Ready for release

_baseline-manuscript.Rmd

@@ -115,7 +115,7 @@ This study analyses baseline data from a cluster-randomised controlled trial tes
 
 Six school units were included in the study. There were four educational tracks in the schools from which students were recruited: 1. Practical Nurse (Nur), 2. Hotel, Restaurant and Catering (HRC), 3. Business and Administration (BA), and 4. Information and Communications Technology (IT). Schools were paired so that there would be matching numbers of students from each educational track for both members of the pair. Blinded randomisation by a statistician was then conducted so that a random member of each pair was selected as intervention school, the other as control school (details reported in @hankonenLetMoveIt2016). Student participants were blind to allocation at baseline.
 
-All conducted analyses and visualisations with accompanying code, can be found in the supplementary website at https://git.io/fNHuf (permalink at [REF]), previously piloted in [@heinoSimpleRationaleprovidingSMS2018]. Source code to reproduce this manuscript and all its figures can be found at https://git.io/fptcC.
+All conducted analyses and visualisations with accompanying code, can be found in the supplementary website at https://git.io/fNHuf (permalink at [REF]), previously piloted in [@heinoSimpleRationaleprovidingSMS2018]. Source code to reproduce this manuscript (written with the R package `papaja` [@austPapajaPreparingAPA2019]), and all its figures can be found at https://git.io/fptcC.
 
 <!-- TODO right before submission -->
 
@@ -133,7 +133,7 @@ In the LMI trial, there were multiple primary outcomes. The primary outcome for
 
 ### Theoretical predictors of PA
 
-The determinants postulated by the program theory included behavioural beliefs (outcome expectations, descriptive norms, intention, self-efficacy/perceived behavioural control), autonomous and controlled motivation, opportunities, action- and coping planning, and behaviour change technique (BCT) use. Participants were allowed to skip questions, and scales were computed as means of all items where responses were available. In other words, answering a single item of a specific scale sufficed. All items, response options, and descriptive statistics of scales are available in the supplementary website (section https://git.io/fAj0e); made using R package `codebook` @arslanHowAutomaticallyDocument for automatic dataset documentation.
+The determinants postulated by the program theory included behavioural beliefs (outcome expectations, descriptive norms, intention, self-efficacy/perceived behavioural control), autonomous and controlled motivation, opportunities, action- and coping planning, and behaviour change technique (BCT) use. Participants were allowed to skip questions, and scales were computed as means of all items where responses were available. In other words, answering a single item of a specific scale sufficed. All items, response options, and descriptive statistics of scales are available in the supplementary website (section https://git.io/fAj0e); made using R package `codebook` [@arslanHowAutomaticallyDocument] for automatic dataset documentation.
 
 ### Statistical analysis
 
@@ -1101,7 +1101,9 @@ In conclusion, this analysis of baseline data from the Let's Move It interventio
 
 ### List of abbreviations  
 
-\noindent PA = Physical activity  
+\noindent 
+
+PA = Physical activity  
 MVPA = Moderate-to-vigorous physical activity  
 SB = Sedentary behaviour  
 BCT = Behaviour change technique  

baseline-datasetup.R

@@ -42,7 +42,7 @@ knitr::opts_chunk$set(echo = TRUE,
                       warning = FALSE,
                       message = FALSE,
                       error = TRUE,
-                      cache = TRUE, 
+                      cache = FALSE, 
                       collapse = TRUE,
                       eval = TRUE,
                       dpi = 300)

baseline-networks.Rmd

@@ -4,97 +4,14 @@ title: "Network analyses"
 
 This section describes network analyses and displays correlation structures in the data. Here, physical activity (PA) is used interchangeably with moderate-to-vigorous physical activity (MVPA); all measures of activity relate to MVPA.
 
