squid: Statistical Quantification of Individual Differences

A simulation-based tool made to help researchers to become familiar with multilevel variations, and to build up sampling designs for their study. This tool has two main objectives: First, it provides an educational tool useful for students, teachers and researchers who want to learn to use mixed-effects models. Users can experience how the mixed-effects model framework can be used to understand distinct biological phenomena by interactively exploring simulated multilevel data. Second, it offers research opportunities to those who are already familiar with mixed-effects models, as it enables the generation of data sets that users may download and use for a range of simulation-based statistical analyses such as power and sensitivity analysis of multilevel and multivariate data.

Author
Hassen Allegue [aut, cre], Yimen G. Araya-Ajoy [aut], Niels J. Dingemanse [aut], Ned A. Dochtermann [aut], Laszlo Z. Garamszegi [aut], Shinichi Nakagawa [aut], Denis Reale [aut], Holger Schielzeth [aut], David F. Westneat [aut]
Date of publication
2016-06-20 07:55:06
Maintainer
Hassen Allegue <hassen.allegue@gmail.com>
License
MIT + file LICENSE
Version
0.1.1
URLs

View on CRAN

Man pages

package-squid
SQUID - Statistical Quantification of Individual Differences:...
squidApp
SQuID application
squidR
Run SQuID without graphical user interface

