Merge pull request #18 from inbo/tidyverse

Tidyverse
inbo · Oct 2, 2018 · d8beeea · d8beeea
2 parents 2f502f9 + 2a508ee
commit d8beeea
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Showing 42 changed files with 288 additions and 1,309 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,9 +1,16 @@
 Package: n2khelper
 Title: Auxiliary Functions for the Analysis and Reporting of the Natura 2000
     Monitoring
-Version: 0.4.1.1
-Date: 2017-11-25
-Authors@R: c(person("Thierry", "Onkelinx", email = "thierry.onkelinx@inbo.be", role = c("aut", "cre")))
+Version: 0.4.2
+Date: 2018-10-02
+Authors@R: c(
+  person(
+    "Thierry", "Onkelinx", role = c("aut", "cre"), 
+    email = "thierry.onkelinx@inbo.be", 
+    comment = c(ORCID = "0000-0001-8804-4216")),
+  person(
+    family = "Research Institute for Nature and Forest",
+    role = c("cph", "fnd"), email = "info@inbo.be"))
 Description: Auxiliary functions for analysing Natura 2000 monitoring data.
 URL: https://doi.org/10.5281/zenodo.835732
 BugReports: https://github.com/inbo/n2khelper/issues
@@ -26,14 +33,11 @@ LazyData: true
 Suggests:
     testthat
 Collate:
-    'gitConnection_class.R'
-    'auto_commit.R'
     'check_character.R'
     'check_dataframe_covariate.R'
     'check_dataframe_variable.R'
     'check_dbtable.R'
     'check_dbtable_variable.R'
-    'check_git_repo.R'
     'check_id.R'
     'check_path.R'
     'check_single_character.R'
@@ -46,20 +50,14 @@ Collate:
     'get_nbn_key.R'
     'get_nbn_key_multi.R'
     'get_nbn_name.R'
+    'gitConnection_class.R'
     'git_connect.R'
     'git_connection.R'
-    'git_recent.R'
-    'git_sha.R'
     'is_chartor.R'
-    'is_git_repo.R'
-    'list_files_git.R'
     'match_nbn_key.R'
     'odbc_connect.R'
     'odbc_get_id.R'
     'odbc_get_multi_id.R'
     'odbc_insert.R'
-    'read_delim_git.R'
     'read_object_environment.R'
-    'remove_files_git.R'
-    'write_delim_git.R'
 RoxygenNote: 6.0.1
diff --git a/NAMESPACE b/NAMESPACE
@@ -5,7 +5,6 @@ export(check_dataframe_covariate)
 export(check_dataframe_variable)
 export(check_dbtable)
 export(check_dbtable_variable)
-export(check_git_repo)
 export(check_id)
 export(check_path)
 export(check_single_character)
@@ -15,31 +14,21 @@ export(check_single_posix)
 export(check_single_probability)
 export(connect_nbn)
 export(connect_result)
+export(connect_ut_db)
 export(cut_date)
 export(get_nbn_key)
 export(get_nbn_key_multi)
 export(get_nbn_name)
 export(git_connect)
 export(git_connection)
 export(is.chartor)
-export(is_git_repo)
 export(match_nbn_key)
 export(odbc_connect)
 export(odbc_get_id)
 export(odbc_get_multi_id)
 export(odbc_insert)
 export(read_object_environment)
 exportClasses(gitConnection)
-exportMethods(auto_commit)
-exportMethods(git_recent)
-exportMethods(git_sha)
-exportMethods(list_files_git)
-exportMethods(read_delim_git)
-exportMethods(remove_files_git)
-exportMethods(write_delim_git)
-importClassesFrom(git2r,cred_ssh_key)
-importClassesFrom(git2r,cred_user_pass)
-importClassesFrom(git2r,git_repository)
 importFrom(DBI,dbExistsTable)
 importFrom(DBI,dbGetInfo)
 importFrom(DBI,dbGetQuery)
@@ -60,27 +49,25 @@ importFrom(dplyr,"%>%")
 importFrom(dplyr,collect)
 importFrom(dplyr,count_)
 importFrom(dplyr,data_frame)
+importFrom(dplyr,filter)
 importFrom(dplyr,filter_)
 importFrom(dplyr,funs)
 importFrom(dplyr,group_by_)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,mutate_)
 importFrom(dplyr,mutate_each_)
+importFrom(dplyr,select)
 importFrom(dplyr,select_)
 importFrom(dplyr,semi_join)
 importFrom(dplyr,slice_)
 importFrom(dplyr,src_postgres)
 importFrom(dplyr,summarise_)
 importFrom(dplyr,tbl)
 importFrom(dplyr,ungroup)
-importFrom(git2r,add)
-importFrom(git2r,commit)
 importFrom(git2r,config)
 importFrom(git2r,cred_ssh_key)
 importFrom(git2r,cred_user_pass)
-importFrom(git2r,hashfile)
-importFrom(git2r,head)
-importFrom(git2r,push)
+importFrom(git2r,in_repository)
 importFrom(git2r,repository)
 importFrom(lazyeval,interp)
 importFrom(lubridate,is.Date)
@@ -89,17 +76,18 @@ importFrom(lubridate,year)
 importFrom(methods,new)
 importFrom(methods,setClass)
 importFrom(methods,setClassUnion)
-importFrom(methods,setGeneric)
-importFrom(methods,setMethod)
+importFrom(methods,setOldClass)
 importFrom(methods,setValidity)
 importFrom(plyr,ddply)
+importFrom(rlang,.data)
+importFrom(rlang,UQ)
 importFrom(stats,aggregate)
 importFrom(stats,as.formula)
 importFrom(stats,na.fail)
+importFrom(tidyr,spread)
 importFrom(tidyr,spread_)
 importFrom(utils,file_test)
-importFrom(utils,read.delim)
-importFrom(utils,read.table)
-importFrom(utils,sessionInfo)
+importFrom(utils,hasName)
+importFrom(utils,head)
 importFrom(utils,tail)
 importFrom(utils,write.table)
diff --git a/R/auto_commit.R b/R/auto_commit.R
diff --git a/R/check_git_repo.R b/R/check_git_repo.R
diff --git a/R/connect_result.R b/R/connect_result.R
@@ -34,3 +34,26 @@ connect_result <- function(username, password, develop = TRUE){
 connect_nbn <- function(){
   odbcDriverConnect(connection = nbn.dsn)
 }
+
+#' connect to the unit test database
+#' @inheritParams dplyr::src_postgres
+#' @export
+#' @importFrom dplyr src_postgres
+connect_ut_db <- function(
+  host = "localhost",
+  dbname = "n2kunittest",
+  user = "unittest_analysis",
+  password = "unittest",
+  port = 5432,
+  ...
+){
+  # nocov start
+  src_postgres(
+    host = host,
+    dbname = dbname,
+    user = user,
+    password = password,
+    ...
+  )
+  # nocov end
+}
diff --git a/R/cut_date.R b/R/cut_date.R
@@ -7,7 +7,7 @@
 #' @export
 #' @importFrom plyr ddply
 #' @importFrom lubridate year is.Date is.POSIXt
-#' @importFrom utils tail
+#' @importFrom utils tail head
 #' @examples
 #' x <- as.POSIXct(
 #'     c("2015-01-01", "2014-01-02", "2013-01-03", "2012-01-31", "2011-02-01", "2012-12-31")