Merge pull request #5 from pmcharrison/consolidate

Consolidate

.gitignore

@@ -8,3 +8,6 @@ tests/testthat/cache/*
 www
 inst/shiny/cache
 .cache
+.DS_Store
+.idea
+.ipynb_checkpoints

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: incon
 Type: Package
 Title: Computational Models of Simultaneous Consonance
-Version: 0.4.1
+Version: 0.5.0
 Author: person("Peter", "Harrison", email = "[email protected]", role = c("aut", "cre"))
 Depends: R (>= 3.4.0)
 Maintainer: Peter Harrison <[email protected]>
@@ -10,42 +10,42 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Imports:
+    assertthat,
     Rdpack (>= 0.11.0),
+    gmp (>= 0.5.13.2),
     hrep (>= 0.10.0.9001),
-    bowl18 (>= 0.1.0),
-    corpdiss (>= 0.1.0.9000),
-    dycon (>= 0.2.0),
-    har18 (>= 0.1.0),
-    jl12 (>= 0.1.0),
-    parn88 (>= 0.2.0),
-    parn94 (>= 0.2.3),
-    stolz15 (>= 0.1.0),
-    wang13 (>= 0.1.1),
+    hht,
     checkmate (>= 1.9.4),
     magrittr (>= 1.5),
     purrr (>= 0.3.2),
     methods,
+    gtools,
+    Rcpp,
+    numbers,
+    phonTools,
     tibble (>= 2.1.3),
     dplyr (>= 0.8.3),
+    rlang (>= 0.4.0),
     zeallot (>= 0.1.0),
     utils
 RdMacros: Rdpack
 Suggests: 
     testthat (>= 2.1.1),
     knitr (>= 1.23),
     DT (>= 0.5),
-    covr (>= 3.2.1)
-RoxygenNote: 6.1.1
+    covr (>= 3.2.1),
+    cowplot,
+    ggplot2 (>= 3.1.0.9000),
+    hcorp,
+    shiny,
+    shinydashboard,
+    shinyjs,
+    tuneR
+RoxygenNote: 7.3.1
 Remotes: 
     pmcharrison/hrep,
-    pmcharrison/bowl18,
-    pmcharrison/corpdiss,
-    pmcharrison/dycon,
-    pmcharrison/har18,
-    pmcharrison/jl12,
-    pmcharrison/parn88,
-    pmcharrison/parn94,
-    pmcharrison/stolz15,
-    pmcharrison/wang13
+    pmcharrison/hcorp
 VignetteBuilder: knitr
 Byte-Compile: yes
+LinkingTo: 
+    Rcpp

