From baa633a54a9bc4840b8a766710558de5f44b9e49 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 28 Feb 2025 19:06:21 +0100
Subject: [PATCH 01/13] typo
---
gitlab-ci/unittests.gitlab-ci.yml | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/gitlab-ci/unittests.gitlab-ci.yml b/gitlab-ci/unittests.gitlab-ci.yml
index d7cf5f9..049611f 100644
--- a/gitlab-ci/unittests.gitlab-ci.yml
+++ b/gitlab-ci/unittests.gitlab-ci.yml
@@ -4,14 +4,14 @@
script:
- Rscript -e 'pak::pkg_install(pkg = c("XML"), upgrade = FALSE)'
- |
- r -e "devtools::load_all();
+ Rscript -e 'devtools::load_all();
options(stacomiR.dbname = "'$PG_DB'",
stacomiR.host = "'$PG_HOST'",
stacomiR.port = "'$PG_PORT'",
stacomiR.user = "'$PG_USER'",
- stacomiR.password ="'PG_USER_PASSWORD'");
- test <- capture.output(devtools::test(reporter='junit')) ;
- XML::saveXML(XML::xmlParse(test[grep('?xml version', test):length(test)]), file = 'public/test.xml')"
+ stacomiR.password ="'$PG_USER_PASSWORD'");
+ test <- capture.output(devtools::test(reporter="junit")) ;
+ XML::saveXML(XML::xmlParse(test[grep("?xml version", test):length(test)]), file = "public/test.xml")''
artifacts:
when: always
# You should set the job that uploads the screenshot to
--
GitLab
From 30c66722194152c7d5294f50f8267dacfebfca1b Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 28 Feb 2025 20:12:47 +0100
Subject: [PATCH 02/13] test
---
gitlab-ci/unittests.gitlab-ci.yml | 17 ++++++++---------
1 file changed, 8 insertions(+), 9 deletions(-)
diff --git a/gitlab-ci/unittests.gitlab-ci.yml b/gitlab-ci/unittests.gitlab-ci.yml
index 049611f..17d6e1a 100644
--- a/gitlab-ci/unittests.gitlab-ci.yml
+++ b/gitlab-ci/unittests.gitlab-ci.yml
@@ -5,22 +5,21 @@
- Rscript -e 'pak::pkg_install(pkg = c("XML"), upgrade = FALSE)'
- |
Rscript -e 'devtools::load_all();
- options(stacomiR.dbname = "'$PG_DB'",
- stacomiR.host = "'$PG_HOST'",
- stacomiR.port = "'$PG_PORT'",
- stacomiR.user = "'$PG_USER'",
- stacomiR.password ="'$PG_USER_PASSWORD'");
- test <- capture.output(devtools::test(reporter="junit")) ;
- XML::saveXML(XML::xmlParse(test[grep("?xml version", test):length(test)]), file = "public/test.xml")''
+ options(stacomiR.dbname = "'${PG_DB}'",
+ stacomiR.host = "'${PG_HOST}'",
+ stacomiR.port = "'${PG_PORT}'",
+ stacomiR.user = "'${PG_USER}'",
+ stacomiR.password ="'${PG_USER_PASSWORD}'");
+ devtools::test(reporter=JunitReporter$new(file = "junit_result.xml"));'
artifacts:
when: always
# You should set the job that uploads the screenshot to
#artifacts:when: always so that it still uploads a screenshot
#when a test fails.
paths:
- - public/test.xml
+ - check
reports:
- junit: public/test.xml
+ junit: check/stacomir.Rcheck/tests/testthat/junit_result.xml
expire_in: 30 days
# en dev
--
GitLab
From fa4b564978bd3f9962ee3cd73abf39f2b3eb1941 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 28 Feb 2025 20:20:31 +0100
Subject: [PATCH 03/13] up
---
.gitignore | 1 +
gitlab-ci/unittests.gitlab-ci.yml | 3 ++-
2 files changed, 3 insertions(+), 1 deletion(-)
diff --git a/.gitignore b/.gitignore
index 479a553..66f9146 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,3 +9,4 @@ stacomir.Rproj
/~import_coe20092015.csv
.dbeaver/project-settings.json
docs
+tests/testthat/junit_result.xml
diff --git a/gitlab-ci/unittests.gitlab-ci.yml b/gitlab-ci/unittests.gitlab-ci.yml
index 17d6e1a..a5dfd47 100644
--- a/gitlab-ci/unittests.gitlab-ci.yml
+++ b/gitlab-ci/unittests.gitlab-ci.yml
@@ -3,6 +3,7 @@
stage: test
script:
- Rscript -e 'pak::pkg_install(pkg = c("XML"), upgrade = FALSE)'
+ - Rscript -e 'cat("PG_HOST = "'${PG_HOST}'"\n")'
- |
Rscript -e 'devtools::load_all();
options(stacomiR.dbname = "'${PG_DB}'",
@@ -19,7 +20,7 @@
paths:
- check
reports:
- junit: check/stacomir.Rcheck/tests/testthat/junit_result.xml
+ junit: tests/testthat/junit_result.xml
expire_in: 30 days
# en dev
--
GitLab
From 2e50e05be731503764d57a56de44620e153a75b3 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 28 Feb 2025 20:27:28 +0100
Subject: [PATCH 04/13] test
---
gitlab-ci/codecov.gitlab-ci.yml | 10 +++++-----
gitlab-ci/unittests.gitlab-ci.yml | 2 +-
2 files changed, 6 insertions(+), 6 deletions(-)
diff --git a/gitlab-ci/codecov.gitlab-ci.yml b/gitlab-ci/codecov.gitlab-ci.yml
index cbd6072..a4eb6cd 100644
--- a/gitlab-ci/codecov.gitlab-ci.yml
+++ b/gitlab-ci/codecov.gitlab-ci.yml
@@ -7,11 +7,11 @@
- Rscript -e 'pak::pak(pkg = ".", upgrade = FALSE)'
- |
Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all();
- options(stacomiR.dbname = "'$PG_DB'",
- stacomiR.host = "'$PG_HOST'",
- stacomiR.port = "'$PG_PORT'",
- stacomiR.user = "'$PG_USER'",
- stacomiR.password ="'PG_USER_PASSWORD'");
+ options(stacomiR.dbname = "'${PG_DB}'",
+ stacomiR.host = "'${PG_HOST}'",
+ stacomiR.port = "'${PG_PORT}'",
+ stacomiR.user = "'${PG_USER}'",
+ stacomiR.password ="'${PG_USER_PASSWORD}'");
covr::gitlab(quiet = FALSE)'
coverage: '/Coverage: \d+\.\d+/'
artifacts:
diff --git a/gitlab-ci/unittests.gitlab-ci.yml b/gitlab-ci/unittests.gitlab-ci.yml
index a5dfd47..4cf2f7f 100644
--- a/gitlab-ci/unittests.gitlab-ci.yml
+++ b/gitlab-ci/unittests.gitlab-ci.yml
@@ -3,7 +3,7 @@
stage: test
script:
- Rscript -e 'pak::pkg_install(pkg = c("XML"), upgrade = FALSE)'
- - Rscript -e 'cat("PG_HOST = "'${PG_HOST}'"\n")'
+ - Rscript -e 'cat("PG_HOST = '${PG_HOST}'\n")'
- |
Rscript -e 'devtools::load_all();
options(stacomiR.dbname = "'${PG_DB}'",
--
GitLab
From a253f99e2fc3a95c69d53b7de0ed1f1722034338 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 28 Feb 2025 21:23:42 +0100
Subject: [PATCH 05/13] up
---
gitlab-ci/unittests.gitlab-ci.yml | 2 --
tests/testthat/helper.R | 14 +++++++-------
2 files changed, 7 insertions(+), 9 deletions(-)
diff --git a/gitlab-ci/unittests.gitlab-ci.yml b/gitlab-ci/unittests.gitlab-ci.yml
index 4cf2f7f..b67e0b5 100644
--- a/gitlab-ci/unittests.gitlab-ci.yml
+++ b/gitlab-ci/unittests.gitlab-ci.yml
@@ -17,8 +17,6 @@
# You should set the job that uploads the screenshot to
#artifacts:when: always so that it still uploads a screenshot
#when a test fails.
- paths:
- - check
reports:
junit: tests/testthat/junit_result.xml
expire_in: 30 days
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index f9ee689..7fa4135 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -3,13 +3,13 @@
# this file is called before testhat so funcion will be available in all test
# https://testthat.r-lib.org/articles/test-fixtures.html#withr-defer-
# could have used with_envvar and local_envvar but had to set them each time
-options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host = "localhost",
- stacomiR.port = "5432",
- stacomiR.user = "stacomi_test",
- stacomiR.password = "stacomi_test"
-)
+# options(
+# stacomiR.dbname = "bd_contmig_nat",
+# stacomiR.host = "localhost",
+# stacomiR.port = "5432",
+# stacomiR.user = "stacomi_test",
+# stacomiR.password = "stacomi_test"
+# )
password <- getOption("stacomiR.password") # if not set will be ""
dbname <- getOption("stacomiR.dbname") # if not set will be ""
user <- getOption("stacomiR.user")
--
GitLab
From bbad86252ea72db8083aa3dfaeb4f283599f1dda Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Fri, 28 Feb 2025 23:39:35 +0100
Subject: [PATCH 06/13] up
---
R/stacomi.R | 203 ++++++++++----------
tests/testthat/helper.R | 8 +-
tests/testthat/test-03-report_df.R | 168 ++++++++--------
tests/testthat/test-05-report_sample_char.R | 6 +-
4 files changed, 195 insertions(+), 190 deletions(-)
diff --git a/R/stacomi.R b/R/stacomi.R
index f4d5a55..253e23a 100644
--- a/R/stacomi.R
+++ b/R/stacomi.R
@@ -1,88 +1,93 @@
#'
-#'
+#'
#' Internal function, tests the connection and if it works loads the stacomi interface
#' @note \code{base} is copied by stacomi into envir_stacomi. Same for \code{database_expected}
-#'
+#'
#' @param ... Other arguments
#' @return Nothing
#' @author Cedric Briand \email{cedric.briand@eptb-vilaine.fr}
#' @keywords internal
load_stacomi <- function(...) {
-
- # assigned when passing through stacomi
- database_expected <- get("database_expected", envir_stacomi) # logical true or false
-
- if (database_expected) {
- sch <- get_schema()
- dbname <- options("stacomiR.dbname")[[1]]
- host <- options("stacomiR.host")[[1]]
- port <- options("stacomiR.port")[[1]]
- user <- options("stacomiR.user")[[1]]
- password <- options("stacomiR.password")[[1]]
- if (user=="") {
- # this is the default options at start
- # if interactive will try to set the options upon loading
- if (interactive()){
- user <- readline(prompt="Enter user: ")
- options("stacomiR.user"=user)
- password <- readline(prompt="Enter password: ")
- options("stacomiR.password"=password)
- } else {
- user <- "group_stacomi"
- password <- "group_stacomi"
- warning('no user set by default, reverted to user <- "postgres" and password <- "postgres",
+ # assigned when passing through stacomi
+ database_expected <- get("database_expected", envir_stacomi) # logical true or false
+
+ if (database_expected) {
+ sch <- get_schema()
+ dbname <- options("stacomiR.dbname")[[1]]
+ host <- options("stacomiR.host")[[1]]
+ port <- options("stacomiR.port")[[1]]
+ user <- options("stacomiR.user")[[1]]
+ password <- options("stacomiR.password")[[1]]
+ if (user == "") {
+ # this is the default options at start
+ # if interactive will try to set the options upon loading
+ if (interactive()) {
+ user <- readline(prompt = "Enter user: ")
+ options("stacomiR.user" = user)
+ password <- readline(prompt = "Enter password: ")
+ options("stacomiR.password" = password)
+ } else {
+ user <- "group_stacomi"
+ password <- "group_stacomi"
+ warning('no user set by default, reverted to user <- "postgres" and password <- "postgres",
you can change it with options("stacomiR.user"=user) and options("stacomiR.password"=password)')
- }
- }
-
-
- con = new("ConnectionDB")
- e = expression(con <- connect(con))
- con = tryCatch(eval(e), error = function(e) e)
- if ("Rcpp::exception"%in%class(con)){
- cat(con$message)
- test <- FALSE
- } else {
- test <- TRUE
- pool::poolClose(con@connection)
- }
-
-
-
- # second test to check that the database is working OK
-
- if (test) {
- requete = new("RequeteDB")
- requete@sql = paste0("select count(*) from ref.tr_taxon_tax")
- message <- NULL
- requete <- stacomirtools::query(requete)
- if (grepl("Error",requete@status)) stop(requete@status)
- if (nrow(requete@query) == 0) {
- # the database link is not working or the
- # schema
- funout(paste(gettext("Problem during the test, connection to the database is established but failed to connect to the right schema argument passed to stacomi",
- domain = "R-stacomiR"), "\n",
- gettext("dbname", domain = "R-stacomiR")," :", dbname, "\n",
- gettext("User", domain = "R-stacomiR"), " :", user, "\n",
- gettext("Port", domain = "R-stacomiR"), " :", port, "\n",
- gettext("Host", domain = "R-stacomiR"), " :", host, "\n",
- gettext("Password", domain = "R-stacomiR"), " :", password),
- gettext("schema", domain = "R-stacomiR"), " :", sch)
- }
-
- } else {
- # the test has failed and the user will be prompted to another
- funout(paste(gettext("Problem when testing the DB connection", domain = "R-stacomiR"),
- gettext("dbname", domain = "R-stacomiR")," :", dbname, "\n",
- gettext("User", domain = "R-stacomiR"), " :", user, "\n",
- gettext("Port", domain = "R-stacomiR"), " :", port, "\n",
- gettext("Host", domain = "R-stacomiR"), " :", host, "\n",
- gettext("Password", domain = "R-stacomiR"), " :", password))
- } # end else test (else == the test didn't pass, we have to change the name and password
- } else {
- # here : database_expected=FALSE we don't want to check the connection
- # at all...
