4.1. Independence Analysis of Categorical Variables Affecting Honey Production
The independence analysis revealed statistically significant associations between management practices and the sociodemographic characteristics of beekeepers. AH was significantly associated with VF. This relationship indicates that more frequent management—defined as inspections every 15 days or less—is linked to achieving two to three harvests per year. Previous studies have reported that frequent hive inspections play a critical role in the early detection of diseases and in monitoring adverse climatic conditions [
15,
16]. These practices contribute to maintaining colony health [
17,
18] and are associated with improved yield outcomes [
19,
20].
Additional economic activities were also associated with both the beekeeper’s level of instruction and the number of annual harvests. Beekeepers with primary tended to combine apiculture with agricultural work, whereas those with secondary or higher diversified into non-agricultural sectors such as crafts or services. These differences may reflect distinct economic sustainability strategies, as well as disparities in access to resources, technical knowledge, market opportunities, and technology adoption [
21,
22]. In Chachapoyas province, the most prevalent economic activities include agriculture, livestock, and tourism [
23]. Beekeepers with lower educational attainment may maintain stronger ties to these traditional sectors, which are embedded in local cultural practices. Diversification into agricultural activities may reduce the time and resources available for apiculture, thereby influencing management frequency and harvest outcomes.
In this context, [
24] reported that in southwestern Ethiopia, beekeepers engaged primarily in traditional practices and with limited technical specialization obtained lower yields, whereas those with greater specialization and organizational capacity achieved higher production and economic returns. These findings support the premise that time availability and resource allocation for specialized management are key factors influencing apiary performance.
4.4. Principal Component Analysis
Principal component analysis revealed that the first component (Dim1), accounting for 37.1% of the total variance, was strongly influenced by variables directly related to beekeeping management: number of hives, beekeeper experience, and AH frequency. These variables may jointly represent an axis of “productive intensity” or “operational scale”. In this regard, a study conducted under Lebanese conditions, using a comprehensive survey and Principal Component Analysis (PCA), revealed that beekeepers’ knowledge, cooperative membership, number of hives, and honey storage practices significantly influenced production [
33]. Furthermore, geographic region affected management practices, as most beekeepers engaged in year-round migratory beekeeping, highlighting both the challenges and opportunities for improving the sector [
33].
The second component (Dim2), which explained 28.1% of the variance, grouped sociocultural variables such as the beekeeper’s instruction and the presence of additional economic activities. This indicates that socioeconomic attributes of producers also contribute to explaining differences among beekeeping systems [
34]. Furthermore, beekeepers’ management philosophy is closely associated with their choice of hive chemicals and overall beekeeping objectives. This suggests that informed decision-making enables beekeepers to adopt management practices suited to their farm size and production philosophy [
35].
In contrast, apiary visit frequency was associated with a distinct third component, emerging as a relevant variable that may reflect its transversal role across both technical management and beekeeper profile dimensions [
36]. Previous studies, such as that of [
37] have demonstrated that management practices and beekeeper characteristics, when analyzed jointly, account for a substantial portion of the variability observed in honey production, thereby supporting the findings of this study. This study demonstrates that management practices and beekeeper characteristics jointly explain a significant proportion of the variability among beekeeping operations. These findings support the notion that variables such as visit frequency can be integrated across both technical and beekeeper profile dimensions to promote sustainable beekeeping [
38].
4.5. Honey Production Estimation Model
The applied linear mixed-effects model enabled simultaneous evaluation of multiple predictors of honey yield while accounting for district-level variability as a random intercept. The inclusion of district as a random effect was statistically justified by its significant contribution to the total variance (
Table 6), highlighting the influence of geographic factors such as local climate, floral availability, and pest pressure on apiary performance [
39].
