fix

taxonomicallyinformedannotation · Jul 21, 2023 · 69e205c · 69e205c
1 parent b0f5e94
commit 69e205c
Showing 1 changed file with 63 additions and 31 deletions.
diff --git a/R/weight_bio.R b/R/weight_bio.R
@@ -313,94 +313,114 @@ weight_bio <-
 
     candidate_domain <- candidates |>
       tidyft::filter(!is.na(candidate_organism_01_domain)) |>
+      tidyft::filter(candidate_organism_01_domain != "notClassified") |>
       tidytable::distinct(
         structure_inchikey_2D,
         candidate_organism_01_domain
       )
 
     candidate_kingdom <- candidates |>
       tidyft::filter(!is.na(candidate_organism_02_kingdom)) |>
+      tidyft::filter(candidate_organism_02_kingdom != "notClassified") |>
       tidytable::distinct(
         structure_inchikey_2D,
         candidate_organism_02_kingdom
       )
 
     candidate_phylum <- candidates |>
       tidyft::filter(!is.na(candidate_organism_03_phylum)) |>
+      tidyft::filter(candidate_organism_03_phylum != "notClassified") |>
       tidytable::distinct(
         structure_inchikey_2D,
         candidate_organism_03_phylum
       )
 
     candidate_class <- candidates |>
       tidyft::filter(!is.na(candidate_organism_04_class)) |>
+      tidyft::filter(candidate_organism_04_class != "notClassified") |>
       tidytable::distinct(
         structure_inchikey_2D,
         candidate_organism_04_class
       )
 
     candidate_order <- candidates |>
       tidyft::filter(!is.na(candidate_organism_05_order)) |>
+      tidyft::filter(candidate_organism_05_order != "notClassified") |>
       tidytable::distinct(
         structure_inchikey_2D,
         candidate_organism_05_order
       )
 
     ## candidate_infraorder <- candidates |>
     ##   tidyft::filter(!is.na(candidate_organism_05_1_infraorder)) |>
+    ## .  tidyft::filter(candidate_organism_05_1_infraorder
+    ## .   != "notClassified") |>
     ##   tidytable::distinct(structure_inchikey_2D,
     ##                   candidate_organism_05_1_infraorder)
 
     candidate_family <- candidates |>
       tidyft::filter(!is.na(candidate_organism_06_family)) |>
+      tidyft::filter(candidate_organism_06_family != "notClassified") |>
       tidytable::distinct(
         structure_inchikey_2D,
         candidate_organism_06_family
       )
 
     ## candidate_subfamily <- candidates |>
     ##   tidyft::filter(!is.na(candidate_organism_06_1_subfamily)) |>
+    ## .  tidyft::filter(candidate_organism_06_1_subfamily
+    ## .   != "notClassified") |>
     ##   tidytable::distinct(structure_inchikey_2D,
     ##                   candidate_organism_06_1_subfamily)
 
     candidate_tribe <- candidates |>
       tidyft::filter(!is.na(candidate_organism_07_tribe)) |>
+      tidyft::filter(candidate_organism_07_tribe != "notClassified") |>
       tidytable::distinct(
         structure_inchikey_2D,
         candidate_organism_07_tribe
       )
 
     ## candidate_subtribe <- candidates |>
     ##   tidyft::filter(!is.na(candidate_organism_07_1_subtribe)) |>
+    ## .  tidyft::filter(candidate_organism_07_1_subtribe
+    ## .   != "notClassified") |>
     ##   tidytable::distinct(structure_inchikey_2D,
     ##                   candidate_organism_07_1_subtribe)
 
     candidate_genus <- candidates |>
       tidyft::filter(!is.na(candidate_organism_08_genus)) |>
+      tidyft::filter(candidate_organism_08_genus != "notClassified") |>
       tidytable::distinct(
         structure_inchikey_2D,
         candidate_organism_08_genus
       )
 
