Commit ⋅ weecology/portalcasting

#
# the datasets here should come from the models selected
#  and not as an argument ... or? maybe not? idk. think this out.
# 
#  i think so
# should the start and end time also come from somewhere else?
#  well, here the end moon is what is looped over
#   not sure this is what i want to happen more generally, tho
#  we want portalcast to iterate over individual casts, but generally
#   i think we want to create a recipe list or something

  return_if_null(models)


@@ -78,7 +83,8 @@

  }

  if (end_moons[nend_moons] != last_moon) {
 # this maybe should happen within cast?
 # this maybe should happen within cast? or maybe we can sidestep it
  # yeah, i would like to avoid refilling the data so many times, how to do?
    messageq(message_break(), "\nResetting data to most up-to-date versions\n", message_break(), quiet = quiet)

    fill_data(main     = main, 

@@ -117,7 +117,7 @@

                                total       = TRUE, 
                                nadot       = TRUE)
  temp_species  <- read_model_controls(main = main, settings = settings)$jags_logistic_competition$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -405,7 +405,7 @@

                                total       = TRUE, 
                                nadot       = TRUE)
  temp_species  <- read_model_controls(main = main, settings = settings)$jags_logistic_competition_covariates$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -692,7 +692,7 @@

                                total       = TRUE, 
                                nadot       = TRUE)
  temp_species  <- read_model_controls(main = main, settings = settings)$jags_logistic_covariates$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -964,7 +964,7 @@

                                total       = TRUE, 
                                nadot       = TRUE)
  temp_species  <- read_model_controls(main = main, settings = settings)$jags_logistic$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -1215,7 +1215,7 @@

                                total       = TRUE, 
                                nadot       = TRUE)
  temp_species  <- read_model_controls(main = main, settings = settings)$jags_RW$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -132,7 +132,7 @@

                                      nadot       = TRUE)

  temp_species  <- read_model_controls(main = main, settings = settings)$AutoArima$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -232,7 +232,7 @@

                                      total       = TRUE, 
                                      nadot       = TRUE)
  temp_species  <- read_model_controls(main = main, settings = settings)$NaiveArima$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -330,7 +330,7 @@

                                      total       = TRUE, 
                                      nadot       = TRUE)
  temp_species  <- read_model_controls(main = main, settings = settings)$ESSS$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -427,7 +427,7 @@

                                      total       = TRUE, 
                                      nadot       = TRUE)
  temp_species  <- read_model_controls(main = main, settings = settings)$nbGARCH$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -537,7 +537,7 @@

                                      total       = TRUE, 
                                      nadot       = TRUE)
  temp_species  <- read_model_controls(main = main, settings = settings)$nbsGARCH$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -670,7 +670,7 @@

                                      total       = TRUE, 
                                      nadot       = TRUE)
  temp_species  <- read_model_controls(main = main, settings = settings)$pevGARCH$species
  if (temp_species == "all") {
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]

@@ -26,7 +26,7 @@

#'
#' @param quiet \code{logical} indicator if progress messages should be quieted.
#'
#' @param verbose \code{logical} indicator of whether or not to print out all of the information (and thus just the tidy messages).
#' @param verbose \code{logical} indicator of whether or not to print out all of the information or just the tidy messages.
#'
#' @return \code{NULL}, \code{\link[base]{invisible}}-ly.
#'

@@ -198,30 +198,30 @@

#' @export
#'
prepare_dataset <- function(name        = "all",
                         main        = ".",
                         settings    = directory_settings(),
                         filename    = "rodents_all.csv",
                         clean       = FALSE,
                         level       = "Site",
                         type        = "Rodents",
                         plots       = "all",
                         unknowns    = FALSE,
                         shape       = "crosstab",
                         time        = "newmoon",
                         output      = "abundance",
                         fillweight  = FALSE,
                         treatment   = NULL,
                         na_drop     = FALSE,
                         zero_drop   = FALSE,
                         min_traps   = 1,
                         min_plots   = 24,
                         effort      = TRUE,
                         species     = base_species(),
                         total       = TRUE,
                         save        = TRUE,
                         overwrite   = TRUE,
                         quiet       = FALSE,
                         verbose     = FALSE) {
                            main        = ".",
                            settings    = directory_settings(),
                            filename    = "rodents_all.csv",
                            clean       = FALSE,
                            level       = "Site",
                            type        = "Rodents",
                            plots       = "all",
                            unknowns    = FALSE,
                            shape       = "crosstab",
                            time        = "newmoon",
                            output      = "abundance",
                            fillweight  = FALSE,
                            treatment   = NULL,
                            na_drop     = FALSE,
                            zero_drop   = FALSE,
                            min_traps   = 1,
                            min_plots   = 24,
                            effort      = TRUE,
                            species     = base_species(),
                            total       = TRUE,
                            save        = TRUE,
                            overwrite   = TRUE,
                            quiet       = FALSE,
                            verbose     = FALSE) {

  return_if_null(name)


