diff --git a/DESCRIPTION b/DESCRIPTION
index 1ec245193d899bcbb550b68a62f8e47a9ade318f..66a936f2374b4f3266bc21a4fa2e3507e3077e56 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,7 +3,7 @@ Title: Kalman Filter for Impulse Noised Outliers
Version: 1.0.0
Authors@R: c(
person("Bertrand", "Cloez", email = "bertrand.cloez@inrae.fr", role = c("aut", "cre")),
- person("Isabelle", "Sanchez", email = "isabelle.sanchez@inra.fr", role = c("ctr")),
+ person("Isabelle", "Sanchez", email = "isabelle.sanchez@inrae.fr", role = c("ctr")),
person("Benedicte", "Fontez", email = "benedicte.fontez@supagro.fr", role = c("ctr")))
Author: Bertrand Cloez [aut, cre],
Isabelle Sanchez [ctr],
@@ -18,6 +18,11 @@ LazyData: TRUE
URL: https://forgemia.inra.fr/isabelle.sanchez/kfino
BugReports: https://forgemia.inra.fr/isabelle.sanchez/kfino/issues
Imports: ggplot2, dplyr
-Suggests: rmarkdown, knitr, RColorBrewer
+Suggests:
+ rmarkdown,
+ knitr,
+ RColorBrewer,
+ testthat (>= 3.0.0)
VignetteBuilder: knitr
RoxygenNote: 7.1.2
+Config/testthat/edition: 3
diff --git a/R/graph_functions.R b/R/graph_functions.R
index 12d4eb533469b6886a0eb03af93911214e4cc049..dfe806af8bddd519cb109fb8d087504dc40471b0 100644
--- a/R/graph_functions.R
+++ b/R/graph_functions.R
@@ -5,7 +5,8 @@
#' qualitative or quantitative display) or prediction
#' @param Tvar char, time variable in the data.frame datain
#' @param Yvar char, variable which was analysed in the data.frame datain
-#' @param Ident char, colname of the individual id to be analyzed
+#' @param Ident char, column name of the individual id to be analyzed
+#' @param title char, a graph title
#'
#' @details The produced graphic can be, according to typeG:
#' \describe{
@@ -45,64 +46,77 @@
#' # predictions on OK values
#' kfino_plot(resuin=resu2,typeG="prediction",
#' Tvar="Day",Yvar="Poids",Ident="IDE")
-kfino_plot<-function(resuin,typeG,
- Tvar,Yvar,Ident){
+kfino_plot<-function(resuin,
+ typeG,
+ Tvar,
+ Yvar,
+ Ident,
+ title=NULL){
- # Tests d'existence
- if (!is.null(resuin[[1]])){
- tp<-as.data.frame(resuin[[1]])
- myIDE<-unique(tp[,Ident])
+ # Existence check
+ if (is.null(resuin[[1]])) {
+ stop("NULL object - No graph to provide. Please check your input object.")
+ }
+ if (!typeG %in% c("quanti","quali","prediction")) {
+ stop("This type is not allowed.")
+ }
+ if (typeG %in% c("prediction","quanti") & is.null(resuin[[2]])) {
+ stop("NULL object - No graph to provide. Please check your input object.")
+ }
+
+ # Some formatting
+ tp<-as.data.frame(resuin[[1]])
+ myIDE<-unique(tp[,Ident])
- if (typeG == "quali"){
- if (!is.null(resuin[[2]])){
- g1<-ggplot(tp,aes_string(x=Tvar))+
- geom_point( aes_string(y=Yvar,color="flag")) +
- geom_line(data=tp[!is.na(tp$prediction),], aes(y=.data$prediction)) +
- geom_line(data=tp[!is.na(tp$prediction),], aes(y=.data$lwr),
- color="green") +
- geom_line(data=tp[!is.na(tp$prediction),], aes(y=.data$upr),
- color="green") +
- scale_color_manual(values =
- c("KO"="purple", "OK" = "black", "Bad"="red")) +
- ggtitle(paste0("kfino outlier detection - ",myIDE))
- } else {
- g1<-ggplot(tp,aes_string(x=Tvar))+
- geom_point( aes_string(y=Yvar,color="flag")) +
- scale_color_manual(values =
- c("KO"="purple", "OK" = "black", "Bad"="red")) +
- ggtitle(paste0("kfino outlier detection - ",myIDE))
- }
- return(g1)
- } else if (typeG == "quanti"){
- if (!is.null(resuin[[2]])){
- g1<-ggplot(tp,aes_string(x=Tvar))+
- geom_point( aes_string(y=Yvar,color="label_pred")) +
+ if (is.null(title)){
+ tp.title1<-paste0("kfino outlier detection - ",myIDE)
+ tp.title2<-paste0("kfino prediction - ",myIDE)
+ } else {
+ tp.title1<-paste0(title," - ",myIDE)
+ tp.title2<-paste0(title," - ",myIDE)
+ }
+
+ # graphics
+ if (typeG == "quali"){
+ if (!is.null(resuin[[2]])){
+ g1<-ggplot(tp,aes_string(x=Tvar))+
+ geom_point( aes_string(y=Yvar,color="flag")) +
geom_line(data=tp[!is.na(tp$prediction),], aes(y=.data$prediction)) +
geom_line(data=tp[!is.na(tp$prediction),], aes(y=.data$lwr),
color="green") +
