citation: | summary | mastif inputs | simulated data | mastSim | treeData and xytree | data summary and maps | model fitting | output summary, lists, and plots | estimates, and predictions in output | plots of output | slow convergence? | multiple seed types per species | specNames and seedNames | mastPlot written to files | my data | diameter effect | year and random effects | prior parameter values | maturation/fecundity data, if available | when trees are sampled less frequently than seeds | adding covariates | flexibility | random individual effects | random groups for years and lags | random effects when there are multiple species | convergence | time series: volatility and periodicity | trouble shooting | references

overview | model summary | data types | effort and weight of discrete data | using gjam | simulated data | my data | sensitivity to predictors | plotting output | flexibility in gjam | heterogeneous effort | specifying censored intervals | prior distribution on coefficients | species-factor levels that do not occur | sample effort in count data | sample effort in composition data | the partition in ordinal data | categorical data | combinations of data types | random effects | missing data, out-of-sample prediction | prediction with heterogenous effort | conditional prediction | conditional parameters | presence-only data with effort | dimension reduction | big-S composition data: fungal endophytes | interactions and indirect effects | joint trait modeling | trait response model (TRM) | input data | traits by species | factors in this example | TRM analysis | interactions and indirect effects | predictive trait model (PTM) | start with species abundance | trouble shooting in PTM | selecting variables | trouble shooting | reference notes | more on parameter dimensions | more on factors in $\mathbf{X}$ | algorithm summary | acknowledgements | references