@@ -1,6 +1,3 @@

# These functions are to be pulled out into the directory orchestration package


#' @title Create the Structure of a Directory and Fill with Content
#'
#' @description Instantiates the necessary folder structure for a directory, writes the setup configuration file, and fills the directory with core content. 

@@ -40,8 +37,12 @@

                       settings = directory_settings(), 
                       quiet    = FALSE){

  core_package_version <- package_version_finder("setup_dir")

  messageq(message_break(), "\nThis is ", core_package_version[["package"]], " v", core_package_version[["version"]], "  ", format(Sys.time(), "%x %T %Z"), "\n", message_break(), quiet = quiet)
  messageq(message_break(), "\nEstablishing directory at\n ", normalizePath(file.path(main = main), mustWork = FALSE), "\n", message_break(), quiet = quiet)


  mapply(FUN          = dir.create, 
         path         = file.path(main, settings$subdirectories),
         recursive    = TRUE,

@@ -51,6 +52,7 @@

                                settings = settings, 
                                quiet    = quiet)

  messageq(message_break(), "\nDirectory successfully instantiated\n", message_break(), quiet = quiet)

}


@@ -67,11 +69,6 @@

                       quiet    = FALSE, 
                       verbose  = FALSE) {

  core_package_version <- package_version_finder("setup_dir")


  messageq(message_break(), "\nThis is ", core_package_version[["package"]], " v", core_package_version[["version"]], quiet = quiet)
  messageq("  ", format(Sys.time(), "%x %T %Z"), "\n", message_break(), quiet = quiet)

  create_dir(main     = main, 
             settings = settings,

@@ -84,7 +81,6 @@

           quiet    = quiet,
           verbose  = verbose)

  messageq(message_break(), "\nDirectory successfully instantiated\n", message_break(), quiet = quiet)

  read_directory_configuration(main     = main,
                               settings = settings,

@@ -972,11 +972,20 @@


  obs           <- read_rodents_table(main     = main, 
                                      settings = settings, 
                                        dataset = gsub("_interp", "", casts_meta$dataset))
                                        dataset = gsub("dm_", "", gsub("_interp", "", casts_meta$dataset)))
  colnames(obs) <- gsub("\\.", "", colnames(obs))

  sp_col  <- is_sp_col(obs, nadot = TRUE, total = TRUE)
  species <- ifnull(species, colnames(obs)[sp_col])

  mod_control <- read_model_controls(main = main, settings = settings)
  model   <- ifnull(model, names(mod_control)[1])
  temp_species <- mod_control[[model]]$species
  if (length(temp_species) == 1 && temp_species == "all") {
    species <- species
  } else {
    species <- species[species %in% temp_species]
  }
  if (length(species) > 1) {
    if ("total" %in% species) {
      species <- "total"

@@ -993,7 +1002,7 @@

  }

  obs     <- obs[ , c("newmoonnumber", species)]
  dataset <- gsub("_interp", "", casts_meta$dataset)
  dataset <- gsub("dm_", "", gsub("_interp", "", casts_meta$dataset))

  if (!is.null(model) && tolower(model) == "ensemble") {


@@ -36,17 +36,18 @@


  nmodels <- length(models)

  if (nmodels == 1) {

    read_model_controls(main     = main, 
                        settings = settings)[[models]]

  } else if (nmodels > 1) {
# want to cut this commented part out but need to make sure it will still work fine or figure out where i need to fix it
#  if (nmodels == 1) {
#
#    read_model_controls(main     = main, 
#                        settings = settings)[[models]]
#
#  } else if (nmodels > 1) {

    read_model_controls(main     = main, 
                        settings = settings)[models]

  }
#  }

}


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R	3,429	3,205	0	224	93.46%
Project Totals (22 files)	3,429	3,205	0	224	93.46%