Regarding fixed effects (
Table 7), significant predictors of honey production included beekeeper experience (
p = 0.0137), number of hives (
p < 0.0001), AH frequency (
p = 0.018), and exclusive dedication to beekeeping (absence of additional economic activities,
p = 0.0481). These results align with patterns identified in univariate and multivariate analyses, confirming that honey yield is closely associated with operational scale, management intensity, and technical specialization [
40]. Among these, hive quantity exhibited the strongest positive effect, reinforcing its role as a structurally determinant variable in production systems. Conversely, variables such as beekeeper instruction and apiary visit frequency did not exhibit statistically significant effects within the model. However, their inclusion improved overall model fit and were retained in the final specification. This indicates that while these variables may exert indirect or interaction-based influence, they do not independently account for substantial variance in honey yield [
41].
Comparable models have been employed in previous studies, where experience, apiary size, and productive specialization were positively associated with higher yield levels, whereas educational attainment and management frequency were not consistently significant in multivariate frameworks [
42]. Recent studies have also incorporated predictive modeling approaches to estimate honey production based on climatic variables, floral resource availability, and management characteristics [
43,
44]. These studies demonstrate the feasibility of yield forecasting and its potential utility for harvest planning and resource optimization, particularly in rural contexts analogous to Chachapoyas.
The apparent divergence among some statistical results can be attributed to the distinct analytical purposes and scopes of the applied methods. For instance, the Chi-square test revealed significant associations between harvest frequency and apiary visit frequency (p < 0.01), as well as between additional economic activities and educational level, indicating that inspection practices and livelihood strategies vary according to managerial and sociodemographic characteristics.
However, when honey production was analyzed using a linear mixed-effects model—which simultaneously incorporates multiple predictors and accounts for district-level variability as a random factor—neither education nor visit frequency exhibited statistically significant direct effects on yield. Although not significant as independent predictors, these variables were retained because they improved the overall model fit according to specific goodness-of-fit criteria.
This contrast reflects the fundamental difference between univariate or bivariate tests and multivariate modeling approaches. While Chi-square analyses detect simple associations, they do not account for confounding or interactive effects. In contrast, multivariate models estimate the adjusted influence of several variables concurrently, offering a more integrated and realistic representation of production dynamics. Consequently, factors that appear significant in isolated analyses may lose direct significance once technical, operational, and spatial sources of variation are controlled. This underscores the complexity of beekeeping systems and suggests the potential influence of latent factors or interactions not explicitly addressed in this study.
Model validation confirmed compliance with key statistical assumptions. The Shapiro–Wilk test applied to residuals (
p = 0.7385) supported normality, and variance inflation factors (VIF < 10) ruled out significant multicollinearity among predictors. Marginal (R
2 = 0.778) and conditional (R
2 = 0.789) coefficients of determination indicated high explanatory power for both fixed and random effects, which is essential in mixed models incorporating unit-level heterogeneity (i.e., apiaries). Logarithmic transformation of the dependent variable during modeling, followed by back-transformation via the exponential function (exp()), improved data distribution and stabilized variance, yielding a more accurate fit. This precision was reflected in the strong correlation between predicted and observed honey yields (R = 0.836,
p < 0.01), as illustrated in
Figure 3. Despite the overall model performance, several outliers were detected. These may be attributable to external factors not explicitly modeled, including variation in management practices, seasonal floral dynamics, or localized climatic anomalies [
45,
46].
The weight information was neither collected nor included as a predictor in the honey production estimation model described. The linear mixed-effects model incorporated variables such as beekeeper experience, number of hives, frequency of agricultural applications, and exclusive dedication to beekeeping; however, weight data were not included as part of the fixed or random effects.
A major limitation of this study is the exclusion of the variable related to surrounding vegetation, which may represent a key determinant of beekeeping productivity. Although a positive relationship was identified between the beekeeper’s educational background and honey yield, future research should incorporate analyses of the productive potential associated with the floristic composition and availability of nectar and pollen resources within the Amazonian landscape. Areas with greater diversity and abundance of melliferous flora are likely to support higher honey yields, regardless of other factors considered. Therefore, the omission of this environmental variable may constrain the generalizability and accuracy of the explanatory model in identifying the true determinants of beekeeping production.