-```{r htmlTemp3, echo=FALSE, eval=FALSE, INCLUDE = FALSE}
-# This chunk was an attempt at html_document2 with code folding... Turned out to be a bit much.
-
-codejs <- readr::read_lines("/mnt/Data/autoentrepreneur/js/codefolding.js")
-collapsejs <- readr::read_lines("/mnt/Data/autoentrepreneur/js/collapse.js")
-transitionjs <- readr::read_lines("/mnt/Data/autoentrepreneur/js/transition.js")
-dropdownjs <- readr::read_lines("/mnt/Data/autoentrepreneur/js/dropdown.js")
-
-htmlhead <- c(
-  paste('
-<script>',
-paste(transitionjs, collapse = "\n"),
-'</script>
-<script>',
-paste(collapsejs, collapse = "\n"),
-'</script>
-<script>',
-paste(codejs, collapse = "\n"),
-'</script>
-<script>',
-paste(dropdownjs, collapse = "\n"),
-'</script>
-<style type="text/css">
-.code-folding-btn { margin-bottom: 4px; }
-.row { display: flex; }
-.collapse { display: none; }
-.in { display:block }
-.pull-right > .dropdown-menu {
-    right: 0;
-    left: auto;
-}
-.open > .dropdown-menu {
-    display: block;
-}
-.dropdown-menu {
-    position: absolute;
-    top: 100%;
-    left: 0;
-    z-index: 1000;
-    display: none;
-    float: left;
-    min-width: 160px;
-    padding: 5px 0;
-    margin: 2px 0 0;
-    font-size: 14px;
-    text-align: left;
-    list-style: none;
-    background-color: #fff;
-    -webkit-background-clip: padding-box;
-    background-clip: padding-box;
-    border: 1px solid #ccc;
-    border: 1px solid rgba(0,0,0,.15);
-    border-radius: 4px;
-    -webkit-box-shadow: 0 6px 12px rgba(0,0,0,.175);
-    box-shadow: 0 6px 12px rgba(0,0,0,.175);
-}
-</style>
-<script>
-$(document).ready(function () {
-  window.initializeCodeFolding("show" === "hide");
-});
-</script>
-', sep = "\n"),
-  paste0('
-<script>
-document.write(\'<div class="btn-group pull-right" style="position: absolute; top: 20%; right: 2%; z-index: 200"><button type="button" class="btn btn-default btn-xs dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="true" data-_extension-text-contrast=""><span>Code</span> <span class="caret"></span></button><ul class="dropdown-menu" style="min-width: 50px;"><li><a id="rmd-show-all-code" href="#">Show All Code</a></li><li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li></ul></div>\')
-</script>
-')
-)
-
-readr::write_lines(htmlhead, path = "/mnt/Data/autoentrepreneur/header.html")
-```
-
-
-```{r setup}
-
-knitr::opts_chunk$set(
-  warning = FALSE, # show warnings during codebook generation
-  message = FALSE, # show messages during codebook generation
-  error = TRUE, # do not interrupt codebook generation in case of errors,
-                # usually makes debugging easier, and sometimes half a codebook
-                # is better than none
-  echo = FALSE,  # don't show the R code,
-  cache = FALSE
-)
+```{r setup, message = FALSE, warning = FALSE}
 
 source("baseline-datasetup.R")
 
 ```
 
 Clicking the "Code"-buttons on the right shows code for each chunk.
+
 $~$
 $~$
 <a id="network"></a>
@@ -4756,7 +4673,7 @@ plot(bootnet_centrality_stability_determinants, perNode=T, "strength")
 bootnet::corStability(bootnet_centrality_stability_determinants)
 ```
 
-### PA network without SDT motivations
+<!-- ### PA network without SDT motivations -->
 
 ```{r, include = FALSE, eval = FALSE}
 # Network without motivation variables
@@ -4790,7 +4707,7 @@ plot(network1, layout = "spring", labels = TRUE, groups = group.spinglass, color
 
 ```
 
-### PA network without BCTs and SDT
+<!-- ### PA network without BCTs and SDT -->
 
 ```{r, include = FALSE, eval = FALSE}
 # Network without motivation variables
@@ -4847,7 +4764,7 @@ plot(nwBoys, label.scale = FALSE, title = "Boys", label.cex = 0.75,
      pieBorder = 1)
 ```
 