- }
+ }
+ }
+
+
+ con <- new("ConnectionDB")
+ e <- expression(con <- connect(con))
+ con <- tryCatch(eval(e), error = function(e) e)
+ if ("Rcpp::exception" %in% class(con)) {
+ cat(con$message)
+ test <- FALSE
+ } else {
+ test <- TRUE
+ pool::poolClose(con@connection)
+ }
+
+
+
+ # second test to check that the database is working OK
+
+ if (test) {
+ requete <- new("RequeteDB")
+ requete@sql <- paste0("select count(*) from ref.tr_taxon_tax")
+ message <- NULL
+ requete <- stacomirtools::query(requete)
+ if (grepl("Error", requete@status)) stop(requete@status)
+ if (nrow(requete@query) == 0) {
+ # the database link is not working or the
+ # schema
+ funout(
+ paste(
+ gettext("Problem during the test, connection to the database is established but failed to connect to the right schema argument passed to stacomi",
+ domain = "R-stacomiR"
+ ), "\n",
+ gettext("dbname", domain = "R-stacomiR"), " :", dbname, "\n",
+ gettext("User", domain = "R-stacomiR"), " :", user, "\n",
+ gettext("Port", domain = "R-stacomiR"), " :", port, "\n",
+ gettext("Host", domain = "R-stacomiR"), " :", host, "\n",
+ gettext("Password", domain = "R-stacomiR"), " :", password
+ ),
+ gettext("schema", domain = "R-stacomiR"), " :", sch
+ )
+ }
+ } else {
+ # the test has failed and the user will be prompted to another
+ funout(paste(
+ gettext("Problem when testing the DB connection", domain = "R-stacomiR"),
+ gettext("dbname", domain = "R-stacomiR"), " :", dbname, "\n",
+ gettext("User", domain = "R-stacomiR"), " :", user, "\n",
+ gettext("Port", domain = "R-stacomiR"), " :", port, "\n",
+ gettext("Host", domain = "R-stacomiR"), " :", host, "\n",
+ gettext("Password", domain = "R-stacomiR"), " :", password
+ ))
+ } # end else test (else == the test didn't pass, we have to change the name and password
+ } else {
+ # here : database_expected=FALSE we don't want to check the connection
+ # at all...
+ }
}
@@ -91,7 +96,7 @@ load_stacomi <- function(...) {
#' stacomi Main launcher for program stacomi
-#'
+#'
#' When \code{database_expected=FALSE} a connection to the database is not expected. Therefore test are run by calling examples object stored in Rdata.
#' To change the language use Sys.setenv(LANG = 'fr') or Sys.setenv(LANG = 'en')
#' @param database_expected Boolean, if \code{TRUE} pre launch tests will be run to test the connection validity
@@ -101,32 +106,34 @@ load_stacomi <- function(...) {
#' @usage stacomi(database_expected=TRUE, datawd = "~", sch = "test")
#' @author Cedric Briand \email{cedric.briand@eptb-vilaine.fr}
#' @examples
-#'
-#' require(stacomiR)
-#' #launch stacomi
-#' \dontrun{
-#' stacomi(database_expected=TRUE, datawd='~',sch= "iav")
+#'
+#' require(stacomiR)
+#' # launch stacomi
+#' \dontrun{
+#' stacomi(database_expected = TRUE, datawd = "~", sch = "iav")
#' }
#' # launch stacomi without connection to the database
-#' stacomi(database_expected=FALSE)
+#' stacomi(database_expected = FALSE)
#' # launch stacomi with options
#' options(
-#' stacomiR.dbname = "bd_contmig_nat",
-#' stacomiR.host = readline(prompt = "Enter host: "),
-#' stacomiR.port = "5432",
-#' stacomiR.user = readline(prompt = "Enter user: "),
-#' stacomiR.password = readline(prompt = "Enter password: ")
-#')
+#' stacomiR.dbname = "bd_contmig_nat",
+#' stacomiR.host = readline(prompt = "Enter host: "),
+#' stacomiR.port = "5432",
+#' stacomiR.user = readline(prompt = "Enter user: "),
+#' stacomiR.password = readline(prompt = "Enter password: ")
+#' )
#' # another usefull option to print all queries run by stacomiR to the console
-#' options('stacomiR.printqueries'= TRUE)
+#' options("stacomiR.printqueries" = TRUE)
#' @export
-stacomi = function(database_expected = TRUE, datawd = "~", sch = "test") {
- assign("database_expected", database_expected, envir = envir_stacomi)
- # values assigned in the envir_stacomi
- assign("datawd", datawd, envir = envir_stacomi)
- assign("sch", paste(sch, ".", sep = ""), envir = envir_stacomi)
- load_stacomi()
- invisible(NULL)
+stacomi <- function(database_expected = TRUE,
+ datawd = tempdir(),
+ sch = "test") {
+ assign("database_expected", database_expected, envir = envir_stacomi)
+ # values assigned in the envir_stacomi
+ assign("datawd", datawd, envir = envir_stacomi)
+ assign("sch", paste(sch, ".", sep = ""), envir = envir_stacomi)
+ load_stacomi()
+ invisible(NULL)
}
@@ -135,7 +142,7 @@ stacomi = function(database_expected = TRUE, datawd = "~", sch = "test") {
#' Working environment for stacomiR created when launching stacomi()
-#'
+#'
#' This is where the graphical interface stores its objects
#' try \code{ls(envir=envir_stacomi)}
#' @keywords environment
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index 7fa4135..1863ef2 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -3,13 +3,7 @@
# this file is called before testhat so funcion will be available in all test
# https://testthat.r-lib.org/articles/test-fixtures.html#withr-defer-
# could have used with_envvar and local_envvar but had to set them each time
-# options(
-# stacomiR.dbname = "bd_contmig_nat",
-# stacomiR.host = "localhost",
-# stacomiR.port = "5432",
-# stacomiR.user = "stacomi_test",
-# stacomiR.password = "stacomi_test"
-# )
+
password <- getOption("stacomiR.password") # if not set will be ""
dbname <- getOption("stacomiR.dbname") # if not set will be ""
user <- getOption("stacomiR.user")
diff --git a/tests/testthat/test-03-report_df.R b/tests/testthat/test-03-report_df.R
index 06ed6b4..bf4b0a4 100644
--- a/tests/testthat/test-03-report_df.R
+++ b/tests/testthat/test-03-report_df.R
@@ -1,95 +1,99 @@
context("report_df")
test_that("Test an instance of report_df", {
- skip_on_cran()
- stacomi(database_expected = FALSE, sch ="test")
- env_set_test_stacomi()
- r_df <- new("report_df")
- r_df <- choice_c(
- r_df,
- 2,
- horodatedebut = "2013-01-01",
- horodatefin = "2013-12-31",
- silent = TRUE
- )
- expect_gt(nrow(r_df@df@data),
- 0,
- label = "There should be data loaded by the choice_c method in the data slot of
- the ref_df slot,nrow(r_df@df@data)")
- expect_s4_class(r_df,
- "report_df")
- expect_error(
- BfDF <- choice_c(
- r_df,
- 2,
- horodatedebut = "2013 01 011",
- horodatefin = "2013-12-31",
- silent = TRUE
- )
- )
- rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
-
- })
+ skip_on_cran()
+ stacomi(database_expected = FALSE, sch = "test")
+ env_set_test_stacomi()
+ r_df <- new("report_df")
+ r_df <- choice_c(
+ r_df,
+ 2,
+ horodatedebut = "2013-01-01",
+ horodatefin = "2013-12-31",
+ silent = TRUE
+ )
+ expect_gt(nrow(r_df@df@data),
+ 0,
+ label = "There should be data loaded by the choice_c method in the data slot of
+ the ref_df slot,nrow(r_df@df@data)"
+ )
+ expect_s4_class(
+ r_df,
+ "report_df"
+ )
+ expect_error(
+ BfDF <- choice_c(
+ r_df,
+ 2,
+ horodatedebut = "2013 01 011",
+ horodatefin = "2013-12-31",
+ silent = TRUE
+ )
+ )
+ rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
+})
test_that("report_df charge method works", {
- skip_on_cran()
- stacomi(database_expected = TRUE, sch ="test")
- env_set_test_stacomi()
- r_df <- new("report_df")
- r_df <- choice_c(
- r_df,
- 2,
- horodatedebut = "2013-01-01",
- horodatefin = "2013-12-31",
- silent = TRUE
- )
- r_df <- charge(r_df, silent = TRUE)
- r_df <- connect(r_df, silent = TRUE)
- expect_equal(nrow(r_df@data), 5)
- rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
-
- })
+ skip_on_cran()
+ stacomi(database_expected = TRUE, sch = "test")
+ env_set_test_stacomi()
+ r_df <- new("report_df")
+ r_df <- choice_c(
+ r_df,
+ 2,
+ horodatedebut = "2013-01-01",
+ horodatefin = "2013-12-31",
+ silent = TRUE
+ )
+ r_df <- charge(r_df, silent = TRUE)
+ r_df <- connect(r_df, silent = TRUE)
+ expect_equal(nrow(r_df@data), 5)
+ rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
+})
test_that("report_df plot method works", {
- stacomi(database_expected = FALSE, sch ="test")
- data(r_df)
- r_df <- r_df
- # expect_error(expr,NA) tests for an absence of error
- expect_no_error({
- invisible(capture.output(plot(r_df, plot.type = "1", silent = TRUE)))
- invisible(capture.output(plot(r_df,
- plot.type = "2",
- silent = TRUE,
- main = "An example title")))
- plot(r_df,
- plot.type = "3",
- silent = TRUE,
- main = "An example title")
- plot(r_df,
- plot.type = "4",
- silent = TRUE,
- main = "An example title")})
- rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
- })
-
+ stacomi(database_expected = FALSE, sch = "test")
+ data(r_df)
+ r_df <- r_df
+ # expect_error(expr,NA) tests for an absence of error
+ expect_no_error({
+ invisible(capture.output(plot(r_df, plot.type = "1", silent = TRUE)))
+ invisible(capture.output(plot(r_df,
+ plot.type = "2",
+ silent = TRUE,
+ main = "An example title"
+ )))
+ plot(r_df,
+ plot.type = "3",
+ silent = TRUE,
+ main = "An example title"
+ )
+ plot(r_df,
+ plot.type = "4",
+ silent = TRUE,
+ main = "An example title"
+ )
+ })
+ rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
+})
test_that("report_df summary method works", {
- skip_on_cran()
- stacomi(database_expected = FALSE, sch ="test")
- data(r_df)
- r_df <- r_df
- #expected <- ifelse(Sys.getlocale(category = "LC_TIME")=="French_France.utf8", "statistiques", "summary")
- expect_output(summary(r_df, silent = TRUE))
- rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
- })
+ skip_on_cran()
+ stacomi(database_expected = FALSE, sch = "test")
+ data(r_df)
+ # r_df <- r_df
+ # expected <- ifelse(Sys.getlocale(category = "LC_TIME")=="French_France.utf8", "statistiques", "summary")
+ expect_output(summary(r_df, silent = TRUE))
+ rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
+})
test_that("report_df print method works", {
- skip_on_cran()
- stacomi(database_expected = FALSE, sch ="test")
- data(r_df)
- r_df <- r_df
- expect_output(print(r_df))
- rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
- })
\ No newline at end of file
+ skip_on_cran()
+ stacomi(database_expected = FALSE, sch = "test")
+ data(r_df)
+ r_df <- r_df
+ expect_output(print(r_df))
+ rm(list = ls(envir = envir_stacomi), envir = envir_stacomi)
+})
diff --git a/tests/testthat/test-05-report_sample_char.R b/tests/testthat/test-05-report_sample_char.R
index 87128d4..680d7f0 100644
--- a/tests/testthat/test-05-report_sample_char.R
+++ b/tests/testthat/test-05-report_sample_char.R
@@ -5,7 +5,7 @@ test_that("Test that view lot_ope_car exists", {
stacomi(database_expected = TRUE, sch = "test")
req <- new("RequeteDB")
sch <- rlang::env_get(envir_stacomi, "sch")
- req@sql <- paste("select * from ", sch, " vue_lot_ope_car limit 10")
+ req@sql <- paste("select * from ", sch, "vue_lot_ope_car limit 10")
req <- stacomirtools::query(req)
result <- req@query
expect_true(nrow(result) > 0)
@@ -80,8 +80,8 @@ test_that("Test charge method for report_sample_char", {
taxa = c("Anguilla anguilla"),
stage = c("AGJ", "CIV"),
par = c(1785, 1786, 1787, "C001"),
- horodatedebut = "2013-01-01",
- horodatefin = "2013-12-31",
+ horodatedebut = "2009-01-01",
+ horodatefin = "2009-12-31",
silent = TRUE
)
)
--
GitLab
From c23a3add1d893b9ead97dded7856ee145bb56e56 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Sat, 1 Mar 2025 17:35:00 +0100
Subject: [PATCH 07/13] up
---
R/stacomi.R | 2 +-
dev/03_deploy.R | 8 +++++++-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/R/stacomi.R b/R/stacomi.R
index 253e23a..3e3bc51 100644
--- a/R/stacomi.R
+++ b/R/stacomi.R
@@ -110,7 +110,7 @@ load_stacomi <- function(...) {
#' require(stacomiR)
#' # launch stacomi
#' \dontrun{
-#' stacomi(database_expected = TRUE, datawd = "~", sch = "iav")
+#' stacomi(database_expected = TRUE, datawd = tempdir(), sch = "iav")
#' }
#' # launch stacomi without connection to the database
#' stacomi(database_expected = FALSE)
diff --git a/dev/03_deploy.R b/dev/03_deploy.R
index bd41850..6346d20 100644
--- a/dev/03_deploy.R
+++ b/dev/03_deploy.R
@@ -18,7 +18,13 @@ rm(list = ls(all.names = TRUE))
devtools::load_all()
Sys.setenv("LANGUAGE" = "en") # otherwise problems when running from Rstudio
-# GO TO helper.R called before everything to change options.
