Nothing

```
# Model variables
nb.IS <- 4
B0 <- 1
X1 <- 2
X2 <- 3
X1X2 <- 4
FullModel_VAR <- list(
# Plot
"Plot" = list( "width" = "600px"
),
# Run Button
"Run" = list( "label" = "RUN",
"icon" = icon("refresh"),
"style" = "primary",
"invalidStyle" = "inverse",
"errorTxt" = "Please make sure to fix all input errors before running the simulation."
),
# ReRun Button
"ReRun" = list( "label" = "re-RUN",
"icon" = icon("refresh"),
"style" = "default",
"invalidStyle" = "inverse",
"errorTxt" = "Please make sure to fix all input errors before running the simulation."
),
# Download sampled data Button
"download_sampled" = list( "label" = "Download Sampled Data"),
# Download raw data Button
"download_raw" = list( "label" = "Download Raw Data"),
# Download R code
"download_Rcode" = list( "label" = "Download R code"),
# save input Button
"save" = list( "label" = "Save"),
# load input Button
"load" = list( "label" = "Load"),
# Simulation time (Tmax)
"Tmax" = list( "label" = "Time",
"infoTxt" = "Simulation time (number of time steps).",
"value" = 100,
"min" = 1,
"max" = "",
"step" = 1,
"errorTxt" = "Simulation time must be an integer superior or equal to 1."
),
# Simulation time (Tmax)
"NP" = list( "label" = "Replicates",
"infoTxt" = "Number of replicates of the simulated world (distinct populations are generated with the same simulation design).",
"value" = 1,
"min" = 1,
"max" = "",
"step" = 1,
"errorTxt" = "Number of replicates must be an integer superior or equal to 1."
),
# Individual number per replicate
"NI" = list( "label" = "Individual(s)",
"infoTxt" = "Numbers of individuals generated within each population (replicate).",
"value" = 5,
"min" = 1,
"max" = "",
"step" = 1,
"errorTxt" = "Number of individuals must be an integer superior or equal to 1.
Number of individuals must also be divisible by the number of higher-level groups."
),
# Number of trait per individual
"NT" = list( "label" = "Trait(s)",
"infoTxt" = "Number of trait(s) within each individual.",
"value" = c("1" = 1,"2" = 2)
),
"NTnames" = c(paste("$",NOT$trait.1,"$"),
paste("$",NOT$trait.2,"$")),
# Number of High-level groups
"NG" = list("label" = "Higher-level groups",
"infoTxt" = "Number of higher-level groups. Number of groups must be lower than number of individuals. Number of individuals must be divisible by number of groups.",
"value" = 1,
"min" = 1,
"max" = "",
"step" = 1,
"modulo" = 5,
"errorTxt" = "Number of higher-level groups must be an integer
between 1 and number of individuals.</br>
Number of individuals must be divisible by
the number of higher-level groups."
),
# Environement variables
"Envnames" = c("X1", "X2", "EG", "ES"),
"Env_preview" = paste0("In SQuID the final output of each environmental effect is standardized
(i.e., $Var(",NOT$env,"=1)$ and $E(",NOT$env,")=0$).
However, the previsualization graph below displays only the generated environmental data before standardization."),
"X1" = list( "state" = list("label" = "Add environment X1",
"infoTxt" = "",
"value" = FALSE),
"share" = list("label" = "Shared environment",
"infoTxt" = "",
"value" = TRUE)
),
"X2" = list( "state" = list("label" = "Add environment X2",
"infoTxt" = "",
"value" = FALSE),
"share" = list("label" = "Shared environment",
"infoTxt" = "",
"value" = TRUE)
),
"X1X2" = list( "state" = list("label" = "Add environment interaction",
"infoTxt" = "",
"value" = FALSE),
"info" = "Interaction between environment X1 and X2 is
available only when both environements are not null."
