Merge pull request #10 from egouldo/pkgdown-setup

pkgdown setup

.Rbuildignore

@@ -5,3 +5,6 @@
 ^\.Rproj\.user$
 _targets.R
 
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.gitignore

@@ -3,4 +3,5 @@
 .RData
 .Ruserdata
 .DS_Store
-*reprex.*
+*reprex.*
+docs

DESCRIPTION

@@ -34,7 +34,36 @@ Imports:
     purrr,
     rlang,
     tidyr,
-    tidyselect
+    tidyselect,
+    orchaRd,
+    pointblank,
+    tibble,
+    broom.mixed, 
+    cli, 
+    data.table, 
+    forcats, 
+    fs, 
+    ggeffects, 
+    ggforestplot, 
+    glue, 
+    here, 
+    lme4, 
+    magick, 
+    metafor, 
+    metaviz, 
+    naniar, 
+    parameters, 
+    parsnip, 
+    performance, 
+    pracma, 
+    progress, 
+    readr, 
+    readxl, 
+    recipes, 
+    sae, 
+    stringr, 
+    timetk, 
+    workflows
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)

R/pred_to_Z.R

@@ -44,7 +44,7 @@ pred_to_Z <- function(back_transformed_data,
     if(!pointblank::test_col_exists(back_transformed_data, 
                                     columns = c("fit", "se.fit"))){
 
-      cli::cli_warn("Eucalyptus Dataframe {.arg back_transformed_data} is missing columns {.val fit} and/or {.val se.fit}. Returning {.val {NA}} for standardized predictions.")
+      cli::cli_warn("Eucalyptus Dataframe {.arg back_transformed_data} is missing columns {.val fit} and/or {.val se.fit}. Returning {.val {NA}} for standardized predictions.") #TODO remove hard-coding, generalise
       return(NA)
     }
     sd_p <- params %>% filter(parameter == "sd") %>% pluck("value")

_pkgdown.yml

@@ -0,0 +1,82 @@
+url: ~
+template:
+  bootstrap: 5
+reference:
+- title: "Unprocessed data cleaning and checking"
+  desc: "Functions for cleaning and QA checking unprocessed analyst data"
+- subtitle: "Miscellaneous cleaning functions"
+  contents:
+    - rm_inf_na
+    - anonymise_teams
+    - clean_response_transformation
+    - assign_transformation_type
+- subtitle: "Working with analyst-provided out-of-sample predictions"
+  desc:
+  contents:
+    - augment_prediction_data
+    - preprocess_prediction_files
+    - preprocess_updated_prediction_files
+    - read_submission_data
+    - starts_with("validate_predictions")
+- title: "Data Processing for Meta-analysis and Modelling"
+  desc: "Calculating and standardising variables for analysis"
+  contents:
+    - est_to_zr
+    - Z_VZ_preds
+    - pred_to_Z
+    - apply_VZ_exclusions
+    - box_cox_transform
+    - log_transform
+    - calculate_deviation_score
+    - calculate_sorensen_diversity_index
+    - apply_sorensen_calc
+    - conversion
+    - conversion_2
+    - convert_predictions
+    - ends_with("_back")
+    - back_transform_response_vars_yi
+    - starts_with("exclude_")
+    - starts_with("subset_fns")
+    - standardise_response
+- title: "Process and create datasets for analysis"
+  desc: "Functions for creating datasets ready for meta-analysis or other analyses"
+  contents:
+    - make_param_table
+    - compute_MA_inputs
+    - compute_metaanalysis_inputs
+    - get_diversity_data
+    - starts_with("prepare_")
+- title: "Model Fitting & Meta-analysis"
+  desc: "Functions for fitting meta-analysis and other models described ion *Gould et al. (2023)*"
+  contents:
+    - starts_with("fit_")
+- title: "Extracting Analysis Outputs & Visualisation"
+  desc: "Functions for extracting model outputs, and visualising analysis results"
+  contents:
+    - gg_forest
+    - starts_with("plot_")
+    - i2_ml
+    - calc_I2_ml
+    - apportion_heterogeneity_ml
+    - compare_ml_MA
+    - get_MA_fit_stats
+    - run_model_checks
+- title: "Scaling Up: Working with data subsets or multiple datasets"
+  desc: >
+    Functions for working with multiple datasets or data subsets within a tidyverse list-column framework.
+- subtitle: "Wrapper Functions"
+  desc: ""
+  contents:
+    - compute_metaanalysis_inputs
+    - meta_analyse_datasets
+    - make_viz
+- subtitle: "Generate data subsets of full ManyEcoEvo or ManyAnalyst dataset"
+  desc: ""
+  contents:
+    - starts_with("generate_")
+- title: "Utility Functions"
+  desc: "Miscelaneous utility functions"
+  contents: 
+    - capwords
+    - hex_key
+    - named_group_split