-### PA network without BCTs and SDT, intention, MVPA, fat%
+<!-- ### PA network without BCTs and SDT, intention, MVPA, fat% -->
 
 ```{r, include = FALSE, eval = FALSE}
 # Network without motivation variables
@@ -4895,7 +4812,7 @@ plot(network1, layout = "spring", labels = TRUE, groups = group.spinglass, color
 
 ```
 
-## Robustness test 
+<!-- ## Robustness test  -->
 
 ```{r, include = FALSE, eval = FALSE}
 
@@ -4917,7 +4834,7 @@ qgraph::centralityPlot(Network)
 qgraph::centralityPlot(Network2)
 ```
 
-## Centrality stability
+<!-- ## Centrality stability -->
 
 ```{r, eval = FALSE}
 boot2 <- bootnet::bootnet(Network1, nBoots = 2500, type = "case", nCores = 2)
@@ -4934,7 +4851,7 @@ plot(boot1, "betweenness")
 plot(boot1, "closeness")
 ```
 
-## Network comparison test: girls and boys
+<!-- ## Network comparison test: girls and boys -->
 
 ```{r, include = FALSE, eval = FALSE}
 
@@ -4972,8 +4889,9 @@ sum(nct_results$einv.pvals$"p-value" < 0.05)  # how many edges are different
 
 ```
 
-## Robustness test 
-```{r, eval = FALSE}
+<!-- ## Robustness test  -->
+
+```{r, include = FALSE, eval = FALSE}
 data <- data %>% dplyr::select(BCT = agreementDependentBCT_T1,
     AUT = autonomous_T1,
     Intn = intention_T1,
@@ -4998,9 +4916,9 @@ qgraph::centralityPlot(Network)
 qgraph::centralityPlot(Network2)
 ```
 
-# Centrality stability
+<!-- # Centrality stability -->
 
-```{r, eval = FALSE}
+```{r, include = FALSE, eval = FALSE}
 boot2 <- bootnet::bootnet(Network, nBoots = 2500, type = "case", nCores = 2)
 bootnet::corStability(boot2)
 
@@ -5227,9 +5145,20 @@ itemGroups <- c(rep("Amotivation", 4),
                 rep("Integrated", 3),
                 rep("Intrinsic", 3))
 
+```
+
+```{r sdt-network-all}
 
 plot(nwAll, groups = itemGroups, nodeNames = itemNames, legend.cex = 0.25)
 
 ```
 
+# Session information
+
+Description of the R environment can be found below.
 
+```{r session-info, results = 'markup'}
+devtools::session_info()
+
+pander::pander(sessionInfo())
+```

baseline-networks_cache/html/__packages

@@ -19,5 +19,3 @@ dplyr
 stringr
 forcats
 ggridges
-shiny
-corrgram

baseline-supplement.Rmd

@@ -1,5 +1,8 @@
 ---
 title: "Descriptive plots"
+output: 
+  html_document: 
+    keep_md: yes
 ---
 
 ```{r include = FALSE, eval = FALSE, echo = FALSE}
@@ -96,7 +99,7 @@ readr::write_lines(htmlhead, path = "/mnt/Data/autoentrepreneur/header.html")
 
 Clicking the "Code"-buttons on the right shows code for each chunk.
 
-To start data analysis, we run a data compilation file to enable compiling the document. This file can be found under the tab "Data setup code" on top of the screen.
+To start data analysis, we run a data compilation file to enable compiling the document. This file can be found [here](https://raw.githubusercontent.com/heinonmatti/baseline-visu/master/baseline-datasetup.R).
 
 ```{r setup, verbose = FALSE, warning = FALSE, message = FALSE}
 
@@ -6370,4 +6373,10 @@ plot1 + plot2
 
 ```
 
+# Session information
 
+Description of the R environment can be found below.
+
+```{r session-info, results = 'markup'}
+devtools::session_info()
+```