+options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = "stacomi_test",
+ stacomiR.password = "stacomi_test"
+)
devtools::test() # this will run load_all() see details about classes below for specific tests
#test_local() # check a package during R CMD check
test <- capture.output(devtools::test(reporter="junit"))
--
GitLab
From d0fa62348e8f4d080882e41ebffa2f66cda6aa22 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Sat, 1 Mar 2025 17:52:37 +0100
Subject: [PATCH 08/13] MAJ doc
---
man/choice_c-report_annual-method.Rd | 2 +-
man/plot-report_mig_mult-missing-method.Rd | 2 +-
man/r_dc.Rd | 2 +-
man/r_df.Rd | 2 +-
man/r_env.Rd | 2 +-
man/r_mig.Rd | 2 +-
man/r_mig_interannual_vichy.Rd | 2 +-
man/report_annual-class.Rd | 8 +-
man/report_dc-class.Rd | 77 +++---
man/report_df-class.Rd | 68 +++--
man/report_env-class.Rd | 50 ++--
man/report_ge_weight-class.Rd | 79 +++---
man/report_mig-class.Rd | 83 +++---
man/report_mig_char-class.Rd | 94 +++----
man/report_mig_env-class.Rd | 67 ++---
man/report_mig_interannual-class.Rd | 289 +++++++++++----------
man/report_mig_mult-class.Rd | 4 +-
man/report_sample_char-class.Rd | 129 ++++-----
man/report_sea_age-class.Rd | 74 +++---
man/report_silver_eel-class.Rd | 72 ++---
man/report_species-class.Rd | 75 +++---
man/stacomi.Rd | 22 +-
22 files changed, 624 insertions(+), 581 deletions(-)
diff --git a/man/choice_c-report_annual-method.Rd b/man/choice_c-report_annual-method.Rd
index 9c5834c..4ef9ffb 100644
--- a/man/choice_c-report_annual-method.Rd
+++ b/man/choice_c-report_annual-method.Rd
@@ -27,7 +27,7 @@ it should match the ref.tr_taxon_tax referential table in the stacomi database,
An object of class \link{report_annual-class} with data selected
}
\description{
-The choice_c method fills in the data slot for classes \link{ref_dc-class}, \link{ref_taxa-class},
+The choice_c method fills in the data slot for classes \link{ref_dc-class}, \link{ref_taxa-class},
\link{ref_stage-class} and two slots of \link{ref_year-class}
}
\author{
diff --git a/man/plot-report_mig_mult-missing-method.Rd b/man/plot-report_mig_mult-missing-method.Rd
index a8cc9b4..183d05f 100644
--- a/man/plot-report_mig_mult-missing-method.Rd
+++ b/man/plot-report_mig_mult-missing-method.Rd
@@ -17,7 +17,7 @@
\arguments{
\item{x}{An object of class report_mig_mult}
-\item{plot.type}{One of 'standard','step','multiple'. Defaut to \code{standard} the standard report_mig with dc and operation displayed, can also be \code{step} or
+\item{plot.type}{One of 'standard','step','multiple','time'. Defaut to \code{standard} the standard report_mig with dc and operation displayed, can also be \code{step} or
\code{multiple}}
\item{color}{Default NULL, argument passed for the plot.type='standard' method. A vector of color in the following order : (1) working, (2) stopped, (3:7) 1...5 types of operation,
diff --git a/man/r_dc.Rd b/man/r_dc.Rd
index 14aaa53..3f39384 100644
--- a/man/r_dc.Rd
+++ b/man/r_dc.Rd
@@ -24,7 +24,7 @@ An object of class report_dc with 4 slots:
\item{libelle}{label corresponding to per_tar_code}
}
}
- \item{df}{the \code{ref_dc} object with 3 slots filled with data corresponding to the iav postgres schema}
+ \item{df}{the \code{ref_dc} object with 3 slots filled with data corresponding to the test postgres schema}
\item{horodatedebut}{the \code{ref_horodate} with horodate set for starting date}
\item{horodatefin}{the \code{ref_horodate} with horodate set for ending date}
}
diff --git a/man/r_df.Rd b/man/r_df.Rd
index 0fcd7c6..10c82e4 100644
--- a/man/r_df.Rd
+++ b/man/r_df.Rd
@@ -23,7 +23,7 @@ An object of class report_df with 4 slots:
\item{libelle}{label corresponding to per_tar_code}
}
}
- \item{df}{the \code{ref_df} object with 3 slots filled with data corresponding to the iav postgres schema}
+ \item{df}{the \code{ref_df} object with 3 slots filled with data corresponding to the test postgres schema}
\item{horodatedebut}{the \code{ref_horodate} with horodate set for starting date}
\item{horodatefin}{the \code{ref_horodate} with horodate set for ending date}'
}
diff --git a/man/r_env.Rd b/man/r_env.Rd
index d2e8aa9..31b8e89 100644
--- a/man/r_env.Rd
+++ b/man/r_env.Rd
@@ -7,7 +7,7 @@
\format{
An object of class \link{report_env-class} with data slot loaded:
\describe{
- \item{stationMesure}{the \code{ref_env} object with 5 slots filled with data corresponding to the iav postgres schema}
+ \item{stationMesure}{the \code{ref_env} object with 5 slots filled with data corresponding to the test postgres schema}
\item{horodatedebut}{object of class \code{ref_horodate-class} : the start date selected}
\item{horodatefin}{object of class \code{ref_horodate-class} : the end date selected}
\item{data}{ A dataframe with 723 rows and 6 variables
diff --git a/man/r_mig.Rd b/man/r_mig.Rd
index e3f0e66..9b72c2e 100644
--- a/man/r_mig.Rd
+++ b/man/r_mig.Rd
@@ -7,7 +7,7 @@
\format{
An object of class report_mig with 8 slots:
\describe{
- \item{dc}{the \code{ref_dc} object with 4 slots filled with data corresponding to the iav postgres schema}
+ \item{dc}{the \code{ref_dc} object with 4 slots filled with data corresponding to the test postgres schema}
\item{taxa}{the \code{ref_taxa} the taxa selected}
\item{stage}{the \code{ref_stage} the stage selected}
\item{timestep}{the \code{ref_timestep_daily} calculated for all 2015}
diff --git a/man/r_mig_interannual_vichy.Rd b/man/r_mig_interannual_vichy.Rd
index 7f062d3..0bbc2c5 100644
--- a/man/r_mig_interannual_vichy.Rd
+++ b/man/r_mig_interannual_vichy.Rd
@@ -7,7 +7,7 @@
\format{
An object of class \link{report_mig_interannual-class} with 7 slots:
\describe{
- \item{dc}{the \code{ref_dc} object with 4 slots filled with data corresponding to the iav postgres schema}
+ \item{dc}{the \code{ref_dc} object with 4 slots filled with data corresponding to the test postgres schema}
\item{taxa}{the \code{ref_taxa} the taxa selected}
\item{stage}{the \code{ref_stage} the stage selected}
\item{start_year}{the \code{ref_timestep_daily} calculated for all 2015}
diff --git a/man/report_annual-class.Rd b/man/report_annual-class.Rd
index 515e871..d795f3a 100644
--- a/man/report_annual-class.Rd
+++ b/man/report_annual-class.Rd
@@ -28,11 +28,11 @@ ref_year allows to choose last year of the report}
\examples{
# launching stacomi without database for demo
stacomi(database_expected=FALSE)
-# the following piece of script will load the Arzal dataset and connected to iav postgres schema
+# the following piece of script will load the Arzal dataset and connected to test postgres schema
# it requires a working database
# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
- stacomi(database_expected=TRUE, sch='iav')
+ stacomi(database_expected=TRUE, sch='test')
if (interactive()){
if (!exists("user")){
user <- readline(prompt="Enter user: ")
@@ -51,8 +51,8 @@ stacomi(database_expected=FALSE)
dc=c(5,6,12),
taxa=c("Anguilla anguilla"),
stage=c("AGJ","AGG"),
- start_year="1996",
- end_year="2015",
+ start_year="2012",
+ end_year="2013",
silent=FALSE)
r_ann<-connect(r_ann)
}
diff --git a/man/report_dc-class.Rd b/man/report_dc-class.Rd
index fb0d806..88ef5bd 100644
--- a/man/report_dc-class.Rd
+++ b/man/report_dc-class.Rd
@@ -29,55 +29,50 @@ class allows to draw graphics allowing an overview of the device operation
}
\examples{
-
-
-# An example that will work only if the database is present
-# and the program installed and comprises the schema iav
+# An example that will work only if the database is present
+# and the program installed and comprises the schema test
# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
+if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.password = password
- )
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.password = password
+ )
+ }
+ stacomi(TRUE, sch = "test")
+ r_dc <- new("report_dc")
+ r_dc <- choice_c(r_dc,
+ 5,
+ horodatedebut = "2012-01-01",
+ horodatefin = "2015-12-31",
+ silent = TRUE
+ )
+ r_dc <- connect(r_dc)
}
- stacomi(TRUE,sch="iav")
- r_dc=new("report_dc")
- r_dc<-choice_c(r_dc,
- 5,
- horodatedebut="2000-01-01",
- horodatefin="2015-12-31",
- silent=TRUE)
- r_dc<-connect(r_dc)
+ ##
-##
-
# this dataset has been loaded by the previous lines
- ###########################################################
-# Without connexion to the database (use dataset r_dc)
+ ###########################################################
+ # Without connexion to the database (use dataset r_dc)
##########################################################
- # this option allows to launch the program without the interface to display
-# some of the program features.
- stacomi(database_expected=FALSE)
+ # this option allows to launch the program without the interface to display
+ # some of the program features.