     ## candidate_subgenus <- candidates |>
     ##   tidyft::filter(!is.na(candidate_organism_08_1_subgenus)) |>
+    ## .  tidyft::filter(candidate_organism_08_1_subgenus
+    ## .   != "notClassified") |>
     ##   tidytable::distinct(structure_inchikey_2D,
     ##                   candidate_organism_08_1_subgenus)
 
     candidate_species <- candidates |>
       tidyft::filter(!is.na(candidate_organism_09_species)) |>
+      tidyft::filter(candidate_organism_09_species != "notClassified") |>
       tidytable::distinct(
         structure_inchikey_2D,
         candidate_organism_09_species
       )
 
     ## candidate_subspecies <- candidates |>
     ##   tidyft::filter(!is.na(candidate_organism_09_1_subspecies)) |>
+    ## .  tidyft::filter(candidate_organism_09_1_subspecies
+    ## .   != "notClassified") |>
     ##   tidytable::distinct(structure_inchikey_2D,
     ##                   candidate_organism_09_1_subspecies)
 
     candidate_varietas <- candidates |>
       tidyft::filter(!is.na(candidate_organism_10_varietas)) |>
+      tidyft::filter(candidate_organism_10_varietas != "notClassified") |>
       tidytable::distinct(
         structure_inchikey_2D,
         candidate_organism_10_varietas
@@ -410,12 +430,13 @@ weight_bio <-
 
