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DESCRIPTION

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Package: hBayesDM
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Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
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Version: 0.7.1
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Date: 2019-01-21
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Version: 0.7.2
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Date: 2019-02-11
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Author:
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Woo-Young Ahn [aut, cre],
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Nate Haines [aut],
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2020
Description:
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Fit an array of decision-making tasks with computational models in
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a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
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various computational models with a single line of coding.
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Ahn et al. (2018) <doi:10.1162/CPSY_a_00002>
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various computational models with a single line of coding
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(Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
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Depends:
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R (>= 3.4.0),
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Rcpp (>= 0.12.0),
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'hBayesDM_model.R'
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'bandit2arm_delta.R'
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'bandit4arm2_kalman_filter.R'
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'bandit4arm_2par_lapse.R'
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'bandit4arm_4par.R'
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'bandit4arm_lapse.R'
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'bandit4arm_lapse_decay.R'
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'bandit4arm_singleA_lapse.R'
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'bart_par4.R'
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'choiceRT_ddm.R'
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'choiceRT_ddm_single.R'

NAMESPACE

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export(HDIofMCMC)
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export(bandit2arm_delta)
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export(bandit4arm2_kalman_filter)
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export(bandit4arm_2par_lapse)
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export(bandit4arm_4par)
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export(bandit4arm_lapse)
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export(bandit4arm_lapse_decay)
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export(bandit4arm_singleA_lapse)
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export(bart_par4)
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export(choiceRT_ddm)
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export(choiceRT_ddm_single)

NEWS.md

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# hBayesDM 0.7.2
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* Add three new models for the bandit4arm task: `bandit4arm_2par_lapse`,
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`bandit4arm_lapse_decay` and `bandit4arm_singleA_lapse`.
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* Fix various (minor) errors.
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# hBayesDM 0.7.1
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* Make it usable without manually loading `rstan`.
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# hBayesDM 0.7.0
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* Now, in default, you should build a Stan file into a binary for the first time to use it. To build all the models on installation, you should set an environmental variable `BUILD_ALL` to `true` before installation.
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* Now all the implemented models are refactored using `hBayesDM_model` function. You don't have to change anything to use them, but developers can easily implement new model now!
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* Now all the implemented models are refactored using `hBayesDM_model` function. You don't have to change anything to use them, but developers can easily implement new models now!
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* We added a Kalman filter model for 4-armed bandit task (`bandit4arm2_kalman_filter`; Daw et al., 2006) and a probability weighting function for general description-based tasks (`dbdm_prob_weight`; Erev et al., 2010; Hertwig et al., 2004; Jessup et al., 2008).
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* Initial values of parameter estimation for some models are updated as plausible values, and the parameter boundaries of several models are fixed (see more on issue #63 and #64 in Github).
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* Exponential and linear models for choice under risk and ambiguity task now have four model regressors: `sv`, `sv_fix`, `sv_var`, and `p_var`.

R/bandit4arm2_kalman_filter.R

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#' @templateVar MODEL_FUNCTION bandit4arm2_kalman_filter
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#' @templateVar CONTRIBUTOR \href{https://zohyos7.github.io}{Yoonseo Zoh}, \href{https://lei-zhang.net/}{Lei Zhang}
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#' @templateVar TASK_NAME 4-Armed Bandit Task (2)
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#' @templateVar TASK_NAME 4-Armed Bandit Task (modified)
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#' @templateVar MODEL_NAME Kalman Filter
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#' @templateVar MODEL_CITE (Daw et al., 2006, Nature)
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#' @templateVar MODEL_TYPE Hierarchical