+ stacomi(database_expected = FALSE)
data("r_dc")
- plot(r_dc,plot.type="1")
- plot(r_dc,plot.type="2")
- plot(r_dc,plot.type="3",main="trial title")
- plot(r_dc,plot.type="4",main="trial title")
-# the following will write in the datawd folder
- summary(r_dc)
-}
-
-
-
+ plot(r_dc, plot.type = "1")
+ plot(r_dc, plot.type = "2")
+ plot(r_dc, plot.type = "3", main = "trial title")
+ plot(r_dc, plot.type = "4", main = "trial title")
+ # the following will write in the datawd folder
+ summary(r_dc)
}
\seealso{
diff --git a/man/report_df-class.Rd b/man/report_df-class.Rd
index c0c1d8d..f7a266a 100644
--- a/man/report_df-class.Rd
+++ b/man/report_df-class.Rd
@@ -38,52 +38,46 @@ the status of either the fishway or DC. In the database four types of operation
\examples{
stacomi(
- database_expected=FALSE)
-# An example that will work with the database installed only and schema iav in the database
+ database_expected = FALSE
+)
+# An example that will work with the database installed only and schema test in the database
# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
- stacomi(
- database_expected=TRUE, sch='iav')
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
- }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.user = password
- )
- r_df=new("report_df")
- r_df<-choice_c(r_df,
- 1,
- horodatedebut="2015-01-01",
- horodatefin="2015-12-31",
- silent=TRUE)
- Sys.setenv(TZ='GMT')
- # the times at Arzal are recorded continuously
- # they are converted to date when a time appears while the hour is changing
- # hence the following
- r_df<-connect(r_df)
+stacomi(
+ database_expected = TRUE, sch = "test"
+)
+if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
+}
+options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+)
+r_df <- new("report_df")
+r_df <- choice_c(r_df,
+ 1,
+ horodatedebut = "2015-01-01",
+ horodatefin = "2015-12-31",
+ silent = TRUE
+)
+r_df <- connect(r_df)
}
data("r_df")
-plot(r_df,plot.type="4")
+plot(r_df, plot.type = "4")
# the following examples work but take a while to compute
\dontrun{
- plot(r_df,plot.type="1")
- plot(r_df,plot.type="2",main="A nice title")
- plot(r_df,plot.type="3",main="A nice title")
+plot(r_df, plot.type = "1")
+plot(r_df, plot.type = "2", main = "A nice title")
+plot(r_df, plot.type = "3", main = "A nice title")
}
-
-
-
-
-
}
\seealso{
Other report Objects:
diff --git a/man/report_env-class.Rd b/man/report_env-class.Rd
index dc7be72..a8d7273 100644
--- a/man/report_env-class.Rd
+++ b/man/report_env-class.Rd
@@ -24,33 +24,35 @@ joined graphs crossing the information from \link{report_mig_mult-class} and \li
\examples{
stacomi(
- database_expected=FALSE)
+ database_expected = FALSE
+)
\dontrun{
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
- }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.user = password
- )
- r_env<-new("report_env")
- r_env<-choice_c(r_env,
- stationMesure=c("temp_gabion","coef_maree"),
- datedebut="2008-01-01",
- datefin="2008-12-31",
- silent=FALSE)
- r_env<-connect(r_env)
-
-}
+if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
+}
+options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+)
+r_env <- new("report_env")
+r_env <- choice_c(r_env,
+ stationMesure = c("temp_gabion", "coef_maree"),
+ datedebut = "2008-01-01",
+ datefin = "2008-12-31",
+ silent = FALSE
+)
+r_env <- connect(r_env)
+
+}
data("r_env")
-plot(r_env,silent=TRUE)
+plot(r_env, silent = TRUE)
}
\seealso{
Other report Objects:
diff --git a/man/report_ge_weight-class.Rd b/man/report_ge_weight-class.Rd
index 53b2e3a..9c356a6 100644
--- a/man/report_ge_weight-class.Rd
+++ b/man/report_ge_weight-class.Rd
@@ -50,55 +50,58 @@ request are from august to august (a glass eel season)
require(stacomiR)
# launching stacomi without selecting the scheme or interface
stacomi(
- database_expected=FALSE, sch='iav')
-# this requires a working database with the schema iav
+ database_expected = FALSE, sch = "test"
+)
+# this requires a working database with the schema test
# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
- stacomi(
- database_expected=TRUE, sch='iav')
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
- }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.user = password
- )
- #create an instance of the class
- r_gew<-new("report_ge_weight")
- r_gew@liste<-charge(object=r_gew@liste,listechoice=c("=1",">1","tous"),label="")
- # here I'm using weights when number are larger than 1i.e.wet weight
- # always choose a date from one year to the next eg 2010 to 2011
- # as the dates are from august to august
- r_gew<-choice_c(r_gew,
- dc=c(6),
- start_year="2009",
- end_year="2015",
- selectedvalue=">1",
- silent=FALSE)
- r_gew<-connect(r_gew)
- r_gew<-calcule(r_gew)
-}
+stacomi(
+ database_expected = TRUE, sch = "test"
+)
+if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
+}
+options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+)
+# create an instance of the class
+r_gew <- new("report_ge_weight")
+r_gew@liste <- charge(object = r_gew@liste, listechoice = c("=1", ">1", "tous"), label = "")
+# here I'm using weights when number are larger than 1i.e.wet weight
+# always choose a date from one year to the next eg 2010 to 2011
+# as the dates are from august to august
+r_gew <- choice_c(r_gew,
+ dc = c(6),
+ start_year = "2009",
+ end_year = "2014",
+ selectedvalue = ">1",
+ silent = FALSE
+)
+r_gew <- connect(r_gew)
+r_gew <- calcule(r_gew)
+}
# load the dataset generated by previous lines
data("r_gew")
# the calculation will fill the slot calcdata
# A ggplot showing the trend in weight
-plot(r_gew, plot.type=1)
+plot(r_gew, plot.type = 1)
# A plot showing both the data and the trend as recorded in the database
-plot(r_gew, plot.type=2)
+plot(r_gew, plot.type = 2)
# Same as plot.type=1 but with size according to size of the sample,
# usefull for wet weights where weight are recorded on a number of glass eel
-plot(r_gew, plot.type=3)
+plot(r_gew, plot.type = 3)
\dontrun{
-# First model with nls, see Guerault and Desaunay (1993)
- model(r_gew,model.type="seasonal")
- model(r_gew,model.type="seasonal1")
+# First model with nls, see Guerault and Desaunay (1993)
+model(r_gew, model.type = "seasonal")
+model(r_gew, model.type = "seasonal1")
}
}
\seealso{
diff --git a/man/report_mig-class.Rd b/man/report_mig-class.Rd
index c1435c6..9149cba 100644
--- a/man/report_mig-class.Rd
+++ b/man/report_mig-class.Rd
@@ -37,75 +37,82 @@ method if any weight are found in the data slot.}
In practise, the report_mig class uses methods (calcule, connect...) from the more elaborate \link{report_mig_mult-class}
}
\examples{
-stacomi(database_expected=FALSE)
+stacomi(database_expected = FALSE)
# If you have a working database
-# the following line of code will create the r_mig dataset from the iav (default)
+# the following line of code will create the r_mig dataset from the test (default)
# schema in the database
-\dontrun{
- stacomi(database_expected=TRUE)
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
- }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.user = password
- )
- stacomi(
- database_expected=TRUE)
- r_mig=new("report_mig")
- r_mig=choice_c(r_mig,
- dc=5,
- taxa=c("Chelon ramada"),
- stage=c("IND"),
- datedebut="2015-01-01",
- datefin="2015-12-31")
- r_mig<-charge(r_mig)
+\dontrun{
+ stacomi(database_expected = TRUE)
+ if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
+ stacomi(database_expected = TRUE)
+ r_mig = new("report_mig")
+ r_mig = choice_c(
+ r_mig,
+ dc = 5,
+ taxa = c("Chelon ramada"),
+ stage = c("IND"),
+ datedebut = "2015-01-01",
+ datefin = "2015-12-31"
+ )
+ r_mig <- charge(r_mig)
# launching charge will also load classes associated with the report
# e.g. report_ope, report_df, report_dc
- r_mig<-connect(r_mig)
+ r_mig <- connect(r_mig)
########################
-# calculations
+ # calculations
########################
- r_mig<-calcule(r_mig,silent=TRUE)
+ r_mig <- calcule(r_mig, silent = TRUE)
}
########################
# loading data
## use the following to get the raw data loaded by the connect method
# not shown there as the database and program might not be installed
-# All three classes report... were created by the charge and connect method
+# All three classes report... were created by the charge and connect method
# of report_mig_mult
# in the previous example
################################
data("r_mig")
data("r_mig_ope")
-assign("report_ope",r_mig_ope,envir=envir_stacomi)
+assign("report_ope", r_mig_ope, envir = envir_stacomi)
data("r_mig_df")
-assign("report_df",r_mig_df,envir=envir_stacomi)
+assign("report_df", r_mig_df, envir = envir_stacomi)
data("r_mig_dc")
-assign("report_dc",r_mig_dc,envir=envir_stacomi)
+assign("report_dc", r_mig_dc, envir = envir_stacomi)
#Individual plot for all DC (standard), taxa and stage where data present
#silent argument to stop all messages
-plot(r_mig,plot.type="standard",silent=TRUE)
+plot(r_mig, plot.type = "standard", silent = TRUE)
#cumulated migration at the station (all stages and DC grouped)
-plot(r_mig,plot.type="step")
+plot(r_mig, plot.type = "step")
# data will be written in the data directory specified in datawd argument to stacomi default "~"
#file
\dontrun{
- summary(r_mig,silent=TRUE)
+ summary(r_mig, silent = TRUE)
}
# this will write the daily report for later in in the reportnMigrationInterannuelle-class
\dontrun{
- write_database(r_mig,silent=TRUE,dbname="bd_contmig_nat",host="localhost",port=5432)
+ write_database(
+ r_mig,
+ silent = TRUE,
+ dbname = "bd_contmig_nat",
+ host = "localhost",
+ port = 5432
+ )
}
}
\seealso{
diff --git a/man/report_mig_char-class.Rd b/man/report_mig_char-class.Rd
index 09354e2..2bc863b 100644
--- a/man/report_mig_char-class.Rd
+++ b/man/report_mig_char-class.Rd
@@ -54,62 +54,66 @@ using interface_report_mig_char function.
require(stacomiR)
stacomi(
- database_expected=FALSE, sch='logrami')
+ database_expected = FALSE
+)
# this requires a database with the schema logrami
# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
- stacomi(database_expected=TRUE, sch='logrami')
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
- }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.user = password
- )
- r_mig_char <- new("report_mig_char")
- # here parqual is not in the list
- # so this is equivalent to parqual=NULL
- # default for echantillon is "with"
- r_mig_char <- choice_c(r_mig_char,
- dc=c(107,108,101),
- taxa=c("Salmo salar"),
- stage=c('5','11','BEC','BER','IND'),
- parquan=c('C001','1786','1785'),
- horodatedebut="2012-01-01",
- horodatefin="2012-12-31",
- silent=FALSE)
- # r_mig_char<-charge(r_mig_char) not necessary there
- r_mig_char <- connect(r_mig_char)
-
-}
+stacomi(database_expected = TRUE, sch = "test")
+if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
+}
+options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+)
+r_mig_char <- new("report_mig_char")
+# here parqual is not in the list
+# so this is equivalent to parqual=NULL
+# default for echantillon is "with"
+r_mig_char <- choice_c(r_mig_char,
+ dc = c(19,20),
+ taxa = c("Salmo salar"),
+ stage = c("5"),
+ parquan = c("C001"),
+ horodatedebut = "2012-01-01",
+ horodatefin = "2012-12-31",
+ silent = FALSE
+)
+# r_mig_char<-charge(r_mig_char) not necessary there
+r_mig_char <- connect(r_mig_char)
+
+}
# load the dataset generated by previous lines
data("r_mig_char")
-r_mig_char<-calcule(r_mig_char, silent=TRUE)
-plot(r_mig_char,plot.type="quant", silent=TRUE)
+r_mig_char <- calcule(r_mig_char, silent = TRUE)
+plot(r_mig_char, plot.type = "quant", silent = TRUE)
# one quantitative parameter found, manual choice of color
-plot(r_mig_char,plot.type="quant",color_parm=c("C001"="red"), silent=TRUE)
+plot(r_mig_char, plot.type = "quant", color_parm = c("C001" = "red"), silent = TRUE)
# age will be plotted as a qualitative variable
# here we split size data accoding to the limit known between different ages from
# scale reading in the Loire
-r_mig_char <- setasqualitative(r_mig_char,par='C001',
- breaks=c(0,675,850,2000),
- labels=c("age 1","age 2","age 3"))
-r_mig_char<-calcule(r_mig_char, silent=TRUE)
-plot(r_mig_char, plot.type="qual", silent=TRUE)
-plot(r_mig_char, plot.type="crossed")
-plot(r_mig_char, plot.type="crossed",
- color_parm=c("age 1"="#379ec6","age 2"="#173957","age 3"="#b09953"))
-xt<-xtable(r_mig_char)
+r_mig_char <- setasqualitative(r_mig_char,
+ par = "C001",
+ breaks = c(0, 675, 850, 2000),
+ labels = c("age 1", "age 2", "age 3")
+)
+r_mig_char <- calcule(r_mig_char, silent = TRUE)
+plot(r_mig_char, plot.type = "qual", silent = TRUE)
+plot(r_mig_char, plot.type = "crossed")
+plot(r_mig_char,
+ plot.type = "crossed",
+ color_parm = c("age 1" = "#379ec6", "age 2" = "#173957", "age 3" = "#b09953")
+)
+xt <- xtable(r_mig_char)
# use method print.xtable to get the output
-
-
}
\seealso{
Other report Objects:
diff --git a/man/report_mig_env-class.Rd b/man/report_mig_env-class.Rd
index 330916b..06aa144 100644
--- a/man/report_mig_env-class.Rd
+++ b/man/report_mig_env-class.Rd
@@ -28,45 +28,48 @@ event of the day is displayed on the annual plot.
\examples{
require(stacomiR)
stacomi(
- database_expected=FALSE)
+ database_expected = FALSE
+)
# the following will load the data provided the user has access to the database
-# with data in the iav example scheme.
+# with data in the test example scheme.
# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
- stacomi(
- database_expected=TRUE)
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
- }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.user = password
- )
- r_mig_env<-new("report_mig_env")
- r_mig_env<-choice_c(r_mig_env,
- dc=c(5,6,12),
- taxa=c("Anguilla anguilla"),
- stage=c("AGJ","AGG","CIV"),
- stationMesure=c("temp_gabion","coef_maree","phases_lune"),
- datedebut="2008-01-01",
- datefin="2008-12-31",
- silent=FALSE)
- r_mig_env<-charge(r_mig_env) # this is necessary to load operations, DF and DC
- r_mig_env<-connect(r_mig_env)
- r_mig_env<-calcule(r_mig_env,silent=TRUE)
-}
+stacomi(
+ database_expected = TRUE
+)
+if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
+}
+options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+)
+r_mig_env <- new("report_mig_env")
+r_mig_env <- choice_c(r_mig_env,
+ dc = c(5, 6, 12),
+ taxa = c("Anguilla anguilla"),
+ stage = c("AGJ", "AGG", "CIV"),
+ stationMesure = c("temp_gabion", "coef_maree", "phases_lune"),
+ datedebut = "2010-01-01",
+ datefin = "2010-12-31",
+ silent = FALSE
+)
+r_mig_env <- charge(r_mig_env) # this is necessary to load operations, DF and DC
+r_mig_env <- connect(r_mig_env)
+r_mig_env <- calcule(r_mig_env, silent = TRUE)
+}
data("r_mig_env")
# An example of plot with custom colors.
plot(r_mig_env,
- color_station=c("temp_gabion"="red","coef_maree"="blue","phases_lune"="pink"),
- color_dc=c("5"="yellow","6"="orange","12"="purple")
+ color_station = c("temp_gabion" = "red", "coef_maree" = "blue", "phases_lune" = "pink"),
+ color_dc = c("5" = "yellow", "6" = "orange", "12" = "purple")
)
}
\seealso{
diff --git a/man/report_mig_interannual-class.Rd b/man/report_mig_interannual-class.Rd
index 6b57353..19f47d3 100644
--- a/man/report_mig_interannual-class.Rd
+++ b/man/report_mig_interannual-class.Rd
@@ -40,182 +40,199 @@ ref_year allows to choose last year of the report}
require(stacomiR)
# launching stacomi without selecting the scheme or interface
stacomi(
- database_expected=FALSE, sch='pmp')
-# If you have connection to the database with the pmp scheme
+ database_expected = FALSE, sch = "pmp"
+)
+# If you have connection to the database with the pmp scheme
# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
- stacomi(database_expected=TRUE, sch="pmp")
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
- }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.user = password
- )
+stacomi(database_expected = TRUE, sch = "pmp")
+if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
+}
+options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+)
- # (longest historical dataset available
- # in France for eel ...) this suppose you have access to the pmp schema...
- # a glimpse of the dataset is still available in the r_mig_interannual dataset
- # loaded in the package...
- r_mig_interannual <- new("report_mig_interannual")
- r_mig_interannual <- choice_c(r_mig_interannual,
- dc=c(16),
- taxa=c("Anguilla anguilla"),
- stage=c("PANG"),
- start_year="1990",
- end_year="2015",
- year_choice=NULL,
- silent=TRUE)
- r_mig_interannual <- charge(r_mig_interannual)
- r_mig_interannual <- connect(r_mig_interannual, check=TRUE)
- r_mig_interannual <- calcule(r_mig_interannual, silent=TRUE)
-}
-#############otherwise use this ######################
+# (longest historical dataset available
+# in France for eel ...) this suppose you have access to the pmp schema...
