult to adjust for multiple confounders simultaneously (however, the curves can be standardized, as a form of adjustment). Standardization is mainly used for one to two variables at the time. Please clarify.

WE HAVE CLARIFIED THIS

9. Does the methods section require all the formula given, or can it be simplified and referenced to original papers instead?

PLOS ONE REQUIRES DETAILED METHODOLOGY, FOR UNDERSTANDING AND REPEATABILITY, HENCE WE RETAIN IT BECAUSE OTHER REVIEWERS ARE HAPPY WITH IT

10. Methods: I don’t understand the “……………………………..(1)” notation in the formulas. Also notation “(i = 1, ………., N)” should perhaps be “(i=1,2,…,N)”. I don’t understand the notation “j= 1; : : : ;P;” or the notation “… … … … … .” or the notation “+ ⋯… … … …+”.

THANK YOU. WE HAVE CORRECTED THESE NOTATIONS AS DIRECTED.

11. Methods row 187: “Odd scale” should be “odds scale” I think?

THANK YOU

12. Methods row 210: The sentence “The position of the internal knots is usually in centiles computed as 100/df.” The placement of knots are at the centiles of event times, I believe.

WE AGREE. THANK YOU. WE HAVE CORRECTED

13. Methods, Dependent variable, row 227: I don’t understand the sentence “The dependent variable is the censored timing (age) of the onset of type-1 diabetes among children. The time was censored on the date of the data collection, emigration and death.” In survival analysis the outcome is two-dimensional and defined by a survival time (with a start and an end), and an event indicator. Please clarify. What does “date of data collection” mean? Is this the date of extraction from the registers?

THANK YOU. WE HAVE CLARIFIED AND CORRECTED THIS.

14. Results: How was the attributable fraction calculated, please explain in the methods section and give a reference.

THANK YOU. WE HAVE ADDED THIS TO THE METHODOLOGY

15. Results, row 270-274: I don’t understand the added value of this section. Why is inference made on crude unadjusted rates? This is better done in adjusted models further down in the results section.

THANK YOU. WE ONLY SHOWED THIS FOR ART VS SPONTANEOUS AND NOT FOR THE ENTIRE COVARIATES. THIS IS NECESSARY FOR READERS TO BE AWARE OF THE DIFFERENCES WITHOUT COVARIATES

16. Results: Row 278: The log rank test is not a test of proportional hazards assumption, I think. Please clarify.

THANK YOU. WE HAVE CORRECTED THIS

________________________________________

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Reviewer #1: No

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Reviewer #4: No

Attachment

Submitted filename: response to reviewers Diabetics.docx

Decision Letter 1

Y Zhan

16 Mar 2021

PONE-D-21-00472R1

Conception modes and risk of Type-1 diabetes among 1985-2015 Swedish birth cohort: How robust are the survival analysis regression models?

PLOS ONE

Dear Dr. Fagbamigbe,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Apr 30 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

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If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

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Y Zhan

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

Reviewer #3: (No Response)

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Partly

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: No

**********

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The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: No

Reviewer #3: No

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: My general comment from the first round of reviews regarding the aim of the study still stands, but if the other reviewers and editors are happy then I have no further comments. The authors have adequately addressed my specific comments.

Reviewer #2: (No Response)

Reviewer #3: Thanks for the opportunity to review this re-submission.

I think the paper has improved in clarity and presentation from the previous submission, but my main concerns have still not been addressed.

Specifically, now that the authors clarified that "This study is a method paper with an application", I think the paper should focus more on the models comparison (which is still just barely discussed):

- The difference in interpretation between accelerated failure time and proportional hazards models is not discussed. Why use one against the other, if they are just a re-parametrisation of each other?

