finding and trying to fix another taxize-plant list bug

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: taxonlookup
 Title: A dynamically-updating versioned taxonomic resource for vascular plants
-Version: 0.3.0
+Version: 0.3.1
 Description: This is a taxon lookup table for land plants.  It is built from a set of scripts that dynamically build a versioned genus-family-order-higher taxa lookup table from canonical sources on the web.  It uses semantic versioning to keep track of changes. 
 Depends: R (>= 3.1.0)
 License: BSD_2_clause + file LICENSE

createlookup.R

@@ -76,6 +76,10 @@ matchPlantListFamiliesToApweb<-function(tplGenera){
   tplGenera$order[tplGenera$family %in% c("Leiosporocerotaceae", "Anthocerotaceae", "Notothyladaceae","Phymatocerotaceae","Dendrocerotaceae")]<-"undetermined_hornwort_order"
   #and the liverworts
   tplGenera$order[tplGenera$family %in% read.delim("source_data/liverwortFamilies.txt",header=FALSE)$V1]<-"undetermined_liverwort_order"
+  #temporary: adjusting for a taxize bug
+  tplGenera$order[tplGenera$family=="Eriocaulaceae"]<-"Poales"
+
+  #setting up a seperate column with ApWeb synonymy
   tplGenera$apweb.family<-tplGenera$family
   badFamilies<-unique(tplGenera$apweb.family[!tplGenera$apweb.family%in%apFamilies$acceptedFamilies&tplGenera$group!="Bryophytes"&tplGenera$apweb.family%in%apFamilies$family])
   tplGenera$apweb.family[tplGenera$apweb.family%in%badFamilies]<-apFamilies$synonym[match(tplGenera$apweb.family,apFamilies$family)][tplGenera$apweb.family%in%badFamilies]

man/add_higher_order.Rd

@@ -14,15 +14,17 @@ add_higher_order(lookup = plant_lookup(include_counts = TRUE),
 corresponds to taxonomic order.}
 }
 \description{
-Augment the genus-family-order lookup table with plant higher order data, from
+Augment the genus-family-order lookup table with plant higher taxa data, from
 http://datadryad.org/resource/doi:10.5061/dryad.63q27
 }
 \details{
 Data for the higher-level taxonomy lookup (http://datadryad.org/resource/doi:10.5061/dryad.63q27.2/1.1) compiled by Dave Tank and colleagues
 
-The format of the lookup is that higher nodes are columns within the data.frame.
+Because of the currently non-nested structure of higher clade information for plants,
+the format of the lookup is also not nested.
+In the lookup the higher nodes are columns within the data.frame.
 If a genus is a descendent of a particular node, the row for that genus repeats
-the node name.  If a genus is not a descendent of that particular node, the cell is left blank.
+the node name (which is also the column name).  If a genus is not a descendent of that particular node, the cell is left blank.
 }
 \examples{
 ##' # see the format of the resource

man/plant_lookup.Rd

@@ -8,7 +8,7 @@
 \title{Plant lookup table}
 \usage{
 plant_lookup(version = plant_lookup_version_current(),
-  include_counts = FALSE)
+  include_counts = FALSE, family.tax = "apweb")
 
 plant_lookup_versions(type = "local")
 
@@ -27,6 +27,11 @@ to the package if you have never downloaded the data before.  With
 "accepted" species within each genus counts as
 \code{number.of.species}.}
 
+\item{family.tax}{= the value "ap.web" will return the family names from apweb
+otherwise the lookup will include the family names from the plant list.
+Currently there are 8 family names that differ between the two sources.
+\code{family.tax}.}
+
 \item{type}{Type of version to return: options are "local"
 (versions installed locally) or "github" (versions available on
 github).  With any luck, "github" is a superset of "local".}
@@ -37,22 +42,23 @@ number of species in each genus.  Data persists across package
 installations.
 }
 \details{
-The data for this lookup primarily comes from two sources:
+The data within this lookup table comes from two sources:
 
 1. The Plant List v1.1. (http://www.theplantlist.org/) for
 accepted genera to families and species richness within each
-genera.  Note that we do not consider hybrids (e.g. Genus x
-species) as species for this count while the plant list summary
+genera.  Note that we do not consider hybrids (e.g. Genus X
+species) as distinct species for this count while the plant list summary
 statistics do, so the the counts from this package will not line up exactly
 with the ones on the TPL website.
 
-2. APWeb (http://www.mobot.org/MOBOT/research/APweb/) for family
-level synonymies and family-to-order for all vascular plant families.
+2. APWeb (http://www.mobot.org/MOBOT/research/APweb/) for family-level
+synonymies and family-to-order for all vascular plant families.
 Note that there is not currently order-level information available for Bryophytes.
 
-3. We correct some spelling
-errors, special character issues, genera listed in multiple families,
-and a few other errors from The Plant List.
+These data are then currated--we correct some spelling
+errors, special character issues, genera listed in multiple families, family-level synonomy,
+and other issues that arise in assembling a resources like this.  Details of the curration
+are at https://github.com/wcornwell/taxonlookup
 }
 \examples{
 #