     log_debug("... domain \n")
     step_dom <- tidytable::left_join(sample_domain, candidate_domain) |>
-      tidyft::filter(candidate_organism_01_domain != "notClassified") |>
+      tidyft::filter(!is.na(sample_organism_01_domain)) |>
       dplyr::filter(
         stringi::stri_detect_regex(
           pattern = candidate_organism_01_domain,
           str = sample_organism_01_domain
-        )
+        ) |
+          sample_organism_01_domain == "notClassified"
       ) |>
       dplyr::mutate(score_biological = score_biological_domain) |>
       tidytable::left_join(
@@ -438,12 +459,13 @@ weight_bio <-
         sample_organism_02_kingdom
       )
     step_kin <- tidytable::left_join(step_kin, candidate_kingdom) |>
-      tidyft::filter(candidate_organism_02_kingdom != "notClassified") |>
+      tidyft::filter(!is.na(candidate_organism_02_kingdom)) |>
       dplyr::filter(
         stringi::stri_detect_regex(
           pattern = candidate_organism_02_kingdom,
           str = sample_organism_02_kingdom
-        )
+        ) |
+          sample_organism_02_kingdom == "notClassified"
       ) |>
       dplyr::mutate(score_biological = score_biological_kingdom) |>
       tidytable::left_join(
@@ -466,12 +488,13 @@ weight_bio <-
         sample_organism_03_phylum
       )
     step_phy <- tidytable::left_join(step_phy, candidate_phylum) |>
-      tidyft::filter(candidate_organism_03_phylum != "notClassified") |>
+      tidyft::filter(!is.na(candidate_organism_03_phylum)) |>
       dplyr::filter(
         stringi::stri_detect_regex(
           pattern = candidate_organism_03_phylum,
           str = sample_organism_03_phylum
-        )
+        ) |
+          sample_organism_03_phylum == "notClassified"
       ) |>
       dplyr::mutate(score_biological = score_biological_phylum) |>
       tidytable::left_join(
@@ -494,12 +517,13 @@ weight_bio <-
         sample_organism_04_class
       )
     step_cla <- tidytable::left_join(step_cla, candidate_class) |>
-      tidyft::filter(candidate_organism_04_class != "notClassified") |>
+      tidyft::filter(!is.na(candidate_organism_04_class)) |>
       dplyr::filter(
         stringi::stri_detect_regex(
           pattern = candidate_organism_04_class,
           str = sample_organism_04_class
-        )
+        ) |
+          sample_organism_04_class == "notClassified"
       ) |>
       dplyr::mutate(score_biological = score_biological_class) |>
       tidytable::left_join(
@@ -522,12 +546,13 @@ weight_bio <-
         sample_organism_05_order
       )
     step_ord <- tidytable::left_join(step_ord, candidate_order) |>
-      tidyft::filter(candidate_organism_05_order != "notClassified") |>
+      tidyft::filter(!is.na(candidate_organism_05_order)) |>
       dplyr::filter(
         stringi::stri_detect_regex(
           pattern = candidate_organism_05_order,
           str = sample_organism_05_order
-        )
+        ) |
+          sample_organism_05_order == "notClassified"
       ) |>
       dplyr::mutate(score_biological = score_biological_order) |>
       tidytable::left_join(
@@ -549,12 +574,12 @@ weight_bio <-
     ##                   sample_organism_05_1_infraorder)
     ## step_ord2 <-
     ##   tidytable::left_join(step_ord2, candidate_infraorder) |>
-    ##   tidyft::filter(candidate_organism_05_1_infraorder !=
-    ## "notClassified") |>
+    ## tidyft::filter(!is.na(candidate_organism_05_1_infraorder)) |>
     ##   dplyr::filter(
     ##     stringi::stri_detect_regex(
     ## pattern = candidate_organism_05_1_infraorder,
-    ## str = sample_organism_05_1_infraorder)
+    ## str = sample_organism_05_1_infraorder) |
+    ## sample_organism_05_1_infraorder == "notClassified"
     ##   ) |>
     ##   dplyr::mutate(score_biological = scoreBiologicalInfraorder) |>
     ##   tidytable::left_join(
@@ -574,12 +599,13 @@ weight_bio <-
         sample_organism_06_family
       )
     step_fam <- tidytable::left_join(step_fam, candidate_family) |>
-      tidyft::filter(candidate_organism_06_family != "notClassified") |>
+      tidyft::filter(!is.na(candidate_organism_06_family)) |>
       dplyr::filter(
         stringi::stri_detect_regex(
           pattern = candidate_organism_06_family,
           str = sample_organism_06_family
-        )
+        ) |
+          sample_organism_06_family == "notClassified"
       ) |>
       dplyr::mutate(score_biological = score_biological_family) |>
       tidytable::left_join(
@@ -600,11 +626,12 @@ weight_bio <-
     ##   tidytable::distinct(structure_inchikey_2D,
     ##                   sample_organism_06_1_subfamily)
     ## step_fam2 <- tidytable::left_join(step_fam2, candidate_subfamily) |>
-    ##   tidyft::filter(candidate_organism_06_1_subfamily != "notClassified") |>
+    ## tidyft::filter(!is.na(candidate_organism_06_1_subfamily)) |>