inst/CITATION

@@ -1,9 +1,29 @@
 citHeader("To cite ManyEcoEvo in publications use:")
 
- @Manual{,
-    title = {ManyEcoEvo: Meta-analyse data from 'Many-Analysts' style studies},
-    author = {Elliot Gould and Hannah S. Fraser and Shinichi Nakagawa and Timothy H. Parker},
-    year = {2023},
-    note = {R package version 1.0.0},
-    url = {https://github.com/egouldo/ManyEcoEvo},
-  }
+bibentry(
+     bibtype = "Article",
+     title = "ManyEcoEvo: Meta-analyse data from ManyAnalyst style studies",
+     author = c(person(given = "Elliot",
+                    family = "Gould",
+                    email =  "elliot.gould@unimelb.edu.au",
+                    role = c("aut", "cre"),
+                    comment = c(ORCID = "https://orcid.org/0000-0002-6585-538X")),
+             person(given = "Hannah S.",
+                    family = "Fraser",
+                    role = "aut",
+                    comment = c(ORCID = "https://orcid.org/0000-0003-2443-4463")),
+             person(given = "Shinichi",
+                    family = "Nakagawa",
+                    role = "aut",
+                    comment = c(ORCID = "https://orcid.org/0000-0002-7765-5182")),
+             person(given = "Timothy H.",
+                    family = "Parker",
+                    role = "aut",
+                    comment = c(ORCID = "https://orcid.org/0000-0003-2995-5284"))
+           ),
+     journal = "TBC",
+     year = "2023",
+     #note = "R package version 1.3-4",
+     #url = "https://CRAN.R-project.org/package=boot",
+     #key = "boot-package"
+     )

renv.lock

@@ -954,6 +954,26 @@
       ],
       "Hash": "4bf4423d2c8b68c93b47e32ec554c2f1"
     },
+    "downlit": {
+      "Package": "downlit",
+      "Version": "0.4.2",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "brio",
+        "desc",
+        "digest",
+        "evaluate",
+        "fansi",
+        "memoise",
+        "rlang",
+        "vctrs",
+        "withr",
+        "yaml"
+      ],
+      "Hash": "79bf3f66590752ffbba20f8d2da94c7c"
+    },
     "dplyr": {
       "Package": "dplyr",
       "Version": "1.1.3",
@@ -2812,6 +2832,36 @@
       ],
       "Hash": "01f28d4278f15c76cddbea05899c5d6f"
     },
+    "pkgdown": {
+      "Package": "pkgdown",
+      "Version": "2.0.7",
+      "Source": "Repository",
+      "Repository": "CRAN",
+      "Requirements": [
+        "R",
+        "bslib",
+        "callr",
+        "cli",
+        "desc",
+        "digest",
+        "downlit",
+        "fs",
+        "httr",
+        "jsonlite",
+        "magrittr",
+        "memoise",
+        "purrr",
+        "ragg",
+        "rlang",
+        "rmarkdown",
+        "tibble",
+        "whisker",
+        "withr",
+        "xml2",
+        "yaml"
+      ],
+      "Hash": "16fa15449c930bf3a7761d3c68f8abf9"
+    },
     "pkgload": {
       "Package": "pkgload",
       "Version": "1.3.2",
@@ -3287,14 +3337,14 @@
     },
     "rlang": {
       "Package": "rlang",
-      "Version": "1.1.1",
+      "Version": "1.1.2",
       "Source": "Repository",
       "Repository": "CRAN",
       "Requirements": [
         "R",
         "utils"
       ],
-      "Hash": "a85c767b55f0bf9b7ad16c6d7baee5bb"
+      "Hash": "50a6dbdc522936ca35afc5e2082ea91b"
     },
     "rmarkdown": {
       "Package": "rmarkdown",