Software tools for systematic reviews

• Covidence

  GW in 2019 has bought a subscription to this Cloud based tool for facilitating screening decisions, used by the Cochrane Collaboration. Register for an account.

• NVIVO for analysis of qualitative research

  NVIVO is used for coding interview data to identify common themes emerging from interviews with several participants. GW faculty, staff, and students may download NVIVO software.

• RedCAP

  RedCAP is software that can be used to create survey forms for research or data collection or data extraction. It has very detailed functionality to enable data exchange with Electronic Health Record Systems, and to integrate with study workflow such as scheduling follow up reminders for study participants.

• Systematic Review Toolbox

  Select the Healthcare discipline and features you want a tool to support.

• SRDR tool from AHRQ

  Free, web-based and has a training environment, tutorials, and example templates of systematic review data extraction forms

• RevMan 5

  RevMan 5 is the desktop version of the software used by Cochrane systematic review teams. RevMan 5 is free for academic use and can be downloaded and configured to run as stand alone software that does not connect with the Cochrane server if you follow the instructions at https://training.cochrane.org/online-learning/core-software-cochrane-reviews/revman/revman-5-download/non-cochrane-reviews

• Rayyan

  Free, web-based tool for collecting and screening citations. It has options to screen with multiple people, masking each other.

• GradePro

  Free, web application to create, manage and share summaries of research evidence (called Evidence Profiles and Summary of Findings Tables) for reviews or guidelines, uses the GRADE criteria to evaluate each paper under review.

• DistillerSR

  Needs subscription. Create coded data extraction forms from templates.

• EPPI Reviewer

  Needs subscription. Like DistillerSR, tool for text mining, data clustering, classification and term extraction

• SUMARI

  Needs subscription. Qualitative data analysis.

• Dedoose

  Needs subscription. Qualitative data analysis, similar to NVIVO in that it can be used to code interview transcripts, identify word co-occurence, cloud based.

• Meta-analysis software for statistical analysis of data for quantitative reviews

  SPSS, SAS, and STATA are popular analytical statistical software that include macros for carrying out meta-analysis. Himmelfarb has SPSS on some 3rd floor computers, and GW affiliates may download SAS to your own laptop from the Division of IT website. To perform mathematical analysis of big data sets there are statistical analysis software libraries in the R programming language available through GitHub and RStudio, but this requires advanced knowledge of the R and Python computer languages and data wrangling/cleaning.

• PRISMA 2020 flow diagram generator

  The PRISMA Statement website has a page listing example flow diagram templates and a link to software for creating PRISMA 2020 flow diagrams using R software.

GW researchers may want to consider using Refworks to manage citations, and GW Box to store the full text PDF's of review articles. You can also use online survey forms such as Qualtrics, RedCAP, or Survey Monkey, to design and create your own coded fillable forms, and export the data to Excel or one of the qualitative analytical software tools listed above.

References:

https://guides.mclibrary.duke.edu/sysreview/types

An overview of review methodology

Writing review manuscripts is not the easiest task. It requires lot of time and extensive work to search the previous related work. Therefore, to do so accurately should be a priority for all academics. However, this task has become increasingly complex. Here, i am trying to define the type of review and guidlines and provide the links for authors so that they can organize well.

Types of Review articles:

According to Snyder et al. 2019, there is three types:

1. Systematic

2. Semi systematic

3. Integrative

While, according to Duke University, There is 14 type of reviews:

1. Critical review

2. Literatur/narrative review

3. Mapping review/ systematic map

4. Meta-analysis

5. Mixed studies review/mixed methods review

6. Overview

7. Qualitative systematic review/qualitative evidence synthesis

8. Rapid review

9. Scoping review

10. State-of-the-art review

11. Systematic review

12. Systematic search and review

13. Systematized review

14. Umbrella review

Guidlines:

There are number of reported standards and guidelines  such as:

1. PRISMA, developed for systematic literature reviews and meta-analyses).

2. RAMSES, developed for systematic narrative reviews.

3. Guidelines for integrative reviews. 

References:

https://www.sciencedirect.com/science/article/pii/S0148296319304564

https://systematicreviewsjournal.biomedcentral.com/articles/10.1186/s13643-016-0343-0

https://www.ncbi.nlm.nih.gov/books/NBK481583/

https://guides.himmelfarb.gwu.edu/systematic_review/types

https://uow.libguides.com/systematic-review/types-of-systematic-reviews

Watch youtube:

https://www.youtube.com/watch?v=FqGGUUnrmhw&ab_channel=Sage

Links for agronomy data scinecs

 1. https://docs.tibco.com/data-science/GUID-FE8CE528-28B3-4898-993D-097A87EF8407-homepage.html

2. https://drs.icar.gov.in/

3. https://www.statmethods.net/

4. https://stats.oarc.ucla.edu/other/dae/

5, https://www.connectedpapers.com/ (for research papers)

Learning climate science

There are some MOOC course on climate science with machine learning by ECMWF:

1. ML in Weather & Climate

2. Concepts of Machine Learning

3. Practical ML applications in Weather & Climate

In addition, ECMWF also teach Data Assimilation  and Numerical weather prediction. I think this is the best place to learn machine learning to annalyze the climate science.

References:

https://lms.ecmwf.int/course/index.php?categoryid=1

https://lms.ecmwf.int/

Is DSSAT crop model ?

 Dear all,

I have noticed that many researcher are reporting that "DSSAT is a model" i.e

Even in conferences, they are mentioning that yield simulation was done using "DSSAT model". 

