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Merge pull request #65 from neuropsychology/dev
prepare CRAN
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| # Contribution Guidelines | ||
| **All people are very much welcome to contribute to code, documentation, testing and suggestions.** | ||
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| `psycho` is a beginner-friendly package. Even if you're new to all this open-source way of life, new to coding and submitting pull requests (PRs), we encourage you to try. You can submit some recommendations in the [issues](https://github.com/neuropsychology/psycho.R/issues) or start coding a function or adding some parameters, fixing a bug or just rewriting a bit so it is more clear, more documented or understandable. Then, do not hesitate to sumbit your changes. We will work together to integrate them :) | ||
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| ## Code | ||
| - Authors of code contribution will be added within the [**authors**](https://github.com/neuropsychology/psycho.R/blob/master/DESCRIPTION) section within the package description. | ||
| - Please document and comment your code, so that the purpose of each step (or code line) is stated in a clear and understandable way. | ||
| - Avoid unnecessary function splitting into smaller bits: it makes testing and reading of the code more difficult (as one must jump between functions and files to understand what's happening). | ||
| - Before submitting a change, please use [**styler**](https://github.com/r-lib/styler) to nicely format your code. |
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| #' Analyze aov objects. | ||
| #' | ||
| #' Analyze aov objects. | ||
| #' | ||
| #' @param x aov object. | ||
| #' @param ... Arguments passed to or from other methods. | ||
| #' | ||
| #' @return output | ||
| #' | ||
| #' @examples | ||
| #' library(psycho) | ||
| #' | ||
| #' df <- psycho::affective | ||
| #' | ||
| #' x <- aov(df$Tolerating ~ df$Sex) | ||
| #' | ||
| #' summary(analyze(x)) | ||
| #' | ||
| #' | ||
| #' @author \href{https://dominiquemakowski.github.io/}{Dominique Makowski} | ||
| #' | ||
| #' @import broom | ||
| #' | ||
| #' @export | ||
| analyze.aov <- function(x, ...) { | ||
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| # TODO: this must be enhanced! | ||
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| # Processing | ||
| # ------------- | ||
| values <- broom::tidy(x) | ||
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| # Text | ||
| # ------------- | ||
| text <- "Not available yet" | ||
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| # Summary | ||
| # ------------- | ||
| summary <- values | ||
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| # Plot | ||
| # ------------- | ||
| plot <- "Not available yet" | ||
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| output <- list(text = text, plot = plot, summary = summary, values = values) | ||
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| class(output) <- c("psychobject", "list") | ||
| return(output) | ||
| } |
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| #' Analyze aov objects. | ||
| #' | ||
| #' Analyze aov objects. | ||
| #' | ||
| #' @param x aov object. | ||
| #' @param ... Arguments passed to or from other methods. | ||
| #' | ||
| #' @return output | ||
| #' | ||
| #' @examples | ||
| #' library(psycho) | ||
| #' library(lavaan) | ||
| #' | ||
| #' model <- ' visual =~ x1 + x2 + x3 | ||
| #' textual =~ x4 + x5 + x6 | ||
| #' speed =~ x7 + x8 + x9 ' | ||
| #' x <- lavaan::cfa(model, data=HolzingerSwineford1939) | ||
| #' | ||
| #' rez <- analyze(x) | ||
| #' print(rez) | ||
| #' | ||
| #' | ||
| #' @author \href{https://dominiquemakowski.github.io/}{Dominique Makowski} | ||
| #' | ||
| #' @seealso | ||
| #' https://www.researchgate.net/post/Whats_the_standard_of_fit_indices_in_SEM | ||
| #' | ||
| #' | ||