R/bandit4arm_2par_lapse.R

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#' @templateVar MODEL_FUNCTION bandit4arm_2par_lapse
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#' @templateVar TASK_NAME 4-Armed Bandit Task
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#' @templateVar MODEL_NAME 3 Parameter Model, without C (choice perseveration), R (reward sensitivity), and P (punishment sensitivity). But with xi (noise)
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#' @templateVar MODEL_CITE (Aylward et al., 2018, PsyArXiv)
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#' @templateVar MODEL_TYPE Hierarchical
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#' @templateVar DATA_COLUMNS "subjID", "choice", "gain", "loss"
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#' @templateVar PARAMETERS "Arew" (reward learning rate), "Apun" (punishment learning rate), "xi" (noise)
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#' @templateVar LENGTH_DATA_COLUMNS 4
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#' @templateVar DETAILS_DATA_1 \item{"subjID"}{A unique identifier for each subject in the data-set.}
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#' @templateVar DETAILS_DATA_2 \item{"choice"}{Integer value representing the option chosen on the given trial: 1, 2, 3, or 4.}
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#' @templateVar DETAILS_DATA_3 \item{"gain"}{Floating point value representing the amount of currency won on the given trial (e.g. 50, 100).}
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#' @templateVar DETAILS_DATA_4 \item{"loss"}{Floating point value representing the amount of currency lost on the given trial (e.g. 0, -50).}
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#'
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#' @template model-documentation
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#'
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#' @export
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#' @include hBayesDM_model.R
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#'
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#' @references
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#' Aylward, Valton, Ahn, Bond, Dayan, Roiser, & Robinson (2018) Altered decision-making under
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#' uncertainty in unmedicated mood and anxiety disorders. PsyArxiv. 10.31234/osf.io/k5b8m
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bandit4arm_2par_lapse <- hBayesDM_model(
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task_name = "bandit4arm",
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model_name = "2par_lapse",
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data_columns = c("subjID", "choice", "gain", "loss"),
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parameters = list("Arew" = c(0, 0.1, 1),
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"Apun" = c(0, 0.1, 1),
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"xi" = c(0, 0.1, 1)),
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preprocess_func = function(raw_data, general_info) {
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# Currently class(raw_data) == "data.table"
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# Use general_info of raw_data
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subjs <- general_info$subjs
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n_subj <- general_info$n_subj
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t_subjs <- general_info$t_subjs
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t_max <- general_info$t_max
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# Initialize (model-specific) data arrays
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rew <- array( 0, c(n_subj, t_max))
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los <- array( 0, c(n_subj, t_max))
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choice <- array(-1, c(n_subj, t_max))
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# Write from raw_data to the data arrays
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for (i in 1:n_subj) {
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subj <- subjs[i]
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t <- t_subjs[i]
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DT_subj <- raw_data[subjid == subj]
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rew[i, 1:t] <- DT_subj$gain
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los[i, 1:t] <- -1 * abs(DT_subj$loss)
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choice[i, 1:t] <- DT_subj$choice
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}
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# Wrap into a list for Stan
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data_list <- list(
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N = n_subj,
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T = t_max,
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Tsubj = t_subjs,
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rew = rew,
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los = los,
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choice = choice
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)
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# Returned data_list will directly be passed to Stan
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return(data_list)
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}
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)
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R/bandit4arm_lapse_decay.R

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#' @templateVar MODEL_FUNCTION bandit4arm_lapse_decay
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#' @templateVar TASK_NAME 4-Armed Bandit Task
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#' @templateVar MODEL_NAME 5 Parameter Model, without C (choice perseveration) but with xi (noise). Added decay rate (Niv et al., 2015, J. Neuro).
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#' @templateVar MODEL_CITE (Aylward et al., 2018, PsyArXiv)
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#' @templateVar MODEL_TYPE Hierarchical
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#' @templateVar DATA_COLUMNS "subjID", "choice", "gain", "loss"
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#' @templateVar PARAMETERS "Arew" (reward learning rate), "Apun" (punishment learning rate), "R" (reward sensitivity), "P" (punishment sensitivity), "xi" (noise), "d" (decay rate)
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#' @templateVar LENGTH_DATA_COLUMNS 4
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#' @templateVar DETAILS_DATA_1 \item{"subjID"}{A unique identifier for each subject in the data-set.}
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#' @templateVar DETAILS_DATA_2 \item{"choice"}{Integer value representing the option chosen on the given trial: 1, 2, 3, or 4.}
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#' @templateVar DETAILS_DATA_3 \item{"gain"}{Floating point value representing the amount of currency won on the given trial (e.g. 50, 100).}
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#' @templateVar DETAILS_DATA_4 \item{"loss"}{Floating point value representing the amount of currency lost on the given trial (e.g. 0, -50).}
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#'
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#' @template model-documentation
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#'
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#' @export
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#' @include hBayesDM_model.R
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#'
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#' @references
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#' Aylward, Valton, Ahn, Bond, Dayan, Roiser, & Robinson (2018) Altered decision-making under
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#' uncertainty in unmedicated mood and anxiety disorders. PsyArxiv. 10.31234/osf.io/k5b8m
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bandit4arm_lapse_decay <- hBayesDM_model(
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task_name = "bandit4arm",
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model_name = "lapse_decay",
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data_columns = c("subjID", "choice", "gain", "loss"),
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parameters = list("Arew" = c(0, 0.1, 1),
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"Apun" = c(0, 0.1, 1),
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"R" = c(0, 1, 30),
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"P" = c(0, 1, 30),
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"xi" = c(0, 0.1, 1),
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"d" = c(0, 0.1, 1)),
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preprocess_func = function(raw_data, general_info) {
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# Currently class(raw_data) == "data.table"
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# Use general_info of raw_data
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subjs <- general_info$subjs
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n_subj <- general_info$n_subj
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t_subjs <- general_info$t_subjs
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t_max <- general_info$t_max
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# Initialize (model-specific) data arrays
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rew <- array( 0, c(n_subj, t_max))
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los <- array( 0, c(n_subj, t_max))
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choice <- array(-1, c(n_subj, t_max))
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# Write from raw_data to the data arrays
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for (i in 1:n_subj) {
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subj <- subjs[i]
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t <- t_subjs[i]
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DT_subj <- raw_data[subjid == subj]
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rew[i, 1:t] <- DT_subj$gain
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los[i, 1:t] <- -1 * abs(DT_subj$loss)
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choice[i, 1:t] <- DT_subj$choice
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}
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# Wrap into a list for Stan
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data_list <- list(
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N = n_subj,
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T = t_max,
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Tsubj = t_subjs,
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rew = rew,
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los = los,
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choice = choice
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)
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# Returned data_list will directly be passed to Stan
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return(data_list)
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}
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)