geom_line(data=tp[!is.na(tp$prediction),], aes(y=.data$upr),
color="green") +
- ggtitle(paste0("kfino outlier detection - ",myIDE))
- return(g1)
- } else {
- print("NULL object - No graph to provide")
- }
- } else if (typeG == "prediction"){
- if (!is.null(resuin[[2]])){
- tp2<-filter(tp,.data$flag == "OK")
-
- g1<-ggplot(tp2,aes_string(x=Tvar))+
- geom_point( aes_string(y=Yvar)) +
- geom_line(data=tp2, aes(y=.data$prediction)) +
- geom_line(data=tp2, aes(y=.data$lwr),color="green") +
- geom_line(data=tp2, aes(y=.data$upr),color="green") +
- ggtitle(paste0("kfino prediction - ",myIDE))
- return(g1)
- } else {
- print("NULL object - No graph to provide")
- }
+ scale_color_manual(values =
+ c("KO"="purple", "OK" = "black", "Bad"="red")) +
+ ggtitle(tp.title1)
+ } else {
+ g1<-ggplot(tp,aes_string(x=Tvar))+
+ geom_point( aes_string(y=Yvar,color="flag")) +
+ scale_color_manual(values =
+ c("KO"="purple", "OK" = "black", "Bad"="red")) +
+ ggtitle(tp.title1)
}
- } else {
- stop("NULL object - No graph to provide")
+ return(g1)
+ } else if (typeG == "quanti"){
+ g1<-ggplot(tp,aes_string(x=Tvar))+
+ geom_point( aes_string(y=Yvar,color="label_pred")) +
+ geom_line(data=tp[!is.na(tp$prediction),], aes(y=.data$prediction)) +
+ geom_line(data=tp[!is.na(tp$prediction),], aes(y=.data$lwr),
+ color="green") +
+ geom_line(data=tp[!is.na(tp$prediction),], aes(y=.data$upr),
+ color="green") +
+ ggtitle(tp.title1)
+ return(g1)
+ } else if (typeG == "prediction"){
+ tp2<-filter(tp,.data$flag == "OK")
+
+ g1<-ggplot(tp2,aes_string(x=Tvar))+
+ geom_point( aes_string(y=Yvar)) +
+ geom_line(data=tp2, aes(y=.data$prediction)) +
+ geom_line(data=tp2, aes(y=.data$lwr),color="green") +
+ geom_line(data=tp2, aes(y=.data$upr),color="green") +
+ ggtitle(tp.title2)
+ return(g1)
}
-}
\ No newline at end of file
+}
+
diff --git a/man/kfino.Rd b/man/kfino.Rd
index ab2fb3466f2a024e5c22331aa0f2a12ba84bc51a..3baabd3b88f63784041461e6965fad54ad69644c 100644
--- a/man/kfino.Rd
+++ b/man/kfino.Rd
@@ -24,7 +24,7 @@ Useful links:
Other contributors:
\itemize{
- \item Isabelle Sanchez \email{isabelle.sanchez@inra.fr} [contractor]
+ \item Isabelle Sanchez \email{isabelle.sanchez@inrae.fr} [contractor]
\item Benedicte Fontez \email{benedicte.fontez@supagro.fr} [contractor]
}
diff --git a/man/kfino_plot.Rd b/man/kfino_plot.Rd
index 50f479ac57581274f0660c54c698616c9a0363e8..f264dc311f0f4dde44f6bdb55e405919208b4536 100644
--- a/man/kfino_plot.Rd
+++ b/man/kfino_plot.Rd
@@ -4,7 +4,7 @@
\alias{kfino_plot}
\title{graphical function}
\usage{
-kfino_plot(resuin, typeG, Tvar, Yvar, Ident)
+kfino_plot(resuin, typeG, Tvar, Yvar, Ident, title = NULL)
}
\arguments{
\item{resuin}{a list resulting of the kfino algorithm}
@@ -16,7 +16,9 @@ qualitative or quantitative display) or prediction}
\item{Yvar}{char, variable which was analysed in the data.frame datain}
-\item{Ident}{char, colname of the individual id to be analyzed}
+\item{Ident}{char, column name of the individual id to be analyzed}
+
+\item{title}{char, a graph title}
}
\value{
a ggplot2 graphic
diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000000000000000000000000000000000000..b38dd0795cf9c6c4384639accc4c8455412190f9
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,4 @@
+library(testthat)
+library(kfino)
+
+test_check("kfino")
diff --git a/tests/testthat/test-outputAlgo.R b/tests/testthat/test-outputAlgo.R
new file mode 100644
index 0000000000000000000000000000000000000000..3a9a5a0735ce35790926cd02b96c80da11458534
--- /dev/null
+++ b/tests/testthat/test-outputAlgo.R
@@ -0,0 +1,14 @@
+test_that("Output type", {
+ data(spring1)
+ resu1<-kfino_fit(datain=spring1,
+ Tvar="dateNum",Yvar="Poids",
+ expertMin=30,expertMax=75,
+ doOptim=FALSE,aa=0.001,sigma2_mm=0.05,
+ K=2,sigma2_pp=5)
+
+ expect_equal(str(resu1),"list")
+ expect_equal(str(resu1[[1]]),"data.frame")
+ expect_equal(str(resu1[[2]]),"data.frame")
+ expect_equal(str(resu1[[3]]),"list")
+ #expect_true(is_SBM(netA))
+})
\ No newline at end of file