Unfortunately, it is wrong. DSSAT is not a model.

Q. Why DSSAT is not a model ?

Ans: As DSSAT website has clearly mentioned that DSSAT is a software application program comprises dynamic crop growth simulation models and intact with soil and water module.

Q. What is model in DSSAT

Ans: DSSAT have several Crop Simulation Models (CSM) such as: CERES for cereal crops, Substor for root crops, CANEGRO for sugarcane, CROPGROW for peanut and oilseed and many more.

Q. So, What is the right way to write/cite or mentioned

Ans: Well, DSSAT have different crop models over 42 crops then it can write as DSSAT-CSM-(Crop model name i.e. CERES or ..). 

However, Aquacrop, GECROS, SPASS, STICS, SIRUS, LINTUL, WOFOST are popular crop models. 

Reference:

https://dssat.net/

Where to get online training on QGIS with R/Python ?

 1. https://www.ceh.ac.uk/training/spatial-analysis-qgis-and-r-introduction-environmental-scientists

2. https://blogs.fu-berlin.de/reseda/r-crash-course/

3. https://www.centerforwildlifestudies.org/courses-1/geospatial-modeling-online-jan-2023

4. https://www.centerforwildlifestudies.org/courses-1/geospatial-modeling-online-jan-2023

5. https://www.agsrt.com/geospatialanalysiswithrandqgis

6. https://cros-legacy.ec.europa.eu/content/scripting-and-programming-geographic-information-systems-qgis-2023_en

7. https://giscourse.online/courses/geostatistics-course-for-beginners-creating-algorithms-with-r-for-qgis/

Some important facts for crop modelling

• Gravitational water, defined as the water that is held at a potential greater than -1/3 bar and freely drain by gravity.

• Capillary water, held by force of attraction between soil particles and water molecules and retained in the  between the water potential -1/3 to -31 bars. 

• Hygroscopic water, water that is held by the soil particles at a suction of more than -31 bars. 

• Available water, water retained between field capacity (-1/3 bar) to permanent wilting point (-15 bars) 

• Soil Water Measurement :

•  Techniques for measuring the soil moisture can be grouped into the following two categories: 

• Direct measurement: gravimetric or thermo-gravimetric procedure

• Indirect measurement : The indirect measurement category includes the following:

• Radiological method – Neutron scattering, gamma attenuation technique (e.g., using neutron moisture meter) 

• Electromagnetic method – Time domain reflectrometry (TDR), TDR FM, Diviner 

•  Tensiometry method – using tensiometer 

• Psychrometer method

Different types of radioactive sources produce the following types of radiation: 

Neutrons 

Gamma rays (Photons) 

Alpha particles 

Beta particles 

Water content of soil is inferred from the dielectric permittivity of the medium. Electrical conductivity is inferred from TDR signal attenuation.

Psychrometer Method approach measures the vapor pressure of the water in equilibrium with the soil and hence measures the total soil-water potential.

• Indirect Estimation of Soil Moisture Characteristic:

• Statistical approaches, which either relate parameters in specific hydraulic models with texture and other soil properties using regression analysis 

• Physico-empirical approaches, which transform the PSD curve into a soil water characteristic curve by relating soil particle size to a corresponding pore diameter in a soil capillary model.

• Factors Affecting Hysteresis The factors influencing hysteresis are the following:

• Pore-size geometry 

• Entrapped air

• Moisture absorption (capillarity) and release (drainage) behavior of the soil 

• Swelling and shrinkage of soil 

• Field methods for determination of saturated hydraulic in the absence of watertable or far above the water-table are as follows:

• Bore-hole constant water level method 

• Permeameter method

• Field Measurement of Ksat

(a) Auger-hole method (for unconfined water-table condition)

 (b) Well-pumping method (under both confined and unconfined condition)

• Measurement of Unsaturated Hydraulic Conductivity:

(a) Instantaneous profile method: The instantaneous profile method for determining unsaturated hydraulic conductivity and diffusivity is based on Darcian analysis of transient soil water content

(b) Internal drainage method 

(c) Saturating unsaturated soil core or column

• The growth cycle of wheat has mainly the following divisions: germination, seedling establishment and leaf production, tillering and head differentiation, stem and head growth, head emergence and flowering, and grain filling and maturity. 

• The phases were germination and emergence (0–8 days), tillering (8–43 days), stem elongation (33–65 days), heading (55–75 days), flowering (61–81 days), and grain formation and ripening (65–115 days) for wheat. 

• Winter wheat has growing period of 120 to 160 days 

• Crown root initiation is most critical stage for irrigation 

• The minimum daily temp for growth  is  50 C 

• The mean daily temp for optimum growth and tillering is in the range of 150-200C 

• Rice grown about 40% of the irrigated area in india

• The optimum temp is required for potato is 18-200 C 

• Water requirement of major crops Crop Water requirement (cm) Crop Water requirement (cm)  Wheat (winter) 30–40,  Wheat (spring) 40–55, Corn 50–70, Rice 110–160 Cotton 70–100, Maize 40–60 (cm) 

• Many methods of scheduling irrigations are used by the farmers. These methods include the following:  Crop observation, “Feeling” the soil, Application of irrigation weekly to bring the water to a set amount (say, 5–7 cm for rice), Rotation basis (provision of irrigation scheme or pump owner), Pan evaporation observation, Check book method/irrigation calendar. 

• Duty is the depth of water required by a crop during its growing period for successfully grown up