R/bandit4arm_singleA_lapse.R

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#' @templateVar MODEL_FUNCTION bandit4arm_singleA_lapse
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#' @templateVar TASK_NAME 4-Armed Bandit Task
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#' @templateVar MODEL_NAME 4 Parameter Model, without C (choice perseveration) but with xi (noise). Single learning rate both for R and P.
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#' @templateVar MODEL_CITE (Aylward et al., 2018, PsyArXiv)
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#' @templateVar MODEL_TYPE Hierarchical
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#' @templateVar DATA_COLUMNS "subjID", "choice", "gain", "loss"
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#' @templateVar PARAMETERS "A" (learning rate), "R" (reward sensitivity), "P" (punishment sensitivity), "xi" (noise)
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#' @templateVar LENGTH_DATA_COLUMNS 4
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#' @templateVar DETAILS_DATA_1 \item{"subjID"}{A unique identifier for each subject in the data-set.}
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#' @templateVar DETAILS_DATA_2 \item{"choice"}{Integer value representing the option chosen on the given trial: 1, 2, 3, or 4.}
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#' @templateVar DETAILS_DATA_3 \item{"gain"}{Floating point value representing the amount of currency won on the given trial (e.g. 50, 100).}
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#' @templateVar DETAILS_DATA_4 \item{"loss"}{Floating point value representing the amount of currency lost on the given trial (e.g. 0, -50).}
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#'
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#' @template model-documentation
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#'
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#' @export
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#' @include hBayesDM_model.R
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#'
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#' @references
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#' Aylward, Valton, Ahn, Bond, Dayan, Roiser, & Robinson (2018) Altered decision-making under
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#' uncertainty in unmedicated mood and anxiety disorders. PsyArxiv. 10.31234/osf.io/k5b8m
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bandit4arm_singleA_lapse <- hBayesDM_model(
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task_name = "bandit4arm",
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model_name = "singleA_lapse",
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data_columns = c("subjID", "choice", "gain", "loss"),
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parameters = list("A" = c(0, 0.1, 1),
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"R" = c(0, 1, 30),
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"P" = c(0, 1, 30),
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"xi" = c(0, 0.1, 1)),
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preprocess_func = function(raw_data, general_info) {
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# Currently class(raw_data) == "data.table"
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# Use general_info of raw_data
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subjs <- general_info$subjs
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n_subj <- general_info$n_subj
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t_subjs <- general_info$t_subjs
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t_max <- general_info$t_max
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# Initialize (model-specific) data arrays
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rew <- array( 0, c(n_subj, t_max))
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los <- array( 0, c(n_subj, t_max))
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choice <- array(-1, c(n_subj, t_max))
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# Write from raw_data to the data arrays
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for (i in 1:n_subj) {
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subj <- subjs[i]
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t <- t_subjs[i]
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DT_subj <- raw_data[subjid == subj]
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rew[i, 1:t] <- DT_subj$gain
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los[i, 1:t] <- -1 * abs(DT_subj$loss)
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choice[i, 1:t] <- DT_subj$choice
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}
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# Wrap into a list for Stan
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data_list <- list(
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N = n_subj,
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T = t_max,
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Tsubj = t_subjs,
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rew = rew,
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los = los,
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choice = choice
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)
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# Returned data_list will directly be passed to Stan
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return(data_list)
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}
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)