- The differences between the fitted model coefficients (in the application) is not presented, so I am not sure the reader can appreciate what happens when a not-flexible-enough parametric form is assumed. Performing a step-wise procedure with AIC/BIC does not assess robustness, to my eyes;

- Still, there is no much reason to use the flexible parametric models if hazard ratios are the measure of interest here - the Cox model would work just fine, without needing any functional form assumption;

- I still don't think there is strong evidence against proportional hazards. The right-hand-side plot of figure 2 doesn't really show violations of the assumptions, as it is hard to identify non-proportional hazards on the survival scale. Furthermore, if the authors believe there are non-proportional hazards, how are they accommodating that into the analysis?

- It's still not possible to compare a partial likelihood model (the Cox model) with models that are fitted using full likelihood with AIC/BIC, that hasn't been corrected;

- I still don't agree with the conclusion that "the methods of analysis may not be connected with the contradictory findings in earlier studies", we just don't know as we don't see the comparison between all the different models that are being studied here. Further to that, we don't know what the true effect is, so we cannot exclude that both the Cox and the Royston-Parmar models get it wrong, I believe?

In conclusion, I still think the paper needs major modifications if the goal is to study the robustness of different survival regression models. If this is a method paper, I think it should focus more on the methodological part rather than on the application (which I think it's still the case).

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PLoS One. 2021 Jun 25;16(6):e0253389. doi: 10.1371/journal.pone.0253389.r004

Author response to Decision Letter 1


14 May 2021

Reviewer #1: My general comment from the first round of reviews regarding the aim of the study still stands, but if the other reviewers and editors are happy then I have no further comments. The authors have adequately addressed my specific comments.

Thank you

Reviewer #2: (No Response)

Thank you

Reviewer #3: Thanks for the opportunity to review this re-submission.

I think the paper has improved in clarity and presentation from the previous submission, but my main concerns have still not been addressed.

Specifically, now that the authors clarified that "This study is a method paper with an application", I think the paper should focus more on the models comparison (which is still just barely discussed):

- The difference in interpretation between accelerated failure time and proportional hazards models is not discussed. Why use one against the other, if they are just a re-parametrisation of each other?

Thank you. We have improved on the model comparison, especially in the discussion part as we have already explained the differences between the models in the introduction

- The differences between the fitted model coefficients (in the application) is not presented, so I am not sure the reader can appreciate what happens when a not-flexible-enough parametric form is assumed. Performing a step-wise procedure with AIC/BIC does not assess robustness, to my eyes;

Than you. The fitted model coefficients have been provided

- Still, there is no much reason to use the flexible parametric models if hazard ratios are the measure of interest here - the Cox model would work just fine, without needing any functional form assumption;

Thank you. The study was to compare different models. As you rightly said the Cox compared favourably with the flexible parametric models, although the latter has lower model fit parameters

- I still don't think there is strong evidence against proportional hazards. The right-hand-side plot of figure 2 doesn't really show violations of the assumptions, as it is hard to identify non-proportional hazards on the survival scale. Furthermore, if the authors believe there are non-proportional hazards, how are they accommodating that into the analysis?

We agree, the study was to compare different models. The proportional models compared well with other models. We have reflected these in our results, discussions, findings and abstracts. Nonetheless, the flexible model, as detailed in the literature, has capability of handling non-proportional hazards. As stated in the methodology, we focussed on the hazard scale of the models to ensure that the estimates from the FPSR and CPH models are comparable.

- It's still not possible to compare a partial likelihood model (the Cox model) with models that are fitted using full likelihood with AIC/BIC, that hasn't been corrected;

This has been corrected

- I still don't agree with the conclusion that "the methods of analysis may not be connected with the contradictory findings in earlier studies", we just don't know as we don't see the comparison between all the different models that are being studied here. Further to that, we don't know what the true effect is, so we cannot exclude that both the Cox and the Royston-Parmar models get it wrong, I believe?

We have changed the sentence to read “Hence the methods of analysis may not be disconnected with the contradictory findings in earlier studies”

In conclusion, I still think the paper needs major modifications if the goal is to study the robustness of different survival regression models. If this is a method paper, I think it should focus more on the methodological part rather than on the application (which I think it's still the case).

Thank you for the constructive comments. As you stated, this study is a method paper with an application. So we have discussed the models and the applications.

