From 460c81150d46a6a871917a2b289bf9eb54ec5199 Mon Sep 17 00:00:00 2001
From: Francesco Sabatini <francesco.sabatini@idiv.de>
Date: Wed, 4 Mar 2020 01:33:47 +0100
Subject: [PATCH] Brushed up Backbone, Created Taxon group. Manual clean
families
---
code/03_TaxonomicBackbone.Rmd | 261 ++++++++++++++++++++++++++--------
1 file changed, 200 insertions(+), 61 deletions(-)
diff --git a/code/03_TaxonomicBackbone.Rmd b/code/03_TaxonomicBackbone.Rmd
index 27e83ce..2611f12 100644
--- a/code/03_TaxonomicBackbone.Rmd
+++ b/code/03_TaxonomicBackbone.Rmd
@@ -58,8 +58,14 @@ mushroom <- c("Mycena", "Boletus", "Russula","Calocybe","Collybia","Amanita","Am
"Sarcodom","Sarcoscyphus","Scleroderma","Stropharia","Tylopilus","Typhula", "Calyptella", "Chrysopsora", "Lacrymaria", "Dermoloma",
"Agaricus","Alnicola", "Amanitina", "Bovista", "Cheilymenia","Clavulinopsis", "Clitocybe", "Entoloma", "Geaster", "Inocybe",
"Laccaria", "Laetiporus", "Lepista", "Macrolepiota", "Macrolepis", "Marasmius", "Panaeolus", "Psathyrella", "Psilocybe",
- "Rickenella", "Sarcoscypha", "Vascellum", "Ramaria",
- "Amphoroblasia", "Amphoroblastia", "Agrocybe")
+ "Rickenella", "Sarcoscypha", "Vascellum", "Ramaria","Amphoroblasia", "Amphoroblastia", "Agrocybe",
+ "Flammulaster", "Phaeocollybia", "Cortinarius", "Lepiota", "Cystoderma",
+ "Armillaria", "Athelia", "Ceraceomyces", "Chlorociboria", "Clavariaceae",
+ "Cystoderma", "Dacrymyces","Dendrographa","Dirina", "Flammulaster","Fomes","Gyrophora",
+ "Kirschsteiniothelia", "Lasallia","Lepiota","Llimoniella","Mazosia","Microthelia","Mollisia",
+ "Multiclavula","Phaeocollybia","Phellinus","Plectocarpon","Pleospora","Ramariopsis","Reinkella",
+ "Roccella","Roccellina","Sigridea","Stereum","Tremella","Tulostoma","Umbilicaria","Unguiculariopsis" ,
+ "Xanthoconium")
```
@@ -1200,7 +1206,7 @@ tpl.submit <- tnrs.res.certain %>% filter(is.na(Accepted_name)) %>% dplyr::selec
nrow(tpl.submit)
write_csv(tpl.submit, path="../_derived/TPL/tpl.submit.csv")
-#dividve in 99 batches
+#divide in 99 batches
indices <- 1:nrow(tpl.submit)
chunks <- split(indices, sort(indices%%99))
@@ -1248,11 +1254,17 @@ save(tpl.ncbi.certain, tpl.ncbi.uncertain, file="../_derived/TNRS_submit/tnrs.it
# Merge the resolved species lists into a Backbone
## Read files
-```{r, eval = T}
+```{r, eval = T, warning=F}
load("../_derived/TNRS_submit/tnrs.iter1.RData")
load("../_derived/TNRS_submit/tnrs.iter2.RData")
load("../_derived/TNRS_submit/tnrs.iter3.RData")
load("../_derived/TNRS_submit/tnrs.iter4.RData")
+
+#Double check of wrong taxa from TNRS
+finalcheck <- c("Salix repens subsp. repens var. repens","Hieracium lachenalii")
+tpl.ncbi.certain <- tpl.ncbi.certain %>%
+ bind_rows(TPL(finalcheck))
+
```
Combine the `certain` data sets:
@@ -1300,11 +1312,11 @@ Backbone <- spec.list.TRY.sPlot %>%
levels=c("Accepted","Synonym", "No opinion","Invalid",
"Illegitimate","Misapplied","Rejected name",
"Unresolved"))) %>%
+ arrange(Taxonomic_status) %>%
+ slice(1) %>%
#delete empty spaces at end of names
mutate(Accepted_name=gsub(pattern=" $", replacement="", x=Accepted_name)) %>%
- mutate(Accepted_name_species=gsub(pattern=" $", replacement="", x=Accepted_name_species)) %>%
- arrange(Taxonomic_status) %>%
- slice(1),
+ mutate(Accepted_name_species=gsub(pattern=" $", replacement="", x=Accepted_name_species)),
by="Name_submitted")
#Double check
nrow(Backbone) == nrow(spec.list.TRY.sPlot)
@@ -1318,7 +1330,7 @@ If names were neither resolved at the accepted or synonym level, set `Status_cor
```{r, eval = T}
Backbone <- Backbone %>%
mutate(Status_correct=fct_collapse(Taxonomic_status,
- Other=c("No opinion","Invalid",
+ Other=c("No opinion","Invalid", "Unresolved",
"Illegitimate","Misapplied","Rejected name"))) %>%
mutate(Status_correct=fct_explicit_na(Status_correct, "No suitable matches found.")) %>%
#Create Name_correct field. Use Accepted names, if any. Otherwise matched names.
