[Stacomir-commits] r483 - pkg/stacomir/vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu May 17 10:00:09 CEST 2018
Author: legrand
Date: 2018-05-17 10:00:09 +0200 (Thu, 17 May 2018)
New Revision: 483
Modified:
pkg/stacomir/vignettes/stacomir.Rmd
pkg/stacomir/vignettes/stacomir.pdf
Log:
Vignette with figures loaded automatically
Modified: pkg/stacomir/vignettes/stacomir.Rmd
===================================================================
--- pkg/stacomir/vignettes/stacomir.Rmd 2018-05-16 13:01:08 UTC (rev 482)
+++ pkg/stacomir/vignettes/stacomir.Rmd 2018-05-17 08:00:09 UTC (rev 483)
@@ -5,8 +5,10 @@
output: rmarkdown::pdf_document
vignette: >
%\VignetteIndexEntry{Vignette Title}
+ %\VignetteEncoding{UTF-8}
%\VignetteEngine{knitr::rmarkdown}
- %\VignetteEncoding{UTF-8}
+editor_options:
+ chunk_output_type: console
---
```{r setup, include = FALSE}
@@ -18,6 +20,7 @@
)
opts_knit$set(message=FALSE, warnings=FALSE,error=FALSE,include=FALSE)
```
+[![CRAN\_Status\_Badge](http://www.r-pkg.org/badges/version/stacomiR)](https://cran.r-project.org/package=stacomiR)
# stacomiR <img src="../man/figures/logo.png" align="right" />
@@ -47,8 +50,10 @@
R-Forge.
```{r , eval=FALSE}
-install.packages("stacomiR") # get the package from CRAN
-install.packages("stacomiR", repos="http://R-Forge.R-project.org") # get the development version
+# get the package from CRAN
+install.packages("stacomiR")
+# get the development version
+install.packages("stacomiR", repos="http://R-Forge.R-project.org")
```
Usage
@@ -271,21 +276,34 @@
periods) (middle), a summary of migration per month (bottom).
-```{r rmmstd,eval=FALSE,echo=TRUE,fig.keep="last"}
-# chunk not evaluated as it produces 5 plot with dev.new() called in a loop
-Sys.setenv(LANG = "fr")
- plot(r_mig_mult,plot.type="standard",silent=TRUE)
+```{r rmmstd,eval=TRUE,echo=TRUE,message=FALSE,fig.keep="last",fig.height = 8, fig.width = 6}
+# 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")
+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)
+r_mig_mult<-calcule(r_mig_mult,silent=TRUE)
+
+# To avoid call to dev.new() which creates a device per stage, DC, taxa, we simplify
+# the object as dev.new() causes knitr to crash:
+r_mig_mult at taxa@data<- r_mig_mult at taxa@data[1,]
+r_mig_mult at stage@data<-r_mig_mult at stage@data[3,]
+r_mig_mult at dc@dc_selectionne<-r_mig_mult at dc@dc_selectionne[3]
+
+plot(r_mig_mult,plot.type="standard",silent=TRUE)
+
```
-![](../man/figures/README-rmmstandard-1.png)
-
Summary of migration for different stages and counting devices
-```{r rmmmult,eval=FALSE,echo=TRUE,fig.keep="all"}
+```{r rmmmult,eval=TRUE,echo=TRUE,fig.height = 4, fig.width = 6}
plot(r_mig_mult,plot.type="multiple",silent=TRUE)
```
-![](../man/figures/README-rmmmult-1.png)
#### Silver eels
@@ -299,7 +317,7 @@
score ([Durif et al.,
2009](http://fishlarvae.org/common/SiteMedia/durif%20et%20al%202009b.pdf))
-```{r silver,eval=TRUE,echo=TRUE,fig.height = 4, fig.width = 6,fig.keep="all"}
+```{r silver,eval=TRUE,echo=TRUE,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
Modified: pkg/stacomir/vignettes/stacomir.pdf
===================================================================
--- pkg/stacomir/vignettes/stacomir.pdf 2018-05-16 13:01:08 UTC (rev 482)
+++ pkg/stacomir/vignettes/stacomir.pdf 2018-05-17 08:00:09 UTC (rev 483)
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[TRUNCATED]
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