+# a glimpse of the dataset is still available in the r_mig_interannual dataset
+# loaded in the package...
+r_mig_interannual <- new("report_mig_interannual")
+r_mig_interannual <- choice_c(r_mig_interannual,
+ dc = c(16),
+ taxa = c("Anguilla anguilla"),
+ stage = c("PANG"),
+ start_year = "1990",
+ end_year = "2015",
+ silent = TRUE
+)
+r_mig_interannual <- charge(r_mig_interannual)
+r_mig_interannual <- connect(r_mig_interannual, check = TRUE)
+r_mig_interannual <- calcule(r_mig_interannual, silent = TRUE)
+}
+############# otherwise use this ######################
# load the dataset generated by previous lines
data("r_mig_interannual")
#######################################################
-# the first plot is of little interest, it allows to see what data
+# the first plot is of little interest, it allows to see what data
# are available... simple lines
# For irregular operations like those reported at the enfrenaux eel ladder....
-plot(r_mig_interannual,plot.type="line", year_choice=2015, silent=TRUE)
+plot(r_mig_interannual, plot.type = "line", year_choice = 2015, silent = TRUE)
# a plot to show the seasonality, this graph may be misleading if the
# migration is not monitored all year round. Note the y unit is not very informative
# you need to have the viridis package loaded to run this example
-plot(r_mig_interannual,plot.type="density",year_choice=2015, silent=TRUE)
+plot(r_mig_interannual, plot.type = "density", year_choice = 2015, silent = TRUE)
+
\dontrun{
- if (requireNamespace("ggplot2", quietly = TRUE)&
- requireNamespace("viridis", quietly = TRUE)){
- g<-get("g",envir=envir_stacomi)
- g+
- ggplot2::scale_fill_manual(values=viridis::viridis(22))+
- ggplot2::ggtitle("Saisonnalite de la migration aux Enfrenaux")
- }
- #############################################
+if (requireNamespace("ggplot2", quietly = TRUE) &
+ requireNamespace("viridis", quietly = TRUE)) {
+ g <- get("g", envir = envir_stacomi)
+ g +
+ ggplot2::scale_fill_manual(values = viridis::viridis(22)) +
+ ggplot2::ggtitle("Saisonnalite de la migration aux Enfrenaux")
+}
+#############################################
# the standard plot is showing daily values
- ###########################################
- plot(r_mig_interannual,plot.type="standard",year_choice=2015,silent=TRUE)
+###########################################
+plot(r_mig_interannual, plot.type = "standard", year_choice = 2015, silent = TRUE)
# Manual edition of the graph produced
- if (requireNamespace("ggplot2", quietly = TRUE)){
- g1<-get("g1",envir=envir_stacomi)
- g1<-g1+ggplot2::ggtitle("Les Enfrenaux")+
- ggplot2::scale_fill_manual(name="Source",
- values=c("purple","#0A0C01"),
- labels = c("historical set","2015 values"))+
- ggplot2::scale_colour_manual(name="Source", values="#B8EA00",
- labels = c("historical mean")) +
- ggplot2::ylab("Nombre d'anguilles")
- print(g1)
- }
- #########################################################
+if (requireNamespace("ggplot2", quietly = TRUE)) {
+ g1 <- get("g1", envir = envir_stacomi)
+ g1 <- g1 + ggplot2::ggtitle("Les Enfrenaux") +
+ ggplot2::scale_fill_manual(
+ name = "Source",
+ values = c("purple", "#0A0C01"),
+ labels = c("historical set", "2015 values")
+ ) +
+ ggplot2::scale_colour_manual(
+ name = "Source", values = "#B8EA00",
+ labels = c("historical mean")
+ ) +
+ ggplot2::ylab("Nombre d'anguilles")
+ print(g1)
+}
+#########################################################
# Another graph to show a "manual" processing of the data
# and their extraction from the data slot
- #########################################################
- if (requireNamespace("ggplot2", quietly = TRUE)&
- requireNamespace("viridis", quietly = TRUE)){
- dat<-fun_date_extraction(r_mig_interannual@data, # data to import
- "bjo_jour", # name of the column where dates are found
- annee=FALSE,
- mois=TRUE,
- semaine =TRUE,
- jour_mois=FALSE)
-# sum per month
- res<-dplyr::select(dat,bjo_valeur,bjo_annee,semaine)
- res<-dplyr::group_by(res,bjo_annee,semaine)
- res<-dplyr::summarize(res,effectif=sum(bjo_valeur))
- ggplot2::ggplot(res, ggplot2::aes(x = semaine, y = bjo_annee,fill=effectif)) +
- ggplot2::geom_tile(colour="black") + ggplot2::coord_fixed() +
- viridis::scale_fill_viridis(begin=0,option="D") + ggplot2::theme_bw()+
- ggplot2::theme(panel.background= ggplot2::element_rect(fill = "#9360A9"),
- panel.grid.major=ggplot2::element_line(colour="#C1DB39"),
- panel.grid.minor=ggplot2::element_line(colour="#7DD632"))+
- ggplot2::ylab("year")+ggplot2::xlab("week")+
- ggplot2::ggtitle("Historical trend at Les Enfrenaux Eel trap")
-
- }
- ###############################################
+#########################################################
+if (requireNamespace("ggplot2", quietly = TRUE) &
+ requireNamespace("viridis", quietly = TRUE)) {
+ dat <- fun_date_extraction(r_mig_interannual@data, # data to import
+ "bjo_jour", # name of the column where dates are found
+ annee = FALSE,
+ mois = TRUE,
+ semaine = TRUE,
+ jour_mois = FALSE
+ )
+ # sum per month
+ res <- dplyr::select(dat, bjo_valeur, bjo_annee, semaine)
+ res <- dplyr::group_by(res, bjo_annee, semaine)
+ res <- dplyr::summarize(res, effectif = sum(bjo_valeur))
+ ggplot2::ggplot(res, ggplot2::aes(x = semaine, y = bjo_annee, fill = effectif)) +
+ ggplot2::geom_tile(colour = "black") +
+ ggplot2::coord_fixed() +
+ viridis::scale_fill_viridis(begin = 0, option = "D") +
+ ggplot2::theme_bw() +
+ ggplot2::theme(
+ panel.background = ggplot2::element_rect(fill = "#9360A9"),
+ panel.grid.major = ggplot2::element_line(colour = "#C1DB39"),
+ panel.grid.minor = ggplot2::element_line(colour = "#7DD632")
+ ) +
+ ggplot2::ylab("year") +
+ ggplot2::xlab("week") +
+ ggplot2::ggtitle("Historical trend at Les Enfrenaux Eel trap")
+}
+###############################################
# barchart with different splitting periods
# the migration is displayed against seasonal data
# extacted from all other years loaded in the report
- ################################################
+################################################
# available arguments for timesplit are "quinzaine" and "mois" and "semaine"
# with the silent=TRUE argument, it's always the latest year that is selected,
# otherwise the user is prompted with a choice, to select the year he wants
# to compare will all others...
- plot(r_mig_interannual,plot.type="barchart",timesplit="quinzaine",year_choice=2015,silent=TRUE)
-# Comparison with historical values. Each year and 2 weeks values
+plot(r_mig_interannual, plot.type = "barchart", timesplit = "quinzaine", year_choice = 2015, silent = TRUE)
+# Comparison with historical values. Each year and 2 weeks values
# is a point on the graph...
- plot(r_mig_interannual,plot.type="pointrange",timesplit="mois",year_choice=2015,silent=TRUE)
- ###############################################
+plot(r_mig_interannual, plot.type = "pointrange", timesplit = "mois", year_choice = 2015, silent = TRUE)
+###############################################
# Step plot
# different years shown in the graph
# the current year (or the selected year if silent=FALSE)
# is displayed with a dotted line
- ################################################
- plot(r_mig_interannual,plot.type="step",year_choice=2015,silent=TRUE)
- if (requireNamespace("ggplot2", quietly = TRUE)&
- requireNamespace("viridis", quietly = TRUE)){
- g<-get("g",envir=envir_stacomi) + ggplot2::theme_minimal()
- g+viridis::scale_color_viridis(discrete=TRUE)+
- ggplot2::ggtitle("Cumulated migration step plot
+################################################
+plot(r_mig_interannual, plot.type = "step", year_choice = 2015, silent = TRUE)
+if (requireNamespace("ggplot2", quietly = TRUE) &
+ requireNamespace("viridis", quietly = TRUE)) {
+ g <- get("g", envir = envir_stacomi) + ggplot2::theme_minimal()
+ g + viridis::scale_color_viridis(discrete = TRUE) +
+ ggplot2::ggtitle("Cumulated migration step plot
at les Enfrenaux eel trap")
-
- }
- ###############################################
+}
+###############################################
# Plots for seasonality of the salmon migration
# using a Loire river dataset (Vichy fishway)
- ################################################
- data("r_mig_interannual_vichy")
+################################################
+data("r_mig_interannual_vichy")
# the following show how data are processed to get
# statistics for seaonal migration, daily values
- r_mig_interannual_vichy<-calcule(r_mig_interannual_vichy,
- timesplit="jour",year_choice=2012,silent=TRUE)
-#r_mig_interannual_vichy@calcdata #check this to see the results
+r_mig_interannual_vichy <- calcule(r_mig_interannual_vichy,
+ timesplit = "jour", year_choice = 2012, silent = TRUE
+)
+# r_mig_interannual_vichy@calcdata #check this to see the results
# statistics for seaonal migration, weekly values
- r_mig_interannual_vichy<-calcule(r_mig_interannual_vichy,timesplit="semaine"
- ,year_choice=2012,silent=TRUE)
-#r_mig_interannual_vichy@calcdata
-
+r_mig_interannual_vichy <- calcule(r_mig_interannual_vichy,
+ timesplit = "semaine",
+ year_choice = 2012, silent = TRUE
+)
+# r_mig_interannual_vichy@calcdata
+
# the plot method also runs the calcule method
- plot(r_mig_interannual_vichy,plot.type="seasonal",
- timesplit="semaine", year_choice=2012, silent=TRUE)
- plot(r_mig_interannual_vichy,plot.type="seasonal",
- timesplit="mois", year_choice=2012, silent=TRUE)
- plot(r_mig_interannual_vichy,plot.type="seasonal",
- timesplit="jour",year_choice=2012, silent=TRUE)
-
-
- ###############################################
+plot(r_mig_interannual_vichy,
+ plot.type = "seasonal",
+ timesplit = "semaine", year_choice = 2012, silent = TRUE
+)
+plot(r_mig_interannual_vichy,
+ plot.type = "seasonal",
+ timesplit = "mois", year_choice = 2012, silent = TRUE
+)
+plot(r_mig_interannual_vichy,
+ plot.type = "seasonal",
+ timesplit = "jour", year_choice = 2012, silent = TRUE
+)
+
+
+###############################################
# Plots for seasonality using another Loire river dataset
-# with the migration of Lampreys (Petromyzon marinus)
+# with the migration of Lampreys (Petromyzon marinus)
# recorded at the the Descarte DF (Vienne)
- ################################################
+################################################
# run this only if you are connected to the logrami dataset
-stacomi(database_expected = TRUE, sch = 'logrami')
- bmi_des<-new("report_mig_interannual")
- bmi_des<-choice_c(bmi_des,
- dc=c(23),
- taxa=c("Petromyzon marinus"),
- stage=c("5"),
- start_year="2007",
- end_year="2014",
- silent=TRUE)
- bmi_des<-connect(bmi_des)
- bmi_des<-calcule(bmi_des,timesplit="semaine")
- plot(bmi_des,plot.type="seasonal",timesplit="semaine",year_choice=2014)
- plot(bmi_des,plot.type="seasonal",timesplit="jour",year_choice=2014)
- plot(bmi_des,plot.type="seasonal",timesplit="mois",year_choice=2014)
-}
-
-
-
+stacomi(database_expected = TRUE, sch = "logrami")
+bmi_des <- new("report_mig_interannual")
+bmi_des <- choice_c(bmi_des,
+ dc = c(23),
+ taxa = c("Petromyzon marinus"),
+ stage = c("5"),
+ start_year = "2007",
+ end_year = "2014",
+ silent = TRUE
+)
+bmi_des <- connect(bmi_des)
+bmi_des <- calcule(bmi_des, timesplit = "semaine")
+plot(bmi_des, plot.type = "seasonal", timesplit = "semaine", year_choice = 2014)
+plot(bmi_des, plot.type = "seasonal", timesplit = "jour", year_choice = 2014)
+plot(bmi_des, plot.type = "seasonal", timesplit = "mois", year_choice = 2014)
+}
}
\seealso{
Other report Objects:
diff --git a/man/report_mig_mult-class.Rd b/man/report_mig_mult-class.Rd
index 0fbd9da..c9c5e0a 100644
--- a/man/report_mig_mult-class.Rd
+++ b/man/report_mig_mult-class.Rd
@@ -51,7 +51,7 @@ stacomi(database_expected=FALSE)
## launches the application in the command line
## here an example of loading
## the following lines will only run if you have the program installed
-## and the iav scheme available in the database
+## and the test scheme available in the database
## this example generates the r_mig_mult dataset
# prompt for user and password but you can set appropriate options for host, port and dbname
\dontrun{
@@ -122,6 +122,8 @@ plot(r_mig_mult,plot.type="standard",silent=TRUE)
# Combined plot for ggplot2
plot(r_mig_mult,plot.type="multiple",silent=TRUE)
