Update docs

dadi_cli/parsers/common_arguments.py

@@ -253,7 +253,7 @@ def add_eps_argument(parser: argparse.ArgumentParser) -> None:
         type=positive_num,
         nargs="+",
         required=False,
-        help="Step sizes to try for Godambe analysis. Default: [0.1, 0.01, 0.001]",
+        help="Step sizes to try for Godambe analysis. Default: [0.1, 0.01, 0.001].",
     )
 
 

docs/userguide/stat.md

@@ -1,5 +1,7 @@
 # Statistical testing
 
+## Bootstrapped spectrum generation
+
 To perform uncertainty analysis, `dadi` offers [an approach](https://dadi.readthedocs.io/en/latest/user-guide/uncertainty-analysis/) using the Godambe Information Matrix (GIM). To utilize this method, users should begin by using the `GenerateFs` subcommand to generate bootstrapped data from VCF files.
 
 In this example, we generate `20` bootstraps using the `--bootstrap` argument to save time, though we recommend users perform `100` bootstraps for more robust results. The `--chunk-size` argument specifies the maximum length of the chromosome chunks, which are then randomly drawn with replacement to create the bootstrapped chromosomes. The `--output` argument sets the prefix for the output files and the directory where the allele frequency spectra from the bootstrapped chromosomes will be stored.
@@ -12,6 +14,8 @@ dadi-cli GenerateFs --vcf examples/data/1KG.YRI.CEU.non.vcf.gz --pop-info exampl
 
 The output files from the above commands can be found in the `bootstrapping_syn` directory for synonymous SNPs and the `bootstrapping_non` directory for non-synonymous SNPs [here](https://github.com/xin-huang/dadi-cli/tree/revision/examples/results/fs). 
 
+## Confidence interval estimation
+
 To estimate the confidence intervals for the demographic parameters, users can use
 
 ```         
@@ -25,3 +29,39 @@ dadi-cli StatDFE --fs ./examples/results/fs/1KG.YRI.CEU.20.nonsynonymous.snps.un
 ```
 
 Three different step sizes are tested when using the GIM. Ideally 95% confidence intervals will be consistent between step sizes.
+
+## Arguments
+
+For the `StatDM` subcommand:
+
+| Argument | Description |
+| - | - |
+| `--fs` | Frequency spectrum of mutations used for inference. To generate the frequency spectrum, please use `dadi-cli GenerateFs`. Can be an HTML link. |
+| `--model` | Name of the demographic model. To check available demographic models, please use `dadi-cli Model`. |
+| `--model-file` | Name of python module file (not including .py) that contains custom models to use. Can be an HTML link. Default: None. |
+| `--grids` | Sizes of grids. Default: Based on sample size. |
+| `--nomisid` | Enable to *not* include a parameter modeling ancestral state misidentification when data are polarized. |
+| `--output` | Name of the output file. |
+| `--constants` | Fixed parameters during the inference or using Godambe analysis. Use -1 to indicate a parameter is NOT fixed. Default: None. |
+| `--eps` | Step sizes to try for Godambe analysis. Default: [0.1, 0.01, 0.001]. |
+| `--demo-popt` | File contains the bestfit demographic parameters, generated by `dadi-cli BestFit`. |
+| `--bootstrapping-dir` | Directory containing boostrapping spectra. |
+| `--logscale` | Determine whether estimating the uncertainties by assuming log-normal distribution of parameters; Default: False. |
+
+For the `StatDFE` subcommand:
+
+| Argument | Description |
+| - | - |
+| `--fs` | Frequency spectrum of mutations used for inference. To generate the frequency spectrum, please use `dadi-cli GenerateFs`. Can be an HTML link. |
+| `--cache1d` | File name of the 1D DFE cache. To generate the cache, please use `dadi-cli GenerateCache`. |
+| `--cache2d` | File name of the 2D DFE cache. To generate the cache, please use `dadi-cli GenerateCache`. |
+| `--pdf1d` | 1D probability density function for the DFE inference. To check available probability density functions, please use `dadi-cli Pdf`. |
+| `--pdf2d` | 2D probability density function for the joint DFE inference. To check available probability density functions, please use `dadi-cli Pdf`. |
+| `--nomisid` | Enable to *not* include a parameter modeling ancestral state misidentification when data are polarized. |
+| `--output` | Name of the output file. |
+| `--constants` | Fixed parameters during the inference or using Godambe analysis. Use -1 to indicate a parameter is NOT fixed. Default: None. |
+| `--eps` | Step sizes to try for Godambe analysis. Default: [0.1, 0.01, 0.001]. |
+| `--dfe-popt` | File containing the bestfit DFE parameters, generated by `dadi-cli BestFit`. |
+| `--bootstrapping-nonsynonymous-dir` | Directory containing boostrapping spectra. |
+| `--bootstrapping-synonymous-dir` | Directory containing boostrapping spectra, required to adjust nonsynonymous theta for differences in synonymous theta. |
+| `--logscale` | Determine whether estimating the uncertainties by assuming log-normal distribution of parameters; Default: False. |