[Stacomir-commits] r607 - in pkg/stacomir: doc vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Nov 15 12:03:09 CET 2021
Author: briand
Date: 2021-11-15 12:03:09 +0100 (Mon, 15 Nov 2021)
New Revision: 607
Removed:
pkg/stacomir/vignettes/stacomir.html
Modified:
pkg/stacomir/doc/stacomir.R
pkg/stacomir/doc/stacomir.Rmd
pkg/stacomir/doc/stacomir.html
pkg/stacomir/vignettes/stacomir.Rmd
Log:
vignette not building in stacomir-rforge
Modified: pkg/stacomir/doc/stacomir.R
===================================================================
--- pkg/stacomir/doc/stacomir.R 2021-11-15 10:21:52 UTC (rev 606)
+++ pkg/stacomir/doc/stacomir.R 2021-11-15 11:03:09 UTC (rev 607)
@@ -1,9 +1,9 @@
## ----setup, include = FALSE---------------------------------------------------
require(knitr)
knitr::opts_chunk$set(
- collapse = TRUE,
- comment = "#>",
- fig.path = "../man/figures/README-"
+ collapse = TRUE,
+ comment = "#>",
+ fig.path = "../man/figures/README-"
)
opts_knit$set(message=FALSE, warnings=FALSE,error=FALSE,include=FALSE)
@@ -21,8 +21,16 @@
# stacomi()
## ---- eval=FALSE--------------------------------------------------------------
-# base=c("my_stacomi_dbname","localhost","5432","myuser","mypassword")
-# stacomi(database_expected = TRUE, base=base)
+# #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
@@ -29,27 +37,29 @@
stacomi(database_expected=FALSE)
## ----eval=FALSE,echo=TRUE-----------------------------------------------------
-# 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)
+# 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=TRUE,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")
+require(stacomiR)
stacomi(
- database_expected=FALSE)
+ database_expected=FALSE)
data("r_mig_mult")
data("r_mig_mult_ope")
assign("report_ope",r_mig_mult_ope,envir=envir_stacomi)
@@ -61,9 +71,9 @@
# 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_selected<-r_mig_mult at dc@dc_selected[3]
+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_selected <- r_mig_mult at dc@dc_selected[3]
plot(r_mig_mult,plot.type="standard",silent=TRUE)
@@ -70,7 +80,7 @@
## ----rmmmult,eval=TRUE,echo=TRUE,fig.height = 4, fig.width = 6----------------
- plot(r_mig_mult,plot.type="multiple",silent=TRUE)
+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)
Modified: pkg/stacomir/doc/stacomir.Rmd
===================================================================
--- pkg/stacomir/doc/stacomir.Rmd 2021-11-15 10:21:52 UTC (rev 606)
+++ pkg/stacomir/doc/stacomir.Rmd 2021-11-15 11:03:09 UTC (rev 607)
@@ -14,9 +14,9 @@
```{r setup, include = FALSE}
require(knitr)
knitr::opts_chunk$set(
- collapse = TRUE,
- comment = "#>",
- fig.path = "../man/figures/README-"
+ collapse = TRUE,
+ comment = "#>",
+ fig.path = "../man/figures/README-"
)
opts_knit$set(message=FALSE, warnings=FALSE,error=FALSE,include=FALSE)
```
@@ -66,12 +66,31 @@
stacomi()
```
-The program can be launched to use from the command line, base is a string
-vector with 5 elements
+The program can be launched with options
+* `stacomiR.dbname`: databasename
+* `stacomiR.host`: the name of the host, default to ["localhost"]
+* `stacomiR.port`: the name of the port, default to ["5432"]
+* `stacomiR.user`: a string with the user name e.g. ["postgres"]
+* `stacomiR.password`: a string with the user password
+* `stacomiR.ODBClink`: a string with name of the ODBC link, this options is used
+ by stacomirtools to use ODBC connexion it is currently deprecated
+* `stacomiR.path`: a string with the path to where some output are written,
+ defaut '~' path to the user document folder in windows
+* `stacomiR.printqueries`: a boolean, default FALSE,
+ with the side effect of printing queries to the console
+
```{r , eval=FALSE}
-base=c("my_stacomi_dbname","localhost","5432","myuser","mypassword")
-stacomi(database_expected = TRUE, base=base)
+#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")