@@ -1338,13 +1350,12 @@ Backbone <- Backbone %>%
summary(Backbone$Status_correct)
summary(Backbone$Rank_correct)
```
+
There are `r sum(is.na(Backbone$Name_correct))` species names for which we found no match in any of the taxonomic resources we used. Yet, for as many as `r sum(Backbone$Rank_correct %in% c("higher", "family", "genus"))` taxa, the matching did not properly resolve the species name, and we only found a match at genus or higher level.
## Complete list of families
-There are `r sum(is.na(Backbone$Accepted_name_family))` records with missing family information.
-### Derive info from other species of the same Genera in the Backbone itself
-Copy family info for taxa resolved at family level.
+There are `r sum(is.na(Backbone$Accepted_name_family))` records with missing family information. Create field `Family_correct`.
```{r}
Backbone <- Backbone %>%
mutate(family.lev=str_extract(word(Name_correct,1), pattern='([^\\s]+aceae)')) %>%
@@ -1356,38 +1367,6 @@ Backbone <- Backbone %>%
# Remaining records with missing family info
sum((is.na(Backbone$Family_correct)))
```
-
-Derive family info from each genus in the backbone, and use this info to complement records from the same genera, but with missing family info.
-```{r}
-genera_families <- Backbone %>%
- filter(Taxonomic_status=="Accepted") %>%
- dplyr::select(Genus_correct, Family_correct) %>%
- rename(family=Family_correct) %>%
- distinct() %>%
- na.omit() %>%
- #for some genera there are multiple families assigned
- # (e.g. in case of unresolved species names )
- # Extract the family names that occurs most often across each genus
- group_by(Genus_correct, family) %>%
- summarize(n=n()) %>%
- arrange(desc(n)) %>%
- slice(1) %>%
- ungroup() %>%
- dplyr::select(-n)
-
-# Assign family derived from backbone to other records
-Backbone <- Backbone %>%
- left_join(genera_families, by="Genus_correct") %>%
- mutate(Family_correct=ifelse( (is.na(Family_correct) & !is.na(family)),
- family,
- Family_correct)) %>%
- dplyr::select(-family)
-
-#Records with missing family info
-sum(is.na(Backbone$Family_correct))
-```
-
-
### Resolve genera with missing family info with `TNRS`
```{r, eval=F}
@@ -1443,11 +1422,27 @@ unzip("/data/sPlot/users/Francesco/Ancillary_Data/Catalogue_of_Life/CatLife2019.
```
-
-
```{r, message=F, warning=F}
cat.life <- read_delim("/data/sPlot/users/Francesco/Ancillary_Data/Catalogue_of_Life/taxa.txt",
- delim="\t")
+ delim="\t",
+ col_types = cols(
+ .default = col_character(),
+ taxonID = col_double(),
+ datasetID = col_double(),
+ acceptedNameUsageID = col_double(),
+ parentNameUsageID = col_double(),
+ superfamily = col_logical(),
+ subgenus = col_logical(),
+ source = col_logical(),
+ namePublishedIn = col_logical(),
+ modified = col_character(),
+ taxonConceptID = col_double(),
+ isExtinct = col_logical()
+ )) %>%
+ #correct family names to match to the standards in TPL
+ mutate(family=ifelse(family=="Fabaceae", "Leguminosae", family)) %>%
+ mutate(family=ifelse(family=="Asteraceae", "Compositae", family))
+
Genera_missing <- Backbone %>%
filter(is.na(Family_correct) & !is.na(Genus_correct)) %>%
dplyr::select(Genus_correct) %>%
@@ -1471,39 +1466,116 @@ sum(is.na(Backbone$Family_correct))
```
After matching the remaining genera with the Catalogue of life there are still `r nrow(Backbone %>% filter(is.na(Family_correct)))` records without Family affiliation, for a total of `r nrow(Backbone %>% filter(is.na(Family_correct)) %>% dplyr::select(Genus_correct) %>% distinct())` genera.
