Hi,
I'm trying to run difftest and I can't get my model to converge (even though all the examples work):
library(phyloseq)
library(corncob)
library(ggplot2)
# ASV data
seq_data = readRDS('ps_object.rds')
# filter out dates after the experiment
seq_data = seq_data %>% phyloseq::subset_samples(Date %in% c("2020.09.01", "2020.06.11", "2020.08.06", "2020.08.19", "2020.07.08", "2020.07.07", "2020.06.25", "2020.07.22", "2020.05.11", "2020.05.29"))
# collapse to phylum data
phy_data = seq_data %>% tax_glom('phylum')
test = bbdml(formula=ASV1~Date,
+ phi.formula=~Date,
+ data=phy_data,
+ taxa_are_rows=T)
> test
Call:
bbdml(formula = ASV1 ~ Date, phi.formula = ~Date, data = phy_data,
... = pairlist(taxa_are_rows = T))
Coefficients associated with abundance:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -3.48050 0.06874 -50.635 < 2e-16 ***
Date2020.05.29 0.14888 0.11188 1.331 0.187
Date2020.06.11 0.49810 0.09036 5.512 4.2e-07 ***
Date2020.06.25 -0.05654 0.08979 -0.630 0.531
Date2020.07.07 0.04556 0.09530 0.478 0.634
Date2020.07.08 0.07992 0.09455 0.845 0.401
Date2020.07.22 0.09872 0.09886 0.999 0.321
Date2020.08.06 0.00730 0.09463 0.077 0.939
Date2020.08.19 0.08539 0.08293 1.030 0.306
Date2020.09.01 0.15254 0.09270 1.646 0.104
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Coefficients associated with dispersion:
Estimate Std. Error t value Pr(>|t|)
(Intercept) -6.62462 0.46342 -14.295 <2e-16 ***
Date2020.05.29 0.65342 0.65156 1.003 0.319
Date2020.06.11 0.11408 0.66311 0.172 0.864
Date2020.06.25 -0.40465 0.65670 -0.616 0.540
Date2020.07.07 -0.03213 0.65362 -0.049 0.961
Date2020.07.08 -0.03100 0.65301 -0.047 0.962
Date2020.07.22 0.16200 0.65495 0.247 0.805
Date2020.08.06 -0.09950 0.65437 -0.152 0.880
Date2020.08.19 -0.73318 0.66298 -1.106 0.272
Date2020.09.01 -0.05732 0.65613 -0.087 0.931
---
Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
Log-likelihood: -648.38
> da_analysis = differentialTest(formula = ~ Date,
+ phi.formula = ~ Date,
+ formula_null = ~ 1,
+ phi.formula.null = ~ Date,
+ test='Wald',
+ boot=F,
+ data=common_phyla)
Error in differentialTest(formula = ~Date, phi.formula = ~Date, formula_null = ~1, :
All models failed to converge!
If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
It doesn't matter how I specify the model, they all fail:
> da_analysis = differentialTest(formula = ~ 1,
+ phi.formula = ~ 1,
+ formula_null = ~ 1,
+ phi.formula.null = ~ 1,
+ test='Wald',
+ boot=F,
+ data=common_phyla)
Error in differentialTest(formula = ~1, phi.formula = ~1, formula_null = ~1, :
All models failed to converge!
If you are seeing this, it is likely that your model is overspecified. This occurs when your sample size is not large enough to estimate all the parameters of your model. This is most commonly due to categorical variables that include many categories.
Alternatively, double-check your values for the arguments `link`, `phi.link`, and `method` to makes sure that they follow the specified options.
To confirm you have fixed the issue, try running a model for a single taxon with bbdml.
Hi, I'm trying to run difftest and I can't get my model to converge (even though all the examples work):
It doesn't matter how I specify the model, they all fail:
Thoughts?