NAMESPACE

@@ -1,9 +1,119 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(as.character,fraction)
+S3method(bowl18_min_freq_dist,default)
+S3method(bowl18_min_freq_dist,fr_chord)
+S3method(complex_sonor,default)
+S3method(complex_sonor,parn94)
+S3method(corpus_dissonance_table,corpus)
+S3method(count_chords,corpus)
+S3method(double,fraction)
+S3method(expand_harmonics,fraction)
+S3method(expand_harmonics,rational_chord)
+S3method(fraction,numeric)
+S3method(gcd,rational_chord)
+S3method(half,fraction)
+S3method(huron_1994,default)
+S3method(huron_1994,int_vec)
+S3method(huron_1994,pc_set)
+S3method(jl_tonal_dissonance,default)
+S3method(jl_tonal_dissonance,pc_set)
+S3method(kl_div_from_uniform,smooth_spectrum)
+S3method(lcm,rational_chord)
+S3method(multiplicity,default)
+S3method(multiplicity,parn94)
+S3method(parn88,default)
+S3method(parn88,pc_set)
+S3method(parn94,default)
+S3method(parn94,sparse_pi_spectrum)
+S3method(pc_harmonicity,default)
+S3method(pc_harmonicity,milne_pc_spectrum)
+S3method(pc_harmonicity,pc_set)
+S3method(peak,milne_pc_spectrum)
+S3method(pitch_salience,default)
+S3method(pitch_salience,parn94)
+S3method(pitch_salience,pitch_salience)
+S3method(print,corpus_dissonance_table)
+S3method(pure_sonor,default)
+S3method(pure_sonor,parn94)
+S3method(rationalise_chord,pi_chord)
+S3method(roughness_hutch,default)
+S3method(roughness_hutch,sparse_fr_spectrum)
+S3method(roughness_seth,default)
+S3method(roughness_seth,sparse_fr_spectrum)
+S3method(roughness_vass,default)
+S3method(roughness_vass,sparse_fr_spectrum)
+S3method(roughness_wang,default)
+S3method(roughness_wang,sparse_fr_spectrum)
+S3method(smooth_log_periodicity,default)
+S3method(smooth_log_periodicity,pi_chord)
+S3method(sweep_harmonic_template,milne_pc_spectrum)
+S3method(sweep_harmonic_template,pc_set)
+S3method(type,corpus_dissonance_table)
+export(bowl18_min_freq_dist)
+export(complex_sonor)
+export(corpus_dissonance)
+export(corpus_dissonance_table)
+export(cosine_similarity)
+export(count_chords)
+export(demo_wang)
+export(get_free_field_threshold)
+export(get_overall_masking_level)
+export(get_partial_masking_level)
+export(get_pure_tone_audibility)
+export(get_pure_tone_audible_level)
+export(get_pure_tone_height)
+export(get_tone_salience)
+export(gill09_harmonicity)
 export(har_19_composite_coef)
+export(huron_1994)
+export(huron_1994_weights)
+export(hutch_cbw)
+export(hutch_dissonance_function)
+export(hutch_g)
+export(hutch_visualise)
+export(hutch_y)
 export(incon)
 export(incon_models)
+export(jl_rule_1)
+export(jl_rule_2)
+export(jl_rule_3)
+export(jl_tonal_dissonance)
+export(kl_div_from_uniform)
 export(list_models)
+export(multiplicity)
+export(parn88)
+export(parn94)
+export(parn94_params)
+export(pc_harmonicity)
+export(peak)
+export(pitch_commonality)
+export(pitch_distance)
+export(pitch_salience)
+export(pure_sonor)
+export(root)
+export(root_ambiguity)
+export(root_support_weights)
+export(roughness_hutch)
+export(roughness_seth)
+export(roughness_vass)
+export(roughness_wang)
+export(smooth_log_periodicity)
+export(sweep_harmonic_template)
+export(sweep_template)
+export(type)
+importFrom(Rcpp,sourceCpp)
+importFrom(Rdpack,reprompt)
 importFrom(magrittr,"%>%")
+importFrom(methods,"is")
+importFrom(methods,.valueClassTest)
+importFrom(methods,new)
+importFrom(rlang,".data")
+importFrom(stats,"approx")
+importFrom(stats,"cor")
+importFrom(stats,"fft")
+importFrom(stats,cor)
 importFrom(tibble,tibble)
+importFrom(utils,"capture.output")
 importFrom(zeallot,"%<-%")
+useDynLib(incon, .registration = TRUE)

NEWS.md

@@ -1,3 +1,8 @@
+# incon 0.5.0
+
+- Consolidated all modelling dependencies into this package, 
+  to avoid having to download so many GitHub repositories on installation.
+
 # incon 0.4.1
 
 - Addressing some minor dependency issues.

R/RcppExports.R

@@ -0,0 +1,19 @@
+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+mod <- function(x, base) {
+    .Call(`_incon_mod`, x, base)
+}
+
+get_index <- function(x, index, offset) {
+    .Call(`_incon_get_index`, x, index, offset)
+}
+
+cosine_similarity_cpp <- function(x, template_, offset) {
+    .Call(`_incon_cosine_similarity_cpp`, x, template_, offset)
+}
+
+sweep_template_cpp <- function(x, template_) {
+    .Call(`_incon_sweep_template_cpp`, x, template_)
+}
+

R/imports.R

@@ -1,5 +1,35 @@
+## usethis namespace: start
+#' @useDynLib incon, .registration = TRUE
+## usethis namespace: end
+NULL
+
+## usethis namespace: start
+#' @importFrom Rcpp sourceCpp
+## usethis namespace: end
+NULL
+
 #' @importFrom magrittr "%>%"
 NULL
 
 #' @importFrom zeallot "%<-%"
 NULL
+
+#' @importFrom methods "is"
+NULL
+
+#' @importFrom stats "approx" "cor" "fft"
+NULL
+
+#' @importFrom tibble tibble
+NULL
+
+#' @importFrom utils "capture.output"
+NULL
+
+#' @importFrom rlang ".data"
+NULL
+
+`.` <- NULL
+
+#' @importFrom Rdpack reprompt
+NULL