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coverage:
  precision: 2
  round: down
  status:
    patch:
      default:
        target: 50%
    project:
      default:
        target: 50%

comment: false

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405	405		total = TRUE,
406	406		nadot = TRUE)
407	407		temp_species <- read_model_controls(main = main, settings = settings)$jags_logistic_competition_covariates$species
408		-	if (temp_species == "all") {
	408	+	if (length(temp_species) == 1 && temp_species == "all") {
409	409		species <- species
410	410		} else {
411	411		species <- species[species %in% temp_species]

692	692		total = TRUE,
693	693		nadot = TRUE)
694	694		temp_species <- read_model_controls(main = main, settings = settings)$jags_logistic_covariates$species
695		-	if (temp_species == "all") {
	695	+	if (length(temp_species) == 1 && temp_species == "all") {
696	696		species <- species
697	697		} else {
698	698		species <- species[species %in% temp_species]

964	964		total = TRUE,
965	965		nadot = TRUE)
966	966		temp_species <- read_model_controls(main = main, settings = settings)$jags_logistic$species
967		-	if (temp_species == "all") {
	967	+	if (length(temp_species) == 1 && temp_species == "all") {
968	968		species <- species
969	969		} else {
970	970		species <- species[species %in% temp_species]

1215	1215		total = TRUE,
1216	1216		nadot = TRUE)
1217	1217		temp_species <- read_model_controls(main = main, settings = settings)$jags_RW$species
1218		-	if (temp_species == "all") {
	1218	+	if (length(temp_species) == 1 && temp_species == "all") {
1219	1219		species <- species
1220	1220		} else {
1221	1221		species <- species[species %in% temp_species]

132	132		nadot = TRUE)
133	133
134	134		temp_species <- read_model_controls(main = main, settings = settings)$AutoArima$species
135		-	if (temp_species == "all") {
	135	+	if (length(temp_species) == 1 && temp_species == "all") {
136	136		species <- species
137	137		} else {
138	138		species <- species[species %in% temp_species]

49	49		#
50	50		# the datasets here should come from the models selected
51	51		# and not as an argument ... or? maybe not? idk. think this out.
52		-	#
	52	+	# i think so
	53	+	# should the start and end time also come from somewhere else?
	54	+	# well, here the end moon is what is looped over
	55	+	# not sure this is what i want to happen more generally, tho
	56	+	# we want portalcast to iterate over individual casts, but generally
	57	+	# i think we want to create a recipe list or something
53	58
54	59		return_if_null(models)
55	60

78	83		}
79	84
80	85		if (end_moons[nend_moons] != last_moon) {
81		-	# this maybe should happen within cast?
	86	+	# this maybe should happen within cast? or maybe we can sidestep it
	87	+	# yeah, i would like to avoid refilling the data so many times, how to do?
82	88		messageq(message_break(), "\nResetting data to most up-to-date versions\n", message_break(), quiet = quiet)
83	89
84	90		fill_data(main = main,

26	26		#'
27	27		#' @param quiet \code{logical} indicator if progress messages should be quieted.
28	28		#'
29		-	#' @param verbose \code{logical} indicator of whether or not to print out all of the information (and thus just the tidy messages).
	29	+	#' @param verbose \code{logical} indicator of whether or not to print out all of the information or just the tidy messages.
30	30		#'
31	31		#' @return \code{NULL}, \code{\link[base]{invisible}}-ly.
32	32		#'

198	198		#' @export
199	199		#'
200	200		prepare_dataset <- function(name = "all",
201		-	main = ".",
202		-	settings = directory_settings(),
203		-	filename = "rodents_all.csv",
204		-	clean = FALSE,
205		-	level = "Site",
206		-	type = "Rodents",
207		-	plots = "all",
208		-	unknowns = FALSE,
209		-	shape = "crosstab",
210		-	time = "newmoon",
211		-	output = "abundance",
212		-	fillweight = FALSE,
213		-	treatment = NULL,
214		-	na_drop = FALSE,
215		-	zero_drop = FALSE,
216		-	min_traps = 1,
217		-	min_plots = 24,
218		-	effort = TRUE,
219		-	species = base_species(),
220		-	total = TRUE,
221		-	save = TRUE,
222		-	overwrite = TRUE,
223		-	quiet = FALSE,
224		-	verbose = FALSE) {
	201	+	main = ".",
	202	+	settings = directory_settings(),
	203	+	filename = "rodents_all.csv",
	204	+	clean = FALSE,
	205	+	level = "Site",
	206	+	type = "Rodents",
	207	+	plots = "all",
	208	+	unknowns = FALSE,
	209	+	shape = "crosstab",
	210	+	time = "newmoon",
	211	+	output = "abundance",
	212	+	fillweight = FALSE,
	213	+	treatment = NULL,
	214	+	na_drop = FALSE,
	215	+	zero_drop = FALSE,
	216	+	min_traps = 1,
	217	+	min_plots = 24,
	218	+	effort = TRUE,
	219	+	species = base_species(),
	220	+	total = TRUE,
	221	+	save = TRUE,
	222	+	overwrite = TRUE,
	223	+	quiet = FALSE,
	224	+	verbose = FALSE) {
225	225
226	226		return_if_null(name)
227	227

