# BLABOR

This project contains the code and raw data linked to the publication 
"Mind the reporting gap: Fostering context awareness in scientific reporting of 
field trials. A Scoping Review", written by Morgane de Toeuf, Cécile Thonar,
Marjolein Visser.

! Output files are not provided with this repository, but after downloading the 
whole repository, including its folder structure, running the code will generate 
all output files and store them in the appropriate folder, with the exception of
flowcharts: the code saving mechanism was sub-optimal. A good way to save them is
by running the code in RStudio, and export the figure from the Viewer Pane.


## Methods --> °°°° !! Add DOI when we get it !! °°°°

All methods are described in detail in the publication (DOI). 
In brief, first, a pool of 88 publications is formed, all observations are made 
on each publication. The list of the 88 articles is shared within supplementary 
materials of the publication. Inclusion criteria are: 
- publication reporting on a field trial held in Europe 
- trials with at least one combination of 2-crop grain legume-cereal intercrops
- publications between 2020 and 2024
- original data (no meta-analysis or review)
Second, we investigate reporting practices within publications. A score of 0 
(omitted) or 1 (reported) is attributed to a series of 16 variables, refered to
in the code as "binary variables" (see description of data set below). 
Finally, we report a series of other observations for each article to comment on
current reporting practices, regarding aspects such as the reporting of past 
farming practices, the sharing of data, etc (see description of data set below).

All analyses are ran in R. Steps of the data analysis are commented within the 
script. The raw data is available, but article references have been 
pseudonymized with ID numbers. The correspondence table between ID numbers and 
article references can be requested to the authors. 

## Description of Files in this repository

### Scripts

** BLABOR_script.r **
Script to replicate all analyses and figures included in the publication. 
Includes computation of new variables and intermediary data frames, as well as 
plotting of all radar charts, flow charts and the binary heatmap, and the 
computation of the hierarchical clustering analysis (HCA). 
There are also a few "quality checks" for intermediate steps, e.g., evaluation 
of the dendrogram provided by the HCA.
All steps are thorougly commented in the script. To run it, you will need to 
install R and to download the raw data "0_data_tidy_pseudo.csv". 
The script was last rendered with the R version 4.5.2.

** BLABOR_suppl_mat.R **
Script to replicate all figures and tables included in the supplementary 
materials. All steps are thorougly commented in the script. To run it, you will 
need to install R and to download the raw data "0_data_tidy_pseudo.csv". 
The script was last rendered with the R version 4.5.2.

### Data set

** 0_data_tidy_pseudo.csv **
id_word                     pseudonymized ID number of the article

plot_exp_station_or_farmer  whether the trial was held on an experimental 
                            station or in a farm [exp_station; farm; NA]
                            
decl_categ                  declared data availability, according to statement 
                            in the publication. 4 categories: no declaration, 
                            data is available upon request to the authors, 
                            data is available within article or supplementary 
                            material, data is available in an openly accessible 
                            repository [no_decl; corresp_author; art_suppl; 
                            Repos]
                            
data_decl                   decl_categ + notes detailing wether the data was 
                            indeed available and what potential issues were
                            
data_avail_factor           same information as in data_decl, but aggregated in 
                            categories [Repos; Repos_no; Repos_seq; 
                            art_suppl_no_raw; art_suppl_raw; 
                            art_suppl_raw_subopt; corresp_author; 
                            corresp_author_privacy; no_decl; no_decl_seq]
                            
past_practices              whether the article mentions past practices (prior 
                            to the years of the trial). Values are either "none"
                            or they contain 2 informations: years over which the 
                            practices are related (e.g., >10y), and which 
                            practice it concerns
                            
past_age                    years over which the practices are related prior to 
                            the trial. 0 when no past practice is reported
                            
past_managt                 Whether management is reported for years before the 
                            trial. Binary variable [1; 0]
past_succession             Whether precrop is reported for years before the 
                            trial (thus crop succession). Binary variable [1; 0]
                            
past_till                   Whether tillage practices are reported for years  
                            before the trial. Binary variable [1; 0]

past_fert                   Whether N fertilization is reported for years  
                            before the trial. Binary variable [1; 0]

past_weed                   Whether weed control measures are reported for years  
                            before the trial. Binary variable [1; 0]
                            (no other practice than those was related prior to
                            the trial)

long_trial                  Whether the publication reports on about a long-term
                            field trial. Binary variable [yes; no]
                            
typo_insects                Whether the article corresponds to an "insect study"
                            (studies insects. See definition in the resuls 
                            section). Binary variable [1; 0]
                            
typo_disease                Whether the article corresponds to a "disease study"
                            (studies diseases. See definition in the resuls 
                            section). Binary variable [1; 0]
                            
typo_microbio               Whether the article corresponds to a "soil study"
                            (studies soil. See definition in the resuls 
                            section). Binary variable [1; 0]
                            
which_management            Under which management the field trial was held. 
                            [conventional; organic; unclear]
                            
texture                     Score for Texture. Binary variable [1; 0]

soil_type                   Score for Soil type. Binary variable [1; 0]

p_h                         Score for pH. Binary variable [1; 0]

soil_c                      Score for Soil C. Binary variable [1; 0]

soil_n                      Score for Soil N. Binary variable [1; 0]

weather                     Score for Weather. Binary variable [1; 0]

yield                       Score for Yield. Binary variable [1; 0]

quality                     Score for Crop quality. Binary variable [1; 0]

pest_disease_score          Score for Pest and Disease control measures. 
                            Binary variable [1; 0]

weed_score                  Score for Weed control measures. Binary variable 
                            [1; 0]

cultivar                    Score for Cultivar. Binary variable [1; 0]

sowing_rates                Score for Sowing Rates. Binary variable [1; 0]

ferti                       Score for N Fertilization. Binary variable [1; 0]

till                        Score for Tillage practices. Binary variable [1; 0]

precrop                     Score for Precrop. Binary variable [1; 0]

management                  Score for Management. Binary variable [1; 0]

control_or_not              Whether pest and disease control measures were 
                            applied. If the report was omitted: "unclear"
                            [unclear; 1; 0]
                            
control_what                Whether the applied pest and disease control measure 
                            was named (e.g., name of the molecule or the product). 
                            Binary values [1; 0]

control_when                Whether the timing of the application of pest and 
                            disease control measures was given. Binary values 
                            [1; 0]

control_quant               Whether the dosage of the application of pest and 
                            disease control measures was given. Binary values 
                            [1; 0]

weeding_or_not              Whether weed control measures were applied. If the 
                            report was omitted: "unclear". [unclear; 1; 0]

weeding_type                Type of weeding that was applied. 0 is for either no
                            application or weeding was not mentioned. 
                            [0; chemical; mechanical; steam]

weed_when                   Whether the timing of the application of weed 
                            control measures was given. Binary values [1; 0]

weed_quant                  Whether the dosage of the application of weed control 
                            measures was given. In the case of mechanical weeding,
                            whether intensity was detailed. Binary values 
                            [1; 0]