graph added

Rscripts/Process_CT_for_Gargantext.Rmd

@@ -18,7 +18,7 @@ name<-"database_d_chavalarias_2020-05-15" # name of the csv to be loaded
 AllData <-read.csv(paste("data/",name,".csv",sep=""),head=TRUE,sep="\t")
 AllData$Inclusion.criteria <- NULL
 AllData$Exclusion.criteria <- NULL
-AllData <- filter(AllData,!is.na(AllData$Registration.date))
+#AllData <- filter(AllData,!is.na(AllData$Registration.date))
 nrow(AllData)
 x <- unique(AllData$Trial.registration.number)
 head(x)[[1]]
@@ -33,7 +33,7 @@ library(stringr)
 Prevention<- filter(AllData,grepl("Prevention",AllData$Study.aim)) # CTs taggés prevention
 Treatments <- filter(AllData,grepl("Treatment",AllData$Study.aim)) # # CTs taggés Treaments
 Posttreatment<- filter(AllData,grepl("Post treatment",AllData$Study.aim)) # CTs taggé Post-Treatment
-print(paste(count(Prevention)," Prevention CTs,", count(Treatments)," Treatments CTs and ",count(Posttreatment)," Post-treatment CTs."))
+print(paste(count(Prevention)," Prevention arms,", count(Treatments)," Treatments arms and ",count(Posttreatment)," Post-treatment arms."))
 ```
 ## Export of data and viz
 Data are exported in several formats. The list of all treatments is also exported assuming that treatments are separated by a '+' signe in the column treatment of the original db.

Rscripts/Process_CT_for_Gargantext.nb.html

@@ -1777,7 +1777,7 @@ $(document).ready(function () {
 <p>First define what is the name of the file to be processed. This file should be in the folder /data</p>
 <!-- rnb-text-end -->
 <!-- rnb-chunk-begin -->
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+<!-- rnb-source-begin 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 -->
 <pre class="r"><code>library(lubridate)
 source(&quot;coronalib.R&quot;) # R libraries 
 name&lt;-&quot;database_d_chavalarias_2020-05-15&quot; # name of the csv to be loaded
@@ -1785,7 +1785,7 @@ name&lt;-&quot;database_d_chavalarias_2020-05-15&quot; # name of the csv to be l
 AllData &lt;-read.csv(paste(&quot;data/&quot;,name,&quot;.csv&quot;,sep=&quot;&quot;),head=TRUE,sep=&quot;\t&quot;)
 AllData$Inclusion.criteria &lt;- NULL
 AllData$Exclusion.criteria &lt;- NULL
-AllData &lt;- filter(AllData,!is.na(AllData$Registration.date))
+#AllData &lt;- filter(AllData,!is.na(AllData$Registration.date))
 nrow(AllData)</code></pre>
 <!-- rnb-source-end -->
 <!-- rnb-output-begin eyJkYXRhIjoiWzFdIDE5MDJcbiJ9 -->
@@ -1807,16 +1807,16 @@ head(x)[[1]]</code></pre>
 <p>Several dataframe are generated according to which are the CTs under study.</p>
 <!-- rnb-text-end -->
 <!-- rnb-chunk-begin -->
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+<!-- rnb-source-begin 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 -->
 <pre class="r"><code>library(dplyr) 
 library(stringr) 
 Prevention&lt;- filter(AllData,grepl(&quot;Prevention&quot;,AllData$Study.aim)) # CTs taggés prevention
 Treatments &lt;- filter(AllData,grepl(&quot;Treatment&quot;,AllData$Study.aim)) # # CTs taggés Treaments
 Posttreatment&lt;- filter(AllData,grepl(&quot;Post treatment&quot;,AllData$Study.aim)) # CTs taggé Post-Treatment
-print(paste(count(Prevention),&quot; Prevention CTs,&quot;, count(Treatments),&quot; Treatments CTs and &quot;,count(Posttreatment),&quot; Post-treatment CTs.&quot;))</code></pre>
+print(paste(count(Prevention),&quot; Prevention arms,&quot;, count(Treatments),&quot; Treatments arms and &quot;,count(Posttreatment),&quot; Post-treatment arms.&quot;))</code></pre>
 <!-- rnb-source-end -->
-<!-- rnb-output-begin eyJkYXRhIjoiWzFdIFwiMjgyICBQcmV2ZW50aW9uIENUcywgMTYwNCAgVHJlYXRtZW50cyBDVHMgYW5kICAxNSAgUG9zdC10cmVhdG1lbnQgQ1RzLlwiXG4ifQ== -->
-<pre><code>[1] &quot;282  Prevention CTs, 1604  Treatments CTs and  15  Post-treatment CTs.&quot;</code></pre>
+<!-- rnb-output-begin eyJkYXRhIjoiWzFdIFwiMjgyICBQcmV2ZW50aW9uIGFybXMsIDE2MDQgIFRyZWF0bWVudHMgYXJtcyBhbmQgIDE1ICBQb3N0LXRyZWF0bWVudCBhcm1zLlwiXG4ifQ== -->
+<pre><code>[1] &quot;282  Prevention arms, 1604  Treatments arms and  15  Post-treatment arms.&quot;</code></pre>
 <!-- rnb-output-end -->
 <!-- rnb-chunk-end -->
 <!-- rnb-text-begin -->
@@ -1880,7 +1880,7 @@ TreatmentsCloud(Treatments)</code></pre>
 <!-- rnb-chunk-end -->
 </div>
 
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