<environment: package:stats>
attr(,"name")
[1] "package:stats"
attr(,"path")
[1] "/opt/R/4.4.2/lib/R/library/stats"Environments
Mini-Lecture 10
Ben Baumer
Smith College
2024-10-17
Environments
Types of environments
What I want you to focus on:
- 7.4.1: Package environments
- 7.4.3: Namespace environments
Less important right now:
- 7.2.4: Super assignment
- 7.3: Recursing over environments
- 7.5: Call stacks
- 7.6: Environments as data structures
7.4: Special Environments
- Package environments: objects provided by the package
- Execution environments: where the function is executed
Package environment for stats
[1] "asOneSidedFormula" "r2dtable" "drop.terms"
[4] "confint.lm" "is.mts" "nlminb"
[7] "alias" "gaussian" "profile"
[10] "ls.diag" "mahalanobis" "rmultinom"
[13] "dpois" "numericDeriv" "makepredictcall"
[16] "qlogis" "loadings" "dlogis"
[19] "nlm" "residuals.glm" "qcauchy"
[22] "nextn" "nls" "plot.stepfun"
[25] "arima0.diag" "dummy.coef" "ftable"
[28] "as.formula" "pairwise.wilcox.test" "time"
[31] "embed" "mantelhaen.test" "dwilcox"
[34] "ar" "oneway.test" "fligner.test"
[37] "bw.bcv" "rWishart" "predict.glm"
[40] "logLik" "confint.default" "AIC"
[43] "rlogis" "bw.ucv" "arima"
[46] "plot.ts" "tsp" "model.extract"
[49] "tsp<-" "stat.anova" "update.formula"
[52] "qbeta" "bw.SJ" "factanal"
[55] "drop.scope" "summary.aov" "optimHess"
[58] ".lm.fit" "cooks.distance" "dnorm"
[61] "psmirnov" "extractAIC" "qbirthday"
[64] "C" "sortedXyData" "D"
[67] "lowess" "varimax" "optimize"
[70] "manova" "deviance" "optim"
[73] "lag.plot" "constrOptim" "splinefunH"
[76] "reformulate" "pacf" "mcnemar.test"
[79] "df" "tsSmooth" "make.link"
[82] "glm.control" "hasTsp" "pgamma"
[85] "addmargins" "dexp" "power.anova.test"
[88] "prop.test" "model.weights" "ave"
[91] "is.stepfun" "heatmap" "stepfun"
[94] "loess.smooth" "window<-" "line"
[97] "qqline" "ar.mle" "residuals"
[100] "lsfit" "get_all_vars" "dt"
[103] "splinefun" "ks.test" "cor"
[106] "add.scope" "ecdf" "pwilcox"
[109] "cov" "dendrapply" "rsignrank"
[112] "bandwidth.kernel" "as.dist" "SSweibull"
[115] "bw.nrd" "start" "plnorm"
[118] "ts.union" "mvfft" "dweibull"
[121] "as.ts" "cor.test" ".checkMFClasses"
[124] "effects" "reorder" "KalmanForecast"
[127] "eff.aovlist" "qgamma" "glm.fit"
[130] "dgamma" "plot.spec.coherency" "cov2cor"
[133] "ls.print" "setNames" "acf2AR"
[136] "add1" "rcauchy" "shapiro.test"
[139] "deriv3" "window" "model.tables"
[142] "model.matrix" ".nknots.smspl" "KalmanLike"
[145] "SSasymp" "predict" "as.stepfun"
[148] "power.prop.test" "t.test" "rstandard"
[151] "binom.test" "cophenetic" "pbeta"
[154] "KalmanRun" "naprint" "qlnorm"
[157] "plclust" "model.response" "dlnorm"
[160] "lag" "spec.pgram" "interaction.plot"
[163] "fitted" "rgeom" "estVar"
[166] "rgamma" "arima0" "loglin"
[169] "ar.yw" "promax" "phyper"
[172] "drop1" "SSfol" "runif"
[175] "family" "quantile" "wilcox.test"
[178] "psignrank" "complete.cases" "offset"
[181] "scatter.smooth" "dmultinom" "rlnorm"
[184] "approx" "naresid" "SSfpl"
[187] "proj" "supsmu" "qqnorm"
[190] "end" "printCoefmat" "princomp"
[193] "dnbinom" "lm.influence" "aggregate.data.frame"
[196] "rect.hclust" "convolve" "ansari.test"
[199] "median.default" "ARMAacf" "poly"
[202] "NLSstRtAsymptote" "power.t.test" "write.ftable"
[205] "qhyper" "polym" "weights"
[208] "dhyper" "contrasts<-" "kernel"
[211] "friedman.test" "acf" "qwilcox"