+
+ plot(r_mig_mult,plot.type="time",silent=TRUE)
# Data will be written in the data directory specified in
# the datawd argument to stacomi, default "~"
summary(r_mig_mult,silent=FALSE)
diff --git a/man/report_sample_char-class.Rd b/man/report_sample_char-class.Rd
index 65f9fba..ba903f9 100644
--- a/man/report_sample_char-class.Rd
+++ b/man/report_sample_char-class.Rd
@@ -42,96 +42,101 @@ of the view vue_lot_ope_car
stacomi( database_expected=FALSE)
# If you have a working database
# the following line of code will create the r_sample_char
-# dataset from the iav (default) schema in the database
+# dataset from the test (default) schema in the database
\dontrun{
- stacomi(database_expected=TRUE) # uses default option sch = 'iav'
- # prompt for user and password, you can set these in the options,
- # including dbname and host
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
- }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.user = password
- )
+ stacomi(database_expected = TRUE) # uses default option sch = 'test'
+ # prompt for user and password, you can set these in the options,
+ # including dbname and host
+ if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
#create an instance of the class
r_sample_char <- new("report_sample_char")
- # the following will load data for size,
+ # the following will load data for size,
# parameters 1786 (total size) C001 (size at video control)
# dc 5 and 6 are fishways located on the Arzal dam
# two stages are selected
- r_sample_char <- choice_c(r_sample_char,
- dc=c(5,6),
- taxa=c("Anguilla anguilla"),
- stage=c("AGJ","CIV"),
- par=c(1785,1786,1787,"C001"),
- horodatedebut="2013-01-01",
- horodatefin="2013-12-31",
- silent=FALSE)
+ r_sample_char <- choice_c(
+ r_sample_char,
+ dc = c(5, 6),
+ taxa = c("Anguilla anguilla"),
+ stage = c("AGJ", "CIV"),
+ par = c(1786, "C001"),
+ horodatedebut = "2013-01-01",
+ horodatefin = "2013-12-31",
+ silent = FALSE
+ )
# two warning produced, ignored if silent=TRUE
r_sample_char <- connect(r_sample_char)
- r_sample_char <- calcule(r_sample_char,silent=TRUE)
+ r_sample_char <- calcule(r_sample_char, silent = TRUE)
-}
+}
# load the dataset generated by previous lines
data("r_sample_char")
# A "violin" plot
-plot(r_sample_char,plot.type="1",silent=TRUE)
+plot(r_sample_char, plot.type = "1", silent = TRUE)
# get the plot from envir_stacomi to change labels for name
# if you use require(ggplot2) the :: argument is not needed
# e.g. write require(ggplot2);g<-get("g",envir=envir_stacomi)
# g+xlab("size")+ylab("year")
-if (requireNamespace("ggplot2", quietly = TRUE)){
- g<-get("g",envir=envir_stacomi)
- g+ggplot2::xlab("size")+ggplot2::ylab("year")
+if (requireNamespace("ggplot2", quietly = TRUE)) {
+ g1 <- get("g1", envir = envir_stacomi)
+ g1 + ggplot2::xlab("size") + ggplot2::ylab("year")
}
-# A boxplot per month
-plot(r_sample_char,plot.type="2",silent=TRUE)
-# A xyplot
-plot(r_sample_char,plot.type="3",silent=TRUE)
+# A boxplot per month (named g2 in envir_stacomi)
+plot(r_sample_char, plot.type = "2", silent = TRUE)
+# A xyplot (named g3 in envir_stacomi)
+plot(r_sample_char, plot.type = "3", silent = TRUE)
\dontrun{
#####################################
-# an example graph created manually from data
+ # an example graph created manually from data
#####################################
-# two variables one on DC, one on stage
-# passing dc information to the stage variable
- r_sample_char@data$std_libelle[r_sample_char@data$ope_dic_identifiant==5]<-
- "Yellow eel (vert. slot fishway)"
- r_sample_char@data$std_libelle[r_sample_char@data$std_libelle=="Anguille jaune"]<-
- "Yellow eel (ramp)"
- r_sample_char@data$std_libelle[r_sample_char@data$std_libelle=="civelle"]<-
- "Glass eel (ramp)"
-# creating a boxplot with custom output : an example
-# again if you use require(ggplot2) the :: argument is not needed
+ # two variables one on DC, one on stage
+ # passing dc information to the stage variable
+ r_sample_char@data$std_libelle[r_sample_char@data$ope_dic_identifiant ==
+ 5] <-
+ "Yellow eel (vert. slot fishway)"
+ r_sample_char@data$std_libelle[r_sample_char@data$std_libelle == "Anguille jaune"] <-
+ "Yellow eel (ramp)"
+ r_sample_char@data$std_libelle[r_sample_char@data$std_libelle == "civelle"] <-
+ "Glass eel (ramp)"
+ # creating a boxplot with custom output : an example
+ # again if you use require(ggplot2) the :: argument is not needed
- if (requireNamespace("ggplot2", quietly = TRUE)){
- g<-ggplot2::ggplot(r_sample_char@data)+
- ggplot2::geom_boxplot(ggplot2::aes(x=annee,
- y =car_valeur_quantitatif,
- fill = std_libelle))+
- ggplot2::xlab("size")+ggplot2::ylab("year")+
- ggplot2::scale_fill_manual("stage & fishway",
- values=c("Yellow eel (vert. slot fishway)"="blue",
- "Yellow eel (ramp)"="turquoise3",
- "Glass eel (ramp)"="Cyan"))+
- ggplot2::theme_bw()
- print(g)
+ if (requireNamespace("ggplot2", quietly = TRUE)) {
+ g <- ggplot2::ggplot(r_sample_char@data) +
+ ggplot2::geom_boxplot(ggplot2::aes(x = annee, y = car_valeur_quantitatif, fill = std_libelle)) +
+ ggplot2::xlab("size") + ggplot2::ylab("year") +
+ ggplot2::scale_fill_manual(
+ "stage & fishway",
+ values = c(
+ "Yellow eel (vert. slot fishway)" = "blue",
+ "Yellow eel (ramp)" = "turquoise3",
+ "Glass eel (ramp)" = "Cyan"
+ )
+ ) +
+ ggplot2::theme_bw()
+ print(g)
}
-# get a simple summary using Hmisc::describe
+ # get a simple summary using Hmisc::describe
summary(r_sample_char)
-# get the command line to create the object using choice_c
-# when the graphical interface has been used
+ # get the command line to create the object using choice_c
+ # when the graphical interface has been used
print(r_sample_char)
}
}
diff --git a/man/report_sea_age-class.Rd b/man/report_sea_age-class.Rd
index f73b724..6e809b1 100644
--- a/man/report_sea_age-class.Rd
+++ b/man/report_sea_age-class.Rd
@@ -48,63 +48,65 @@ This class is displayed by interface_report_sea_age
\examples{
require(stacomiR)
-stacomi(
- database_expected=FALSE)
+stacomi(database_expected = FALSE)
# If you have a working database
-# the following line of code will create the r_seaa dataset
+# the following line of code will create the r_seaa dataset
# from the logrami schema in the database
\dontrun{
- stacomi(database_expected=TRUE, sch='logrami')
- # overrides the default option sch = 'iav'
- # prompt for user and password, you can set these in the options,
- # including dbname and host
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
- }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.user = password
- )
+ stacomi(database_expected = TRUE, sch = 'test')
+ # prompt for user and password, you can set these in the options,
+ # including dbname and host
+ if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
#create an instance of the class
- r_seaa<-new("report_sea_age")
- r_seaa<-choice_c(r_seaa,
- dc=c(107,108,101),
- horodatedebut="2012-01-01",
- horodatefin="2012-12-31",
- limit1hm=675,
- limit2hm=875,
- silent=FALSE
+ r_seaa <- new("report_sea_age")
+ r_seaa <- choice_c(
+ r_seaa,
+ dc = c(19, 20),
+ horodatedebut = "2012-01-01",
+ horodatefin = "2012-12-31",
+ stage = c('5'),
+ par = c('C001', 'A124'),
+ limit1hm = 675,
+ limit2hm = 875,
+ silent = FALSE
)
- r_seaa<-connect(r_seaa)
- r_seaa<-calcule(r_seaa)
+ r_seaa <- connect(r_seaa)
+ r_seaa <- calcule(r_seaa)
-}
+}
# load the dataset generated by previous lines
# Salmons from the loire on two dams
data("r_seaa")
# the calculation will fill the slot calcdata
-# stages are in r_seaa@calcdata[["6"]][,"stage"]
+# stages are in r_seaa@calcdata[["6"]][,"stage"]
#look at data structure using str(r_seaa@calcdata[["6"]])
# plot data to confirm the split by limits is correct
-plot(r_seaa, plot.type=1)
+plot(r_seaa, plot.type = 1)
# if there are several dc, data it split by dc
-plot(r_seaa, plot.type=2)
+plot(r_seaa, plot.type = 2)
\dontrun{
-# print a summary statistic, and save the output in a list for later use
- stats<-summary(r_seaa)
+ # print a summary statistic, and save the output in a list for later use
+ stats <- summary(r_seaa)
write_database(r_seaa)
}
+
}
\seealso{
Other report Objects:
diff --git a/man/report_silver_eel-class.Rd b/man/report_silver_eel-class.Rd
index b09fe4f..1b5a164 100644
--- a/man/report_silver_eel-class.Rd
+++ b/man/report_silver_eel-class.Rd
@@ -48,64 +48,66 @@ This class is displayed by interface_report_silver_eel
\examples{
# launching stacomi without selecting the scheme or interface
-stacomi( database_expected=FALSE)
+stacomi(database_expected = FALSE)
# the following script will load data from the two Anguillere monitored in the Somme
# If you have a working database
-# the following line of code will create the r_silver dataset
+# the following line of code will create the r_silver dataset
# from the "fd80." schema in the database
\dontrun{
- stacomi(database_expected=TRUE, sch="fd80.") # overrides the default option sch = 'iav'
- # prompt for user and password, you can set these in the options,
- # including dbname and host
- if (interactive()){
- if (!exists("user")){
- user <- readline(prompt="Enter user: ")
- password <- readline(prompt="Enter password: ")
- }
- }
- options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host ="localhost",
- stacomiR.port = "5432",
- stacomiR.user = user,
- stacomiR.user = password
- )
-
+ stacomi(database_expected = TRUE, sch = "fd80.") # overrides the default option sch = 'iav'
+ # prompt for user and password, you can set these in the options,
+ # including dbname and host
+ if (interactive()) {
+ if (!exists("user")) {
+ user <- readline(prompt = "Enter user: ")
+ password <- readline(prompt = "Enter password: ")
+ }
+ }
+ options(
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = "localhost",
+ stacomiR.port = "5432",
+ stacomiR.user = user,
+ stacomiR.user = password
+ )
+
#create an instance of the class
- r_silver<-new("report_silver_eel")
- r_silver<-choice_c(r_silver,
- dc=c(2,6),
- horodatedebut="2010-09-01",
- horodatefin="2016-10-04",
- silent=FALSE)
- r_silver<-connect(r_silver)
-}
+ r_silver <- new("report_silver_eel")
+ r_silver <- choice_c(
+ r_silver,
+ dc = c(2, 6),
+ horodatedebut = "2010-09-01",
+ horodatefin = "2016-10-04",
+ silent = FALSE
+ )
+ r_silver <- connect(r_silver)
+}
# load the dataset generated by previous lines
data("r_silver")
# the calculation will fill the slot calcdata
-r_silver<-calcule(r_silver)
-# stages are in r_silver@calcdata[["6"]][,"stage"]
+r_silver <- calcule(r_silver)
+# stages are in r_silver@calcdata[["6"]][,"stage"]
#look at data structure using str(r_silver@calcdata[["6"]])
# standard plot as drawn by Laurent Beaulaton (Analyse des donnees d'argenture acquises en France)
# showing Durif's stage according to size and eye diameter
-plot(r_silver, plot.type=1)
+plot(r_silver, plot.type = 1)
# number per month or year and Durif's stage (year if number of dc >1)
-plot(r_silver, plot.type="2")
+plot(r_silver, plot.type = "2")
# plot showing fulton's coefficient, and size weight graphs
-# inspired from Acou et al., 2009
+# inspired from Acou et al., 2009
# Differential Production and Condition Indices of Premigrant
# Eels in Two Small Atlantic Coastal Catchments
# of France
-plot(r_silver, plot.type="3")
+plot(r_silver, plot.type = "3")
# get a list of summary data and print output to screen
-plot(r_silver, plot.type="4")
+plot(r_silver, plot.type = "4")
# print a summary statistic, and save the output in a list for later use
-stats<-summary(r_silver)
+stats <- summary(r_silver)
}
\seealso{
Other report Objects:
diff --git a/man/report_species-class.Rd b/man/report_species-class.Rd
index a396d61..d25295e 100644
--- a/man/report_species-class.Rd
+++ b/man/report_species-class.Rd
@@ -36,53 +36,60 @@ year/week/month.
\examples{
# launching stacomi without selecting the scheme or interface
-stacomi( database_expected=FALSE)
-# the following script will load data
+stacomi(database_expected = FALSE)
+# the following script will load data
# from the two Anguillere monitored in the Somme
# If you have a working database
-# the following line of code will create the bilesp dataset from the "iav."
+# the following line of code will create the bilesp dataset from the "test."