```
@@ -246,21 +265,22 @@
```{r ,eval=FALSE,echo=TRUE}
- 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)
+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)
```
The previous line generates data not only about the report_mig_mult class,
@@ -281,8 +301,9 @@
```{r rmmstd,eval=TRUE,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")
+require(stacomiR)
stacomi(
- database_expected=FALSE)
+ database_expected=FALSE)
data("r_mig_mult")
data("r_mig_mult_ope")
assign("report_ope",r_mig_mult_ope,envir=envir_stacomi)
@@ -294,9 +315,9 @@
# 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_selected<-r_mig_mult at dc@dc_selected[3]
+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_selected <- r_mig_mult at dc@dc_selected[3]
plot(r_mig_mult,plot.type="standard",silent=TRUE)
@@ -306,7 +327,7 @@
```{r rmmmult,eval=TRUE,echo=TRUE,fig.height = 4, fig.width = 6}
- plot(r_mig_mult,plot.type="multiple",silent=TRUE)
+plot(r_mig_mult,plot.type="multiple",silent=TRUE)
```
Modified: pkg/stacomir/doc/stacomir.html
===================================================================
--- pkg/stacomir/doc/stacomir.html 2021-11-15 10:21:52 UTC (rev 606)
+++ pkg/stacomir/doc/stacomir.html 2021-11-15 11:03:09 UTC (rev 607)
@@ -12,7 +12,7 @@
<meta name="author" content="Marion Legrand, Cedric Briand" />
-<meta name="date" content="2021-11-12" />
+<meta name="date" content="2021-11-15" />
<title>StacomiR- A package for fish migration monitoring</title>
@@ -141,7 +141,7 @@
<h1 class="title toc-ignore">StacomiR- A package for fish migration monitoring</h1>
<h4 class="author">Marion Legrand, Cedric Briand</h4>
-<h4 class="date">2021-11-12</h4>
+<h4 class="date">2021-11-15</h4>
@@ -163,9 +163,27 @@
<h2>Usage</h2>
<p>Launch the graphical interface</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">stacomi</span>()</span></code></pre></div>
-<p>The program can be launched to use from the command line, base is a string vector with 5 elements</p>
-<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>base<span class="ot">=</span><span class="fu">c</span>(<span class="st">"my_stacomi_dbname"</span>,<span class="st">"localhost"</span>,<span class="st">"5432"</span>,<span class="st">"myuser"</span>,<span class="st">"mypassword"</span>)</span>
-<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="fu">stacomi</span>(<span class="at">database_expected =</span> <span class="cn">TRUE</span>, <span class="at">base=</span>base)</span></code></pre></div>
+<p>The program can be launched with options</p>
+<ul>
+<li><code>stacomiR.dbname</code>: databasename</li>
+<li><code>stacomiR.host</code>: the name of the host, default to [“localhost”]</li>
+<li><code>stacomiR.port</code>: the name of the port, default to [“5432”]</li>
+<li><code>stacomiR.user</code>: a string with the user name e.g. [“postgres”]</li>
+<li><code>stacomiR.password</code>: a string with the user password</li>
+<li><code>stacomiR.ODBClink</code>: a string with name of the ODBC link, this options is used by stacomirtools to use ODBC connexion it is currently deprecated</li>
+<li><code>stacomiR.path</code>: a string with the path to where some output are written, defaut ‘~’ path to the user document folder in windows</li>
+<li><code>stacomiR.printqueries</code>: a boolean, default FALSE, with the side effect of printing queries to the console</li>
+</ul>
+<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="co">#here is an example to connect with interactive use</span></span>
+<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a><span class="fu">options</span>(</span>
+<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a> <span class="at">stacomiR.dbname =</span> <span class="st">"bd_contmig_nat"</span>,</span>
+<span id="cb3-4"><a href="#cb3-4" aria-hidden="true" tabindex="-1"></a> <span class="at">stacomiR.host =</span> <span class="fu">readline</span>(<span class="at">prompt =</span> <span class="st">"Enter host: "</span>),</span>