[214] "filter" "lm.fit" "rpois"
[217] "cmdscale" "factor.scope" "Gamma"
[220] "pweibull" "pchisq" "ksmooth"
[223] "symnum" "smooth" "quasipoisson"
[226] "ppr" "spec.ar" "pnbinom"
[229] "coefficients" "model.offset" "dbeta"
[232] "SSasympOff" "pbirthday" "replications"
[235] "ar.ols" "rhyper" "spectrum"
[238] "lm" "expand.model.frame" "kernapply"
[241] "bw.nrd0" "stl" "loess"
[244] "IQR" "qgeom" "contr.helmert"
[247] "na.pass" "toeplitz" "pairwise.t.test"
[250] "dist" ".getXlevels" "NLSstClosestX"
[253] "getInitial" "sigma" "qchisq"
[256] "contr.poly" "dchisq" "spline"
[259] "qunif" "confint" "pairwise.table"
[262] "SSasympOrig" "pexp" "plot.spec.phase"
[265] "medpolish" "density.default" "ptukey"
[268] "cancor" "Box.test" "TukeyHSD"
[271] "rnorm" "poisson" "var.test"
[274] "bartlett.test" "na.fail" "summary.stepfun"
[277] "model.frame" "covratio" "contrasts"
[280] "ar.burg" "residuals.lm" "df.residual"
[283] "ts.intersect" "power" "SSlogis"
[286] "glm" "rchisq" "getCall"
[289] "chisq.test" "model.matrix.lm" "coef"
[292] "step" "ppoints" "vcov"
[295] ".preformat.ts" "qqplot" "DF2formula"
[298] "update.default" "qtukey" "qpois"
[301] "quade.test" "df.kernel" "influence"
[304] "qsmirnov" "cutree" "pf"
[307] "poisson.test" "case.names" "frequency"
[310] "tsdiag" "qweibull" "NLSstLfAsymptote"
[313] "kmeans" "weighted.residuals" "mauchly.test"
[316] "napredict" "qexp" "deriv"
[319] "var" "aggregate.ts" "rwilcox"
[322] "SSbiexp" "pt" "rsmirnov"
[325] "qf" "xtabs" "kruskal.test"
[328] "median" "as.hclust" "termplot"
[331] "rweibull" "resid" "pgeom"
[334] "qnbinom" "se.contrast" "summary.manova"
[337] "prcomp" "preplot" "plot.ecdf"
[340] "arima.sim" "lm.wfit" "ccf"
[343] "is.leaf" "na.action" "screeplot"
[346] "approxfun" "NLSstAsymptotic" "order.dendrogram"
[349] "cycle" "qt" "rf"
[352] "punif" "quasi" "ts.plot"
[355] "cov.wt" "mood.test" "PP.test"
[358] "is.empty.model" "loess.control" "decompose"
[361] "aggregate" "BIC" "reshape"
[364] "makeARIMA" "ARMAtoMA" "weighted.mean"
[367] "pbinom" "selfStart" "SSgompertz"
[370] "qnorm" "inverse.gaussian" "na.omit"
[373] "sd" "rt" "fft"
[376] "dcauchy" "fivenum" "toeplitz2"
[379] "relevel" "summary.glm" "rexp"
[382] "monthplot" "dfbeta" "diffinv"
[385] "nobs" "SSmicmen" "is.ts"
[388] "dummy.coef.lm" "hatvalues" "variable.names"
[391] "Pair" "model.frame.default" "anova"
[394] "simulate" "dffits" "model.matrix.default"
[397] "contr.SAS" "contr.treatment" "as.dendrogram"
[400] "prop.trend.test" "predict.lm" "ppois"
[403] "pcauchy" "smoothEnds" "qbinom"
[406] "hat" "p.adjust" ".MFclass"
[409] "dbinom" "terms.formula" "spec.taper"
[412] "HoltWinters" "ts" "na.exclude"
[415] "dsignrank" "is.tskernel" "fitted.values"
[418] "qsignrank" "integrate" "optimise"
[421] "binomial" "KalmanSmooth" ".vcov.aliased"
[424] "deltat" "SSD" "p.adjust.methods"
[427] "smooth.spline" "summary.lm" "rstudent"
[430] "dgeom" "density" "hclust"
[433] "terms" "fisher.test" "rbinom"
[436] "isoreg" "nls.control" "formula"
[439] "contr.sum" "uniroot" "quasibinomial"
[442] "dfbetas" "na.contiguous" "influence.measures"
[445] "dunif" "pairwise.prop.test" "rnbinom"
[448] "rbeta" "pnorm" "knots"
[451] "cpgram" "biplot" "mad"
[454] "runmed" "read.ftable" "plogis"
[457] "delete.response" "aov" "update"
[460] "StructTS" What users see: the search path
Namespaces via sd()
- Note the environment!
