hugomflavio / actel

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Showing 2 of 5 files from the diff.
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NEWS.md has changed.
DESCRIPTION has changed.

@@ -431,7 +431,7 @@
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  p <- p + ggplot2::facet_grid(. ~ variable, scales = "free_x")
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  p <- p + ggplot2::theme(axis.text.x = ggplot2::element_text(angle = 45, vjust = 1, hjust = 1))
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  p <- p + ggplot2::labs(x = "", y = "")
434 -
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/dotplots.png"), width = 6, height = (1.3 + 0.115 * (nrow(t2) - 1)))
434 +
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/dotplots.png"), width = 6, height = (1.3 + 0.115 * (nrow(t2) - 1)), limitsize = FALSE)
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  appendTo("debug", "Terminating printDotplots.")
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}
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@@ -483,7 +483,7 @@
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  p <- p + ggplot2::scale_y_continuous(limits = c(0, 1), expand = c(0, 0, 0.05, 0))
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  p <- p + ggplot2::labs(x = "", y = "Survival")
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  the.width <- max(2, sum(grepl("Disap.", colnames(section.overview))) * nrow(section.overview))
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  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/survival.png"), width = the.width, height = 4)
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  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/survival.png"), width = the.width, height = 4, limitsize = FALSE)
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  appendTo("debug", "Terminating printSurvivalGraphic.")
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}
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@@ -704,7 +704,7 @@
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      }
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    }
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    # Save
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    ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, ".", extension), width = the.width, height = the.height)  # better to save in png to avoid point overlapping issues
707 +
    ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, ".", extension), width = the.width, height = the.height, limitsize = FALSE)  # better to save in png to avoid point overlapping issues
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    if (counter %% 2 == 0) {
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      individual.plots <<- paste0(individual.plots, "![](", tempdir(), "/actel_report_auxiliary_files/", tag, ".", extension, "){ width=", the.width * 10, "% }\n")
@@ -1271,7 +1271,7 @@
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      p <- p + ggplot2::scale_fill_manual(values = as.vector(cbPalette)[1:length(unique(plotdata$Group))], drop = FALSE)
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    }
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    ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", i,"_days.png"), width = 10, height = length(unique(plotdata$variable)) * 2)
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    ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", i,"_days.png"), width = 10, height = length(unique(plotdata$variable)) * 2, limitsize = FALSE)
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  })
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}
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@@ -1377,7 +1377,7 @@
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  p <- p + ggplot2::labs(x = "", y = "n")
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  p <- p + ggplot2::scale_y_continuous(expand = c(0, 0, 0.05, 0))
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  the.width <- max(2, (ncol(input) - 1) * nrow(input) * 0.7)
1380 -
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_section.png"), width = the.width, height = 4)
1380 +
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_section.png"), width = the.width, height = 4, limitsize = FALSE)
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}
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#' Print a simple barplot with the number of tags last seen at each section
@@ -1409,7 +1409,7 @@
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  p <- p + ggplot2::coord_flip()
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  p <- p + ggplot2::guides(fill = ggplot2::guide_legend(reverse = TRUE))
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  the.height <- max(2, ((length(levels(status.df$Very.last.array)) - 1) * 0.5))
1412 -
  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_arrays.png"), width = 6, height = the.height)
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  ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/last_arrays.png"), width = 6, height = the.height, limitsize = FALSE)
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}
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#' Print sensor data for each individual tag
@@ -1488,7 +1488,7 @@
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      }
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      # Save
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      ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, "_sensors.", extension), width = the.width, height = the.height)  # better to save in png to avoid point overlapping issues
1491 +
      ggplot2::ggsave(paste0(tempdir(), "/actel_report_auxiliary_files/", tag, "_sensors.", extension), width = the.width, height = the.height, limitsize = FALSE)  # better to save in png to avoid point overlapping issues
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      n.plots <- n.plots + 1
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      if (n.plots %% 2 == 0) {

