Added fancy stx_query() function

R/example_code.R

@@ -0,0 +1,94 @@
+# filter_dt() -----------------------------------
+taxa.dt = stx_taxa()
+colnames(taxa.dt) # inspect column names to filter for
+
+# Specify taxonomy columns for which tax filtering can be applied.
+# Make sure that list names match the column names in your data table!
+var_ls = list(
+  family = "Cyprinidae",
+  genus  = c("Daphnia","Ceriodaphnia")
+)
+
+tax.out = filter_dt( taxa.dt, var_ls, silent = FALSE)
+View(tax.out) # inspect the output
+
+
+# stx_query() ---------------------------------
+
+# Example 1) - Basic stx_query() call
+# will return results filtered for default endpoint_group = c("XX50", "NOEX", "LOEX") and duration_unit = "h"
+dt = stx_query(verbose = T)
+
+# If you wish to filter for different endpoint groups, you can specify them in the query.
+stx_catalog()$endpoint_group # to view available endpoint groups
+dt1 = stx_query(endpoint_group = c("Bioconc","MATC","MCIG"))
+
+# if you wish to keep all duration_unit and endpoint_groups, set them to NULL. 
+dt2 = stx_query(duration_unit = NULL, endpoint_group = NULL, verbose = T) 
+# including "NR" (not reported) values. This is everything you can retrieve via stx_data() as well. 
+dt3 = stx_query(duration_unit = NULL, endpoint_group = NULL, verbose = T, rm_na = F) 
+
+
+# Example 2) - Filter for specific taxonomic groups
+# Filter for fish and algae for an exposure duration of 12 to 120 hours and concentration unit in g/l for endpoint group XX50 (50% effect/lethality values)
+stx_catalog()$group # to get an idea about available taxonomic groups
+stx_catalog()$concentration_unit
+dt4 = stx_query(
+  verbose = T, 
+  endpoint_group = "XX50",
+  duration = c(12, 120),
+  concentration_unit = "g/l", 
+  tax_group  = c("fish","algae")
+)
+
+
+# Example 3) - Filter for specific genus and chemical compounds + append reference data
+# make sure to extract only EC50/LC50 values from 12 - 96 hours and of comparable concentration units
+dt5 = stx_query(
+  verbose = T,
+  cas_number = c("1071-83-6","63-25-2","138261-41-3"), # glyphosate, carbaryl and imidacloprid 
+  endpoint_group = "XX50", # to get only 50% effect/lethality values
+  duration = c(12, 96),
+  concentration_unit = "g/l", 
+  tax_genus = c("Danio","Daphnia","Ceriodaphnia","Chironomus"),
+  include_reference = TRUE
+)
+
+
+# Example 4) - filter for specific taxonomic families and append reference data + more taxonomic lineage information
+stx_catalog()$family # get an idea about which family to use by inspecting the taxa catalog
+colnames(stx_taxa())[-1] # all possible taxonomic columns to extract from stx_taxa()
+
+dt6 = stx_query(
+  verbose = T, 
+  endpoint_group = "XX50",
+  duration = c(12, 120),
+  concentration_unit = "g/l", 
+  tax_family = c("Cyprinidae","Salmonidae","Daphniidae"),
+  tax_columns = c("group","taxon","genus","family","order","class","habitat"), # to get more taxonomic lineage information
+  include_reference = TRUE
+)
+
+
+# Example 5) - Specific data selection
+# get ALL LC50 values for 96 - 120 h of exposure for zebra fish (Danio rerio)
+danio = stx_query(
+  endpoint_group = "XX50",
+  duration = c(96, 120),
+  effect = "mortality",
+  concentration_unit = "g/l",
+  concentration_type = "active ingredient",
+  tax_genus = "Danio",
+  include_reference = TRUE
+)
+
+# get ALL LC50 values for 24 - 48 h of exposure for Daphnia
+dmag = stx_query(
+  endpoint_group = "XX50",
+  duration = c(24, 48),
+  effect = "mortality",
+  concentration_unit = "g/l",
+  concentration_type = "active ingredient",
+  tax_genus = "Daphnia",
+  include_reference = TRUE
+)