+<span id="cb3-5"><a href="#cb3-5" aria-hidden="true" tabindex="-1"></a> <span class="at">stacomiR.port =</span> <span class="st">"5432"</span>,</span>
+<span id="cb3-6"><a href="#cb3-6" aria-hidden="true" tabindex="-1"></a> <span class="at">stacomiR.user =</span> <span class="fu">readline</span>(<span class="at">prompt =</span> <span class="st">"Enter user: "</span>),</span>
+<span id="cb3-7"><a href="#cb3-7" aria-hidden="true" tabindex="-1"></a> <span class="at">stacomiR.password =</span> <span class="fu">readline</span>(<span class="at">prompt =</span> <span class="st">"Enter password: "</span>)</span>
+<span id="cb3-8"><a href="#cb3-8" aria-hidden="true" tabindex="-1"></a>)</span>
+<span id="cb3-9"><a href="#cb3-9" aria-hidden="true" tabindex="-1"></a><span class="co"># the schema of connection is passed by sch</span></span>
+<span id="cb3-10"><a href="#cb3-10" aria-hidden="true" tabindex="-1"></a><span class="fu">stacomi</span>(<span class="at">database_expected =</span> <span class="cn">TRUE</span>, <span class="at">sch=</span> <span class="st">"iav"</span>)</span></code></pre></div>
</div>
<div id="data-structure" class="section level2">
<h2>Data structure</h2>
@@ -321,48 +339,50 @@
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="do">## launches the application in the command line without connection to the database</span></span>
<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a><span class="fu">stacomi</span>(<span class="at">database_expected=</span><span class="cn">FALSE</span>) </span></code></pre></div>
<p>The following code is only run when there is a connection to the database. The program will create an object of the class report_mig_mult, and run it for several DC, here 5 is a vertical slot fishway, and 6 and 12 are two glass eel trapping ladder located at the Arzal dam in the Vilaine river (France). We are evaluating the migration of all stages of eel (glass eel CIV, yellow eel AGJ and silver eel AGG). Glass eel and yellow eel migrate to the watershed while silver eels are migrating back to the ocean. Data are loaded from the database with the <code>charge</code> method and the <code>calcule</code> method will interpolate daily migration from monitoring operations which do not necessarily span a day, and convert the glass eel weight in numbers.</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a> <span class="fu">stacomi</span>(</span>
-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a> <span class="at">database_expected=</span><span class="cn">TRUE</span>) </span>
-<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> r_mig_mult<span class="ot">=</span><span class="fu">new</span>(<span class="st">"report_mig_mult"</span>)</span>
-<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a> r_mig_mult<span class="ot">=</span><span class="fu">choice_c</span>(r_mig_mult,</span>
-<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a> <span class="at">dc=</span><span class="fu">c</span>(<span class="dv">5</span>,<span class="dv">6</span>,<span class="dv">12</span>),</span>
-<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a> <span class="at">taxa=</span><span class="fu">c</span>(<span class="st">"Anguilla anguilla"</span>),</span>
-<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a> <span class="at">stage=</span><span class="fu">c</span>(<span class="st">"AGG"</span>,<span class="st">"AGJ"</span>,<span class="st">"CIV"</span>),</span>
-<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a> <span class="at">datedebut=</span><span class="st">"2011-01-01"</span>,</span>
-<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a> <span class="at">datefin=</span><span class="st">"2011-12-31"</span>)</span>
