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Merge pull request #41 from USEPA/develop
CRAN v5.5.1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,6 @@ | ||
| Package: spsurvey | ||
| Title: Spatial Sampling Design and Analysis | ||
| Version: 5.5.0 | ||
| Version: 5.5.1 | ||
| Authors@R: c( | ||
| person("Michael", "Dumelle", role=c("aut","cre"), | ||
| email = "[email protected]", comment = c(ORCID = "0000-0002-3393-5529")), | ||
|
|
@@ -40,5 +40,5 @@ BugReports: https://github.com/USEPA/spsurvey/issues | |
| VignetteBuilder: knitr | ||
| Encoding: UTF-8 | ||
| LazyData: true | ||
| RoxygenNote: 7.1.2 | ||
| RoxygenNote: 7.2.3 | ||
| NeedsCompilation: no | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,125 @@ | ||
| # contrast_analysis <- function(dframe, vars, siteID = NULL, weight = "weight", xcoord, ycoord, vartype = "Local", | ||
| # conf = 95, statistics = c("Mean", "Total")) { | ||
| # | ||
| # | ||
| # | ||
| # if (is.null(siteID)) { | ||
| # siteID <- "siteID" | ||
| # dframe$siteID <- paste("site", seq_len(nrow(dframe)), sep = "-") | ||
| # } | ||
| # | ||
| # # create design object | ||
| # stratum_ind <- FALSE | ||
| # stratumID <- NULL | ||
| # cluster_ind <- FALSE | ||
| # clusterID <- NULL | ||
| # weight1 <- NULL | ||
| # sizeweight <- FALSE | ||
| # sweight <- NULL | ||
| # sweight1 <- NULL | ||
| # fpcfactor_ind <- FALSE | ||
| # fpcsize <- NULL | ||
| # Ncluster <- NULL | ||
| # stage1size <- NULL | ||
| # jointprob <- NULL | ||
| # | ||
| # design <- survey_design( | ||
| # dframe, siteID, weight, stratum_ind, stratumID, cluster_ind, clusterID, | ||
| # weight1, sizeweight, sweight, sweight1, fpcfactor_ind, fpcsize, Ncluster, | ||
| # stage1size, vartype, jointprob | ||
| # ) | ||
| # | ||
| # all_vars <- all.vars(vars) | ||
| # # incorporate form when all_vars has only length one (function of single variable)? | ||
| # # what about three variables? Function to assign matrix to localmean_cov? | ||
| # vars_form <- paste(all_vars, collapse = " + ") | ||
| # | ||
| # if (vartype == "Local") { | ||
| # local_weights <- localmean_weight(x = dframe[[xcoord]], y = dframe[[ycoord]], prb = 1 / dframe[[weight]]) | ||
| # } | ||
| # | ||
| # if ("Mean" %in% statistics) { | ||
| # rslt <- svymean(make.formula(vars_form), design) | ||
| # rslt_con <- svycontrast(rslt, vars) | ||
| # if (vartype == "Local") { | ||
| # tw <- sum(dframe[[weight]]) | ||
| # local_vars <- do.call(cbind, lapply(all_vars, function(x) get_local_vars(dframe, weight, x, rslt, "Mean"))) | ||
| # cov_mx <- localmean_cov(local_vars, local_weights) / tw^2 | ||
| # derivs <- lapply(all_vars, D, expr = vars) | ||
| # grad <- rbind(get_grad(all_vars, derivs, rslt)) | ||
| # se_val <- sqrt(grad %*% cov_mx %*% t(grad)) | ||
| # } | ||
| # | ||
| # if (vartype == "SRS") { | ||
| # se_val <- SE(rslt_con) | ||
| # } | ||
| # | ||
| # mean_df <- data.frame(Estimate = rslt_con[1], StdError = se_val, LCB95 = rslt_con[1] - 1.96 * se_val, UCB95 = rslt_con[1] + 1.96 * se_val) | ||
| # } | ||
| # | ||
| # | ||
| # if ("Total" %in% statistics) { | ||
| # rslt <- svytotal(make.formula(vars_form), design) | ||
| # rslt_con <- svycontrast(rslt, vars) | ||
| # if (vartype == "Local") { | ||
| # tw <- sum(dframe[[weight]]) | ||
| # local_vars <- do.call(cbind, lapply(all_vars, function(x) get_local_vars(dframe, weight, x, rslt, "Total"))) | ||
| # cov_mx <- localmean_cov(local_vars, local_weights) | ||
| # derivs <- lapply(all_vars, D, expr = vars) | ||
| # grad <- rbind(get_grad(all_vars, derivs, rslt)) | ||
| # se_val <- sqrt(grad %*% cov_mx %*% t(grad)) | ||
| # } | ||
| # | ||
| # if (vartype == "SRS") { | ||
| # se_val <- SE(rslt_con) | ||
| # } | ||
| # | ||
| # tot_df <- data.frame(Estimate = rslt_con[1], StdError = se_val, LCB95 = rslt_con[1] - 1.96 * se_val, UCB95 = rslt_con[1] + 1.96 * se_val) | ||
| # | ||
| # } | ||
| # | ||
| # contr_out <- list() | ||
| # | ||
| # if ("Mean" %in% statistics) { | ||
| # contr_out$Mean <- mean_df | ||
| # } else { | ||
| # contr_out$Mean <- NULL | ||
| # } | ||
| # | ||
| # if ("Total" %in% statistics) { | ||
| # contr_out$Total <- tot_df | ||
| # } else { | ||
| # contr_out$Total <- NULL | ||
| # } | ||
| # | ||
| # contr_out | ||
| # | ||
| # } | ||
| # | ||
| # get_grad <- function(all_vars, derivs, svyout) { | ||
| # | ||
| # # hoping for no name conflict with .use suffix | ||
| # grad.use.spsurvey <- rep(0, length(all_vars)) | ||
| # derivs.use.spsurvey <- derivs | ||
| # svyout.use.spsurvey <- svyout | ||
| # | ||
| # for (x in all_vars) { | ||
| # assign(x, svyout.use.spsurvey[[x]]) | ||
| # } | ||
| # | ||
| # for (i in seq_along(grad.use.spsurvey)) { | ||
| # grad.use.spsurvey[i] <- eval(derivs.use.spsurvey[[i]]) | ||
| # } | ||
| # grad.use.spsurvey | ||
| # } | ||
| # | ||
| # get_local_vars <- function(dframe, weight, var, rslt, statistic) { | ||
| # if (statistic == "Mean") { | ||
| # val <- (dframe[[var]] - rslt[[var]]) * dframe[[weight]] | ||
| # } | ||
| # | ||
| # if (statistic == "Total") { | ||
| # val <- dframe[[var]] * dframe[[weight]] | ||
| # } | ||
| # val | ||
| # } |
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