Attachment

Submitted filename: response to reviewers Diabetics r2.docx

Decision Letter 2

Y Zhan

28 May 2021

PONE-D-21-00472R2

Comparison of the performances of survival analysis regression models for analysis of conception modes and risk of Type-1 diabetes among 1985-2015 Swedish birth cohort

PLOS ONE

Dear Dr. Fagbamigbe,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Jul 12 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

  • A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.

  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.

  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your revised manuscript.

Kind regards,

Y Zhan

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #3: (No Response)

**********

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The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #3: Partly

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #3: No

**********

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The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #3: No

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #3: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #3: Thank you for the opportunity to re-review this manuscript.

Overall, I think the focus of the manuscript has greatly improved: I have only a few (relatively) minor comments left to address, which are outlined below.

* "Model selection criteria" section, page 10, robustness of the model wasn't really assessed anywhere, so I would suggest removing that and focussing on fit of the models to the available data.

* "Test of equality of incidence rates of type-1 diabetes" section, page 12, I would suggest reporting the rate difference per 1,000 person-years (or 100,000, as the authors prefer) to improve readability, as the currently reported rates have up to 6 significant digits.

* Again, if the PH assumption is violated, then all PH models yield (possibly) wrong results and non-proportional hazards need to be incorporated in the models. I still don't think Figure 2 shows evident violations of PH, but if the authors believe so, then the analysis (and all the fitted models in the manuscript) need to be updated to reflect this. This is the most important issue that the authors should focus on, in my opinion.

* "Comparison of the models" section, page 14, estimates for PH and AFT models are not directly comparable (as the authors state in the methods section, page 7-8). Therefore, comparing the magnitude of the fitted coefficients does not make sense - this needs to be corrected.

* "Discussion" section, page 18, AIC and BIC for the Cox model are higher because it uses partial likelihood - therefore it's an unfair comparison. This has been fixed elsewhere in the manuscript, but not here; I think it needs to be adjusted here too.

* Line 450, page 19, there's a typo - I think the author references there is Rutherford, not Rutherfold.

* "Strength and limitation" section, I think that (as mentioned before) robustness is not really studied here, so I would reword there.

* "Conclusion" section, please mention that the models performed similarly in this specific setting, but there's no guarantee that this will be the case with other data sources or with other diseases. It's hard to generalise these findings to other settings. It would also be great if the authors could discuss non-poportional hazards: as above-mentioned, they first state that there are non-PH but then use PH (or AFT) models, this needs to be adjusted. A general discussion of non-PH as a strength of FPMs (where it's easy to incorporate this) is also welcome - otherwise, I see no reason to not use the Cox model if relative risk is the main measure of interest and non-PH are ignored.

* Some additional comments: 1) Panel D of Figure 1 is hard to read (and I think the caption "the lines for 'father not diabetic'..." is cut off?), and 2) the names in the first column of figure 5 should be updated to be more descriptive (not just the variable name used in Stata).

**********

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Reviewer #3: No

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

PLoS One. 2021 Jun 25;16(6):e0253389. doi: 10.1371/journal.pone.0253389.r006

Author response to Decision Letter 2


1 Jun 2021

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Thank you. We have worked on this and ensured that all references are complete and correct. The old references 31 and 53 have been removed (there was no need for replacement) while old references 18, 32,35,36,28 t0 40 and 42 have been updated

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #3: Thank you for the opportunity to re-review this manuscript.

Overall, I think the focus of the manuscript has greatly improved: I have only a few (relatively) minor comments left to address, which are outlined below.

* "Model selection criteria" section, page 10, robustness of the model wasn't really assessed anywhere, so I would suggest removing that and focussing on fit of the models to the available data.

We have removed the issue about robustness and focussed on fit of the models to the available data.

* "Test of equality of incidence rates of type-1 diabetes" section, page 12, I would suggest reporting the rate difference per 1,000 person-years (or 100,000, as the authors prefer) to improve readability, as the currently reported rates have up to 6 significant digits.