-### Manually fix residual, known issues
+### Manually fix some known issues
```{r}
Backbone <- Backbone %>%
mutate(Family_correct=replace(Family_correct,
- list=word(Accepted_name_species, 1)=="Coptidium",
+ list=Genus_correct=="Coptidium",
values="Ranunculaceae")) %>%
mutate(Family_correct=replace(Family_correct,
- list=word(Accepted_name_species, 1)=="Balanocarpus",
+ list=Genus_correct=="Balanocarpus",
values="Dipterocarpaceae" )) %>%
mutate(Family_correct=replace(Family_correct,
- list=word(Accepted_name_species, 1)=="Cardaminopsis",
+ list=Genus_correct=="Cardaminopsis",
values="Brassicaceae" )) %>%
mutate(Family_correct=replace(Family_correct,
- list=word(Accepted_name_species, 1)=="Carpolepis",
+ list=Genus_correct=="Carpolepis",
values="Myrtaceae" )) %>%
mutate(Family_correct=replace(Family_correct,
- list=word(Accepted_name_species, 1)=="Cathartolinum",
+ list=Genus_correct=="Cathartolinum",
values="Linaceae" )) %>%
mutate(Family_correct=replace(Family_correct,
- list=word(Accepted_name_species, 1)=="Didiscus",
+ list=Genus_correct=="Didiscus",
values="Araliaceae" )) %>%
mutate(Family_correct=replace(Family_correct,
- list=word(Accepted_name_species, 1)=="Grammadenia",
+ list=Genus_correct=="Grammadenia",
values="Primulaceae" )) %>%
mutate(Family_correct=replace(Family_correct,
- list=word(Accepted_name_species, 1)=="Antholoma",
- values="Elaeocarpaceae" ))
+ list=Genus_correct=="Antholoma",
+ values="Elaeocarpaceae" )) %>%
+ mutate(Family_correct=replace(Family_correct,
+ list=Genus_correct=="Odontarrhena",
+ values="Brassicaceae" )) %>%
+ mutate(Family_correct=replace(Family_correct,
+ list=Genus_correct=="Trichinium",
+ values="Amaranthaceae" )) %>%
+ mutate(Family_correct=replace(Family_correct,
+ list=Genus_correct=="Limonium",
+ values="Plumbaginaceae" )) %>%
+ mutate(Family_correct=replace(Family_correct,
+ list=Genus_correct=="Eunanus",
+ values="Phrymaceae" )) %>%
+ mutate(Family_correct=replace(Family_correct,
+ list=Genus_correct=="Sunaptea",
+ values="Dipterocarpaceae" )) %>%
+ mutate(Family_correct=replace(Family_correct,
+ list=Genus_correct=="Aconogonon",
+ values="Polygonaceae" )) %>%
+ mutate(Family_correct=replace(Family_correct,
+ list=Genus_correct=="Cajophora",
+ values="Loasaceae" )) %>%
+ mutate(Family_correct=replace(Family_correct,
+ list=Genus_correct=="Calobota",
+ values="Leguminosae" )) %>%
+ mutate(Family_correct=replace(Family_correct,
+ list=Genus_correct=="Alsine",
+ values="Caryophyllaceae" )) %>%
+ mutate(Family_correct=replace(Family_correct,
+ list=Genus_correct=="Cyanococcus",
+ values="Ericaceae" )) %>%
+ mutate(Family_correct=ifelse(Family_correct %in% c("Papilionaceae", "Fabaceae"),
+ "Leguminosae", Family_correct)) %>%
+ mutate(Family_correct=ifelse(Family_correct=="Asteraceae", "Compositae", Family_correct)) %>%
+ mutate(Family_correct=ifelse(Family_correct=="Unknown", NA, Family_correct))
#Records with missing family info
sum(is.na(Backbone$Family_correct))
```
+### Derive info from other species of the same Genera in the Backbone itself
+Derive family info from each genus in the backbone, and use this info to complement records from the same genera, but with missing family info.