function (x, na.rm = FALSE)
sqrt(var(if (is.vector(x) || is.factor(x)) x else as.double(x),
na.rm = na.rm))
<bytecode: 0x55cd1bc1abb0>
<environment: namespace:stats>Namespace environments
[[1]] $ <env: imports:stats>
[[2]] $ <env: namespace:base>
[[3]] $ <env: global> [[1]] $ <env: package:rlang>
[[2]] $ <env: package:stats>
[[3]] $ <env: package:graphics>
[[4]] $ <env: package:grDevices>
[[5]] $ <env: package:utils>
[[6]] $ <env: package:datasets>
[[7]] $ <env: package:methods>
[[8]] $ <env: Autoloads>
[[9]] $ <env: package:base>
[[10]] $ <env: empty>What developers see: the full picture
Huh?
Keep these in mind
- Package environments (i.e., the search path) control what is available to users
- Namespace environments control what is available to developers
- (this will start to make more sense once we start developing packages!)
namespace:macleish
functions that the
macleishdevelopers createdmay or may not be exported
[1] ".__global__" "mass_gis"
[3] "phenocam_image_url_midday" ".packageName"
[5] "phenocam_info" "phenocam_image_url"
[7] "phenocam_download" "phenocam_read_monthly_midday_urls"
[9] "etl_extract.etl_macleish" "phenocam_read_day_urls"
[11] ".__NAMESPACE__." "macleish_intersect"
[13] "etl_transform.etl_macleish" ".__S3MethodsTable__."
[15] "etl_transform_help" imports:macleish
- objects from other packages that
macleishdevelopers use
[1] 322 [1] "slice_max" "expr"
[3] "src" "db_desc"
[5] "group_by_drop_default" "db_commit"
[7] "coalesce" "data_frame"
[9] "summarize_if" "mutate_"
[11] "db_create_index" "join_by"
[13] "check_dbplyr" "src_tbls"
[15] "db_query_rows" "dense_rank"
[17] "slice_head" "tbl"
[19] "last_col" "consecutive_id"
[21] "first" "arrange"
[23] "dplyr_row_slice" "read_csv"
[25] "sql_semi_join" "is.grouped_df"
[27] "summarise_each" "group_vars"
[29] "bind_cols" "last_dplyr_warnings"
[31] "distinct_at" "mutate_all"
[33] "relocate" "compute"
[35] "mutate_if" "distinct_"
[37] "group_indices_" "eval_tbls2"
[39] "smart_upload" "rename_all"
[41] "count" "src_mysql_cnf"
[43] "do_" "do"
[45] "cumany" "recode_factor"
[47] "wrap_dbplyr_obj" "same_src"
[49] "top_frac" "select_vars"
[51] "desc" "db_create_indexes"
[53] "lead" "mutate_at"
[55] "as_tibble" "distinct_prepare"
[57] "src_sqlite" "distinct_if"
[59] "add_row" ".data"
[61] "etl_transform" "cur_column"
[63] "semi_join" "filter_if"
[65] "sql_translate_env" "arrange_"
[67] "case_match" "sql_set_op"
[69] "eval_tbls" "ensyms"
[71] "arrange_at" "add_count"
[73] "dplyr_reconstruct" "slice_min"
[75] "new_rowwise_df" "cross_join"
[77] "setequal" "select"
[79] "distinct_all" "src_local"
[81] "as.tbl" "summarise"
[83] "type_sum" "db_drop_table"
[85] "rows_patch" "cur_data"
[87] "row_number" "groups"
[89] "anti_join" "tbl_vars"
[91] "cur_group_id" "st_intersection"
[93] "auto_copy" "sql_subquery"
[95] "group_indices" "progress_estimated"
[97] "transmute_all" "all_of"
[99] "new_grouped_df" "add_tally_"
[101] "enquo" "group_data"
[103] "contains" "rows_insert"
[105] "all_equal" "group_split"
[107] "tbl_ptype" "glimpse"
[109] "inner_join" "db_insert_into"
[111] "db_save_query" "etl_load"
[113] "etl" "id"
[115] "summarise_all" "st_transform"
[117] "ensym" "db_begin"
[119] "left_join" "everything"
[121] "summarize_each_" "valid_year_month"
[123] "dplyr_col_modify" "compare_tbls2"
[125] "filter" "enquos"
[127] "union_all" "summarize_all"