),
# Stochastic environmental effect
"sto" = list( "state" = list("label" = "Add stochastic environment effect",
"infoTxt" = "Generate a stochastic environmental effect following a normal distribution with mean 0 and variance that you could input below.",
"value" = FALSE),
"share" = list("label" = "Shared environment",
"infoTxt" = "If checked stochastic (and auto-correlated) environmental effect will be general to all individuals otherwise will be specific (different among individuals).",
"value" = TRUE)
),
# Environemental effect variance (stochastic)
"stoV" = list( "label" = "Variance",
"infoTxt" = "Environmental effect variance of a normal distribution around mean 0.",
"value" = 1,
"min" = 0,
"max" = "",
"step" = 0.01,
"errorTxt" = "Environmental effect variance must be a positive number."
),
# Environemental autocorrelation effect
"sto_autocor_state" = list("label" = "Add autocorrelation",
"infoTxt" = "Incorporate auto-correlation within the stochastic and normal environmental values.",
"value" = FALSE
),
# Environemental decay effect correlation
"stoCorr" = list( "label" = "Correlation",
"infoTxt" = "Correlation value between two consecutive environmental values (note that a decay rate is applied on correlation values and will decreases them more the time between environmental values is large).",
"value" = 0.5,
"min" = 0,
"max" = 1,
"step" = 0.01,
"errorTxt" = "Environemental decay effect (correlation) must be a positive proportion"
),
# Linear environmental effect
"lin" = list( "state" = list("label" = "Add linear environmental effect",
"infoTxt" = "Generate an environmental effect with linear trend.",
"value" = FALSE),
"share" = list("label" = "Shared environment",
"infoTxt" = "If checked linear environmental effect will be general to all individuals otherwise will be specific (different among individuals).",
"value" = TRUE)
),
# Linear environemental effect intercept
"linI" = list( "label" = "Intercept",
"infoTxt" = "Environmental effect intercept.",
"value" = 0,
"min" = "",
"max" = "",
"step" = 0.01,
"errorTxt" = "Environmental effect intercept must be a number."
),
# Linear environemental effect slope
"linS" = list( "label" = "Slope",
"infoTxt" = "Environmental effect slope.",
"value" = 0.1,
"min" = "",
"max" = "",
"step" = 0.01,
"errorTxt" = "Environmental effect slope must be a number."
),
# Cyclic environmental effect
"cyc" = list( "state" = list("label" = "Add cyclic environmental effect",
"infoTxt" = "Generate an environmental effect with a cyclic pattern.",
"value" = FALSE),
"share" = list("label" = "Shared environment",
"infoTxt" = "If checked cyclic environmental effect will be general to all individuals otherwise will be specific (different among individuals).",
"value" = TRUE)
),
# Cyclic environemental effect Amplitude
"cycA" = list( "label" = "Amplitude",
"infoTxt" = "Environmental effect amplitude.",
"value" = 10,
"min" = "",
"max" = "",
"step" = 0.01,
"errorTxt" = "Environmental effect amplitude must be a number."
),
# Cyclic environemental effect Period
"cycP" = list( "label" = "Period",
"infoTxt" = "Environmental effect period.",
"value" = 25,
"min" = "",
"max" = "",
"step" = 0.01,
"errorTxt" = "Environmental effect period must be a number."
),
# Cyclic environemental effect Horizontal shift
"cycH" = list( "label" = "Horizontal shift",
"infoTxt" = "Environmental effect horizontal shift.",
"value" = 0,
"min" = "",
"max" = "",
"step" = 0.01,
"errorTxt" = "Environmental effect horizontal shift must be a number."
),
# Cyclic environemental effect Vertical shift
"cycV" = list( "label" = "Vertical shift",
"infoTxt" = "Environmental effect vertical shift.",
"value" = 0,
"min" = "",
"max" = "",
"step" = 0.01,
"errorTxt" = "Environmental effect vertical shift must be a number."
),
# Residual variance (Ve)
"Ve" = list("label" = "Residual variance",
"infoTxt" = "Variance of unaccounted effect on the phenotype.",
"value" = 0.05,
"min" = 0,
"max" = "",
"step" = 0.01,
"errorTxt" = "Residual variance must be a positive number."
),
# Higher-level grouping variance (VG)
"VG" = list("label" = "Higher-level grouping variance",
"infoTxt" = "Higher-level grouping variance.",
"value" = 0,
"min" = 0,
"max" = "",
"step" = 0.01,
"errorTxt" = "Higher-level grouping variance must be a positive number."
