removed extraneous fxns and fixed test

diazrenata · Jul 23, 2020 · d2ae99f · d2ae99f
1 parent 64a8248
commit d2ae99f
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Showing 14 changed files with 46,436 additions and 46,657 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -4,8 +4,6 @@ export("%>%")
 export(add_dis)
 export(add_singletons)
 export(add_singletons_dataset)
-export(assign_macdb_manips)
-export(assign_portal_manips)
 export(count_below)
 export(count_elements)
 export(dis_wrapper)
@@ -50,7 +48,6 @@ importFrom(gmp,sum.bigz)
 importFrom(here,here)
 importFrom(magrittr,"%>%")
 importFrom(portalr,plant_abundance)
-importFrom(purrr,map_int)
 importFrom(rmarkdown,render)
 importFrom(tidyr,gather)
 importFrom(vegan,diversity)

diff --git a/R/manips.R b/R/manips.R
diff --git a/analysis/helper_scripts/kernels.R b/analysis/helper_scripts/kernels.R
diff --git a/analysis/helper_scripts/manips_scrap.R b/analysis/helper_scripts/manips_scrap.R
diff --git a/analysis/helper_scripts/mcdb_kernels.R b/analysis/helper_scripts/mcdb_kernels.R
diff --git a/analysis/helper_scripts/scrap.R b/analysis/helper_scripts/scrap.R
diff --git a/man/assign_macdb_manips.Rd b/man/assign_macdb_manips.Rd
diff --git a/man/assign_portal_manips.Rd b/man/assign_portal_manips.Rd
diff --git a/submit_portal_manip_pipeline.sbatch b/submit_portal_manip_pipeline.sbatch
diff --git a/submit_portal_pipeline.sbatch b/submit_portal_pipeline.sbatch
diff --git a/submit_portal_rodents_pipeline.sbatch b/submit_portal_rodents_pipeline.sbatch
diff --git a/tests/testthat/test05_diversity_indices.R b/tests/testthat/test05_diversity_indices.R
@@ -35,7 +35,7 @@ test_that("individual and site DIs work", {
   di_obs <- pull_di(di_many)
 
   expect_true(is.data.frame(di_obs))
-  expect_true(ncol(di_obs) == ncol(di_many) + 7)
+  expect_true(ncol(di_obs) == ncol(di_many) + 19)
   expect_true(nrow(di_obs) == 1)
   expect_true(di_obs$nsamples == nrow(di_many) - 1)
   expect_true(di_obs$source[1] == "observed")