In wallace: A Modular Platform for Reproducible Modeling of Species Niches and Distributions

```{asis, echo = {{occs_queryDb_knit & !occs_citation_knit}}, eval = {{occs_queryDb_knit & !occs_citation_knit}}, include = {{occs_queryDb_knit & !occs_citation_knit}}}

Obtain Occurrence Data

You searched the r "{{occDb_rmd}}" database for r "{{spName}}", limited to r {{occNum_rmd}} records. You decided to remove occurrences without uncertainty information? r {{uncertainty_rmd}}

```{asis, echo = {{occs_queryDb_knit & occs_citation_knit}}, eval = {{occs_queryDb_knit & occs_citation_knit}}, include = {{occs_queryDb_knit & occs_citation_knit}}}
### Obtain Occurrence Data
You searched the `r "{{occDb_rmd}}"` database for *`r "{{spName}}"`*, limited to `r {{occNum_rmd}}` records, using the citation option. You decided to remove occurrences without uncertainty information? `r {{uncertainty_rmd}}`

```r}, include = {{occs_queryDb_knit & !occs_citation_knit}}}

Query selected database for occurrence records

queryDb_{{spAbr}} <- occs_queryDb( spNames = "{{spName}}", occDb = "{{occDb_rmd}}", occNum = {{occNum_rmd}}, RmUncertain = {{uncertainty_rmd}}) occs_{{spAbr}} <- queryDb_{{spAbr}}${{sp}}$cleaned

```r}, include = {{occs_queryDb_knit & occs_citation_knit}}}
# Query selected database for occurrence records
queryDb_{{spAbr}} <- occs_queryDb(
  spNames = "{{spName}}", 
  occDb = "{{occDb_rmd}}", 
  doCitations = {{doCitations_rmd}},
  gbifUser = "{{gbifUser_rmd}}", 
  gbifEmail = "{{gbifEmail_rmd}}",
  # Please type your GBIF password 
  gbifPW = "",
  RmUncertain = {{uncertainty_rmd}})
occs_{{spAbr}} <- queryDb_{{spAbr}}${{sp}}$cleaned
# Print DOI and date of your search 
queryDb_{{spAbr}}${{sp}}$citation

wallace documentation built on April 4, 2025, 5:21 a.m.