Comments (4)
Hello Ricardo,
could you please install the last github version, and if the problem persists specify
. Print out the input dataset immediately before the bug occurs
. Paste the code immediately leading to the bug
. Print out of the output, if any
. Print out of the complete error/warning message, if any
. sessionInfo()
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- Thanks for the reply!
- After installation with GitHub (sccomp version 1.3.4), sccomp_glm recognizes "contrasts".
- However, a new issue appears. When I run the scomp_glm, the following comes out:
sccomp says: outlier identification first pass - step 1/3 [ETA: ~20s]
Exception: Variable beta_random_intercept missing (in 'model_glm_multi_beta_binomial_generate_date' at line 45)
sccomp says: outlier identification second pass - step 2/3 [ETA: ~60s]
Exception: Variable beta_random_intercept missing (in 'model_glm_multi_beta_binomial_generate_date' at line 45)
sccomp says: outlier-free model fitting - step 3/3 [ETA: ~20s]
sccomp says: the composition design matrix has columns: (Intercept), GroupASD, GroupCOVID19, GroupEpilepsy, GroupHealthy, GroupLBD, GroupMS
sccomp says: the variability design matrix has columns: (Intercept)
- I tried to reinstall the package in its complex version (devtools::install_github("stemangiola/sccomp@cmdstanr")), and the following error appears during the installation:
installing source package ‘sccomp’ ...
using staged installation
SYNTAX ERROR, MESSAGE(S) FROM PARSER:
error in 'model_glm_multi_beta_binomial' at line 47, column 26
45: ) {
46:
47: return beta_binomial_lupmf(
^
48: slice_y |
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I see. that's a problem with windows. I will solve it tomorrow and keep you posted.
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Check of #73 are almost complete. Hopefully, this release will solve your problems.
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Related Issues (20)
- dirichlet_multinomial noise model doesn't seem to function HOT 4
- Interaction terms in sccomp_glm HOT 12
- Warings from sccomp_remove_outliers() when sample size is large HOT 1
- Does sccomp require replicates ? HOT 2
- Relationship between CI, minimal effect threshold, and FDR on plots$credible_intervals_1D HOT 2
- Fig 3B and 3 group comparisson HOT 1
- question: scope of the statistical model HOT 6
- sccomp_boxplot() errors when passing a factor variable HOT 3
- custom ggplot theme misses theme element HOT 1
- sccomp plot method -> rstan::gqs throws warning HOT 3
- question about lumping or selecting compositional data HOT 1
- Interpretation when both bars are highlighted versus one HOT 14
- Warning message: In validityMethod(object) HOT 9
- Warning message when duplicated samples HOT 8
- use of inv_logit vs softmax HOT 3
- throw error if missing values due to pivoting long HOT 3
- Best strategy for differential composition estimation in integrated Seurat object HOT 1
- stanfit correspondence parameters variable names HOT 18
- FDR calculation HOT 3
- Question about "test_composition_above_logit_fold_change" parameter in sccomp_glm HOT 3
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