Files in this package

squid
squid/inst
squid/inst/shiny-squid
squid/inst/shiny-squid/ui.R
squid/inst/shiny-squid/server.R
squid/inst/shiny-squid/www
squid/inst/shiny-squid/www/pictures
squid/inst/shiny-squid/www/pictures/shared_vs_unshared_examples.pdf
squid/inst/shiny-squid/www/pictures/logo_1.png
squid/inst/shiny-squid/www/pictures/shared_vs_unshared_examples.jpg
squid/inst/shiny-squid/www/pictures/group_pic.jpg
squid/inst/shiny-squid/www/pictures/infinity.gif
squid/inst/shiny-squid/www/pictures/modules.png
squid/inst/shiny-squid/www/pictures/underConstruction_pic.pdf
squid/inst/shiny-squid/www/pictures/Environment_examples.jpg
squid/inst/shiny-squid/www/pictures/underConstruction_pic.png
squid/inst/shiny-squid/www/pictures/Vit_examples.jpg
squid/inst/shiny-squid/www/pictures/logo_2.png
squid/inst/shiny-squid/www/css
squid/inst/shiny-squid/www/css/stylesheet.css
squid/inst/shiny-squid/www/css/tableinput.css
squid/inst/shiny-squid/www/css/jquery.qtip.css
squid/inst/shiny-squid/www/xml
squid/inst/shiny-squid/www/xml/qtip.xml
squid/inst/shiny-squid/www/js
squid/inst/shiny-squid/www/js/googleAnalytics.js
squid/inst/shiny-squid/www/js/myScript.js
squid/inst/shiny-squid/www/js/tableinput.js
squid/inst/shiny-squid/www/js/jquery.qtip.js
squid/inst/shiny-squid/www/js/jquery.1.11.1.js
squid/inst/shiny-squid/www/info
squid/inst/shiny-squid/www/info/Modules_Info_NR.html
squid/inst/shiny-squid/www/info/Info_Dtime_Trait.html
squid/inst/shiny-squid/www/info/Info_unknown.html
squid/inst/shiny-squid/www/info/Info_VtInput.html
squid/inst/shiny-squid/www/info/info_B.html
squid/inst/shiny-squid/www/info/Info_Drec_Trait.html
squid/inst/shiny-squid/www/info/info_share.html
squid/inst/shiny-squid/www/info/Info_Drec_Ind.html
squid/inst/shiny-squid/www/info/Info_NR.html
squid/inst/shiny-squid/www/info/Info_auto_V.html
squid/inst/shiny-squid/www/info/Modules_Info_Vme.html
squid/inst/shiny-squid/www/info/Info_Vk.html
squid/inst/shiny-squid/www/info/Info_NK.html
squid/inst/shiny-squid/www/info/Info_environmentType.html
squid/inst/shiny-squid/www/info/Info_Vit.html
squid/inst/shiny-squid/www/info/Info_NT.html
squid/inst/shiny-squid/www/info/Info_Time_sampling.html
squid/inst/shiny-squid/www/info/Modules_Info_Vi.html
squid/inst/shiny-squid/www/info/Modules_Info_NI.html
squid/inst/shiny-squid/www/info/Info_Tmax.html
squid/inst/shiny-squid/www/info/Info_ran_Mu.html
squid/inst/shiny-squid/www/info/Info_ran_V.html
squid/inst/shiny-squid/www/info/Info_lin_Intercep.html
squid/inst/shiny-squid/www/info/Info_Dtime_Ind.html
squid/inst/shiny-squid/www/info/Info_env_preview.html
squid/inst/shiny-squid/www/info/Info_Vind.html
squid/inst/shiny-squid/www/info/Info.html
squid/inst/shiny-squid/www/info/Info_NI.html
squid/inst/shiny-squid/www/info/Info_lin_slope.html
squid/inst/shiny-squid/www/info/Info_auto_Mu.html
squid/inst/shiny-squid/www/info/Info_NP.html
squid/inst/shiny-squid/www/info/Modules_Info_Bes.html
squid/inst/shiny-squid/www/info/Info_known.html
squid/inst/shiny-squid/www/info/Info_Vm.html
squid/inst/shiny-squid/figures
squid/inst/shiny-squid/figures/sampling_vit_0.1.png
squid/inst/shiny-squid/figures/env_shared.png
squid/inst/shiny-squid/figures/sampling_vit_0.75.png
squid/inst/shiny-squid/figures/sampling_same_nb.png
squid/inst/shiny-squid/figures/sampling_same_nb_time.png
squid/inst/shiny-squid/figures/env_non-shared.png
squid/inst/shiny-squid/figures/sampling_all_different.png
squid/inst/shiny-squid/source
squid/inst/shiny-squid/source/server
squid/inst/shiny-squid/source/server/modules
squid/inst/shiny-squid/source/server/modules/module1
squid/inst/shiny-squid/source/server/modules/module1/SVRMod1Step3.R
squid/inst/shiny-squid/source/server/modules/module1/SVRMod1Step2.R
squid/inst/shiny-squid/source/server/modules/module1/SVRMod1Step1.R
squid/inst/shiny-squid/source/server/modules/module1/SVRMod1Step4.R
squid/inst/shiny-squid/source/server/modules/module3
squid/inst/shiny-squid/source/server/modules/module3/SVRMod3Step1.R
squid/inst/shiny-squid/source/server/modules/module3/SVRMod3Step3.R
squid/inst/shiny-squid/source/server/modules/module3/SVRMod3Step2.R
squid/inst/shiny-squid/source/server/modules/SVRmodules.R
squid/inst/shiny-squid/source/server/modules/module6
squid/inst/shiny-squid/source/server/modules/module6/SVRMod6Step2.R
squid/inst/shiny-squid/source/server/modules/module6/SVRMod6Step1.R
squid/inst/shiny-squid/source/server/modules/module6/SVRMod6Step3.R
squid/inst/shiny-squid/source/server/fullmodel
squid/inst/shiny-squid/source/server/fullmodel/SVRGetBMatrix.R
squid/inst/shiny-squid/source/server/fullmodel/SVRGetModelEquation.R
squid/inst/shiny-squid/source/server/fullmodel/SVRGetSummaryVariances.R
squid/inst/shiny-squid/source/server/fullmodel/SVRGetVindMatrix.R
squid/inst/shiny-squid/source/server/fullmodel/SVRDispayModelEquation.R
squid/inst/shiny-squid/source/server/fullmodel/SVRFullModel.R
squid/inst/shiny-squid/source/SVRsource.R
squid/inst/shiny-squid/source/variables
squid/inst/shiny-squid/source/variables/modules
squid/inst/shiny-squid/source/variables/modules/VARmodules.R
squid/inst/shiny-squid/source/variables/general
squid/inst/shiny-squid/source/variables/general/VARgeneral.R
squid/inst/shiny-squid/source/variables/fullmodel
squid/inst/shiny-squid/source/variables/fullmodel/VARfullmodel.R