),
# Number of trait expressions (NR)
"NR" = list( "label" = "Records",
"infoTxt" = "Mean number of records over the population.",
"value" = 20,
"min" = 1,
"max" = 100,
"step" = 1,
"errorTxt" = "Number of records must be an integer between 1 and the sampling time length."
),
# Sampling time length
"SampTime" = list( "label" = "Sampling time length",
"infoTxt" = "Sampling time length for each individual within the population (negatively function to the among-individual variance in timing of sampling).",
"value" = "",
"errorTxt" = ""
),
# Among-individual variance in timing of sampling
"Vhsi" = list( "label" = "Among-individual variance in timing of sampling",
"infoTxt" = "Among-individual variance in timing of sampling.",
"value" = 0.0,
"min" = 0.0,
"max" = 0.95,
"step" = 0.01,
"errorTxt" = "Among-individual variance in timing of sampling must be a number between 0 and 0.95."
),
# Sampling time length
"SampDesign_preview" = list( "label" = "Preview of the sampling design",
"infoTxt" = "Preview of the sampling design defined by the user.",
"value" = "",
"errorTxt" = ""
),
# Mean Environemental effect
"B" = list( "label" = "Population mean values",
"infoTxt" = "Population mean values (fixed intercepts and slopes for each trait).",
"value" = matrix(rep(0,nb.IS),1),
"min" = "",
"max" = "" ,
"errorTxt" = "Population mean values must be numbers."),
"Bnames" = c(paste0("$",EQ$mean0.1,"$"),
paste0("$",EQ$mean1.1,"$"),
paste0("$",EQ$mean2.1,"$"),
paste0("$",EQ$mean12.1,"$"),
paste0("$",EQ$mean0.2,"$",sep=""),
paste0("$",EQ$mean1.2,"$"),
paste0("$",EQ$mean2.2,"$"),
paste0("$",EQ$mean12.2,"$")),
"Vind" = list( "label" = "Individual Variance/Correlation matrix",
"infoTxt" = "Individual Variance/Correlation matrix. Variances are on the matrix diagonal and correlation values are below the matrix diagonal.",
"value" = matrix(rep(0,(nb.IS)^2),nb.IS),
"min" = -1,
"max" = 1 ,
"diagmin" = 0,
"diagmax" = "",
"errorTxt" = "text",
"errorTxt1" = "Variance values must be a positive number.",
"errorTxt2" = "Correlation values must be a number between -1 and 1.") ,
"Vindnames" = c(paste0("$",EQ2$dev0.1,"$"),
paste0("$",EQ2$dev1.1,"$"),
paste0("$",EQ2$dev2.1,"$"),
paste0("$",EQ2$dev12.1,"$"),
paste0("$",EQ2$dev0.2,"$"),
paste0("$",EQ2$dev1.2,"$"),
paste0("$",EQ2$dev2.2,"$"),
paste0("$",EQ2$dev12.2,"$")),
"Checkbox_NbRecords" = list( "infoTxt" = "Number of records sampled."),
"NR_ind" = list( "label" = "Same among individuals",
"infoTxt" = "If checked: same number of records among individuals.",
"value" = TRUE,
"errorTxt" = "text"
),
"NR_trait" = list( "label" = "Same among traits within individuals",
"infoTxt" = "If checked: same number of records among traits within individuals.",
"value" = TRUE,
"errorTxt" = "text"
),
"Checkbox_SamTime" = list( "infoTxt" = "Time when records are sampled."),
"ST_ind" = list( "label" = "Same among individuals",
"infoTxt" = "If checked: same sampling times among individuals.",
"value" = TRUE,
"errorTxt" = "text"
),
"ST_trait" = list( "label" = "Same among traits within individuals",
"infoTxt" = "If checked: same sampling times among traits within individuals.",
"value" = TRUE,
"errorTxt" = "text"
)
)
diag(FullModel_VAR$Vind$value) <- c(0.5,0.1,0.1,0.1)
```

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