Merge pull request #5 from NorwegianVeterinaryInstitute/develop

NVIdb v0.5.2

Author: PetterHopp

.Rbuildignore

@@ -14,3 +14,4 @@
 ^\.git$
 ^\.gitignore$
 ^\.Rhistory$
+^CODE_OF_CONDUCT\.md$

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the overall
+community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards
+of acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies
+when an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at [INSERT CONTACT
+METHOD]. All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series of
+actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or permanent
+ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior, harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within the
+community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0,
+available at https://www.contributor-covenant.org/version/2/0/
+code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at https://
+www.contributor-covenant.org/translations.

CONTRIBUTING.md

@@ -2,7 +2,7 @@
 
 Thank you for taking interest in contributing to *NVIdb*. 
 
-There are four ways you can contribute to the development of *NVIdb*: reporting a bug, fixing documentation errors, contributing new code, or commenting on issues/pull requests. Note that the majority of these activities do not require you to be proficient in R.
+There are several ways you can contribute to the development of *NVIdb*: reporting a bug, fixing documentation errors, contributing new code, or commenting on issues/pull requests. Note that the majority of these activities do not require you to be proficient in R.
 
 All new code or documentation must be approved by @PetterHopp. 
 
@@ -106,16 +106,21 @@ If you want to contribute code, you are welcome to do so. Please try to adhere t
 
 *   You should add yourself as a contributor to the `DESCRIPTION`.
 
-*   If you can, also write a test. *NVIdb* uses [testthat](https://cran.r-project.org/package=testthat) for tests.
-
-*   If you're adding new parameters or a new function, you'll also need
+*   If you're adding a new function or new arguments to an existing function, you'll also need
     to document them. *NVIdb* uses [roxygen2](https://cran.r-project.org/package=roxygen2), with
 [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html),
 for documentation. Make sure to re-run `devtools::document()` on the code before submitting. 
+
+*   *NVIdb* uses functions from [checkmate](https://CRAN.R-project.org/package=checkmate) package  for argument checking. Adding argument checking for new functions and/or arguments will be highly appreciated.
 
-*   Also run `devtools::check()` to make sure your function doesn't imply downstream errors or warnings. 
+*   If you can, also write a test. *NVIdb* uses [testthat](https://cran.r-project.org/package=testthat) for tests.
 
+*   Also run `devtools::check()` to make sure your function doesn't imply downstream errors or warnings. 
 
+### Code of Conduct
+  
+  Please note that the NVIdb project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.
+  
 ### References
 Based on [CONTRIBUTING to poppr](https://github.com/grunwaldlab/poppr/blob/main/CONTRIBUTING.md) by @zkamvar and [CONTRIBUTING to dittodb](https://raw.githubusercontent.com/ropensci/dittodb/main/CONTRIBUTING.mdd) by @jonkeane.
 

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: NVIdb
 Title: Facilitating use of Norwegian Veterinary Institute's databases
-Version: 0.5.1
-Date: 2021-04-08
+Version: 0.5.2
+Date: 2021-04-24
 Authors@R: 
   c(person(given = "Petter",
            family = "Hopp",
@@ -19,8 +19,9 @@ Description: The Norwegian Veterinary Institute has several internal databases a
     package comprises four categories of functions: 
     1) Manage credentials (i.e. password and username), 
     2) Login functions for database services, 
-    3) Read, copy and update different in-house data registers,
-    4) Translate codes into descriptions.
+    3) Read, copy and update different in-house data registers, 
+    4) Translate codes into descriptions. 
+    NVIdb is dependant of NVIconfig which has to be installed manually from GitHub.
 URL: https://github.com/NorwegianVeterinaryInstitute/NVIdb
 BugReports: https://github.com/NorwegianVeterinaryInstitute/NVIdb/issues
 Depends: R (>= 3.5.0)

NEWS

@@ -1,3 +1,13 @@
+NVIdb 0.5.2 - (2021-04-24)
+--------------------------
+
+Bug fixes:
+
+- The selection statement when selecing PJS-codes, for example hensiktkode, is now correct also in he case that only codes with sub-levels are included.
+
+- Corrected add_kommune_fylke so that Møre og Romsdal and Nordland are added correctly to fylkenr 15 and 18, respectively, in the case that gjeldende_fylkenr and/or gjeldende_fylke are added to fylkenr
+
+
 NVIdb 0.5.1 - (2021-04-08)
 --------------------------
 