+```{r}
+genera_families <- Backbone %>%
+ filter(Taxonomic_status=="Accepted") %>%
+ dplyr::select(Genus_correct, Family_correct) %>%
+ rename(family=Family_correct) %>%
+ distinct() %>%
+ na.omit() %>%
+ #for some genera there are multiple families assigned
+ # (e.g. in case of unresolved species names )
+ # Extract the family names that occurs most often across each genus
+ group_by(Genus_correct, family) %>%
+ summarize(n=n()) %>%
+ arrange(desc(n)) %>%
+ slice(1) %>%
+ ungroup() %>%
+ dplyr::select(-n)
-### Create field `Name_short`
+# Assign family derived from backbone to other records
+Backbone <- Backbone %>%
+ left_join(genera_families, by="Genus_correct") %>%
+ mutate(Family_correct=ifelse( (is.na(Family_correct) & !is.na(family)),
+ family,
+ Family_correct)) %>%
+ dplyr::select(-family)
+
+#Records with missing family info
+sum(is.na(Backbone$Family_correct))
+```
+
+### Delete records assigned to mushroom families, if any
+```{r}
+mushroom.families <- c("Physalacriaceae", "Clavariaceae","Agaricaceae","Roccellaceae",
+ "Atheliaceae","Meruliaceae","Helotiaceae", "Dacrymycetaceae", "Boletaceae",
+ "Cortinariaceae", "Polyporaceae", "Umbilicariaceae" , "Pleosporaceae",
+ "Leotiaceae","Dermateaceae", "Hymenochaetaceae","Stereaceae","Tremellaceae")
+Backbone <- Backbone %>%
+ filter(!Genus_correct %in% mushroom) %>%
+ filter(!Family_correct %in% mushroom.families)
+```
+
+
+
+## Create field `Name_short`
Shorten names that have more than two words and where the second word is a x. If there is no species name available, fill in with either genus or family info
```{r}
Backbone <- Backbone %>%
@@ -1523,8 +1595,8 @@ sum(is.na(Backbone$Name_correct))
```
-## Create Field `is_vascular_plant`
-Assign all families that belong to `Tracheophyta` to category `is_vascular_species`, based on `The Catalogue of Life`
+## Create field `is_vascular_plant` and `Taxon group`
+Attach phylum information from `The Catalogue of Life`.
```{r}
Backbone <- Backbone %>%
left_join(cat.life %>%
@@ -1532,11 +1604,77 @@ Backbone <- Backbone %>%
distinct() %>%
na.omit() %>%
rename(Family_correct=family),
- by="Family_correct") %>%
- mutate(is_vascular_species=ifelse(phylum=="Tracheophyta", T, F))
+ by="Family_correct")
+```
+Create fields `is_vascular_species` and `Taxon group` based on list of family manually classified, and on phyla from `The Catalogue of Life`.
+Assign all families that belong to `Tracheophyta` to category `is_vascular_species`, based on
+```{r}
+vascular <- c("Leguminosae" , "Alliaceae", "Bombacaceae" ,"Taxodiaceae",
+ "Aceraceae", "Centrolepidaceae","Callitrichaceae" ,"Flacourtiaceae",
+ "Compositae", "Asclepiadaceae", "Papilionaceae","Tiliaceae",
+ "Mimosaceae" , "Xanthorrhoeaceae","Arthropteridaceae",
+ "Valerianaceae", "Grammitidaceae" ,"Anarthriaceae", "Caesalpiniaceae",
+ "Chenopodiaceae", "Corylaceae", "Diervillaceae", "Dipsacaceae","Guttiferae",
+ "Haptanthaceae", "Hymenophyllopsidaceae", "Isoëtaceae","Labiatae",
+ "Lactoridaceae","Lemnaceae","Selaginaceae","Sterculiaceae","Myoporaceae",
+ "Myrsinaceae" ,"Pyrolaceae", "Rhoipteleaceae" ,"Xanthoceraceae")
+lichens <- c("Acarosporaceae" , "Parmeliaceae", "Physciaceae", "Lichinaceae",
+ "Caliciaceae", "Lecanoraceae", "Venturiaceae" ,"Sphaerophoraceae" ,