| #' @importFrom lavaan parameterEstimates fitmeasures | ||
| #' | ||
| #' @export | ||
| analyze.lavaan <- function(x, ...) { | ||
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| # TODO: this must be enhanced! | ||
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| # Processing | ||
| # ------------- | ||
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| # TODO: tWait for broom to implement methods for lavaan objects! | ||
| values <- list() | ||
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| indices <- lavaan::fitmeasures(x) | ||
| for (index in names(indices)) { | ||
| values[index] <- indices[index] | ||
| } | ||
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| # awang2012 | ||
| # https://www.researchgate.net/post/Whats_the_standard_of_fit_indices_in_SEM | ||
| if (values$cfi >= 0.9) { | ||
| cfi <- "satisfactory" | ||
| } else { | ||
| cfi <- "poor" | ||
| } | ||
| if (values$rmsea <= 0.08) { | ||
| rmsea <- "satisfactory" | ||
| } else { | ||
| rmsea <- "poor" | ||
| } | ||
| if (values$gfi >= 0.9) { | ||
| gfi <- "satisfactory" | ||
| } else { | ||
| gfi <- "poor" | ||
| } | ||
| if (values$tli >= 0.9) { | ||
| tli <- "satisfactory" | ||
| } else { | ||
| tli <- "poor" | ||
| } | ||
| if (values$nfi >= 0.9) { | ||
| nfi <- "satisfactory" | ||
| } else { | ||
| nfi <- "poor" | ||
| } | ||
| fit <- data.frame( | ||
| Index = c("RMSEA", "CFI", "GFI", "TLI", "NFI", "Chisq"), | ||
| Value = c(values$rmsea, values$cfi, values$gfi, values$tli, values$nfi, values$chisq), | ||
| Interpretation = c(rmsea, cfi, gfi, tli, nfi, NA), | ||
| Treshold = c("< .08", "> .9", "> .9", "> .9", "> .9", NA) | ||
| ) | ||
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| # Text | ||
| # ------------- | ||
| if ("satisfactory" %in% fit$Interpretation) { | ||
| satisfactory <- fit %>% | ||
| filter_("Interpretation == 'satisfactory'") %>% | ||
| mutate_("Index" = "paste0(Index, ' (', format_digit(Value), ' ', Treshold, ')')") %>% | ||
| select_("Index") %>% | ||
| pull() %>% | ||
| paste0(collapse = ", ") | ||
| satisfactory <- paste0("The ", satisfactory, " show satisfactory indices of fit.") | ||
| } else { | ||
| satisfactory <- "" | ||
| } | ||
| if ("poor" %in% fit$Interpretation) { | ||
| poor <- fit %>% | ||
| filter_("Interpretation == 'poor'") %>% | ||
| mutate_( | ||
| "Treshold" = 'stringr::str_replace(Treshold, "<", "SUP")', | ||
| "Treshold" = 'stringr::str_replace(Treshold, ">", "INF")', | ||
| "Treshold" = 'stringr::str_replace(Treshold, "SUP", ">")', | ||
| "Treshold" = 'stringr::str_replace(Treshold, "INF", "<")' | ||
| ) %>% | ||
| mutate_("Index" = "paste0(Index, ' (', format_digit(Value), ' ', Treshold, ')')") %>% | ||
| select_("Index") %>% | ||
| pull() %>% | ||
| paste0(collapse = ", ") | ||
| poor <- paste0("The ", poor, " show poor indices of fit.") | ||
| } else { | ||
| poor <- "" | ||
| } | ||
| text <- paste(satisfactory, poor) | ||
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| # Summary | ||
| # ------------- | ||
| summary <- lavaan::parameterEstimates(x) %>% | ||
| as_data_frame() %>% | ||
| tibble::rownames_to_column() %>% | ||
| mutate_("term" = "paste(lhs, op, rhs)") %>% | ||
| rename( | ||
| "estimate" = "est", | ||
| "Operator" = "op", | ||
| "std.error" = "se", | ||
| "p.value" = "pvalue", | ||
| "statistic" = "z", | ||
| "CI_lower" = "ci.lower", | ||
| "CI_upper" = "ci.upper" | ||
| ) %>% | ||
| select_("term", "Operator", "everything()", "-rowname", "-lhs", "-rhs") | ||
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| # Plot | ||
| # ------------- | ||
| plot <- "Not available yet" | ||
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| output <- list(text = text, plot = plot, summary = summary, values = values) | ||
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| class(output) <- c("psychobject", "list") | ||
| return(output) | ||
| } |
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