Built site for prolfqua@1.6.2: 81eb50a

Author: wolski

CLAUDE.html

@@ -68,17 +68,23 @@ autoload is disabled.
         └── Returns a Facade with uniform API:
             $get_contrasts(), $get_missing(), $get_Plotter(), $to_wide()
 
-### Facade Pattern (`ContrastsFacades.R`, `build_contrast_analysis.R`)
+### Facade Pattern (`ContrastsFacades.R`, `ContrastsChildToParentFacades.R`, `build_contrast_analysis.R`)
 
 [`build_contrast_analysis()`](https://wolski.github.io/prolfqua/reference/build_contrast_analysis.md)
 is the recommended entry point. Each method dispatches to a Facade class
 that wires strategy → model → contrasts → moderation internally.
 
-**Aggregated input** (protein-level, `subject_Id == hierarchy_keys`):
-`lm`, `rlm`, `lm_missing`, `lm_impute`, `limma`, `deqms`, `firth`
+Facades split by input/output hierarchy shape:
 
-**Nested input** (peptide-level, `subject_Id` is strict subset of
-`hierarchy_keys`): `lmer`, `ropeca`
+**Aggregated input** (same-level, protein → protein FC;
+`subject_Id == hierarchy_keys`) — `R/ContrastsFacades.R`: `lm`, `rlm`,
+`lm_missing`, `lm_impute`, `limma`, `limma_impute`, `limma_voom`,
+`limma_voom_impute`, `deqms`, `deqms_voom`, `firth`, `limpa`
+
+**Nested input** (child → parent, peptide/precursor → protein FC;
+`subject_Id` is strict subset of `hierarchy_keys`) —
+`R/ContrastsChildToParentFacades.R`: `lmer_nested`, `ropeca_nested`,
+`firth_nested`, `limpa_nested`
 
 ### Weights & `nr_children`
 
@@ -216,8 +222,8 @@ downstream packages.
 `options(prolfqua.vectorize = TRUE)` activates vectorized
 implementations of `compute_contrast` and `linfct_matrix_contrasts`
 (matrix multiplication instead of per-row loops). Affects all Wald test
-facades (lm, rlm, firth, lmer) and limma’s linfct path. Results are
-numerically identical. Default is `FALSE`.
+facades (lm, rlm, firth, firth_nested, lmer_nested) and limma’s linfct
+path. Results are numerically identical. Default is `FALSE`.
 
 ## Testing
 

CLAUDE.md

@@ -529,7 +529,7 @@ sessionInfo()
     ##  [34] grid_4.5.2             jomo_2.7-6             xtable_1.8-8          
     ##  [37] mice_3.19.0            ggplot2_4.0.3          scales_1.4.0          
     ##  [40] iterators_1.0.14       MASS_7.3-65            cli_3.6.6             
-    ##  [43] crayon_1.5.3           UpSetR_1.4.0           rmarkdown_2.31        
+    ##  [43] crayon_1.5.3           UpSetR_1.4.1           rmarkdown_2.31        
     ##  [46] ragg_1.5.2             reformulas_0.4.4       generics_0.1.4        
     ##  [49] otel_0.2.0             httr_1.4.8             minqa_1.2.8           
     ##  [52] cachem_1.1.0           operator.tools_1.6.3.1 splines_4.5.2         

articles/Comparing2Groups.html

@@ -425,32 +425,31 @@ proteins that plain lm could not estimate
 
 ## Peptide-input facades
 
-The mixed-effects `lmer` facade and `ropeca` require lower-level
-measurements below the analysis subject. The `firth` facade can also
-operate directly on peptide-level `LFQData`. `firth` is shown a second
-time here on purpose, because it can also be fitted on peptide input.
-All three still return protein-level contrasts.
+The mixed-effects `lmer_nested` facade and `ropeca_nested` require
+lower-level measurements below the analysis subject. The `firth_nested`
+facade is the peptide-input variant of `firth` shown above. All three
+still return protein-level contrasts.
 
 ``` r
 fa_lmer_2f <- build_contrast_analysis(
   lfq_peptide_2f,
   "~ Subgroup + (1 | peptide_Id) + (1 | sampleName)",
   contrasts_2f,
-  method = "lmer"
+  method = "lmer_nested"
 )
 
 fa_ropeca_2f <- build_contrast_analysis(
   lfq_peptide_2f,
   "~ Subgroup",
   contrasts_2f,
-  method = "ropeca"
+  method = "ropeca_nested"
 )
 
 fa_firth_peptide_2f <- build_contrast_analysis(
   lfq_peptide_2f,
   "~ Subgroup",
   contrasts_2f,
-  method = "firth"
+  method = "firth_nested"
 )
 ```
 
@@ -474,11 +473,11 @@ results_peptide_2f |>
 ```
 
     ## # A tibble: 3 × 2
-    ##   facade n_results
-    ##   <chr>      <int>
-    ## 1 firth        240
-    ## 2 lmer         179
-    ## 3 ropeca       231
+    ##   facade        n_results
+    ##   <chr>             <int>
+    ## 1 firth_nested        240
+    ## 2 lmer_nested         179
+    ## 3 ropeca_nested       231
 
 ``` r
 ggplot(results_peptide_2f, aes(x = diff, y = -log10(p.value), color = significant)) +
@@ -560,7 +559,7 @@ sessionInfo()
     ## [31] nnet_7.3-20            grid_4.5.2             jomo_2.7-6            
     ## [34] mice_3.19.0            scales_1.4.0           iterators_1.0.14      
     ## [37] MASS_7.3-65            cli_3.6.6              crayon_1.5.3          
-    ## [40] UpSetR_1.4.0           rmarkdown_2.31         ragg_1.5.2            
+    ## [40] UpSetR_1.4.1           rmarkdown_2.31         ragg_1.5.2            
     ## [43] reformulas_0.4.4       generics_0.1.4         otel_0.2.0            
     ## [46] httr_1.4.8             minqa_1.2.8            cachem_1.1.0          
     ## [49] operator.tools_1.6.3.1 splines_4.5.2          vctrs_0.7.3