+ "Verrucariaceae", "Tricholomataceae","Baeomycetaceae",
+ "Catillariaceae" ,"Megasporaceae","Ramalinaceae","Pilocarpaceae" ,
+ "Teloschistaceae","Candelariaceae","Rhizocarpaceae","Lecideaceae",
+ "Icmadophilaceae","Cladoniaceae","Collemataceae","Pannariaceae" ,
+ "Lobariaceae", "Ophioparmaceae" ,"Psoraceae","Stereocaulaceae",
+ "Massalongiaceae","Peltigeraceae","Nephromataceae")
+lichen.genera <- c("Amygdalaria", "Anamylospora", "Arthonia", "Pertusaria", "Pyrenula","Opegrapha",
+ "Ochrolechia", "Graphis", "Micarea", "Porpidia", "Arthopyrenia", "Graphina", "Anisomeridium",
+ "Mycobilimbia","Peltula", "Thelotrema", "Arthothelium", "Diploschistes", "Strigula",
+ "Trichothelium", "Melaspilea", "Phaeographis", "Thelenella", "Chaenothecopsis","Fuscidea",
+ "Dactylospora", "Gyalecta", "Myriotrema", "Placynthium")
+mosses <- c("Pilotrichaceae", "Chonecoleaceae", "Hypopterygiaceae", "Scorpidiaceae",
+ "Balantiopsaceae", "Mesoptychiaceae","Octoblepharaceae" ,"Takakiaceae")
+algae_diatoms <- c("Sargassaceae", "Chordaceae", "Cocconeidaceae", "Desmarestiaceae",
+ "Chordariaceae", "Dinobryaceae", "Diploneidaceae", "Ectocarpaceae",
+ "Fragilariaceae","Sphacelariaceae","Vaucheriaceae" ,
+ "Amphipleuraceae", "Fucaceae", "Gomphonemataceae", "Melosiraceae",
+ "Laminariaceae","Acinetosporaceae" ,"Botryochloridaceae",
+ #diatoms below
+ "Thalassiosiraceae", "Cymbellaceae", "Naviculaceae","Bacillariaceae")
+Backbone <- Backbone %>%
+ mutate(is_vascular_species=ifelse(phylum=="Tracheophyta", T, F)) %>%
+ mutate(is_vascular_species=replace(is_vascular_species,
+ list=Family_correct %in% vascular,
+ values=T)) %>%
+ mutate(`Taxon group`="Unknown") %>%
+ mutate(`Taxon group`=ifelse((!is.na(is_vascular_species) & is_vascular_species==T),
+ "Vascular Plant", `Taxon group`)) %>%
+ mutate(`Taxon group`=replace(`Taxon group`,
+ list=Family_correct %in% lichens,
+ values="Lichen")) %>%
+ mutate(`Taxon group`=replace(`Taxon group`,
+ list=Genus_correct %in% lichen.genera,
+ values="Lichen")) %>%
+ mutate(`Taxon group`=replace(`Taxon group`,
+ list=Family_correct %in% algae_diatoms,
+ values="Alga")) %>%
+ mutate(`Taxon group`=replace(`Taxon group`,
+ list=phylum %in% c("Glaucophyta", "Rhodophyta", "Charophyta", "Chlorophyta"),
+ values="Alga")) %>%
+ mutate(`Taxon group`=replace(`Taxon group`,
+ list=Family_correct %in% mosses,
+ values="Moss")) %>%
+ mutate(`Taxon group`=replace(`Taxon group`,
+ list=phylum %in% c("Bryophyta", "Bryophyta", "Anthocerotophyta" ),
+ values="Moss")) %>%
+ mutate(is_vascular_species=ifelse(`Taxon group` %in% c("Moss", "Alga", "Lichen"),
+ F, is_vascular_species))
+table(Backbone$`Taxon group`, exclude=NULL)
table(Backbone$is_vascular_species, exclude=NULL)
```
+
+
+
## Export Backbone
```{r echo=F}
knitr::kable(Backbone %>%
@@ -1596,6 +1734,7 @@ knitr::kable(Backbone %>%
*Name_short* - First two words of `Name_correct`
*phylum* - As derived from `The Catalogue of Life`
*is_vascular_species* - As derived based on selection of `phylum` from `The Catalogue of Life`
+*`Taxon group`* - Taxon group, as in Turboveg. 'Vascular plant', 'Moss' (include liverworts), 'Lichen', 'Algae', 'Unknown
```{r}
save(Backbone, file="../_output/Backbone3.0.RData")
--
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