squid/inst/shiny-squid/source/UIsource.R
squid/inst/shiny-squid/source/inputs
squid/inst/shiny-squid/source/inputs/getSelectInput.R
squid/inst/shiny-squid/source/inputs/getSliderInput.R
squid/inst/shiny-squid/source/inputs/getCheckboxInput.R
squid/inst/shiny-squid/source/inputs/getEnvironmentInput.R
squid/inst/shiny-squid/source/inputs/getNumericInput.R
squid/inst/shiny-squid/source/pages
squid/inst/shiny-squid/source/pages/portal
squid/inst/shiny-squid/source/pages/portal/UIportal.R
squid/inst/shiny-squid/source/pages/modules
squid/inst/shiny-squid/source/pages/modules/module1
squid/inst/shiny-squid/source/pages/modules/module1/UIMod1Step4.R
squid/inst/shiny-squid/source/pages/modules/module1/UIMod1Step3.R
squid/inst/shiny-squid/source/pages/modules/module1/UIMod1Step1.R
squid/inst/shiny-squid/source/pages/modules/module1/UIMod1Step2.R
squid/inst/shiny-squid/source/pages/modules/module3
squid/inst/shiny-squid/source/pages/modules/module3/UIMod3Step1.R
squid/inst/shiny-squid/source/pages/modules/module3/UIMod3Step3.R
squid/inst/shiny-squid/source/pages/modules/module3/UIMod3Step2.R
squid/inst/shiny-squid/source/pages/modules/UImodules.R
squid/inst/shiny-squid/source/pages/modules/module6
squid/inst/shiny-squid/source/pages/modules/module6/UIMod6Step2.R
squid/inst/shiny-squid/source/pages/modules/module6/UIMod6Step3.R
squid/inst/shiny-squid/source/pages/modules/module6/UIMod6Step1.R
squid/inst/shiny-squid/source/pages/fullModel
squid/inst/shiny-squid/source/pages/fullModel/UIfullModel.R
squid/inst/shiny-squid/source/pages/fullModel/UIspecificEnvironment.R
squid/inst/shiny-squid/source/pages/fullModel/UIenvironment.R
squid/inst/shiny-squid/source/pages/fullModelSbyS
squid/inst/shiny-squid/source/pages/fullModelSbyS/UIfullModelSbySDescriptionBivariateSummary.R
squid/inst/shiny-squid/source/pages/fullModelSbyS/UIfullModelSbySDescriptionFullModel.R
squid/inst/shiny-squid/source/pages/fullModelSbyS/UIfullModelSbyS.R
squid/inst/shiny-squid/source/pages/fullModelSbyS/UIfullModelSbySDescriptionSummary.R
squid/inst/shiny-squid/source/pages/fullModelSbyS/UIfullModelSbySOutput.R
squid/inst/shiny-squid/source/pages/fullModelSbyS/UIfullModelEquation_2.R
squid/inst/shiny-squid/source/pages/fullModelSbyS/UIfullModelEquation.R
squid/inst/shiny-squid/source/pages/fullModelSbyS/UIfullModelVarianceEquation.R
squid/inst/shiny-squid/source/pages/fullModelSbyS/UIfullModelSbySDescriptionSamplingDesign.R
squid/inst/shiny-squid/source/pages/fullModelSbyS/UIfullModelSbySInput.R
squid/inst/shiny-squid/source/utilities
squid/inst/shiny-squid/source/utilities/displayRCode.R
squid/inst/shiny-squid/source/utilities/testInput.R
squid/inst/shiny-squid/source/utilities/showEnvironment.R
squid/inst/shiny-squid/source/utilities/getTable.R
squid/inst/shiny-squid/source/utilities/underConstruction.R
squid/inst/shiny-squid/source/utilities/testInputBMatrix.R
squid/inst/shiny-squid/source/utilities/matrixInput2.R
squid/inst/shiny-squid/source/utilities/error_msg.R
squid/inst/shiny-squid/source/utilities/warning_msg.R
squid/inst/shiny-squid/source/utilities/disableActionButton.R
squid/inst/shiny-squid/source/utilities/withMathJax2.R
squid/inst/shiny-squid/source/utilities/getIcon.R
squid/inst/shiny-squid/source/utilities/testInteger.R
squid/inst/shiny-squid/source/utilities/testInputVindMatrix.R
squid/inst/shiny-squid/source/utilities/info_msg.R
squid/inst/shiny-squid/source/utilities/actionButtonLink.R
squid/inst/shiny-squid/source/utilities/powerAnalysis.R
squid/inst/shiny-squid/source/utilities/multiplot.R
squid/inst/shiny-squid/source/utilities/runningIndicator.R
squid/inst/shiny-squid/source/utilities/Cor2CovMatrix.R
squid/inst/shiny-squid/source/utilities/runPowerAnalysis.R
squid/inst/shiny-squid/source/utilities/matrixInputVind.R
squid/inst/shiny-squid/source/utilities/matrixInputB.R
squid/inst/shiny-squid/source/utilities/getLabel.R
squid/inst/shiny-squid/source/utilities/actionButton2.R
squid/inst/shiny-squid/source/text
squid/inst/shiny-squid/source/text/portal
squid/inst/shiny-squid/source/text/portal/TXTportal.R
squid/inst/shiny-squid/source/text/modules
squid/inst/shiny-squid/source/text/modules/TXTmodule6.R
squid/inst/shiny-squid/source/text/modules/TXTmodule3.R
squid/inst/shiny-squid/source/text/modules/TXTmodule1.R
squid/inst/shiny-squid/source/text/fullmodel
squid/inst/shiny-squid/source/text/fullmodel/TXTfullmodel.R
squid/inst/shiny-squid/source/text/fullmodel/vignette.Rmd
squid/inst/shiny-squid/source/text/fullmodel/vignette.html
squid/inst/shiny-squid/test.R
squid/tests
squid/tests/testthat.R
squid/tests/testthat
squid/tests/testthat/test_squidR.R
squid/NAMESPACE
squid/NEWS.md
squid/R
squid/R/getTxUniform.R
squid/R/getNRI.R
squid/R/error_management.R
squid/R/getFullData.R
squid/R/repmat.R
squid/R/plotEnvironment.R
squid/R/displayResults.R
squid/R/setVariables.R
squid/R/squidR.R
squid/R/check_one_integer.R
squid/R/multiplot.R
squid/R/Cor2CovMatrix.R
squid/R/check_matrix.R
squid/R/decayRate.R
squid/R/createEnvironment.R
squid/R/squidApp.R
squid/R/check_one_numeric.R
squid/R/setEnvironments.R
squid/R/check_one_boolean.R
squid/R/reshapeMat.R
squid/R/getIndMatrix.R
squid/R/getEnvironment.R
squid/R/getSampledData.R
squid/README.md
squid/MD5
squid/DESCRIPTION
squid/man
squid/man/package-squid.Rd
squid/man/squidApp.Rd
squid/man/squidR.Rd
squid/LICENSE