NEWS

# Changes in version 1.7.7 (2023-07-26)

## Minor changes

* Better distinction between internal and exported functions
* Website polishing; phyloseq files moved to supplements behind link

# Changes in version 1.5.1 (2022-12-28)

## Major changes

* Rewrote the package to generate TreeSE outputs from simulator functions
* Updated examples and other functionality accordingly


# Changes in version 1.3.5 (2022-05-30)

## New arguments
added `names_species` in `randomA`, `randomE`, `simulateConsumerResource`,
`simulateGLV`, `simulateHubbellRates`, `simulateRicker`, `simulateSOI`, and
`simulateStochasticLogistic` functions.

added `names_resources` in  `randomE` and `simulateConsumerResource` functions.

## `randomA`
1. added parameter `interactions` and 5 interaction types to customize values
and proportions of interspecies interactions

2. added `scale_off_diagonal `to avoid exponential growth in certain gLV
modeling scenarios

3. added `list_A `to enable generating groups of species in simulation

## `randomE`
1. added trophic levels and trophic preferences

2. added `exact` to switch the number of resources to consume/produce between a
poisson distribution and the exact number

## Simulations
CRM, GLV, HubbellRates, and Logistic
1. added control of stochasticity, external events, migration from the
metacommunity, and the extend of measurement errors to all these simulations

2. added microbial trophic levels (an implicit inter-species interaction) in
`simulateConsumerResource`

3. put together result matrix and some parameters into a list containing the
first element named 'matrix' to store the counts of species in the community

## Support plot using miaViz
Example could be found in `simulateConsumerResource`,
`simulateGLV`, `simulateHubbellRates`, `simulateStochasticLogistic` functions.

## Function documentations
shared templates of documentation in man-roxygen to avoid duplication

other minor improvements

# What's changed

1. ways to customize the distribution in `randomA` and `randomE`
2. tests using previous data formats

# Changes in version 0.99.0 (2021-09-29)
+ Three simulation models and three functions are added
+ Submitted to Bioconductor