-<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a> r_mig_mult<span class="ot"><-</span><span class="fu">charge</span>(r_mig_mult)</span>
-<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a> <span class="co"># launching charge will also load classes associated with the report</span></span>
-<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a> <span class="co"># e.g. report_ope, report_df, report_dc</span></span>
-<span id="cb5-13"><a href="#cb5-13" aria-hidden="true" tabindex="-1"></a> r_mig_mult<span class="ot"><-</span><span class="fu">connect</span>(r_mig_mult)</span>
-<span id="cb5-14"><a href="#cb5-14" aria-hidden="true" tabindex="-1"></a> <span class="co"># calculations </span></span>
-<span id="cb5-15"><a href="#cb5-15" aria-hidden="true" tabindex="-1"></a> r_mig_mult<span class="ot"><-</span><span class="fu">calcule</span>(r_mig_mult,<span class="at">silent=</span><span class="cn">TRUE</span>)</span></code></pre></div>
+<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="fu">require</span>(stacomiR)</span>
+<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a><span class="fu">stacomi</span>(</span>
+<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a> <span class="at">database_expected=</span><span class="cn">TRUE</span>) </span>
+<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>r_mig_mult<span class="ot">=</span><span class="fu">new</span>(<span class="st">"report_mig_mult"</span>)</span>
+<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>r_mig_mult<span class="ot">=</span><span class="fu">choice_c</span>(r_mig_mult,</span>
+<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a> <span class="at">dc=</span><span class="fu">c</span>(<span class="dv">5</span>,<span class="dv">6</span>,<span class="dv">12</span>),</span>
+<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a> <span class="at">taxa=</span><span class="fu">c</span>(<span class="st">"Anguilla anguilla"</span>),</span>
+<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a> <span class="at">stage=</span><span class="fu">c</span>(<span class="st">"AGG"</span>,<span class="st">"AGJ"</span>,<span class="st">"CIV"</span>),</span>
+<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a> <span class="at">datedebut=</span><span class="st">"2011-01-01"</span>,</span>
+<span id="cb5-10"><a href="#cb5-10" aria-hidden="true" tabindex="-1"></a> <span class="at">datefin=</span><span class="st">"2011-12-31"</span>)</span>
+<span id="cb5-11"><a href="#cb5-11" aria-hidden="true" tabindex="-1"></a>r_mig_mult<span class="ot"><-</span><span class="fu">charge</span>(r_mig_mult)</span>
+<span id="cb5-12"><a href="#cb5-12" aria-hidden="true" tabindex="-1"></a><span class="co"># launching charge will also load classes associated with the report</span></span>
+<span id="cb5-13"><a href="#cb5-13" aria-hidden="true" tabindex="-1"></a><span class="co"># e.g. report_ope, report_df, report_dc</span></span>
+<span id="cb5-14"><a href="#cb5-14" aria-hidden="true" tabindex="-1"></a>r_mig_mult<span class="ot"><-</span><span class="fu">connect</span>(r_mig_mult)</span>
+<span id="cb5-15"><a href="#cb5-15" aria-hidden="true" tabindex="-1"></a><span class="co"># calculations </span></span>
+<span id="cb5-16"><a href="#cb5-16" aria-hidden="true" tabindex="-1"></a>r_mig_mult<span class="ot"><-</span><span class="fu">calcule</span>(r_mig_mult,<span class="at">silent=</span><span class="cn">TRUE</span>)</span></code></pre></div>
<p>The previous line generates data not only about the report_mig_mult class, but also runs dependent classes which describe how the fishway (DF) and counting devices (DC) have been operated. Sometimes there are no data but only because the camera was not working. There are also information about the operations (e.g. periods at wich a trap content has been evaluated). Here we load what would have been generated if we had run the previous lines.</p>
