Update docs

docs/userguide/stat.md

@@ -16,23 +16,25 @@ The output files from the above commands can be found in the `bootstrapping_syn`
 
 ## Confidence interval estimation
 
-To estimate the confidence intervals for the demographic parameters, users can use
+After obtaining bootstrapped spetra, users can estimate the confidence intervals for the demographic or DFE parameters.
+
+For our [demographic inference example](https://dadi-cli.readthedocs.io/en/revision/userguide/demog/), users can use the following command to estimate the confidence intervals for the demographic parameters:
 
 ```         
-dadi-cli StatDM --fs ./examples/results/fs/1KG.YRI.CEU.20.synonymous.snps.unfold.fs --model split_mig --demo-popt ./examples/results/demog/1KG.YRI.CEU.20.split_mig.demog.params.InferDM.bestfits --grids 60 80 100 --bootstrapping-dir ./examples/results/fs/bootstrapping_syn/ --output ./examples/results/stat/1KG.YRI.CEU.20.split_mig.bestfit.demog.params.godambe.ci
+dadi-cli StatDM --fs examples/results/fs/1KG.YRI.CEU.20.syn.unfolded.fs --model split_mig --demo-popt examples/results/demog/1KG.YRI.CEU.20.split_mig.demog.params.InferDM.bestfits --grids 60 80 100 --bootstrapping-dir examples/results/fs/bootstrapping_syn/ --output examples/results/stat/1KG.YRI.CEU.20.split_mig.bestfit.demog.params.godambe.ci
 ```
 
-To estimate the confidence intervals for the joint DFE parameters, users can use
+For our [DFE inference example](https://dadi-cli.readthedocs.io/en/revision/userguide/dfe/), users can use the following command to estimate the confidence intervals for the 1d DFE parameters:
 
 ```         
-dadi-cli StatDFE --fs ./examples/results/fs/1KG.YRI.CEU.20.nonsynonymous.snps.unfold.fs --dfe-popt ./examples/results/dfe/1KG.YRI.CEU.20.split_mig.dfe.1D_lognormal.params.InferDFE.bestfits --cache1d ./examples/results/caches/1KG.YRI.CEU.20.split_mig.sel.single.gamma.spectra.bpkl --pdf1d lognormal --bootstrapping-nonsynonymous-dir ./examples/results/fs/bootstrapping_non/ --bootstrapping-synonymous-dir ./examples/results/fs/bootstrapping_non/ --output ./examples/results/stat/1KG.YRI.CEU.20.split_mig.bestfit.dfe.1D_lognormal.params.godambe.ci
+dadi-cli StatDFE --fs examples/results/fs/1KG.YRI.CEU.20.non.unfolded.fs --dfe-popt examples/results/dfe/1KG.YRI.CEU.20.split_mig.dfe.1D_lognormal.params.InferDFE.bestfits --cache1d examples/results/caches/1KG.YRI.CEU.20.split_mig_sel_single_gamma.spectra.bpkl --pdf1d lognormal --bootstrapping-nonsynonymous-dir examples/results/fs/bootstrapping_non/ --bootstrapping-synonymous-dir examples/results/fs/bootstrapping_non/ --output examples/results/stat/1KG.YRI.CEU.20.split_mig.bestfit.dfe.1D_lognormal.params.godambe.ci
 ```
 
 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:
+### `StatDM`
 
 | Argument | Description |
 | - | - |
@@ -48,7 +50,7 @@ For the `StatDM` subcommand:
 | `--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:
+### `StatDFE`
 
 | Argument | Description |
 | - | - |

examples/results/stat/1KG.YRI.CEU.20.split_mig.bestfit.demog.params.godambe.ci

@@ -0,0 +1,12 @@
+Estimated 95% uncerts (theta adj), with step size 0.1): [0.0652234  0.01448371 0.02478827 0.07938722 0.00287734]
+Lower bounds of 95% confidence interval : [2.16878752 0.50740874 0.26407614 1.13594438 0.01764644]
+Upper bounds of 95% confidence interval : [2.29923431 0.53637617 0.31365269 1.29471882 0.02340113]
+
+Estimated 95% uncerts (theta adj), with step size 0.01): [0.07667109 0.02254708 0.02647544 0.07385703 0.00264314]
+Lower bounds of 95% confidence interval : [2.15733983 0.49934538 0.26238897 1.14147457 0.01788065]
+Upper bounds of 95% confidence interval : [2.310682   0.54443953 0.31533986 1.28918863 0.02316693]
+
+Estimated 95% uncerts (theta adj), with step size 0.001): [0.05868048 0.00972338 0.00409709 0.01693387 0.00291598]
+Lower bounds of 95% confidence interval : [2.17533044 0.51216908 0.28476733 1.19839773 0.0176078 ]
+Upper bounds of 95% confidence interval : [2.2926914  0.53161583 0.29296151 1.23226547 0.02343977]
+

examples/results/stat/1KG.YRI.CEU.20.split_mig.bestfit.dfe.1D_lognormal.params.godambe.ci

@@ -0,0 +1,12 @@
+Estimated 95% uncerts (theta adj), with step size 0.1): [4.96117706e+00 9.75414635e+00 7.45526698e-03]
+Lower bounds of 95% confidence interval : [ 0.74663106 -1.81945177  0.00901819]
+Upper bounds of 95% confidence interval : [10.66898517 17.68884093  0.02392873]
+
+Estimated 95% uncerts (theta adj), with step size 0.01): [0.43131608 0.913255   0.0019672 ]
+Lower bounds of 95% confidence interval : [5.27649204 7.02143958 0.01450626]
+Upper bounds of 95% confidence interval : [6.1391242  8.84794958 0.01844066]
+
+Estimated 95% uncerts (theta adj), with step size 0.001): [0.07007612 0.18519903 0.00193263]
+Lower bounds of 95% confidence interval : [5.637732   7.74949554 0.01454083]
+Upper bounds of 95% confidence interval : [5.77788423 8.11989361 0.01840609]
+