| Type: | Package |
| Title: | Fit Neutral Community Model to Microbiome or Ecological Data |
| Version: | 0.1.0 |
| Description: | Provides tools for fitting the neutral community model (NCM) to assess the role of stochastic processes in community assembly. The package implements the framework of Sloan et al. (2006) <doi:10.1111/j.1462-2920.2005.00956.x>, enabling users to evaluate neutral dynamics in ecological and microbial communities. |
| License: | GPL (≥ 3) |
| Encoding: | UTF-8 |
| LazyData: | true |
| Depends: | R (≥ 3.5) |
| Imports: | dplyr, Hmisc, minpack.lm |
| RoxygenNote: | 7.3.3 |
| URL: | https://github.com/h-xuanjiu/ncmR |
| NeedsCompilation: | no |
| Packaged: | 2026-04-06 00:38:00 UTC; 15225 |
| Author: | Yuxuan He  [aut,
cre, cph] |
| Maintainer: | Yuxuan He <heyuxuan0525@outlook.com> |
| Repository: | CRAN |
| Date/Publication: | 2026-04-10 13:50:02 UTC |
Example OTU table and grouping information for NCM demonstration
Description
A simulated dataset containing an OTU table (ASV counts) and corresponding
group labels. The data are intended to illustrate the usage of the
fit_ncm function.
Usage
example_data
Format
A list with two components:
- otu
A data frame with 15 rows (samples) and 2000 columns (ASVs). Row names are sample identifiers, column names are ASV identifiers. Values represent counts of each ASV in each sample.
- grp
A data frame with 15 rows and 1 column named
group. Row names correspond to the samples inotu. Thegroupcolumn contains character labels ("A", "A", ..., etc.) indicating group membership for each sample.
Source
Simulated data for package examples.
Fit Neutral Community Model (NCM) with optional grouping and total pooling
Description
Fit Neutral Community Model (NCM) with optional grouping and total pooling
Usage
fit_ncm(
otu,
grp = NULL,
group_col = "group",
groups = NULL,
simplify = TRUE,
return_model = FALSE,
...
)
Arguments
otu |
OTU table, rows = samples, columns = species (data.frame or matrix) |
grp |
Optional data.frame with rownames = sample IDs, and one column specifying group membership. If NULL, all samples in otu are used as one group. |
group_col |
Column name in grp that contains group labels (default "group"). |
groups |
Character vector of group names to analyze. If NULL and grp is provided, the function fits models for each group AND for all samples combined (total). If non-NULL, only those groups are analyzed (no total model). |
simplify |
If TRUE and only one model is fitted, return the model list directly (not nested). |
return_model |
Whether to return the nlsLM model object (default FALSE to save space). |
... |
Additional arguments passed to nlsLM (e.g., lower, upper, control). |
Value
A list containing model results. If multiple models, a named list with keys: - "all" (if total model fitted) and group names. Each value is a list with: m, N, Nm, ci, rsqr, predictions, (model optional).
Examples
# Load example data
data(example_data)
otu <- example_data$otu
grp <- example_data$grp
# 1. No grouping: fit the total model using all samples
res_total <- fit_ncm(otu)
print(paste("m =", round(res_total$m, 4)))
print(paste("R^2 =", round(res_total$rsqr, 4)))
head(res_total$predictions)
# 2. With grouping: fit models for all groups + total
res_all <- fit_ncm(otu, grp)
# 3. Only specific groups (no total model), returns a single model object
res_sub <- fit_ncm(otu, grp, groups = "A")
res_sub$status_summary
Print summary of NCM model
Description
Print summary of NCM model
Usage
## S3 method for class 'summary_ncm'
print(x, ...)
Arguments
x |
An object of class "summary_ncm". |
... |
Additional arguments (not used). |
Value
No return value, called for side effects. Prints a formatted table of NCM results to the console.
Print summary of NCM group results
Description
Print summary of NCM group results
Usage
## S3 method for class 'summary_ncm_group'
print(x, ...)
Arguments
x |
An object of class "summary_ncm_group". |
... |
Additional arguments (not used). |
Value
No return value, called for side effects. Prints a formatted table of NCM group results to the console.
Summary method for NCM objects
Description
Summary method for NCM objects
Usage
## S3 method for class 'NCM'
summary(object, ...)
Arguments
object |
An object of class "NCM" (single model). |
... |
Additional arguments (not used). |
Value
An object of class "summary_ncm" containing key model statistics.
Summary method for NCM group results
Description
Summary method for NCM group results
Usage
## S3 method for class 'NCM_group'
summary(object, ...)
Arguments
object |
An object of class "NCM_group" (list of NCM objects). |
... |
Additional arguments (not used). |
Value
An object of class "summary_ncm_group" containing summary for each group.