R/add_kommune_fylke.R

@@ -112,7 +112,7 @@ add_kommune_fylke <- function(data,
   code_2_new <- unique(translation_table[, c(unname(code_column), unname(new_column))])
 
   if (code_column == "fylkenr") {
-    code_2_new <- merge(code_2_new, translation_table[, c(new_column, "komnr")], by = c(new_column))
+    code_2_new <- merge(code_2_new, translation_table[, c("fylkenr", new_column, "komnr")], by = c("fylkenr", new_column))
     code_2_new <- stats::aggregate(stats::as.formula(paste("komnr", "~", paste(c(code_column, new_column), collapse = " + "))), data = code_2_new, FUN = length)
 
     # For fylkenr, select the fylke where most kommuner is within the fylke. This to avoid fylkenr to be translated to fylker

R/build_query_hensikt.R

@@ -22,7 +22,7 @@
 #'
 
 build_query_hensikt <- function(year, hensikt, db = "PJS") {
-
+  
   # Argument checking
   # Object to store check-results
   checks <- checkmate::makeAssertCollection()
@@ -32,38 +32,38 @@ build_query_hensikt <- function(year, hensikt, db = "PJS") {
   checkmate::assert_choice(db, choices = c("PJS"), add = checks)
   # Report check-results
   checkmate::reportAssertions(checks)
-
+  
   select_year <- NVIdb::build_sql_select_year(year = year, varname = "aar")
-
+  
   select_hensikt <- NVIdb::build_sql_select_code(values = hensikt, varname = "hensiktkode")
   # select_hensikt <- paste0("hensiktkode in ('", paste(hensikt, collapse = "', '"), "')")
-
+  
   selection_v2_sak_m_res <- paste("SELECT * FROM v2_sak_m_res",
-                                   "WHERE", select_year , "AND",
-                                   "(",
-                                   select_hensikt,
-                                   ")" )
-
+                                  "WHERE", select_year , "AND",
+                                  "(",
+                                  select_hensikt,
+                                  ")" )
+  
   select_year <- NVIdb::build_sql_select_year(year = year, varname = "sak.aar")
-
+  
   select_hensikt <- NVIdb::build_sql_select_code(values = hensikt, varname = "sak.hensiktkode")
   # select_hensikt <- paste0("sak.hensiktkode in ('", paste(hensikt, collapse = "', '"), "')")
-
+  
   selection_sakskonklusjon <- paste("SELECT v_sakskonklusjon.*,",
-                                             "sak.mottatt_dato, sak.uttaksdato, sak.sak_avsluttet, sak.hensiktkode,",
-                                             "sak.eier_lokalitetstype, sak.eier_lokalitetnr",
-                                     "FROM v_innsendelse AS sak",
-                                     "INNER JOIN v_sakskonklusjon",
-                                     "ON (v_sakskonklusjon.aar = sak.aar AND",
-                                         "v_sakskonklusjon.ansvarlig_seksjon = sak.ansvarlig_seksjon AND",
-                                         "v_sakskonklusjon.innsendelsesnummer = sak.innsendelsesnummer)",
-                                     "WHERE", select_year, "AND (",
-                                     select_hensikt,
-                                     ")")
-
+                                    "sak.mottatt_dato, sak.uttaksdato, sak.sak_avsluttet, sak.hensiktkode,",
+                                    "sak.eier_lokalitetstype, sak.eier_lokalitetnr",
+                                    "FROM v_innsendelse AS sak",
+                                    "INNER JOIN v_sakskonklusjon",
+                                    "ON (v_sakskonklusjon.aar = sak.aar AND",
+                                    "v_sakskonklusjon.ansvarlig_seksjon = sak.ansvarlig_seksjon AND",
+                                    "v_sakskonklusjon.innsendelsesnummer = sak.innsendelsesnummer)",
+                                    "WHERE", select_year, "AND (",
+                                    select_hensikt,
+                                    ")")
+  
   select_statement <- list("selection_v2_sak_m_res" = selection_v2_sak_m_res,
                            "selection_sakskonklusjon" = selection_sakskonklusjon)
-
+  
   return(select_statement)
 }