# schema in the database
\dontrun{
- bilesp<-new("report_species")
+ bilesp <- new("report_species")
# split is one of "none", "year", "week", "month
- bilesp<-choice_c(bilesp,
- dc=c(5,6,12),
- split="year",
- start_year="2008",
- end_year="2012",
- silent=FALSE)
+ bilesp <- choice_c(
+ bilesp,
+ dc = c(5, 6, 12),
+ split = "year",
+ start_year = "2009",
+ end_year = "2012",
+ silent = FALSE
+ )
bilesp <- connect(bilesp)
bilesp <- calcule(bilesp)
- plot(bilesp, plot.type="pie", silent=FALSE)
- plot(bilesp, plot.type="barplot", silent=FALSE)
- bilesp <- choice_c(bilesp,
- dc=c(5,6,12),
- split="month",
- start_year="2015",
- end_year="2016",
- silent=FALSE)
+ plot(bilesp, plot.type = "pie", silent = FALSE)
+ plot(bilesp, plot.type = "barplot", silent = FALSE)
+ bilesp <- choice_c(
+ bilesp,
+ dc = c(5, 6, 12),
+ split = "month",
+ start_year = "2009",
+ end_year = "2012",
+ silent = FALSE
+ )
bilesp <- charge(bilesp)
bilesp <- connect(bilesp)
- plot(bilesp, plot.type="pie", silent=FALSE)
- plot(bilesp, plot.type="barplot", silent=FALSE)
+ bilesp <- calcule(bilesp)
+ plot(bilesp, plot.type = "pie", silent = FALSE)
+ plot(bilesp, plot.type = "barplot", silent = FALSE)
#length(unique(bilesp@calcdata$taxa_stage)) # 15
# here creating a vector of length 15 with nice blending colours
- if (requireNamespace("grDevices", quietly = TRUE)) {
- mycolorrampblue <-
- grDevices::colorRampPalette(c("#395B74", "#010F19"))
- mycolorrampyellow <-
- grDevices::colorRampPalette(c("#B59C53", "#271D00"))
- mycolorrampred <-
- grDevices::colorRampPalette(c("#B56F53", "#270B00"))
- color<-c(mycolorrampblue(5),
- mycolorrampyellow(5),
- mycolorrampred(5))
- plot(bilesp,plot.type="barplot",color=color,silent=TRUE)
- }
+ if (requireNamespace("grDevices", quietly = TRUE)) {
+ mycolorrampblue <-
+ grDevices::colorRampPalette(c("#395B74", "#010F19"))
+ mycolorrampyellow <-
+ grDevices::colorRampPalette(c("#B59C53", "#271D00"))
+ mycolorrampred <-
+ grDevices::colorRampPalette(c("#B56F53", "#270B00"))
+ color <- c(mycolorrampblue(3),
+ mycolorrampyellow(3),
+ mycolorrampred(4))
+ plot(bilesp,
+ plot.type = "barplot",
+ color = color,
+ silent = TRUE)
+ }
summary(bilesp)
-}
-
+}
}
\seealso{
Other report Objects:
diff --git a/man/stacomi.Rd b/man/stacomi.Rd
index 8da2106..eb13dc5 100644
--- a/man/stacomi.Rd
+++ b/man/stacomi.Rd
@@ -22,23 +22,23 @@ To change the language use Sys.setenv(LANG = 'fr') or Sys.setenv(LANG = 'en')
}
\examples{
- require(stacomiR)
-#launch stacomi
- \dontrun{
-stacomi(database_expected=TRUE, datawd='~',sch= "iav")
+require(stacomiR)
+# launch stacomi
+\dontrun{
+stacomi(database_expected = TRUE, datawd = tempdir(), sch = "iav")
}
# launch stacomi without connection to the database
-stacomi(database_expected=FALSE)
+stacomi(database_expected = FALSE)
# launch stacomi with options
options(
- stacomiR.dbname = "bd_contmig_nat",
- stacomiR.host = readline(prompt = "Enter host: "),
- stacomiR.port = "5432",
- stacomiR.user = readline(prompt = "Enter user: "),
- stacomiR.password = readline(prompt = "Enter password: ")
+ stacomiR.dbname = "bd_contmig_nat",
+ stacomiR.host = readline(prompt = "Enter host: "),
+ stacomiR.port = "5432",
+ stacomiR.user = readline(prompt = "Enter user: "),
+ stacomiR.password = readline(prompt = "Enter password: ")
)
# another usefull option to print all queries run by stacomiR to the console
- options('stacomiR.printqueries'= TRUE)
+options("stacomiR.printqueries" = TRUE)
}
\author{
Cedric Briand \email{cedric.briand@eptb-vilaine.fr}
--
GitLab
From 4cf6c2686450851f8c414b5cff5ee58f7c970307 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Sat, 1 Mar 2025 19:54:32 +0100
Subject: [PATCH 09/13] up
---
dev/03_deploy.R | 2 +-
gitlab-ci/codecov.gitlab-ci.yml | 11 +++-
gitlab-ci/helper.R | 16 +++++
tests/testthat/helper.R | 2 +
vignettes/stacomir.R | 105 --------------------------------
5 files changed, 27 insertions(+), 109 deletions(-)
create mode 100644 gitlab-ci/helper.R
delete mode 100644 vignettes/stacomir.R
diff --git a/dev/03_deploy.R b/dev/03_deploy.R
index 6346d20..4d83762 100644
--- a/dev/03_deploy.R
+++ b/dev/03_deploy.R
@@ -21,7 +21,7 @@ Sys.setenv("LANGUAGE" = "en") # otherwise problems when running from Rstudio
options(
stacomiR.dbname = "bd_contmig_nat",
stacomiR.host = "localhost",
- stacomiR.port = "5432",
+ stacomiR.port = "5435",
stacomiR.user = "stacomi_test",
stacomiR.password = "stacomi_test"
)
diff --git a/gitlab-ci/codecov.gitlab-ci.yml b/gitlab-ci/codecov.gitlab-ci.yml
index a4eb6cd..2a07ea9 100644
--- a/gitlab-ci/codecov.gitlab-ci.yml
+++ b/gitlab-ci/codecov.gitlab-ci.yml
@@ -6,12 +6,17 @@
- Rscript -e 'pak::pkg_install(pkg = c("covr", "DT"), upgrade = FALSE)'
- Rscript -e 'pak::pak(pkg = ".", upgrade = FALSE)'
- |
- Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all();
- options(stacomiR.dbname = "'${PG_DB}'",
+ Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all();
+ txt_option <- "options(stacomiR.dbname = "'${PG_DB}'",
stacomiR.host = "'${PG_HOST}'",
stacomiR.port = "'${PG_PORT}'",
stacomiR.user = "'${PG_USER}'",
- stacomiR.password ="'${PG_USER_PASSWORD}'");
+ stacomiR.password ="'${PG_USER_PASSWORD}'")";
+ source("gitlab-ci/helper.R");
+ copier_option(
+ file_path = "tests/testthat/helper.R",
+ new_text = txt_option
+ )
covr::gitlab(quiet = FALSE)'
coverage: '/Coverage: \d+\.\d+/'
artifacts:
diff --git a/gitlab-ci/helper.R b/gitlab-ci/helper.R
new file mode 100644
index 0000000..5d24a74
--- /dev/null
+++ b/gitlab-ci/helper.R
@@ -0,0 +1,16 @@
+copier_option <- function(
+ file_path = "chemin/vers/votre/fichier.txt",
+ old_text = "# options here for codecov",
+ new_text = "mon code"
+) {
+ # Lire le contenu du fichier
+ file_content <- readLines(file_path, encoding = "UTF-8")
+
+ # Remplacer le texte
+ new_content <- gsub(old_text, new_text, file_content)
+
+ # Écrire le nouveau contenu dans le fichier
+ writeLines(new_content, file_path)
+
+ cat("Remplacement effectué avec succès dans le fichier :", file_path, "\n")
+}
diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
index 1863ef2..b07e1eb 100644
--- a/tests/testthat/helper.R
+++ b/tests/testthat/helper.R
@@ -4,6 +4,8 @@
# https://testthat.r-lib.org/articles/test-fixtures.html#withr-defer-
# could have used with_envvar and local_envvar but had to set them each time
+# options here for codecov
+
password <- getOption("stacomiR.password") # if not set will be ""
dbname <- getOption("stacomiR.dbname") # if not set will be ""
user <- getOption("stacomiR.user")
diff --git a/vignettes/stacomir.R b/vignettes/stacomir.R
deleted file mode 100644
index 5a35e17..0000000
--- a/vignettes/stacomir.R
+++ /dev/null
@@ -1,105 +0,0 @@
-## ----setup, include = FALSE---------------------------------------------------
-require(knitr)
-knitr::opts_chunk$set(
- collapse = TRUE,
- comment = "#>",
- fig.path = "../man/figures/README-"
-)
-opts_knit$set(message=FALSE, warnings=FALSE,error=FALSE,include=FALSE)
-
-## ----echo=FALSE, include=FALSE------------------------------------------------
-library(stacomiR)
-
-
-## ---- eval=FALSE--------------------------------------------------------------
-# # get the package from CRAN
-# install.packages("stacomiR")
-# # get the development version
-# install.packages("stacomiR", repos="http://R-Forge.R-project.org")
-
-## ---- eval=FALSE--------------------------------------------------------------
-# stacomi()
-
-## ---- eval=FALSE--------------------------------------------------------------
-# #here is an example to connect with interactive use
-# options(
-# stacomiR.dbname = "bd_contmig_nat",
-# stacomiR.host = readline(prompt = "Enter host: "),
-# stacomiR.port = "5432",
-# stacomiR.user = readline(prompt = "Enter user: "),
-# stacomiR.password = readline(prompt = "Enter password: ")
-# )
-# # the schema of connection is passed by sch
-# stacomi(database_expected = TRUE, sch= "iav")
-
-## ---- eval=TRUE, echo=TRUE----------------------------------------------------
-## launches the application in the command line without connection to the database
-stacomi(database_expected=FALSE)
-
-## ----eval=FALSE,echo=TRUE-----------------------------------------------------
-# require(stacomiR)
-# stacomi(
-# database_expected=TRUE)
-# r_mig_mult=new("report_mig_mult")
-# r_mig_mult=choice_c(r_mig_mult,
-# dc=c(5,6,12),
-# taxa=c("Anguilla anguilla"),
-# stage=c("AGG","AGJ","CIV"),
-# datedebut="2011-01-01",
-# datefin="2011-12-31")
-# r_mig_mult<-charge(r_mig_mult)
-# # launching charge will also load classes associated with the report
-# # e.g. report_ope, report_df, report_dc
-# r_mig_mult<-connect(r_mig_mult)
-# # calculations
-# r_mig_mult<-calcule(r_mig_mult,silent=TRUE)
-
-## ----rmmstd,eval=FALSE,echo=TRUE,message=FALSE,fig.height=6,fig.with=8--------
-# # Without a connection at the database we can launch these lines to generate the graph
-# # To obtain titles in french use Sys.setenv(LANG = "fr")
-# # the
-# require(stacomiR)
-# stacomi(
-# database_expected=FALSE)
-# data("r_mig_mult")
-# data("r_mig_mult_ope")
-# assign("report_ope",r_mig_mult_ope,envir=envir_stacomi)
-# data("r_mig_mult_df")
-# assign("report_df",r_mig_mult_df,envir=envir_stacomi)
-# data("r_mig_mult_dc")
-# assign("report_dc",r_mig_mult_dc,envir=envir_stacomi)
-# # The two lines below avoid an error in MacOSX, the r_mig_mult currently has CET
-# # which for some reason provides a failure when testing the vignette in MaxOSX (twice the same date in seq.POSIXt)
-# attr(r_mig_mult@data$ope_date_debut, "tzone") <- "UTC"
-# attr(r_mig_mult@data$ope_date_fin, "tzone") <- "UTC"
-# r_mig_mult <- calcule(r_mig_mult,silent=TRUE)
-#
-#
-# # restrict to glass eel
-# r_mig_mult@stage@stage_selected <- r_mig_mult@stage@stage_selected[3]
-# r_mig_mult@dc@dc_selected <- r_mig_mult@dc@dc_selected[3]
-# r_mig_mult <- calcule(r_mig_mult,silent=TRUE)
-# plot(r_mig_mult, plot.type="standard", silent=TRUE)
-
-## ----rmmmult,eval=TRUE,echo=TRUE,fig.height = 4, fig.width = 6----------------
-
-plot(r_mig_mult,plot.type="multiple",silent=TRUE)
-
-## ----silver,eval=TRUE,echo=TRUE,message=FALSE,warning=FALSE,fig.height = 4, fig.width = 6,fig.keep="all"----
-require(stacomiR)
-data("coef_durif")
-# load a dataset of class report_silver_eel with data slot already prepared
-# here is an example of output
-data("r_silver")
-r_silver <- calcule(r_silver)
-plot(r_silver, plot.type="3")
-#######################################
-# To use the function fun_stage_durif manually
-# create a matrix with columns BL","W","Dv","Dh","FL"
-#############################################
-# here it is extracted from the data at hand
-silver_eel<-as.matrix(r_silver@calcdata[[1]][,c("BL","W","Dv","Dh","FL")])
-head(silver_eel) # to see the first lines
-stage <- fun_stage_durif(silver_eel) # apply the function to the matrix
-stage[1:10] # look at the first 10 elements in vector silver
-
--
GitLab
From 9e075bc8f61625633980945eaaa8f3accd15b942 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Sun, 2 Mar 2025 10:59:41 +0100
Subject: [PATCH 10/13] up
---
gitlab-ci/codecov.gitlab-ci.yml | 9 +++++----
1 file changed, 5 insertions(+), 4 deletions(-)
diff --git a/gitlab-ci/codecov.gitlab-ci.yml b/gitlab-ci/codecov.gitlab-ci.yml
index 2a07ea9..d15981d 100644
--- a/gitlab-ci/codecov.gitlab-ci.yml
+++ b/gitlab-ci/codecov.gitlab-ci.yml
@@ -8,10 +8,11 @@
- |
Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all();
txt_option <- "options(stacomiR.dbname = "'${PG_DB}'",
- stacomiR.host = "'${PG_HOST}'",
- stacomiR.port = "'${PG_PORT}'",
- stacomiR.user = "'${PG_USER}'",
- stacomiR.password ="'${PG_USER_PASSWORD}'")";
+ txt_option <- paste0("options(stacomiR.dbname = '", ${PG_DB},"',
+ stacomiR.host = '", ${PG_HOST},"',
+ stacomiR.port = '", ${PG_PORT},"',
+ stacomiR.user = '", ${PG_USER},"',
+ stacomiR.password = '", ${PG_USER_PASSWORD}, "')");
source("gitlab-ci/helper.R");
copier_option(
file_path = "tests/testthat/helper.R",
--
GitLab
From 339d4e82615ff5d030edd24a5438e3616be36cdf Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Sun, 2 Mar 2025 11:44:28 +0100
Subject: [PATCH 11/13] up
---
R/stacomi.R | 2 +-
README.md | 16 ++++++++++------
dev/03_deploy.R | 2 +-
gitlab-ci/check.gitlab-ci.yml | 7 ++++++-
gitlab-ci/codecov.gitlab-ci.yml | 1 -
inst/examples/report_mig_interannual-example.R | 16 ++++++++++++++--
inst/examples/report_sample_char-example.R | 4 +++-
man/report_mig_interannual-class.Rd | 16 ++++++++++++++--
man/report_sample_char-class.Rd | 4 +++-
man/stacomi.Rd | 2 +-
10 files changed, 53 insertions(+), 17 deletions(-)
diff --git a/R/stacomi.R b/R/stacomi.R
index 3e3bc51..a7c3bbb 100644
--- a/R/stacomi.R
+++ b/R/stacomi.R
@@ -103,7 +103,7 @@ load_stacomi <- function(...) {
#' @param datawd The data working directory
#' @param sch The schema in the stacomi database default 'test'.