R/bart_par4.R

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#' @templateVar MODEL_FUNCTION bart_par4
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#' @templateVar CONTRIBUTOR \href{https://ccs-lab.github.io/team/harhim-park/}{Harhim Park}, \href{https://ccs-lab.github.io/team/jaeyeong-yang/}{Jaeyeong Yang}, \href{https://ccs-lab.github.io/team/ayoung-lee/}{Ayoung Lee}, \href{https://ccs-lab.github.io/team/jeongbin-oh/}{Jeongbin Oh}, \href{https://ccs-lab.github.io/team/jiyoon-lee/}{Jiyoon Lee}, \href{https://ccs-lab.github.io/team/junha-jang/}{Junha Jang}
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#' @templateVar TASK_NAME Balloon Analogue Risk Task
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#' @templateVar TASK_CITE (Ravenzwaaij et al., 2011, Journal of Mathematical Psychology)
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#' @templateVar TASK_CITE (Ravenzwaaij et al., 2011)
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#' @templateVar MODEL_NAME Re-parameterized version (by Harhim Park & Jaeyeong Yang) of BART Model (Ravenzwaaij et al., 2011) with 4 parameters
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#' @templateVar MODEL_TYPE Hierarchical
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#' @templateVar DATA_COLUMNS "subjID", "pumps", "explosion"

R/dbdm_prob_weight.R

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#' @templateVar MODEL_FUNCTION dbdm_prob_weight
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#' @templateVar CONTRIBUTOR \href{https://ccs-lab.github.io/team/yoonseo-zoh/}{Yoonseo Zoh}
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#' @templateVar TASK_NAME Description Based Decison Making Task
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#' @templateVar MODEL_NAME Probability Weight Function
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#' @templateVar MODEL_CITE (Erev et al., 2010; Hertwig et al., 2004; Jessup et al., 2008)