@@ -1026,22 +1026,36 @@
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  # check sensor names
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  if (!expect_integer) { 
1029 -
    if(!any(grepl("^Sensor.unit$", colnames(bio)))) {
1029 +
    if (!any(grepl("^Sensor.unit$", colnames(bio)))) {
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      appendTo(c("Screen", "Warning"), "Tags with multiple sensors are listed in the biometrics, but a 'Sensor.unit' column could not be found. Skipping sensor unit assignment.")
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    } 
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    else {
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      bio$Sensor.unit <- as.character(bio$Sensor.unit) #failsafe in case all values are numeric, or NA.
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      A <- sapply(strsplit(bio$Signal, "|", fixed = TRUE), length)
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      pre_B <- strsplit(bio$Sensor.unit, "|", fixed = TRUE)
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      B <- sapply(pre_B, length)
1038 -
      B[sapply(pre_B, is.na)] <- 0
1039 -
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      if (any(A != B))
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        stopAndReport("The number of provided sensor units and signals do not match for ", 
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          ifelse(sum(A != B) <= 10,
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                 paste0("row(s) ", paste0(which(A != B), collapse = ", ")), 
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                 paste0(sum(A != B), " row(s)")),
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      bio$Sensor.unit <- as.character(bio$Sensor.unit) # failsafe in case all values are numeric, or NA.
1034 +
      bio$Sensor.unit[bio$Sensor.unit == ''] <- NA_character_
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1036 +
      if (any(link <- na.as.false(startsWith(bio$Sensor.unit, '|'))))
1037 +
        appendTo(c('screen', 'warning'), paste0("The Sensor.unit information in ",
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          ifelse(sum(link) <= 10,
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                 paste0("row(s) ", paste0(which(link), collapse = ", ")), 
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                 paste0(sum(link), " row(s)")),
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          " of the biometrics starts with a '|' character. Could you have forgotten to include a sensor unit?"))
1042 +
1043 +
      if (any(link <- na.as.false(endsWith(bio$Sensor.unit, '|'))))
1044 +
        appendTo(c('screen', 'warning'), paste0("The Sensor.unit information in ",
1045 +
          ifelse(sum(link) <= 10,
1046 +
                 paste0("row(s) ", paste0(which(link), collapse = ", ")), 
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                 paste0(sum(link), " row(s)")),
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          " of the biometrics ends with a '|' character. Could you have forgotten to include a sensor unit?"))
1049 +
1050 +
      signals_per_tag <- sapply(strsplit(bio$Signal, "|", fixed = TRUE), length) # number of signals per tag
1051 +
      aux <- strsplit(bio$Sensor.unit, "|", fixed = TRUE)
1052 +
      sensors_per_tag <- sapply(aux, length)
1053 +
1054 +
      if (any(link <- signals_per_tag != sensors_per_tag))
1055 +
        stopAndReport("The number of provided sensor units does not match the number of signals for ", 
1056 +
          ifelse(sum(link) <= 10,
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                 paste0("row(s) ", paste0(which(link), collapse = ", ")), 
1058 +
                 paste0(sum(link), " row(s)")),
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          " of the biometrics.")
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    }
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  }
@@ -1623,9 +1637,13 @@
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    } else { # otherwise, prepare tag name and include sensor units if present
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      trimmed_list_names <<- c(trimmed_list_names, paste0(the_codespace, "-", min(bio_aux$Signal_expanded[[i]])))
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      output <- my.list[list_matches]
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1641 +
      # Find Sensor.unit column in the biometrics
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      if (any(grepl("^Sensor.unit$", colnames(bio)))) {
1643 +
        # Replace sensor units...
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        for (j in 1:length(output)) {
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          sensor_index <- match(extractSignals(names(output)[j]), bio_aux$Signal_expanded[[i]])
1646 +
          # but only if the the sensor unit provided is not NA
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          if (!is.na(bio_aux$Sensor.unit_expanded[[i]][sensor_index])) {
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            output[[j]]$Sensor.Unit <- rep(bio_aux$Sensor.unit_expanded[[i]][sensor_index], nrow(output[[j]]))
1631 1649
          }

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Files Coverage
R -0.13% 93.12%
Project Totals (15 files) 93.12%
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