Thank you. We agree with you. We have removed the column with up to 6 digits

* Again, if the PH assumption is violated, then all PH models yield (possibly) wrong results and non-proportional hazards need to be incorporated in the models. I still don't think Figure 2 shows evident violations of PH, but if the authors believe so, then the analysis (and all the fitted models in the manuscript) need to be updated to reflect this. This is the most important issue that the authors should focus on, in my opinion.

Thank you for pointing this out. We have now updated our text to indicate that PH assumptions were not violated

* "Comparison of the models" section, page 14, estimates for PH and AFT models are not directly comparable (as the authors state in the methods section, page 7-8). Therefore, comparing the magnitude of the fitted coefficients does not make sense - this needs to be corrected.

We agree totally. We have corrected this statement

* "Discussion" section, page 18, AIC and BIC for the Cox model are higher because it uses partial likelihood - therefore it's an unfair comparison. This has been fixed elsewhere in the manuscript, but not here; I think it needs to be adjusted here too.

Thank you. We have fixed the sentence

* Line 450, page 19, there's a typo - I think the author references there is Rutherford, not Rutherfold.

Thank you. We have corrected this

* "Strength and limitation" section, I think that (as mentioned before) robustness is not really studied here, so I would reword there.

We appreciate this concern. Yes, we have removed robustness across the manuscript and replaced with model fit

* "Conclusion" section, please mention that the models performed similarly in this specific setting, but there's no guarantee that this will be the case with other data sources or with other diseases. It's hard to generalise these findings to other settings. It would also be great if the authors could discuss non-poportional hazards: as above-mentioned, they first state that there are non-PH but then use PH (or AFT) models, this needs to be adjusted. A general discussion of non-PH as a strength of FPMs (where it's easy to incorporate this) is also welcome - otherwise, I see no reason to not use the Cox model if relative risk is the main measure of interest and non-PH are ignored.

Thank you for this suggestion. It has been incorporated appropriately in the discussion and conclusion sections

* Some additional comments: 1) Panel D of Figure 1 is hard to read (and I think the caption "the lines for 'father not diabetic'..." is cut off?), and 2) the names in the first column of figure 5 should be updated to be more descriptive (not just the variable name used in Stata).

Thank you for the constructive comments. We have fixed this. Actually, the lines for father not diabetic and mother not diabetic overlapped.

Also, we have reproduced the forest plots to ensure easy reading.

Attachment

Submitted filename: response to reviewers Diabetics r3.docx

Decision Letter 3

Y Zhan

4 Jun 2021

Comparison of the performances of survival analysis regression models for analysis of conception modes and risk of Type-1 diabetes among 1985-2015 Swedish birth cohort

PONE-D-21-00472R3

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Acceptance letter

Y Zhan

18 Jun 2021

PONE-D-21-00472R3

Comparison of the performances of survival analysis regression models for analysis of conception modes and risk of Type-1 diabetes among 1985-2015 Swedish birth cohort

Dear Dr. Fagbamigbe:

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Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    Attachment

    Submitted filename: response to reviewers Diabetics.docx

    Attachment

    Submitted filename: response to reviewers Diabetics r2.docx

    Attachment

    Submitted filename: response to reviewers Diabetics r3.docx

    Data Availability Statement

    Ethical permission was given from the Regional Ethical Committee (bjorn.rydevik@gu.se) at the University of Gothenburg (Dnr 214-12, T422-12, T516-15, T233-16, T300-17, T1144-17, T121-18). The Swedish National Board of Health and Welfare obtained informed written consent from patients to have data/samples from their medical records used in research. We followed the prescribed ethical regulations on confidentiality when the database was accessed in October 2019. The Swedish National Board of Health and Welfare, and Statistics Sweden (SCB) placed ethical restrictions on sharing the data publicly as the data contain potentially identifying or sensitive patient information. The restriction was concurred to by the Regional Ethical Committee at the University of Gothenburg, Sweden.


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