R/hBayesDM.R

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#' Hierarchical Bayesian Modeling of Decision-Making Tasks
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#' @docType package
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#' @name hBayesDM-package
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#' @aliases hBayesDM
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#' @useDynLib hBayesDM, .registration = TRUE
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#'
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#' @aliases hBayesDM
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#' @useDynLib hBayesDM, .registration = TRUE
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#'
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#' @import methods
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#' @import Rcpp
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#' @description
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#' Fit an array of decision-making tasks with computational models in a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of various computational models with a single line of coding.
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#' Bolded tasks, followed by their respective models, are itemized below.
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#'
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#' Bolded tasks, followed by their respective models, are itemized below.
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#'
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#' \describe{
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#' \item{\strong{Bandit}}{2-Armed Bandit (Rescorla-Wagner (delta)) --- \link{bandit2arm_delta} \cr
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#' 4-Armed Bandit with fictive updating + reward/punishment sensitvity (Rescorla-Wagner (delta)) --- \link{bandit4arm_4par} \cr
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#' 4-Armed Bandit with fictive updating + reward/punishment sensitvity + lapse (Rescorla-Wagner (delta)) --- \link{bandit4arm_lapse}}
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#' \item{\strong{Bandit2}}{Kalman filter --- \link{bandit4arm2_kalman_filter}}
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#' \item{\strong{Choice RT}}{Drift Diffusion Model --- \link{choiceRT_ddm} \cr
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#' Drift Diffusion Model for a single subject --- \link{choiceRT_ddm_single} \cr
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#' Linear Ballistic Accumulator (LBA) model --- \link{choiceRT_lba} \cr
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#' Linear Ballistic Accumulator (LBA) model for a single subject --- \link{choiceRT_lba_single}}
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#' \item{\strong{Choice under Risk and Ambiguity}}{Exponential model --- \link{cra_exp} \cr
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#' Linear model --- \link{cra_linear}}
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#' \item{\strong{Description-Based Decision Making}}{probability weight function --- \link{dbdm_prob_weight}}
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#' \item{\strong{Delay Discounting}}{Constant Sensitivity --- \link{dd_cs} \cr
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#' Constant Sensitivity for single subject --- \link{dd_cs_single} \cr
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#' Constant Sensitivity for a single subject --- \link{dd_cs_single} \cr
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#' Exponential --- \link{dd_exp} \cr
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#' Hyperbolic --- \link{dd_hyperbolic} \cr
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#' Hyperbolic for single subject --- \link{dd_hyperbolic_single}}
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#' Hyperbolic for a single subject --- \link{dd_hyperbolic_single}}
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#' \item{\strong{Orthogonalized Go/Nogo}}{RW + Noise --- \link{gng_m1} \cr
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#' RW + Noise + Bias --- \link{gng_m2} \cr
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#' RW + Noise + Bias + Pavlovian Bias --- \link{gng_m3} \cr
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#' RW(modified) + Noise + Bias + Pavlovian Bias --- \link{gng_m4}}
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#' \item{\strong{Iowa Gambling}}{Prospect Valence Learning-DecayRI --- \link{igt_pvl_decay} \cr
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#' \item{\strong{Iowa Gambling}}{Outcome-Representation Learning --- \link{igt_orl} \cr
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#' Prospect Valence Learning-DecayRI --- \link{igt_pvl_decay} \cr
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#' Prospect Valence Learning-Delta --- \link{igt_pvl_delta} \cr
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#' Value-Plus_Perseverance --- \link{igt_vpp}}
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#' \item{\strong{Peer influence task}}{OCU model --- \link{peer_ocu}}
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#' \item{\strong{Probabilistic Reversal Learning}}{Fictitious Update --- \link{prl_fictitious} \cr
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#' \item{\strong{Probabilistic Reversal Learning}}{Experience-Weighted Attraction --- \link{prl_ewa} \cr
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#' Fictitious Update --- \link{prl_fictitious} \cr
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#' Fictitious Update w/o alpha (indecision point) --- \link{prl_fictitious_woa} \cr
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#' Fictitious Update and multiple blocks per subject --- \link{prl_fictitious_multipleB} \cr
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#' Experience-Weighted Attraction --- \link{prl_ewa} \cr
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#' Reward-Punishment --- \link{prl_rp} \cr
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#' Reward-Punishment and multiple blocks per subject --- \link{prl_rp_multipleB} \cr
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#' Fictitious Update with separate learning for Reward-Punishment --- \link{prl_fictitious_rp} \cr
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#' Fictitious Update with separate learning for Reward-Punishment w/o alpha (indecision point) --- \link{prl_fictitious_rp_woa}}
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#' \item{\strong{Probabilistic Selection Task}}{Q-learning with two learning rates --- \link{pst_gainloss_Q}}
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#' \item{\strong{Risk Aversion}}{Prospect Theory (PT) --- \link{ra_prospect} \cr
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#' PT without a loss aversion parameter --- \link{ra_noLA} \cr
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#' PT without a risk aversion parameter --- \link{ra_noRA}}
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#' \item{\strong{Ultimatum Game}}{Ideal Bayesian Observer --- \link{ug_bayes} \cr
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#' Rescorla-Wagner (delta) --- \link{ug_delta}}
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#' \item{\strong{Choice/Reaction time}}{Drift Diffusion Model --- \link{choiceRT_ddm} \cr
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#' Drift Diffusion Model for single subject --- \link{choiceRT_ddm_single} \cr
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#' Linear Ballistic Accumulator --- \link{choiceRT_lba} \cr
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#' Linear Ballistic Accumulator for single subject --- \link{choiceRT_lba_single}}
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#' \item{\strong{Risky Decision Task}}{Happiness model --- \link{rdt_happiness}}
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#' \item{\strong{Two-Step task}}{Full model (7 parameters) --- \link{ts_par7} \cr
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#' 6 parameter model (without eligibility trace, lambda) --- \link{ts_par6} \cr
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#' 4 parameter model --- \link{ts_par4}}
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#'
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#' \item{\strong{Ultimatum Game}}{Ideal Bayesian Observer --- \link{ug_bayes} \cr
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#' Rescorla-Wagner (delta) --- \link{ug_delta}}
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#'
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#' }
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#'
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#' @seealso
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#'
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#' @seealso
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#' For tutorials and further readings, visit : \url{http://rpubs.com/CCSL/hBayesDM}.
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#'
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#' @references
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#' Please cite as:
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#'
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#' @references
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#' Please cite as:
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#' Ahn, W.-Y., Haines, N., & Zhang, L. (2017). Revealing neuro-computational mechanisms of reinforcement learning and decision-making with the hBayesDM package. \emph{Computational Psychiatry}. 1, 24-57. https://doi.org/10.1162/CPSY_a_00002
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#'
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#' @author
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#' Woo-Young Ahn \email{wooyoung.ahn@@gmail.com}
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#' Woo-Young Ahn \email{wahn55@@snu.ac.kr}
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#'
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#' Nathaniel Haines \email{haines.175@@osu.edu}
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#'

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