#' @return Nothing, called for its side effect of loading
-#' @usage stacomi(database_expected=TRUE, datawd = "~", sch = "test")
+#' @usage stacomi(database_expected=TRUE, datawd = tempdir(), sch = "test")
#' @author Cedric Briand \email{cedric.briand@eptb-vilaine.fr}
#' @examples
#'
diff --git a/README.md b/README.md
index 98ecdf5..4a0d8eb 100644
--- a/README.md
+++ b/README.md
@@ -54,10 +54,10 @@ database.
``` r
library(stacomiR)
-#> Le chargement a nécessité le package : stacomirtools
-#> Le chargement a nécessité le package : RODBC
-#> Le chargement a nécessité le package : DBI
-#> Le chargement a nécessité le package : pool
+#> Loading required package: stacomirtools
+#> Loading required package: RODBC
+#> Loading required package: DBI
+#> Loading required package: pool
stacomi(database_expected = FALSE)
```
@@ -77,8 +77,8 @@ options(
stacomiR.dbname = "bd_contmig_nat",
stacomiR.host ="localhost",
stacomiR.port ="5432",
- stacomiR.user = "postgres",
- stacomiR.password = "postgres"
+ stacomiR.user = "stacomi_test",
+ stacomiR.password = "stacomi_test"
)
stacomi(database_expected = TRUE)
# set up a basic report for eel two stages (yellow and silver) annual number in pass 5, 6, 12 (fishway, left bank eel pass, right bank eel pass)
@@ -92,6 +92,10 @@ r_ann <- choice_c(
start_year ="1996",
end_year = "2015",
silent = TRUE)
+#> Warning in .local(object, ...): Attention, year 1996 is not available in the
+#> database, available years : none
+#> Warning in .local(object, ...): Attention, year 2015 is not available in the
+#> database, available years : none
r_ann <- connect(r_ann, silent = TRUE)
options(o)
```
diff --git a/dev/03_deploy.R b/dev/03_deploy.R
index 4d83762..6346d20 100644
--- a/dev/03_deploy.R
+++ b/dev/03_deploy.R
@@ -21,7 +21,7 @@ Sys.setenv("LANGUAGE" = "en") # otherwise problems when running from Rstudio
options(
stacomiR.dbname = "bd_contmig_nat",
stacomiR.host = "localhost",
- stacomiR.port = "5435",
+ stacomiR.port = "5432",
stacomiR.user = "stacomi_test",
stacomiR.password = "stacomi_test"
)
diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml
index 3714e3e..289d50d 100644
--- a/gitlab-ci/check.gitlab-ci.yml
+++ b/gitlab-ci/check.gitlab-ci.yml
@@ -6,7 +6,12 @@
stage: check
script:
- mkdir -p public/check
- - r -e 'devtools::load_all();devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")'
+ - |
+ r -e '
+ Sys.setenv('_R_CHECK_SYSTEM_CLOCK_' = 0);
+ devtools::load_all();
+ devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")
+ '
artifacts:
when: always
paths:
diff --git a/gitlab-ci/codecov.gitlab-ci.yml b/gitlab-ci/codecov.gitlab-ci.yml
index d15981d..cebbd5f 100644
--- a/gitlab-ci/codecov.gitlab-ci.yml
+++ b/gitlab-ci/codecov.gitlab-ci.yml
@@ -7,7 +7,6 @@
- Rscript -e 'pak::pak(pkg = ".", upgrade = FALSE)'
- |
Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all();
- txt_option <- "options(stacomiR.dbname = "'${PG_DB}'",
txt_option <- paste0("options(stacomiR.dbname = '", ${PG_DB},"',
stacomiR.host = '", ${PG_HOST},"',
stacomiR.port = '", ${PG_PORT},"',
diff --git a/inst/examples/report_mig_interannual-example.R b/inst/examples/report_mig_interannual-example.R
index 7e0e1b2..2a4181b 100644
--- a/inst/examples/report_mig_interannual-example.R
+++ b/inst/examples/report_mig_interannual-example.R
@@ -121,10 +121,22 @@ if (requireNamespace("ggplot2", quietly = TRUE) &
# with the silent=TRUE argument, it's always the latest year that is selected,
# otherwise the user is prompted with a choice, to select the year he wants
# to compare will all others...
-plot(r_mig_interannual, plot.type = "barchart", timesplit = "quinzaine", year_choice = 2015, silent = TRUE)
+plot(
+ r_mig_interannual,
+ plot.type = "barchart",
+ timesplit = "quinzaine",
+ year_choice = 2015,
+ silent = TRUE
+)
# Comparison with historical values. Each year and 2 weeks values
# is a point on the graph...
-plot(r_mig_interannual, plot.type = "pointrange", timesplit = "mois", year_choice = 2015, silent = TRUE)
+plot(
+ r_mig_interannual,
+ plot.type = "pointrange",
+ timesplit = "mois",
+ year_choice = 2015,
+ silent = TRUE
+)
###############################################
# Step plot
# different years shown in the graph
diff --git a/inst/examples/report_sample_char-example.R b/inst/examples/report_sample_char-example.R
index 07a35f8..e73a437 100644
--- a/inst/examples/report_sample_char-example.R
+++ b/inst/examples/report_sample_char-example.R
@@ -78,7 +78,9 @@ plot(r_sample_char, plot.type = "3", silent = TRUE)
if (requireNamespace("ggplot2", quietly = TRUE)) {
g <- ggplot2::ggplot(r_sample_char@data) +
- ggplot2::geom_boxplot(ggplot2::aes(x = annee, y = car_valeur_quantitatif, fill = std_libelle)) +
+ ggplot2::geom_boxplot(
+ ggplot2::aes(x = annee, y = car_valeur_quantitatif, fill = std_libelle)
+ ) +
ggplot2::xlab("size") + ggplot2::ylab("year") +
ggplot2::scale_fill_manual(
"stage & fishway",
diff --git a/man/report_mig_interannual-class.Rd b/man/report_mig_interannual-class.Rd
index 19f47d3..ae967b9 100644
--- a/man/report_mig_interannual-class.Rd
+++ b/man/report_mig_interannual-class.Rd
@@ -160,10 +160,22 @@ if (requireNamespace("ggplot2", quietly = TRUE) &
# with the silent=TRUE argument, it's always the latest year that is selected,
# otherwise the user is prompted with a choice, to select the year he wants
# to compare will all others...
-plot(r_mig_interannual, plot.type = "barchart", timesplit = "quinzaine", year_choice = 2015, silent = TRUE)
+plot(
+ r_mig_interannual,
+ plot.type = "barchart",
+ timesplit = "quinzaine",
+ year_choice = 2015,
+ silent = TRUE
+)
# Comparison with historical values. Each year and 2 weeks values
# is a point on the graph...
-plot(r_mig_interannual, plot.type = "pointrange", timesplit = "mois", year_choice = 2015, silent = TRUE)
+plot(
+ r_mig_interannual,
+ plot.type = "pointrange",
+ timesplit = "mois",
+ year_choice = 2015,
+ silent = TRUE
+)
###############################################
# Step plot
# different years shown in the graph
diff --git a/man/report_sample_char-class.Rd b/man/report_sample_char-class.Rd
index ba903f9..08acf26 100644
--- a/man/report_sample_char-class.Rd
+++ b/man/report_sample_char-class.Rd
@@ -118,7 +118,9 @@ plot(r_sample_char, plot.type = "3", silent = TRUE)
if (requireNamespace("ggplot2", quietly = TRUE)) {
g <- ggplot2::ggplot(r_sample_char@data) +
- ggplot2::geom_boxplot(ggplot2::aes(x = annee, y = car_valeur_quantitatif, fill = std_libelle)) +
+ ggplot2::geom_boxplot(
+ ggplot2::aes(x = annee, y = car_valeur_quantitatif, fill = std_libelle)
+ ) +
ggplot2::xlab("size") + ggplot2::ylab("year") +
ggplot2::scale_fill_manual(
"stage & fishway",
diff --git a/man/stacomi.Rd b/man/stacomi.Rd
index eb13dc5..0acdceb 100644
--- a/man/stacomi.Rd
+++ b/man/stacomi.Rd
@@ -4,7 +4,7 @@
\alias{stacomi}
\title{stacomi Main launcher for program stacomi}
\usage{
-stacomi(database_expected=TRUE, datawd = "~", sch = "test")
+stacomi(database_expected=TRUE, datawd = tempdir(), sch = "test")
}
\arguments{
\item{database_expected}{Boolean, if \code{TRUE} pre launch tests will be run to test the connection validity}
--
GitLab
From 0eb1b5fd705b5125f60bb1d13dd8675ea9fab610 Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Sun, 2 Mar 2025 12:26:12 +0100
Subject: [PATCH 12/13] up
---
gitlab-ci/check.gitlab-ci.yml | 2 +-
gitlab-ci/update_check.gitlab-ci.yml | 7 ++++++-
2 files changed, 7 insertions(+), 2 deletions(-)
diff --git a/gitlab-ci/check.gitlab-ci.yml b/gitlab-ci/check.gitlab-ci.yml
index 289d50d..8aa145c 100644
--- a/gitlab-ci/check.gitlab-ci.yml
+++ b/gitlab-ci/check.gitlab-ci.yml
@@ -8,7 +8,7 @@
- mkdir -p public/check
- |
r -e '
- Sys.setenv('_R_CHECK_SYSTEM_CLOCK_' = 0);
+ Sys.setenv("_R_CHECK_SYSTEM_CLOCK_" = 0);
devtools::load_all();
devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")
'
diff --git a/gitlab-ci/update_check.gitlab-ci.yml b/gitlab-ci/update_check.gitlab-ci.yml
index 2e32a75..44383f0 100644
--- a/gitlab-ci/update_check.gitlab-ci.yml
+++ b/gitlab-ci/update_check.gitlab-ci.yml
@@ -7,7 +7,12 @@
script:
- mkdir -p public/check
- Rscript -e 'renv::update()'
- - r -e 'devtools::load_all();devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")'
+ - |
+ r -e '
+ Sys.setenv("_R_CHECK_SYSTEM_CLOCK_" = 0);
+ devtools::load_all();
+ devtools::check(document = FALSE, args = "--no-tests", check_dir="public/check")
+ '
artifacts:
when: always
paths:
--
GitLab
From c7b229680fcf955875348284323db1c57ec7e95d Mon Sep 17 00:00:00 2001
From: Laurent BEAULATON <laurent.beaulaton@ofb.gouv.fr>
Date: Sun, 2 Mar 2025 13:07:53 +0100
Subject: [PATCH 13/13] up
---
gitlab-ci/codecov.gitlab-ci.yml | 15 +++++++++------
1 file changed, 9 insertions(+), 6 deletions(-)
diff --git a/gitlab-ci/codecov.gitlab-ci.yml b/gitlab-ci/codecov.gitlab-ci.yml
index cebbd5f..2094399 100644
--- a/gitlab-ci/codecov.gitlab-ci.yml
+++ b/gitlab-ci/codecov.gitlab-ci.yml
@@ -6,17 +6,20 @@
- Rscript -e 'pak::pkg_install(pkg = c("covr", "DT"), upgrade = FALSE)'
- Rscript -e 'pak::pak(pkg = ".", upgrade = FALSE)'
- |
- Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all();
- txt_option <- paste0("options(stacomiR.dbname = '", ${PG_DB},"',
- stacomiR.host = '", ${PG_HOST},"',
- stacomiR.port = '", ${PG_PORT},"',
- stacomiR.user = '", ${PG_USER},"',
- stacomiR.password = '", ${PG_USER_PASSWORD}, "')");
+ Rscript -e '
+ txt_option <- paste0("options(stacomiR.dbname = \"'${PG_DB}'\",
+ stacomiR.host = \"'${PG_HOST}'\",
+ stacomiR.port = \"'${PG_PORT}'\",
+ stacomiR.user = \"'${PG_USER}'\",
+ stacomiR.password = \"'${PG_USER_PASSWORD}'\")");
source("gitlab-ci/helper.R");
copier_option(
file_path = "tests/testthat/helper.R",
new_text = txt_option
)
+ '
+ - |
+ Rscript -e 'Sys.setenv("NOT_CRAN"= "true"); devtools::load_all();
covr::gitlab(quiet = FALSE)'
coverage: '/Coverage: \d+\.\d+/'
artifacts:
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GitLab