<p>One graph per DC, taxa and stage. Below as an example, the glass eel migration in weight and number (top), the periods and type of operation for DF and DC, and the operation (trapping periods) (middle), a summary of migration per month (bottom).</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Without a connection at the database we can launch these lines to generate the graph</span></span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="co"># To obtain titles in french use Sys.setenv(LANG = "fr")</span></span>
-<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="fu">stacomi</span>(</span>
-<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a> <span class="at">database_expected=</span><span class="cn">FALSE</span>) </span>
-<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a><span class="fu">data</span>(<span class="st">"r_mig_mult"</span>)</span>
-<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a><span class="fu">data</span>(<span class="st">"r_mig_mult_ope"</span>)</span>
-<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a><span class="fu">assign</span>(<span class="st">"report_ope"</span>,r_mig_mult_ope,<span class="at">envir=</span>envir_stacomi)</span>
-<span id="cb6-8"><a href="#cb6-8" aria-hidden="true" tabindex="-1"></a><span class="fu">data</span>(<span class="st">"r_mig_mult_df"</span>)</span>
-<span id="cb6-9"><a href="#cb6-9" aria-hidden="true" tabindex="-1"></a><span class="fu">assign</span>(<span class="st">"report_df"</span>,r_mig_mult_df,<span class="at">envir=</span>envir_stacomi)</span>
-<span id="cb6-10"><a href="#cb6-10" aria-hidden="true" tabindex="-1"></a><span class="fu">data</span>(<span class="st">"r_mig_mult_dc"</span>)</span>
-<span id="cb6-11"><a href="#cb6-11" aria-hidden="true" tabindex="-1"></a><span class="fu">assign</span>(<span class="st">"report_dc"</span>,r_mig_mult_dc,<span class="at">envir=</span>envir_stacomi)</span>
-<span id="cb6-12"><a href="#cb6-12" aria-hidden="true" tabindex="-1"></a>r_mig_mult <span class="ot"><-</span> <span class="fu">calcule</span>(r_mig_mult,<span class="at">silent=</span><span class="cn">TRUE</span>) </span>
-<span id="cb6-13"><a href="#cb6-13" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb6-14"><a href="#cb6-14" aria-hidden="true" tabindex="-1"></a><span class="co"># To avoid call to dev.new() which creates a device per stage, DC, taxa, we simplify </span></span>
-<span id="cb6-15"><a href="#cb6-15" aria-hidden="true" tabindex="-1"></a><span class="co"># the object as dev.new() causes knitr to crash:</span></span>
-<span id="cb6-16"><a href="#cb6-16" aria-hidden="true" tabindex="-1"></a>r_mig_mult<span class="sc">@</span>taxa<span class="sc">@</span>data<span class="ot"><-</span> r_mig_mult<span class="sc">@</span>taxa<span class="sc">@</span>data[<span class="dv">1</span>,]</span>
-<span id="cb6-17"><a href="#cb6-17" aria-hidden="true" tabindex="-1"></a>r_mig_mult<span class="sc">@</span>stage<span class="sc">@</span>data<span class="ot"><-</span>r_mig_mult<span class="sc">@</span>stage<span class="sc">@</span>data[<span class="dv">3</span>,]</span>
-<span id="cb6-18"><a href="#cb6-18" aria-hidden="true" tabindex="-1"></a>r_mig_mult<span class="sc">@</span>dc<span class="sc">@</span>dc_selectionne<span class="ot"><-</span>r_mig_mult<span class="sc">@</span>dc<span class="sc">@</span>dc_selectionne[<span class="dv">3</span>]</span>
-<span id="cb6-19"><a href="#cb6-19" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb6-20"><a href="#cb6-20" aria-hidden="true" tabindex="-1"></a><span class="fu">plot</span>(r_mig_mult,<span class="at">plot.type=</span><span class="st">"standard"</span>,<span class="at">silent=</span><span class="cn">TRUE</span>)</span></code></pre></div>
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/stacomir -r 607
More information about the Stacomir-commits
mailing list