1		-	# These functions are to be pulled out into the directory orchestration package
2		-
3		-
4	1		#' @title Create the Structure of a Directory and Fill with Content
5	2		#'
6	3		#' @description Instantiates the necessary folder structure for a directory, writes the setup configuration file, and fills the directory with core content.

40	37		settings = directory_settings(),
41	38		quiet = FALSE){
42	39
	40	+	core_package_version <- package_version_finder("setup_dir")
	41	+
	42	+	messageq(message_break(), "\nThis is ", core_package_version[["package"]], " v", core_package_version[["version"]], " ", format(Sys.time(), "%x %T %Z"), "\n", message_break(), quiet = quiet)
43	43		messageq(message_break(), "\nEstablishing directory at\n ", normalizePath(file.path(main = main), mustWork = FALSE), "\n", message_break(), quiet = quiet)
44	44
	45	+
45	46		mapply(FUN = dir.create,
46	47		path = file.path(main, settings$subdirectories),
47	48		recursive = TRUE,

51	52		settings = settings,
52	53		quiet = quiet)
53	54
	55	+	messageq(message_break(), "\nDirectory successfully instantiated\n", message_break(), quiet = quiet)
54	56
55	57		}
56	58

84	81		quiet = quiet,
85	82		verbose = verbose)
86	83
87		-	messageq(message_break(), "\nDirectory successfully instantiated\n", message_break(), quiet = quiet)
88	84
89	85		read_directory_configuration(main = main,
90	86		settings = settings,

972	972
973	973		obs <- read_rodents_table(main = main,
974	974		settings = settings,
975		-	dataset = gsub("_interp", "", casts_meta$dataset))
	975	+	dataset = gsub("dm_", "", gsub("_interp", "", casts_meta$dataset)))
976	976		colnames(obs) <- gsub("\\.", "", colnames(obs))
977	977
978	978		sp_col <- is_sp_col(obs, nadot = TRUE, total = TRUE)
979	979		species <- ifnull(species, colnames(obs)[sp_col])
	980	+
	981	+	mod_control <- read_model_controls(main = main, settings = settings)
	982	+	model <- ifnull(model, names(mod_control)[1])
	983	+	temp_species <- mod_control[[model]]$species
	984	+	if (length(temp_species) == 1 && temp_species == "all") {
	985	+	species <- species
	986	+	} else {
	987	+	species <- species[species %in% temp_species]
	988	+	}
980	989		if (length(species) > 1) {
981	990		if ("total" %in% species) {
982	991		species <- "total"

993	1002		}
994	1003
995	1004		obs <- obs[ , c("newmoonnumber", species)]
996		-	dataset <- gsub("_interp", "", casts_meta$dataset)
	1005	+	dataset <- gsub("dm_", "", gsub("_interp", "", casts_meta$dataset))
997	1006
998	1007		if (!is.null(model) && tolower(model) == "ensemble") {
999	1008

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36	36
37	37		nmodels <- length(models)
38	38
39		-	if (nmodels == 1) {
40		-
41		-	read_model_controls(main = main,
42		-	settings = settings)[[models]]
43		-
44		-	} else if (nmodels > 1) {
	39	+	# want to cut this commented part out but need to make sure it will still work fine or figure out where i need to fix it
	40	+	# if (nmodels == 1) {
	41	+	#
	42	+	# read_model_controls(main = main,
	43	+	# settings = settings)[[models]]
	44	+	#
	45	+	# } else if (nmodels > 1) {
45	46
46	47		read_model_controls(main = main,
47	48		settings = settings)[models]
48	49
49		-	}
	50	+	# }
50	51
51	52		}
52	53

1	coverage:
2	precision: 2
3	round: down
4	status:
5	patch:
6	default:
7	target: 50%
8	project:
9	default:
10	target: 50%
11
12	comment: false

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