[129] "slice_tail" "where"
[131] "n" "quo"
[133] "add_count_" "summarize_each"
[135] "show_query" "group_cols"
[137] "summarise_at" "n_distinct"
[139] "transmute_at" "extract_date_from_filename"
[141] "rename" "reframe"
[143] "select_vars_" "etl_cleanup"
[145] "near" "pick"
[147] "num_range" "sym"
[149] "n_groups" "across"
[151] "all_vars" "select_all"
[153] "dbWipe" "slice"
[155] "na_if" "select_if"
[157] "grouped_df" "tbl_df"
[159] "tally_" "is.src"
[161] "etl_extract" "intersect"
[163] "db_type" "db_create_table"
[165] "%>%" "mutate_each"
[167] "group_keys" "add_rownames"
[169] "rename_vars" "etl_init"
[171] "dbRunScript" "select_at"
[173] "is.tbl" "arrange_all"
[175] "summarize" "quo_name"
[177] "cummean" "rename_with"
[179] "group_map" "current_vars"
[181] "with_groups" "syms"
[183] "last" "rowwise"
[185] "group_size" "union"
[187] "nth" "match_files_by_year_months"
[189] "src_postgres" "enexprs"
[191] "dim_desc" "transmute"
[193] "any_of" "transmute_if"
[195] "case_when" "arrange_if"
[197] "order_by" "with_order"
[199] "group_rows" "any_vars"
[201] "head" "db_analyze"
[203] "db_data_type" "as_data_frame"
[205] "top_n" "add_tally"
[207] "enexpr" "db_query_fields"
[209] "download.file" "tribble"
[211] "group_trim" "between"
[213] "select_" "lag"
[215] "mutate_each_" "find_schema"
[217] "percent_rank" "distinct"
[219] "as_label" "group_by_prepare"
[221] "db_explain" "summarise_each_"
[223] "tbl_nongroup_vars" "bench_tbls"
[225] "etl_create" "is_grouped_df"
[227] "right_join" "summarise_if"
[229] "filter_" "cur_group_rows"
[231] "src_mysql" "summarize_at"
[233] "lst" "etl_update"
[235] "rows_delete" "combine"
[237] "ntile" "location"
[239] "symdiff" "sql_escape_string"
[241] "rename_vars_" "nest_by"
[243] "db_rollback" "quos"
[245] "filter_at" "collapse"
[247] "db_write_table" "db_has_table"
[249] "unzip" "starts_with"
[251] "ungroup" "group_by"
[253] "funs" "vars"
[255] "if_all" "tibble"
[257] "slice_sample" "recode"
[259] "validate_rowwise_df" "rename_"
[261] "cur_group" "group_nest"
[263] "filter_all" "one_of"
[265] "src_df" "summarise_"
[267] "group_by_" "copy_to"
[269] "ends_with" "is.etl"
[271] "smart_download" "cur_data_all"
[273] "if_else" "setdiff"
[275] "transmute_" "funs_"
[277] "summarize_" "failwith"
[279] "ymd_hms" "compare_tbls"
[281] "sample_frac" "matches"
[283] "st_read" "group_by_all"
[285] "create_etl_package" "write_csv"
[287] "explain" "rename_if"
[289] "sample_n" "group_by_if"
[291] "validate_grouped_df" "common_by"
[293] "group_walk" "changes"
[295] "make_tbl" "rows_upsert"
[297] "cume_dist" "ident"
[299] "rows_append" "rows_update"
[301] "select_var" "db_list_tables"
[303] "rename_at" "sql_escape_ident"
[305] "group_by_at" "pull"
[307] "mutate" "nest_join"
[309] "slice_" "count_"
[311] "group_modify" "if_any"
[313] "tally" "c_across"
[315] "bind_rows" "collect"
[317] "cumall" "min_rank"
[319] "sql_select" "sql"
[321] "full_join" "sql_join" package:macleish
objects that
macleishusers can seeexported objects
[1] "macleish_layers" "mass_gis"
[3] ".Depends" "maple_sap"
[5] "whately_2015" "phenocam_image_url_midday"
[7] "phenocam_image_url" "phenocam_info"
[9] "orchard_2015" "phenocam_read_monthly_midday_urls"
[11] "phenocam_read_day_urls" "macleish_intersect"
[13] "tree_diameter1" "tree_diameter2"
[15] "etl_transform_help" Now
Homework
Reading quiz on Moodle
SDS 410