     ##   dplyr::filter(
     ##     stringi::stri_detect_regex(
     ## pattern = candidate_organism_06_1_subfamily,
-    ## str = sample_organism_06_1_subfamily)
+    ## str = sample_organism_06_1_subfamily) |
+    ## sample_organism_06_1_subfamily == "notClassified"
     ##   ) |>
     ##   dplyr::mutate(score_biological = scoreBiologicalSubfamily) |>
     ##   tidytable::left_join(
@@ -624,12 +651,13 @@ weight_bio <-
         sample_organism_07_tribe
       )
     step_tri <- tidytable::left_join(step_tri, candidate_tribe) |>
-      tidyft::filter(candidate_organism_07_tribe != "notClassified") |>
+      tidyft::filter(!is.na(candidate_organism_07_tribe)) |>
       dplyr::filter(
         stringi::stri_detect_regex(
           pattern = candidate_organism_07_tribe,
           str = sample_organism_07_tribe
-        )
+        ) |
+          sample_organism_07_tribe == "notClassified"
       ) |>
       dplyr::mutate(score_biological = score_biological_tribe) |>
       tidytable::left_join(
@@ -652,11 +680,12 @@ weight_bio <-
     ##     sample_organism_07_1_subtribe
     ##   )
     ## step_tri2 <- tidytable::left_join(step_tri2, candidate_subtribe) |>
-    ##   tidyft::filter(candidate_organism_07_1_subtribe != "notClassified") |>
+    ## tidyft::filter(!is.na(candidate_organism_07_1_subtribe)) |>
     ##   dplyr::filter(
     ##     stringi::stri_detect_regex(
     ## pattern = candidate_organism_07_1_subtribe,
-    ## str = sample_organism_07_1_subtribe)
+    ## str = sample_organism_07_1_subtribe) |
+    ## sample_organism_07_1_subtribe == "notClassified"
     ##   ) |>
     ##   dplyr::mutate(score_biological = scoreBiologicalSubtribe) |>
     ##   tidytable::left_join(
@@ -676,12 +705,13 @@ weight_bio <-
         sample_organism_08_genus
       )
     step_gen <- tidytable::left_join(step_gen, candidate_genus) |>
-      tidyft::filter(candidate_organism_08_genus != "notClassified") |>
+      tidyft::filter(!is.na(candidate_organism_08_genus)) |>
       dplyr::filter(
         stringi::stri_detect_regex(
           pattern = candidate_organism_08_genus,
           str = sample_organism_08_genus
-        )
+        ) |
+          sample_organism_08_genus == "notClassified"
       ) |>
       dplyr::mutate(score_biological = score_biological_genus) |>
       tidytable::left_join(
@@ -703,11 +733,12 @@ weight_bio <-
     ##                   sample_organism_08_1_subgenus)
     ## step_gen2 <-
     ##   tidytable::left_join(step_gen2, candidate_subgenus) |>
-    ##   tidyft::filter(candidate_organism_08_1_subgenus != "notClassified") |>
+    ## tidyft::filter(!is.na(sample_organism_08_1_subgenus)) |>
     ##   dplyr::filter(
     ##     stringi::stri_detect_regex(
     ## pattern = candidate_organism_08_1_subgenus,
-    ## str = sample_organism_08_1_subgenus)
+    ## str = sample_organism_08_1_subgenus) |
+    ## sample_organism_08_1_subgenus == "notClassified"
     ##   ) |>
     ##   dplyr::mutate(score_biological = scoreBiologicalSubgenus) |>
     ##   tidytable::left_join(
@@ -727,12 +758,13 @@ weight_bio <-
         sample_organism_09_species
       )
     step_spe <- tidytable::left_join(step_spe, candidate_species) |>
-      tidyft::filter(candidate_organism_09_species != "notClassified") |>
+      tidyft::filter(!is.na(candidate_organism_09_species)) |>
       dplyr::filter(
         stringi::stri_detect_regex(
           pattern = candidate_organism_09_species,
           str = sample_organism_09_species
-        )
+        ) |
+          sample_organism_09_species == "notClassified"
       ) |>
       dplyr::mutate(score_biological = score_biological_species) |>
       tidytable::left_join(
@@ -754,12 +786,12 @@ weight_bio <-
     ##                   sample_organism_09_1_subspecies)
     ## step_spe2 <-
     ##   tidytable::left_join(step_spe2, candidate_subspecies) |>
-    ##   tidyft::filter(candidate_organism_09_1_subspecies !=
-    ## "notClassified") |>
+    ## tidyft::filter(!is.na(candidate_organism_09_1_subspecies)) |>
     ##   dplyr::filter(
     ##     stringi::stri_detect_regex(
     ## pattern = candidate_organism_09_1_subspecies,
-    ## str = sample_organism_09_1_subspecies)
+    ## str = sample_organism_09_1_subspecies) |
+    ## sample_organism_09_1_subspecies == "notClassified"
     ##   ) |>
     ##   dplyr::mutate(score_biological = scoreBiologicalSubspecies) |>
     ##   tidytable::left_join(
@@ -779,7 +811,7 @@ weight_bio <-
         sample_organism_10_varietas
       )
     step_var <- tidytable::left_join(step_var, candidate_varietas) |>
-      tidyft::filter(candidate_organism_10_varietas != "notClassified") |>
+      tidyft::filter(!is.na(candidate_organism_10_varietas)) |>
       dplyr::filter(
         stringi::stri_detect_regex(
           pattern = candidate_organism_10_varietas,